SLDB

Speech/Language Disorders Database

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Genetic loci linked to speech and language phenotypes

  • Click column headers to sort. Click to expand any row to see more details about the study and linkage result.
  • Click the Pubmed IDs in the last column to link out to the primary research article.
Cytogenetic region Disorder Brief Phenotype Reference Year
13q21 SLI Nonword repetition Bartlett et al 2002

Additional Phenotype Details: 
Standardized tests for nonword repetition (NWR) include the Children's Test of Nonword Repetition (CNRep, Gathercole et al 1994), the nonword repetition test (NRT, Dollaghan & Campbell 1998), and the Nonword Repetition subtest of the Comprehensive Test of Phonological Processing (Wagner et al. 1999).

References

Gathercole SE, Willis CS, Baddeley AD, Emslie H. The Children’s Test of Nonword Repetition: a test of phonological working memory. Memory 1994;2:103-27.

Dollaghan, C., & Campbell, T. F. (1998). Nonword repetition and child language impairment. Journal of Speech, Language, and Hearing Research, 41, 1136–1146

Wagner, R. K., Torgesen, J. K., & Rashotte, C. A. (1999). Comprehensive test of phonological processing. Austin, TX: PRO-ED.

Basic Study Type:  Linkage study

Study Cohort: 
Summary:

86 individuals from 5 families
Genetic data from all; phenotypic data from 73

Details:

"The sample consisted of branches of five Canadian families of Celtic ancestry that were originally identified during a linkage study of schizophrenia (Brzustowicz et al. 2000) and were noted to have a history of language or reading impairments. A total of 73 subjects were phenotyped with language/reading measures, and these plus 13 additional subjects (86 total) had DNA available. The largest family (n = 34 phenotypes and DNA) was not directly part of the schizophrenia study, because they are related to a branch of a family segregating schizophrenia only by a marriage, which should preclude any subject for this study from sharing a schizophrenia locus by descent. . . After all family members who agreed to participate were tested, families were included in the study if at least two members met the criteria for an SLI proband."

Genotyping Methods: 
Automated fluorescent microsatellite analysis.

"DNA was extracted from peripheral blood samples by the GenePure system (Gentra Systems). Buccal-swab DNA was extracted by use of cell lysis buffer and incubation as described by Laird et al. (1991), followed by NH4OAc precipitation and suspension in tris ethylenediaminetetraacetic acid
(TE). Genotyping was conducted in our laboratory and the laboratories of the Center for Inherited Disease Research (CIDR) at Johns Hopkins University in Baltimore. Initial genotyping of 381 markers from the Weber Screening Set, version 6.0, spanning the genome at an average spacing of 9 cM and average heterozygosity of 0.76 was conducted by CIDR by use of automated fluorescent microsatellite analysis (see the CIDR Web site for further details) on 69 subjects. Follow-up genotyping was performed in our laboratory with these and 17 additional subjects, as described elsewhere (Brzustowicz et al. 1997). Two additional markers on chromosome 13 (D13S1317 and D13S1306), one marker on chromosome 2 (D2S352), and one marker on chromosome 17 (D17S809), were also genotyped. PCR primers were ordered from Research Genetics as part of the Human Map Pairs set or were redesigned from the Genome Database locus sequence with the assistance of the Primer 3 program."

Analysis Methods: 
Parametric analysis: "The language impairment, reading impairment, and clinical impairment
phenotypes were each analyzed under both a dominant and a recessive model of inheritance, for a total of six analyses."

Also calculated posterior probability of linkage (PPL), and performed twopoint linkage analysis, multipoint linkage analysis, and heterogeneity testing.

Other Details: 
Criteria for diagnosis of SLI:

SLQ of <=85 on the TOLD, PIQ >=80 on the Wechsler Intelligence Scale, normal hearing (based on self- or parental-report), "no motor impairments or oral structural deviations affecting speech or non-speech movement of the articulators," and no diagnosis of autism, schizophrenia, psychoses, or neurological disorders.

Markers:  D13S800

17q23 SLI Nonword repetition Bartlett et al 2002

Additional Phenotype Details: 
Standardized tests for nonword repetition (NWR) include the Children's Test of Nonword Repetition (CNRep, Gathercole et al 1994), the nonword repetition test (NRT, Dollaghan & Campbell 1998), and the Nonword Repetition subtest of the Comprehensive Test of Phonological Processing (Wagner et al. 1999).

References

Gathercole SE, Willis CS, Baddeley AD, Emslie H. The Children’s Test of Nonword Repetition: a test of phonological working memory. Memory 1994;2:103-27.

Dollaghan, C., & Campbell, T. F. (1998). Nonword repetition and child language impairment. Journal of Speech, Language, and Hearing Research, 41, 1136–1146

Wagner, R. K., Torgesen, J. K., & Rashotte, C. A. (1999). Comprehensive test of phonological processing. Austin, TX: PRO-ED.

Basic Study Type:  Linkage study

Study Cohort: 
Summary:

86 individuals from 5 families
Genetic data from all; phenotypic data from 73

Details:

"The sample consisted of branches of five Canadian families of Celtic ancestry that were originally identified during a linkage study of schizophrenia (Brzustowicz et al. 2000) and were noted to have a history of language or reading impairments. A total of 73 subjects were phenotyped with language/reading measures, and these plus 13 additional subjects (86 total) had DNA available. The largest family (n = 34 phenotypes and DNA) was not directly part of the schizophrenia study, because they are related to a branch of a family segregating schizophrenia only by a marriage, which should preclude any subject for this study from sharing a schizophrenia locus by descent. . . After all family members who agreed to participate were tested, families were included in the study if at least two members met the criteria for an SLI proband."

Genotyping Methods: 
Automated fluorescent microsatellite analysis.

"DNA was extracted from peripheral blood samples by the GenePure system (Gentra Systems). Buccal-swab DNA was extracted by use of cell lysis buffer and incubation as described by Laird et al. (1991), followed by NH4OAc precipitation and suspension in tris ethylenediaminetetraacetic acid
(TE). Genotyping was conducted in our laboratory and the laboratories of the Center for Inherited Disease Research (CIDR) at Johns Hopkins University in Baltimore. Initial genotyping of 381 markers from the Weber Screening Set, version 6.0, spanning the genome at an average spacing of 9 cM and average heterozygosity of 0.76 was conducted by CIDR by use of automated fluorescent microsatellite analysis (see the CIDR Web site for further details) on 69 subjects. Follow-up genotyping was performed in our laboratory with these and 17 additional subjects, as described elsewhere (Brzustowicz et al. 1997). Two additional markers on chromosome 13 (D13S1317 and D13S1306), one marker on chromosome 2 (D2S352), and one marker on chromosome 17 (D17S809), were also genotyped. PCR primers were ordered from Research Genetics as part of the Human Map Pairs set or were redesigned from the Genome Database locus sequence with the assistance of the Primer 3 program."

Analysis Methods: 
Parametric analysis: "The language impairment, reading impairment, and clinical impairment
phenotypes were each analyzed under both a dominant and a recessive model of inheritance, for a total of six analyses."

Also calculated posterior probability of linkage (PPL), and performed twopoint linkage analysis, multipoint linkage analysis, and heterogeneity testing.

Other Details: 
Criteria for diagnosis of SLI:

SLQ of <=85 on the TOLD, PIQ >=80 on the Wechsler Intelligence Scale, normal hearing (based on self- or parental-report), "no motor impairments or oral structural deviations affecting speech or non-speech movement of the articulators," and no diagnosis of autism, schizophrenia, psychoses, or neurological disorders.

Markers:  D17S1290

2p22 SLI Expressive language skills Bartlett et al 2002

Additional Phenotype Details: May be assessed using the expressive language scale of the Clinical Evaluation of Language Fundamentals (CELF-R) battery (Semel et al. 1992).

Reference

Semel EM, Wiig EH, Secord W (1992) Clinical evaluation of language fundamentals—revised. Phychological Corporation, San Antonio.

Basic Study Type:  Linkage study

Study Cohort: 
Summary:

86 individuals from 5 families
Genetic data from all; phenotypic data from 73

Details:

"The sample consisted of branches of five Canadian families of Celtic ancestry that were originally identified during a linkage study of schizophrenia (Brzustowicz et al. 2000) and were noted to have a history of language or reading impairments. A total of 73 subjects were phenotyped with language/reading measures, and these plus 13 additional subjects (86 total) had DNA available. The largest family (n = 34 phenotypes and DNA) was not directly part of the schizophrenia study, because they are related to a branch of a family segregating schizophrenia only by a marriage, which should preclude any subject for this study from sharing a schizophrenia locus by descent. . . After all family members who agreed to participate were tested, families were included in the study if at least two members met the criteria for an SLI proband."

Genotyping Methods: 
Automated fluorescent microsatellite analysis.

"DNA was extracted from peripheral blood samples by the GenePure system (Gentra Systems). Buccal-swab DNA was extracted by use of cell lysis buffer and incubation as described by Laird et al. (1991), followed by NH4OAc precipitation and suspension in tris ethylenediaminetetraacetic acid
(TE). Genotyping was conducted in our laboratory and the laboratories of the Center for Inherited Disease Research (CIDR) at Johns Hopkins University in Baltimore. Initial genotyping of 381 markers from the Weber Screening Set, version 6.0, spanning the genome at an average spacing of 9 cM and average heterozygosity of 0.76 was conducted by CIDR by use of automated fluorescent microsatellite analysis (see the CIDR Web site for further details) on 69 subjects. Follow-up genotyping was performed in our laboratory with these and 17 additional subjects, as described elsewhere (Brzustowicz et al. 1997). Two additional markers on chromosome 13 (D13S1317 and D13S1306), one marker on chromosome 2 (D2S352), and one marker on chromosome 17 (D17S809), were also genotyped. PCR primers were ordered from Research Genetics as part of the Human Map Pairs set or were redesigned from the Genome Database locus sequence with the assistance of the Primer 3 program."

Analysis Methods: 
Parametric analysis: "The language impairment, reading impairment, and clinical impairment
phenotypes were each analyzed under both a dominant and a recessive model of inheritance, for a total of six analyses."

Also calculated posterior probability of linkage (PPL), and performed twopoint linkage analysis, multipoint linkage analysis, and heterogeneity testing.

Other Details: 
Criteria for diagnosis of SLI:

SLQ of <=85 on the TOLD, PIQ >=80 on the Wechsler Intelligence Scale, normal hearing (based on self- or parental-report), "no motor impairments or oral structural deviations affecting speech or non-speech movement of the articulators," and no diagnosis of autism, schizophrenia, psychoses, or neurological disorders.

Markers:  D2S405

18q Impaired speech and language Bouquillon et al 0

Basic Study Type:  - FISH (fluorescent in situ hybridization)

Study Cohort: 
Summary:

Caucasian girl with psychomotor delay, impaired speech and language

Caucasian man with impaired speech and possible mental retardation (hyperkinesia made cognitive assessments difficult)

Patient 1

"A 4-year-old girl was referred to us for psychomotor delay. She was the first child of healthy non-consanguineous Caucasian parents, both of whom were 25 years old at the time of delivery. Her 15-month-old younger sister was healthy. The pregnancy had been uneventful. The patient was born at 39 weeks’ gestation. Her birth weight was 3070 g (-0.5 SDS), birth length was 49 cm (0 SDS), and head circumference was 36 cm (+1.5 SDS). She presented a developmental delay. There was no notion of hypotonia during early childhood, she was able to sit at about 10 months and walked at the age of 22 months, her speech was severely delayed and she communicated only by signs. No hearing impairment was detected by behavioural tests or by two otoacoustic emissions tests. Hyperactivity, impulsivity and encopresis were noted. Psychometric testing at the age of 5 years and 2 months (WPPSI-R) showed moderate mental retardation, with verbal IQ at 48, performance IQ at 52 and overall IQ at 45. On examination at the age of 5 years, her weight was 17 kg (0 SDS), her height was 103 cm (-1 SDS) and her head circumference was 50 cm (0 SDS). We noted short and downslanting palpebral fissures, a small nose with anteverted nostrils, prominent ears, an ogival palate, microstomia (Fig. 1A) and long and thin fingers. She had clinodactyly of the fifth fingers. At 10 years of age, language assessment showed an impaired phonological discrimination in oral speech reception, a disorder of understanding, especially for sentences (-6 SDS for the TROG -Test for Reception of Grammar) and in a lesser extent for words (-1.7 SDS for the French adaptation of the PPVT-R - Peabody Picture Vocabulary Test-Revised), for the narratives (-2 SDS for kikou 3-8-PECSN, a protocol for assessment of syntactic and narrative understanding) and low reading level. Speech evaluation revealed a severe oro-facial dyspraxia, with disorders of articulation, contrasting with a desire to communicate and a correct level of vocabulary. Brain MRI showed a very thin corpus callosum without other abnormalities. X-rays of hand and thorax were normal. Ophthalmic examination revealed hypermetropy and mild astigmatism."

Patient 2

"A 20-year-old manwas referred for hypotonia at 6 months of age to the pediatric department. He was the first child of non-consanguineous Caucasian parents. He was born at 38 weeks of gestation weighing 3500 g (0 SDS) and with a birth length of 50 cm (0 SDS); no recorded data on head circumference were available. He had febrile seizures between 13 months and 4 years of age. He was diagnosed with coeliac disease at the age of 2 years and received a low-gluten diet until the age of 4 years. He also had an inguinal hernia, flat feet in valgus position and clinodactyly of the 5th fingers. He could sit at 24 months and walked unaided at 27 months. The first words appeared at 28 months. At 4 years, the patient could speak only five words, his vocabulary increased to nearly 30 mono or disyllabic words at 20 years of age. He could obey simple orders but he expressed his desires only by signs. No hearing impairment was detected by behavioural tests. He was considered moderately mentally retarded. He was hyperkinetic with heteroaggressivity, continuous moving and gesticulation making it difficult cognitive assessments. His height was 170 cm (-1 SDS), his weight was 66 kg (+0.5 SDS), and his head circumference was 55 cm (0 SDS). Facial dysmorphism with oval face, low hair implantation on the forehead, horizontal eyebrows and synophris, bilateral ptosis, horizontal and narrow palpebral fissures were noted. A large mouth with thin upper lip, smooth philtrum, everted lower lip, and retrognathism are depicted in Fig. 1B. He had large ears with a fissure on the anterior face of the lobules and a long and triangular neck."

Genotyping Methods: 
Patient 1:
"FISH analysis using bacterial artificial chromosome (BAC) clone RP11-164M8 localized in 18q12.3 (37,305,508-37,482,541) confirmed the deletion."

Patient 2:
"The deletion was confirmed by means of FISH probes RP11-25C13 (35,489,794-35,657,085) (NCBI Build 36) and RP11-748M14 (chr18:43,589,519-43,745,379) (NCBI Build 36)."

Markers: 

18q12.3 Impaired speech Bouquillon et al 0

Basic Study Type:  - FISH (fluorescent in situ hybridization)

Study Cohort: 
Summary:

Caucasian girl with psychomotor delay, impaired speech and language

Caucasian man with impaired speech and possible mental retardation (hyperkinesia made cognitive assessments difficult)

Patient 1

"A 4-year-old girl was referred to us for psychomotor delay. She was the first child of healthy non-consanguineous Caucasian parents, both of whom were 25 years old at the time of delivery. Her 15-month-old younger sister was healthy. The pregnancy had been uneventful. The patient was born at 39 weeks’ gestation. Her birth weight was 3070 g (-0.5 SDS), birth length was 49 cm (0 SDS), and head circumference was 36 cm (+1.5 SDS). She presented a developmental delay. There was no notion of hypotonia during early childhood, she was able to sit at about 10 months and walked at the age of 22 months, her speech was severely delayed and she communicated only by signs. No hearing impairment was detected by behavioural tests or by two otoacoustic emissions tests. Hyperactivity, impulsivity and encopresis were noted. Psychometric testing at the age of 5 years and 2 months (WPPSI-R) showed moderate mental retardation, with verbal IQ at 48, performance IQ at 52 and overall IQ at 45. On examination at the age of 5 years, her weight was 17 kg (0 SDS), her height was 103 cm (-1 SDS) and her head circumference was 50 cm (0 SDS). We noted short and downslanting palpebral fissures, a small nose with anteverted nostrils, prominent ears, an ogival palate, microstomia (Fig. 1A) and long and thin fingers. She had clinodactyly of the fifth fingers. At 10 years of age, language assessment showed an impaired phonological discrimination in oral speech reception, a disorder of understanding, especially for sentences (-6 SDS for the TROG -Test for Reception of Grammar) and in a lesser extent for words (-1.7 SDS for the French adaptation of the PPVT-R - Peabody Picture Vocabulary Test-Revised), for the narratives (-2 SDS for kikou 3-8-PECSN, a protocol for assessment of syntactic and narrative understanding) and low reading level. Speech evaluation revealed a severe oro-facial dyspraxia, with disorders of articulation, contrasting with a desire to communicate and a correct level of vocabulary. Brain MRI showed a very thin corpus callosum without other abnormalities. X-rays of hand and thorax were normal. Ophthalmic examination revealed hypermetropy and mild astigmatism."

Patient 2

"A 20-year-old manwas referred for hypotonia at 6 months of age to the pediatric department. He was the first child of non-consanguineous Caucasian parents. He was born at 38 weeks of gestation weighing 3500 g (0 SDS) and with a birth length of 50 cm (0 SDS); no recorded data on head circumference were available. He had febrile seizures between 13 months and 4 years of age. He was diagnosed with coeliac disease at the age of 2 years and received a low-gluten diet until the age of 4 years. He also had an inguinal hernia, flat feet in valgus position and clinodactyly of the 5th fingers. He could sit at 24 months and walked unaided at 27 months. The first words appeared at 28 months. At 4 years, the patient could speak only five words, his vocabulary increased to nearly 30 mono or disyllabic words at 20 years of age. He could obey simple orders but he expressed his desires only by signs. No hearing impairment was detected by behavioural tests. He was considered moderately mentally retarded. He was hyperkinetic with heteroaggressivity, continuous moving and gesticulation making it difficult cognitive assessments. His height was 170 cm (-1 SDS), his weight was 66 kg (+0.5 SDS), and his head circumference was 55 cm (0 SDS). Facial dysmorphism with oval face, low hair implantation on the forehead, horizontal eyebrows and synophris, bilateral ptosis, horizontal and narrow palpebral fissures were noted. A large mouth with thin upper lip, smooth philtrum, everted lower lip, and retrognathism are depicted in Fig. 1B. He had large ears with a fissure on the anterior face of the lobules and a long and triangular neck."

Genotyping Methods: 
Patient 1:
"FISH analysis using bacterial artificial chromosome (BAC) clone RP11-164M8 localized in 18q12.3 (37,305,508-37,482,541) confirmed the deletion."

Patient 2:
"The deletion was confirmed by means of FISH probes RP11-25C13 (35,489,794-35,657,085) (NCBI Build 36) and RP11-748M14 (chr18:43,589,519-43,745,379) (NCBI Build 36)."

Markers: 

6p21.3 Dyslexia Susceptibility to developmental dyslexia Cardon et al 1994

Additional Phenotype Details: Typical diagnostic criteria for dyslexia include remarkable deviation from population mean on age-appropriate standardized reading and spelling tests, such as those in the Wechsler intelligence tests. Reading tests may include oral reading and non-word reading.

Usually, a Performance Intelligence Quotient (PIQ) of at least 70 or 80 on the age-appropriate Weschler test is also a criterion.

References (fourth editions of these tests are also now available):

Wechsler D. 1991. Wechsler intelligence scale for children- third edition (WISC-III). San Antonio: The Psychological Corporation.

Wechsler D. 1997. Wechsler Adult Intelligence Scale-III (WAIS-III). San Antonio: The Psychological Corporation.

Basic Study Type:  Linkage study

Study Cohort: 
Summary: 358 individuals, 19 families; plus 50 families in a twin sample

"Our kindred sibling sample comprises 358 individuals from 19 families who were chosen from a variety of sources, including clinics and private schools specializing in RD. . . The twins sample comprises 50 families drawn from the Colorado twin study of RD (3). The twins range in age from 8 to 20 years (mean, 12.16 years)."

Genotyping Methods: 
"We used polymerase chain reaction (PCR) to obtain. . .DNA markers [on the short arm of chromosome 6 in bands 6p21.31-p21.1 in the region of the HLA loci] for the kindred sibships and replicated the genotyping in the independent twin sample. Five markers having H [greater than or equal to] 0.60 were typed: D6S89, D6S109, D6S105, TNFB, and D6S87 (Table 1). The marker TNFB is closest to BF (separated by 0.8 cM) and is also located within the HLA complex. We used these five markers in a two-point interval mapping procedure (12) to analyze the discriminant scores for RD in both the kindred and the twin samples."

Analysis Methods: 
The authors used (1) a two-point interval mapping procedure that extends the sib-pair approach of Haseman and Elston to accomodate interval mapping, and (2) two extensions of DeFries and Fulker's regression model.

Other Details: 
Inclusion criteria (Kindred sibling sample):

"Selection criteria included an extended family history of specific RD, as diagnosed by reading performance at least 2 years below expected grade level and in a pattern consistent with autosomal dominant inheritance (10)."

Inclusion criteria (Twin sample):

"Twin pairs in which at least one member had a positive school history of reading problems were objectively and systematically selected through cooperating school districts."

Phenotypic measures:

The composite score for reading performance was calculated for subjects with a verbal or performance IQ of >=90.

For the twin sample, quantitative traits on which the composite score was based were: Reading recognition, reading comprehension, and spelling scores in the Peabody individual achievement tests (PIAT). Weights for these scores were "computed from an independent sample of RD and control nontwin children."

"A comparable measure was constructed from the psychometric data obtained on the kindred sample."

Markers:  D6S105

18q Expressive language skills Cody et al 2007

Additional Phenotype Details: May be assessed using the expressive language scale of the Clinical Evaluation of Language Fundamentals (CELF-R) battery (Semel et al. 1992).

Reference

Semel EM, Wiig EH, Secord W (1992) Clinical evaluation of language fundamentals—revised. Phychological Corporation, San Antonio.

Basic Study Type:  - Gene sequencing - FISH (Fluorescent in situ hybridization)

Study Cohort: 
Summary: Five children with proximal deletions in 18q.

- Male with developmental delays and other medical problems
- Male with oral motor delay and other medical problems
- Female with oral apraxia, expressive language delay and other medical problems
- Female with expressive language delay and other medical problems
- Male with global developmental delays, slight discrepancy between expressive and receptive language skills (receptive skills better preserved), and other medical problems


Participant: 18q-129
"This male patient was born to a 33-year-old G2P1 mother. Paternal age was 39 at delivery. The pregnancy was generally unremarkable, with the exception of a maternal sinus infection requiring antibiotics. Labor was induced at 40 weeks. The delivery was complicated by maternal hemorrhage, meconium staining, and fetal decelerations caused by a short umbilical cord. Forceps were required for the delivery. He weighed 2,806 g at birth, was 47 cm in length, and had a head circumference of 33.5 cm. He required supplemental oxygen for 10–15 min after birth. Apgars were 3 and 7 at 1 and 5 min, and 10 at 10 min. He had bilateral cryptorchidism and a minimal umbilical hernia. From birth, he had a history of feeding problems secondary to low muscle tone, suck-swallow coordination problems, tongue protrusion, and reflux. As a result of these feeding problems, he was diagnosed with failure to thrive. At 2 months, a skeletal survey was completed that showed no major skeletal anomalies. An echocardiogram completed at 4 months of age was normal. At 11 months, his feeding problems necessitated the placement of a G-tube and fundoplication. At 11 months, he was diagnosed with a seizure disorder that is currently treated by phenobarbitol and Lamictal®. At approximately 1 year of age, he developed worsening obstructive sleep apnea, requiring a tonsillectomy and adenoidectomy with alveopalatal pharyngoplasty. He had PE tubes placed at 18 months due to recurrent otitis media. He had esotropia that was surgically corrected at 20 months. Other medical problems included several bouts with pneumonia; profound plagiocephaly requiring a helmet for correction, torticollis, eczema, and orthopedic anomalies requiring AFOs. He had significant developmental delays. He rolled over at 7 months, sat independently at 9 months, crawled at 18½ months, and walked at 4 years. He started receiving Early Intervention Services at approximately 6 months of age, including speech, occupational, and physical therapy. At 6 years 7 months, the patient was evaluated at UTHSCSA. An MRI showed a small corpus callosum and enlargement of both lateral ventricles and the third ventricle, possibly related to callosal hypoplasia. There was also fourth ventricle enlargement with some abnormal signal. Endocrinology evaluation was negative for growth hormone deficiency. Thyroid testing was also completed. TSH level was normal, but T4 was below normal. Neurological examination identified spastic cerebral palsy. Otologic examination did not show any structural defects, although he did have a large tongue. ABR showed a mild hearing loss bilaterally. It was suspected that this was primarily conductive hearing loss due to the presence of PE tubes."

Participant: 18q-140
"The patient was born to a 39-year-old G2P1 woman. There was maternal use of Zoloft ®, Ambien ®, and Zyrtec ® as well as some social drinking in the first 2 or 3 weeks following conception. The pregnancy was further complicated by Rh incompatibility. An amniocentesis was performed secondary to advanced maternal age; the results were reported as 46,XY. A prenatal ultrasound showed hydronephrosis. Patient was born at 39 weeks gestation following a vacuum-assisted delivery. He weighed 3,175 g at birth and had Apgar scores of 8 at 1 min and 9 at 5 min. He required supplemental oxygen for several minutes after birth as well as phototherapy for jaundice. Shortly after birth, a voiding cystourethrogram identified bilateral Hutch diverticuli. For the first 7 months of life, he had feeding difficulties. These difficulties were attributed to oral motor delays, generalized hypotonia, and recurrent kidney infections, resulting in failure to thrive. However, following double ureter reimplantation at 7 months, his growth improved significantly. At 10 months of age, plagiocephaly was noted, but did not require intervention. He had an MRI at 16 months that demonstrated hypoplastic corpus callosum and delayed myelination. A vision screen at 20 months was normal.He had a history of recurrent otitis media and had PE tubes placed at 22 months.
"The patient sat without support at 8 months and walked alone at 20 months. He started receiving weekly physical therapy at 8 months and occupational and speech therapy between 12 and 18 months of age. At 12 months, an evaluation by a developmental pediatrician confirmed global developmental delays, with the most significant area of delay in prelinguistic language production. A feeding team evaluation at 15 months of age identified a continuing oral motor delay. Contributing factors included hypotonia and global developmental delays as well as an abnormal suckle transport pattern, resulting in food getting stuck to the roof of the mouth.
"The patient was evaluated at UTHSCSA at 23 months of age. An MRI confirmed delayed myelination and a small corpus callosum and identified right-sided maxillary sinus disease, and bilateral mastoiditis. A mild hearing loss was detected on ABR, consistent with the presence of PE tubes. Otologic evaluation was otherwise normal. A neurology exam identified coordination and gait difficulties as well as ptosis and decreased reflexes. The endocrinology evaluation was negative for growth hormone deficiency. Total T3 and T4 as well as TSH levels were normal."

Participant: 18q-138
"This female patient was born to a 37-year-old G2P1 mother. Paternal age was 35. The pregnancy was complicated by maternal hypothyroidism treated with Synthroid ®. The mother underwent an amniocentesis due to advanced maternal age; the results were reported as 46,XX. The patient was born at 41 weeks following labor induction. The delivery was complicated by meconium staining. The patient’s birth weight was 3,770 g, and she required supplemental oxygen immediately following birth. However, Apgar scores were 9 at 1 min and 10 at 5 min. For several weeks after birth, she had problems with breast feeding due to a decrease in lingual, labial, and buccal strength and coordination secondary to low tone. Feeding was also complicated by a partial tongue tie, a high palate, and a slightly short frenulum. She developed febrile seizures at approximately 16 months of age. These later developed into complex seizures that are currently managed by Keppra ®. She had a history of blunt head trauma at 26 months, and a follow-up CT scan was normal. An MRI completed at 31 months was normal. At 34 months, an ABR and tympanometry were performed and were both normal. Lastly, there is a history of skin problems, including scabies, contact dermatitis, and seborrhea. Per parental report, the patient had no history of vision abnormalities. She has never been evaluated for growth hormone deficiency.
"Developmentally, the patient sat alone at 6 months and rolled over at 7 months. She crawled at 12 months, cruised at 14 months, and stood without support and walked at 19 months. She spoke her first word at 12 months. She received speech, occupational, and physical therapy on a weekly basis starting at approximately 24 months. A speech-language evaluation at 27 months identified a moderate-to-severe expressive communication/language disorder, based on the MacArthur Communicative Development Inventory: Words and Gestures. At 30 months, a second evaluation by a developmental pediatrician indicated that while receptive skills were actually advanced, expressive communication skills were delayed by approximately 1 year. During this evaluation, the patient was diagnosed with oral apraxia."

Participant: 18q-126
"This female was born to a 26-year-old G2P1 mother; the father was 25 years old at time of the delivery. The patient was born at 39 weeks, 5 days and weighed 3,442 g. The delivery was complicated by the passage of meconium during labor. The patient required supplemental oxygen for several minutes following birth. She also had a low core body temperature that was responsive to a warmer. She had Apgar scores of 8 at 1 min and 9 at 5 min. The neonatal period was characterized by colic and feeding problems; she had poor tongue movement and a tendency to pool food in the mouth. Hypotonia was also noted during childhood and was thought to contribute to the patient’s developmental delays. Starting at 19 months, she required AFOs secondary to the hypotonia. Based on repeated visually reinforcement audiometry evaluations, she had normal hearing. At 21 months of age, an ataxic gait was noted. Per the parents’ report, a vision test showed a mild myopia.
"Developmentally, the patient had global delays. She rolled over at 9 months of age; sat between 18 and 24 months, and stood and walked independently at approximately 24 months. An evaluation by a developmental pediatrician at 21 months indicated global delays. However, based on the Preschool Language Skill-3 Scale, her expressive language was her largest deficit, suggesting developmental apraxia of speech. She had also been diagnosed with ADHD. She started receiving speech, occupational, and physical therapy at approximately 14 months of age.
"The patient was evaluated at UTHSCSA at the age of 6 years, 1 month. MRI was normal. Otologic examination and ABR were also normal. An endocrinology evaluation did not identify growth hormone deficiency. In addition, she had normal T4, TSH, and prolactin levels."

Participant: 18q-104
"This male was born to a 34-year-old G1P0 mother following a pregnancy complicated by maternal hypertension and flu. A prenatal ultrasound revealed concern for hydronephrosis. Paternal age at delivery was 37 years. The patient was born at 38 weeks gestation weighing 2,722 g, and birth length was 44.5 cm. The delivery was complicated by a maternal fever. He had Apgar scores of 8 at 1 min and 9 at 5 min. In the first week of life, he had some transient feeding difficulties that resolved without intervention. A renal ultrasound performed at 1 month revealed no abnormalities. During infancy, he was noted to have mild to moderate hypotonia in the trunk and all four extremities, possibly contributing to developmental delays. At 4 months, brachycephaly was noted and required a dynamic orthotic cranioplasty band. At 20 months, a bone age study showed a bone age of between 6 and 12 months. Other medical complications included recurrent ear infections, which required the placement of PE tubes at 3 years and 1 month. At 1 year 4 months, he had an MRI with no structural abnormalities.
"The patient sat without support at 8 months of age and rolled at 10 months. He started crawling at approximately 17 months. At 17 months, the patient started receiving early intervention services, including speech, physical, and occupational therapy on a weekly basis. These services have continued to the present day. At 24 months, a developmental evaluation indicated persistent global deficits. A slight discrepancy was noted between receptive and expressive language skills, with receptive skills being better preserved.
"The patient visited UTHSCSA on two separate occasions, the most recent being at the age of 3 years and 9 months. At this age, an MRI revealed normal myelination as well as mild, right-sided mastoiditis. Behavioral audiometry indicated normal hearing. Otologic examination identified no structural abnormalities. An endocrinology evaluation did not identify a growth hormone failure, and he had normal T4 and TSH levels."

Genotyping Methods: 
"Molecular analysis includes microsatellite PCR, quantitative PCR, and FISH using BAC clones as probes. Microsatellite PCR has been described previously [Cody et al., 1997].
"Quantitative PCR was carried out using iQ-SYBR Green PCR Supermix with the iCycler iQ Real-Time PCR Detection System (Bio-Rad Laboratories, Hercules, CA). All samples were run in triplicate and quantification was performed using the DDCt method. The fractional Ct values at which the amount of amplified target DNA reaches a fixed threshold is directly related to the amount of starting target DNA. The PCR primer sets were designed by us and their locations on chromosome 18 are shown in Table I (see the online Table I at http://www.interscience.wiley.com/jpages/1552-4825/suppmat/index.html).
"FISH analysis was performed on metaphase spreads of participant lymphocytes. Chromosome 18 was identified using alpha-satellite probes (Vysis, DesPlaines, IL). BAC clones used as FISH probes from the region of interest were identified by their location on chromosome 18 using the UCSC Genome Browser (http://genome.ucsc.edu) and NCBI Human Genome Resources (http://www.ncbi.nlm.nih.gov)."

Markers: 

6p21.3 Dyslexia Phoneme awareness Deffenbacher et al 2004

Additional Phenotype Details: 

May be measured by any of several tasks, such as phoneme reversal or phoneme deletion. For example, Newbury et al 2011 used the Spoonerisms Test from the Phonological Assessment battery (PhAB), while Parracchini et al 2008 used a phoneme deletion test from the Auditory Analysis Task.

References

Gallagher A, Frederickson N (1995) The phonological assessment battery (PhAB): an initial assessment of its theoretical and practical utility. Educ Child Psychol 12:53–67

Newbury DF, Paracchini S, Scerri TS, Winchester L, Addis L, Richardson AJ, Walter J, Stein JF, Talcott JB, Monaco AP (2011) Investigation of dyslexia and SLI risk variants in reading- and language-impaired subjects. Behavior Genetics 41, 90-104.

Paracchini S, Steer CD, Buckingham LL, Morris AP, Ring S, Scerri T, Stein J, Pembrey ME, Ragoussis J, Golding J, Monaco AP (2008) Association of the KIAA0319 dyslexia susceptibility gene with reading skills in the general population. The American Journal Of Psychiatry 165, 1576-84.

Rosner J, Simon DP: The Auditory Analysis Test: an initial report. J Learning Disabilities 1971; 4:40–48

Basic Study Type: Linkage and association studies

Study Cohort: - DZ and MZ twin pairs (where at least one twin had a history of reading problems) and their families
- 1,559 individuals (349 nuclear families)
- Recruited from Colorado school districts

- Linkage study used all subjects
- Association study used 114 families (those with at least one child with a phenotypic score <=2 SD below mean)

Genotyping Methods: Linkage study

"Twenty-two dinucleotide repeat markers were selected for genotyping spanning 22 Mb (22 cM) on chromosome 6p21.3 (Table 1). DNA was extracted from blood or buccal samples collected from
parents and offspring. Genotyping was carried out with multiplexed fluorescently labeled primers on an ABI 3700 DNA Analyzer (Applied Biosystems). Allele calls were made by using Genotyper software version 3.7 (Applied Biosystems), and inheritance checking was performed with Genetic Analysis System (GAS) software, version 2.0 (A. Young, Oxford University, 1993–1995). The error
function in Merlin (Abecasis et al. 2002) was used to flag potential genotyping errors for re-analysis."

Association study

"SNPs were selected from the ABI Assays-on-Demand website, which offers optimized TaqMan assays for validated SNPs. SNPs were chosen based on heterozygosity, marker spacing, and a preferential location within candidate genes. Table 2 lists the 31 SNPs that were genotyped. The selected SNPs span ten genes that cluster within ~680 kb of our linkage interval, giving an average marker density of ~21 kb. SNPs were genotyped by TaqMan assay with Fam and Vic labeled MGB probes. Polymerase chain reactions were set up according to the manufacturer’s protocol and thermocycled in T-Gradient thermo-cyclers (Biometra). Endpoint fluorescent readings and allele calling were carried out on an ABI 7000 sequence detection system (SDS) with 7000SDS software (Applied Biosystems). Inheritance and error checking of allele calls were carried out as above with GAS and Merlin, respectively."

Analysis Methods: Linkage study

- Multipoint identity-by-descent values computed using GeneHunter
- Single-point linkage analysis using SIBPAL, implemented in S.A.G.E.
- Analysis performed on all 708 sib-pairs, and on samples with severe scores (at least one sib with one score 20th percentile or lower)
- S.A.G.E. implements revised Haseman-Elston analysis (using both squared trait difference and mean-corrected trait sum)
- Multipoint analysis used non-parametric lod score in GeneHunter, DeFries-Fulker basic method in QMS2, revised H-E method in QMS2
- Significance critierion for linkage: P<=0.05 and z>=1.5

Association study

- FBAT (family-based association test) with dominant and additive models
- QTDT (Quantitative Traits Disequilibrium Test) using orthogonal (Abecasis et al 2000), Allison (1997), and Rabinowitz (1997) models
- Orthogonal and Allison tests used variance components framework modeling environmental, additive, and polygenic effects
- QTDT significance levels based on 1,000 Monte Carlo permutations
- Intermarker LD using LD (GOLD) (Abecasis and Cookson 2000)
- Founder haplotypes and recombinations using Simwalk2
- Haplotypes analyzed using GeneHunter TDT option with 4-marker sliding window
- TDT significance calculated with 1,000 permutations with perm1 option in GeneHunter
- Four-marker haplotypes showing association analyzed using FBAT on markers in isolation

Other Details: Exclusion criteria:

"Subjects with sensory deficits, neurological, or emotional problems were excluded from the sample."

Phenotypes (all quantitative)

- DISC score assessing overall reading ability.
- Component phenotypes (tests described in Gayán et al. 1999):
Phoneme awareness
Phonological decoding
Single-word reading
Orthographic coice

Markers:  D6S1554 ,  D6S1571

6p21.3 Dyslexia Single-word reading Deffenbacher et al 2004

Additional Phenotype Details: Possible measures include the single-word reading subtest of Wechsler Objective Reading Dimensions
(WORD), and the British Ability Scales (BAS) test of single-word reading.


References

Elliot CD, Murray DJ, Pearson LS (1979) The British ability scales. NFER, Slough, UK

Rust J, Golombok S, Trickey G (1993) Wechsler objective reading dimensions. Psychological Corporation, Sidcup.

Basic Study Type: Linkage and association studies

Study Cohort: - DZ and MZ twin pairs (where at least one twin had a history of reading problems) and their families
- 1,559 individuals (349 nuclear families)
- Recruited from Colorado school districts

- Linkage study used all subjects
- Association study used 114 families (those with at least one child with a phenotypic score <=2 SD below mean)

Genotyping Methods: Linkage study

"Twenty-two dinucleotide repeat markers were selected for genotyping spanning 22 Mb (22 cM) on chromosome 6p21.3 (Table 1). DNA was extracted from blood or buccal samples collected from
parents and offspring. Genotyping was carried out with multiplexed fluorescently labeled primers on an ABI 3700 DNA Analyzer (Applied Biosystems). Allele calls were made by using Genotyper software version 3.7 (Applied Biosystems), and inheritance checking was performed with Genetic Analysis System (GAS) software, version 2.0 (A. Young, Oxford University, 1993–1995). The error
function in Merlin (Abecasis et al. 2002) was used to flag potential genotyping errors for re-analysis."

Association study

"SNPs were selected from the ABI Assays-on-Demand website, which offers optimized TaqMan assays for validated SNPs. SNPs were chosen based on heterozygosity, marker spacing, and a preferential location within candidate genes. Table 2 lists the 31 SNPs that were genotyped. The selected SNPs span ten genes that cluster within ~680 kb of our linkage interval, giving an average marker density of ~21 kb. SNPs were genotyped by TaqMan assay with Fam and Vic labeled MGB probes. Polymerase chain reactions were set up according to the manufacturer’s protocol and thermocycled in T-Gradient thermo-cyclers (Biometra). Endpoint fluorescent readings and allele calling were carried out on an ABI 7000 sequence detection system (SDS) with 7000SDS software (Applied Biosystems). Inheritance and error checking of allele calls were carried out as above with GAS and Merlin, respectively."

Analysis Methods: Linkage study

- Multipoint identity-by-descent values computed using GeneHunter
- Single-point linkage analysis using SIBPAL, implemented in S.A.G.E.
- Analysis performed on all 708 sib-pairs, and on samples with severe scores (at least one sib with one score 20th percentile or lower)
- S.A.G.E. implements revised Haseman-Elston analysis (using both squared trait difference and mean-corrected trait sum)
- Multipoint analysis used non-parametric lod score in GeneHunter, DeFries-Fulker basic method in QMS2, revised H-E method in QMS2
- Significance critierion for linkage: P<=0.05 and z>=1.5

Association study

- FBAT (family-based association test) with dominant and additive models
- QTDT (Quantitative Traits Disequilibrium Test) using orthogonal (Abecasis et al 2000), Allison (1997), and Rabinowitz (1997) models
- Orthogonal and Allison tests used variance components framework modeling environmental, additive, and polygenic effects
- QTDT significance levels based on 1,000 Monte Carlo permutations
- Intermarker LD using LD (GOLD) (Abecasis and Cookson 2000)
- Founder haplotypes and recombinations using Simwalk2
- Haplotypes analyzed using GeneHunter TDT option with 4-marker sliding window
- TDT significance calculated with 1,000 permutations with perm1 option in GeneHunter
- Four-marker haplotypes showing association analyzed using FBAT on markers in isolation

Other Details: Exclusion criteria:

"Subjects with sensory deficits, neurological, or emotional problems were excluded from the sample."

Phenotypes (all quantitative)

- DISC score assessing overall reading ability.
- Component phenotypes (tests described in Gayán et al. 1999):
Phoneme awareness
Phonological decoding
Single-word reading
Orthographic coice

Markers:  D6S1554 ,  D6S1571 ,  D6S1588 ,  D6S1597 ,  D6S1663 ,  D6S276 ,  D6S461

6p21.3 Dyslexia Orthographic coding Deffenbacher et al 2004

Additional Phenotype Details: May be assessed by a forced word choice test as in Olson et al 1994, requiring "(identification of a correctly spelt word from two phonologically equivalent options, e.g. rane vs rain" (Newbury et al 2011).

Basic Study Type: Linkage and association studies

Study Cohort: - DZ and MZ twin pairs (where at least one twin had a history of reading problems) and their families
- 1,559 individuals (349 nuclear families)
- Recruited from Colorado school districts

- Linkage study used all subjects
- Association study used 114 families (those with at least one child with a phenotypic score <=2 SD below mean)

Genotyping Methods: Linkage study

"Twenty-two dinucleotide repeat markers were selected for genotyping spanning 22 Mb (22 cM) on chromosome 6p21.3 (Table 1). DNA was extracted from blood or buccal samples collected from
parents and offspring. Genotyping was carried out with multiplexed fluorescently labeled primers on an ABI 3700 DNA Analyzer (Applied Biosystems). Allele calls were made by using Genotyper software version 3.7 (Applied Biosystems), and inheritance checking was performed with Genetic Analysis System (GAS) software, version 2.0 (A. Young, Oxford University, 1993–1995). The error
function in Merlin (Abecasis et al. 2002) was used to flag potential genotyping errors for re-analysis."

Association study

"SNPs were selected from the ABI Assays-on-Demand website, which offers optimized TaqMan assays for validated SNPs. SNPs were chosen based on heterozygosity, marker spacing, and a preferential location within candidate genes. Table 2 lists the 31 SNPs that were genotyped. The selected SNPs span ten genes that cluster within ~680 kb of our linkage interval, giving an average marker density of ~21 kb. SNPs were genotyped by TaqMan assay with Fam and Vic labeled MGB probes. Polymerase chain reactions were set up according to the manufacturer’s protocol and thermocycled in T-Gradient thermo-cyclers (Biometra). Endpoint fluorescent readings and allele calling were carried out on an ABI 7000 sequence detection system (SDS) with 7000SDS software (Applied Biosystems). Inheritance and error checking of allele calls were carried out as above with GAS and Merlin, respectively."

Analysis Methods: Linkage study

- Multipoint identity-by-descent values computed using GeneHunter
- Single-point linkage analysis using SIBPAL, implemented in S.A.G.E.
- Analysis performed on all 708 sib-pairs, and on samples with severe scores (at least one sib with one score 20th percentile or lower)
- S.A.G.E. implements revised Haseman-Elston analysis (using both squared trait difference and mean-corrected trait sum)
- Multipoint analysis used non-parametric lod score in GeneHunter, DeFries-Fulker basic method in QMS2, revised H-E method in QMS2
- Significance critierion for linkage: P<=0.05 and z>=1.5

Association study

- FBAT (family-based association test) with dominant and additive models
- QTDT (Quantitative Traits Disequilibrium Test) using orthogonal (Abecasis et al 2000), Allison (1997), and Rabinowitz (1997) models
- Orthogonal and Allison tests used variance components framework modeling environmental, additive, and polygenic effects
- QTDT significance levels based on 1,000 Monte Carlo permutations
- Intermarker LD using LD (GOLD) (Abecasis and Cookson 2000)
- Founder haplotypes and recombinations using Simwalk2
- Haplotypes analyzed using GeneHunter TDT option with 4-marker sliding window
- TDT significance calculated with 1,000 permutations with perm1 option in GeneHunter
- Four-marker haplotypes showing association analyzed using FBAT on markers in isolation

Other Details: Exclusion criteria:

"Subjects with sensory deficits, neurological, or emotional problems were excluded from the sample."

Phenotypes (all quantitative)

- DISC score assessing overall reading ability.
- Component phenotypes (tests described in Gayán et al. 1999):
Phoneme awareness
Phonological decoding
Single-word reading
Orthographic coice

Markers:  D6S105 ,  D6S1554 ,  D6S1571 ,  D6S1588 ,  D6S1663 ,  D6S1683 ,  D6S258 ,  D6S273 ,  D6S276 ,  D6S306 ,  D6S461 ,  MOG

6p21.3 Dyslexia Discriminant score for reading Deffenbacher et al 2004

Additional Phenotype Details: Weighted composite of the reading recognition, reading comprehension, and spelling subtests of the PIAT (Peabody individual achievement test), used in: Meng et al 2005, DCDC2 is associated with reading disability and modulates neuronal development in the brain. Proceedings Of The National Academy Of Sciences Of The United States Of America 102, 17053-8.

Basic Study Type: Linkage and association studies

Study Cohort: - DZ and MZ twin pairs (where at least one twin had a history of reading problems) and their families
- 1,559 individuals (349 nuclear families)
- Recruited from Colorado school districts

- Linkage study used all subjects
- Association study used 114 families (those with at least one child with a phenotypic score <=2 SD below mean)

Genotyping Methods: Linkage study

"Twenty-two dinucleotide repeat markers were selected for genotyping spanning 22 Mb (22 cM) on chromosome 6p21.3 (Table 1). DNA was extracted from blood or buccal samples collected from
parents and offspring. Genotyping was carried out with multiplexed fluorescently labeled primers on an ABI 3700 DNA Analyzer (Applied Biosystems). Allele calls were made by using Genotyper software version 3.7 (Applied Biosystems), and inheritance checking was performed with Genetic Analysis System (GAS) software, version 2.0 (A. Young, Oxford University, 1993–1995). The error
function in Merlin (Abecasis et al. 2002) was used to flag potential genotyping errors for re-analysis."

Association study

"SNPs were selected from the ABI Assays-on-Demand website, which offers optimized TaqMan assays for validated SNPs. SNPs were chosen based on heterozygosity, marker spacing, and a preferential location within candidate genes. Table 2 lists the 31 SNPs that were genotyped. The selected SNPs span ten genes that cluster within ~680 kb of our linkage interval, giving an average marker density of ~21 kb. SNPs were genotyped by TaqMan assay with Fam and Vic labeled MGB probes. Polymerase chain reactions were set up according to the manufacturer’s protocol and thermocycled in T-Gradient thermo-cyclers (Biometra). Endpoint fluorescent readings and allele calling were carried out on an ABI 7000 sequence detection system (SDS) with 7000SDS software (Applied Biosystems). Inheritance and error checking of allele calls were carried out as above with GAS and Merlin, respectively."

Analysis Methods: Linkage study

- Multipoint identity-by-descent values computed using GeneHunter
- Single-point linkage analysis using SIBPAL, implemented in S.A.G.E.
- Analysis performed on all 708 sib-pairs, and on samples with severe scores (at least one sib with one score 20th percentile or lower)
- S.A.G.E. implements revised Haseman-Elston analysis (using both squared trait difference and mean-corrected trait sum)
- Multipoint analysis used non-parametric lod score in GeneHunter, DeFries-Fulker basic method in QMS2, revised H-E method in QMS2
- Significance critierion for linkage: P<=0.05 and z>=1.5

Association study

- FBAT (family-based association test) with dominant and additive models
- QTDT (Quantitative Traits Disequilibrium Test) using orthogonal (Abecasis et al 2000), Allison (1997), and Rabinowitz (1997) models
- Orthogonal and Allison tests used variance components framework modeling environmental, additive, and polygenic effects
- QTDT significance levels based on 1,000 Monte Carlo permutations
- Intermarker LD using LD (GOLD) (Abecasis and Cookson 2000)
- Founder haplotypes and recombinations using Simwalk2
- Haplotypes analyzed using GeneHunter TDT option with 4-marker sliding window
- TDT significance calculated with 1,000 permutations with perm1 option in GeneHunter
- Four-marker haplotypes showing association analyzed using FBAT on markers in isolation

Other Details: Exclusion criteria:

"Subjects with sensory deficits, neurological, or emotional problems were excluded from the sample."

Phenotypes (all quantitative)

- DISC score assessing overall reading ability.
- Component phenotypes (tests described in Gayán et al. 1999):
Phoneme awareness
Phonological decoding
Single-word reading
Orthographic coice

Markers:  D6S1554 ,  D6S276 ,  D6S461

16q23.1-16q24.2 SLI Tense marking Falcaro et al 2008

Basic Study Type:  Linkage study

Study Cohort: 
Summary:

"The sample considered in this paper consists. . .of 93 probands (68 males and 25 females) and their first-degree relatives, where the minimum age for participation was 6 years. Probands had a mean age of 14 years and 5 months (age range: 13 years and 1 months to 16 years and 2 months). There were 300 first-degree relatives: 93 fathers, 93 mothers, 35 male/24 female siblings over the age of 16 years and 26 male/29 female siblings between the ages of 6 and 16 years. The mean age was 44 years and 1 month for parents, 18 years and 8 months for older siblings and 12 years and 4 months for younger siblings."

Only 40 of the 93 families were genotyped, as "families with no full siblings (n = 27) or only non-consenting siblings (n = 16) or where the proband had co-occurring medical illness such as autism (n = 8), had non-Caucasian ancestry (n = 1) or contributed to a previous SLIC collection (n = 1) were excluded."

Details:

"Participants were originally part of the Manchester Language Study (Conti-Ramsden & Botting 1999a,b; Conti-Ramsden et al. 1997). Probands were recruited from 118 language units attached to English mainstream schools. All language units catering for primary school year 2 children were contacted. Centres enrolling children with global delay or hearing impairments were excluded, and two centres declined to participate. Approximately half of the children attending a language unit for at least 50% of the week were randomly sampled, yielding 242 children (185 males and 57 females) aged between 6 years and 2 months and 7 years and 10 months. These children were then reassessed at approximately 8 years and 11 years of age and also at 14 years of age when assessment was extended to first-degree relatives. Of the 124 (51%) families who agreed to take part in the study, 11 were not assessed because of alterations in family circumstances. From the 113 fully consenting and assessed families, 93 were selected for participation in the present study based on the following proband criteria [see "Other"]."

Genotyping Methods: 
"DNA was extracted using standard protocols and quantified with Pico Green (Molecular Probes, Eugene, OR, USA). If necessary, samples were pre-amplified using Genomiphi DNA amplification kits (GE Healthcare, Amersham, UK). Eight microsatellite markers were amplified across a 10.5-Mb region of chromosome 16q (16q23.1–16q24.2) and nine microsatellite markers from a 23.5-Mb region of chromosome 19 (19q12–19q13.42). DNA was amplified using fluorescently labelled primers (Applied Biosystems, MWG Biotech, Foster City, CA, USA). Polymerase chain reaction products were pooled allowing concurrent detection by ABI 3700 sequencers (Applied Biosystems). Data were extracted using GENESCAN (version 3.1) and GENOTYPER (version 2.0) software (Applied Biosystems), manually verified and checked for inconsistencies within GENETIC ANALYSIS software (version 2, A. Young). Marker haplotypes were generated within GENEHUNTER 2.0 (Kruglyak et al. 1996), and all chromosomes showing an excessive number of recombinations were re-examined at the genotype level. The Integrated Genotyping System (R. Mott) was used for the storage of genotypic data. Sex-averaged maps were taken from the deCODE (Iceland) company’s genetic map (Kong et al. 2002) supplemented with data from the human genome map (University of California, Santa Cruz). Markers were selected on average one every 10 cM."

Analysis Methods: 
Linkage analysis was performed both with a Tobit DeFries-Fulker model and with a standard Haseman-Elston (1972) model. "For the peaks of the LOD scores, we also computed empirical P values using Monte Carlo permutation testing."

Other Details: 
Diagnostic criteria:

Probands have "performance IQ of 80 or more and a minimum of one concurrent standardized language test score that fell at least 1 SD below the population mean at one of the longitudinal assessment stages." Tests included the non-word repetition (NWR) task, the past tense (PT) task, and expressive language scores on the CELF-R (Semel et al 1987).

Other criteria:

"No sensory neural hearing loss.
English as a first language.
No record of a medical condition likely to affect language.
No record of a co-morbid diagnosis of autism."

Markers: 

16q23.1-16q24.2 SLI Nonword repetition Falcaro et al 2008

Additional Phenotype Details: 
Standardized tests for nonword repetition (NWR) include the Children's Test of Nonword Repetition (CNRep, Gathercole et al 1994), the nonword repetition test (NRT, Dollaghan & Campbell 1998), and the Nonword Repetition subtest of the Comprehensive Test of Phonological Processing (Wagner et al. 1999).

References

Gathercole SE, Willis CS, Baddeley AD, Emslie H. The Children’s Test of Nonword Repetition: a test of phonological working memory. Memory 1994;2:103-27.

Dollaghan, C., & Campbell, T. F. (1998). Nonword repetition and child language impairment. Journal of Speech, Language, and Hearing Research, 41, 1136–1146

Wagner, R. K., Torgesen, J. K., & Rashotte, C. A. (1999). Comprehensive test of phonological processing. Austin, TX: PRO-ED.

Basic Study Type:  Linkage study

Study Cohort: 
Summary:

"The sample considered in this paper consists. . .of 93 probands (68 males and 25 females) and their first-degree relatives, where the minimum age for participation was 6 years. Probands had a mean age of 14 years and 5 months (age range: 13 years and 1 months to 16 years and 2 months). There were 300 first-degree relatives: 93 fathers, 93 mothers, 35 male/24 female siblings over the age of 16 years and 26 male/29 female siblings between the ages of 6 and 16 years. The mean age was 44 years and 1 month for parents, 18 years and 8 months for older siblings and 12 years and 4 months for younger siblings."

Only 40 of the 93 families were genotyped, as "families with no full siblings (n = 27) or only non-consenting siblings (n = 16) or where the proband had co-occurring medical illness such as autism (n = 8), had non-Caucasian ancestry (n = 1) or contributed to a previous SLIC collection (n = 1) were excluded."

Details:

"Participants were originally part of the Manchester Language Study (Conti-Ramsden & Botting 1999a,b; Conti-Ramsden et al. 1997). Probands were recruited from 118 language units attached to English mainstream schools. All language units catering for primary school year 2 children were contacted. Centres enrolling children with global delay or hearing impairments were excluded, and two centres declined to participate. Approximately half of the children attending a language unit for at least 50% of the week were randomly sampled, yielding 242 children (185 males and 57 females) aged between 6 years and 2 months and 7 years and 10 months. These children were then reassessed at approximately 8 years and 11 years of age and also at 14 years of age when assessment was extended to first-degree relatives. Of the 124 (51%) families who agreed to take part in the study, 11 were not assessed because of alterations in family circumstances. From the 113 fully consenting and assessed families, 93 were selected for participation in the present study based on the following proband criteria [see "Other"]."

Genotyping Methods: 
"DNA was extracted using standard protocols and quantified with Pico Green (Molecular Probes, Eugene, OR, USA). If necessary, samples were pre-amplified using Genomiphi DNA amplification kits (GE Healthcare, Amersham, UK). Eight microsatellite markers were amplified across a 10.5-Mb region of chromosome 16q (16q23.1–16q24.2) and nine microsatellite markers from a 23.5-Mb region of chromosome 19 (19q12–19q13.42). DNA was amplified using fluorescently labelled primers (Applied Biosystems, MWG Biotech, Foster City, CA, USA). Polymerase chain reaction products were pooled allowing concurrent detection by ABI 3700 sequencers (Applied Biosystems). Data were extracted using GENESCAN (version 3.1) and GENOTYPER (version 2.0) software (Applied Biosystems), manually verified and checked for inconsistencies within GENETIC ANALYSIS software (version 2, A. Young). Marker haplotypes were generated within GENEHUNTER 2.0 (Kruglyak et al. 1996), and all chromosomes showing an excessive number of recombinations were re-examined at the genotype level. The Integrated Genotyping System (R. Mott) was used for the storage of genotypic data. Sex-averaged maps were taken from the deCODE (Iceland) company’s genetic map (Kong et al. 2002) supplemented with data from the human genome map (University of California, Santa Cruz). Markers were selected on average one every 10 cM."

Analysis Methods: 
Linkage analysis was performed both with a Tobit DeFries-Fulker model and with a standard Haseman-Elston (1972) model. "For the peaks of the LOD scores, we also computed empirical P values using Monte Carlo permutation testing."

Other Details: 
Diagnostic criteria:

Probands have "performance IQ of 80 or more and a minimum of one concurrent standardized language test score that fell at least 1 SD below the population mean at one of the longitudinal assessment stages." Tests included the non-word repetition (NWR) task, the past tense (PT) task, and expressive language scores on the CELF-R (Semel et al 1987).

Other criteria:

"No sensory neural hearing loss.
English as a first language.
No record of a medical condition likely to affect language.
No record of a co-morbid diagnosis of autism."

Markers: 

19q12-19q13.42 SLI Tense marking Falcaro et al 2008

Basic Study Type:  Linkage study

Study Cohort: 
Summary:

"The sample considered in this paper consists. . .of 93 probands (68 males and 25 females) and their first-degree relatives, where the minimum age for participation was 6 years. Probands had a mean age of 14 years and 5 months (age range: 13 years and 1 months to 16 years and 2 months). There were 300 first-degree relatives: 93 fathers, 93 mothers, 35 male/24 female siblings over the age of 16 years and 26 male/29 female siblings between the ages of 6 and 16 years. The mean age was 44 years and 1 month for parents, 18 years and 8 months for older siblings and 12 years and 4 months for younger siblings."

Only 40 of the 93 families were genotyped, as "families with no full siblings (n = 27) or only non-consenting siblings (n = 16) or where the proband had co-occurring medical illness such as autism (n = 8), had non-Caucasian ancestry (n = 1) or contributed to a previous SLIC collection (n = 1) were excluded."

Details:

"Participants were originally part of the Manchester Language Study (Conti-Ramsden & Botting 1999a,b; Conti-Ramsden et al. 1997). Probands were recruited from 118 language units attached to English mainstream schools. All language units catering for primary school year 2 children were contacted. Centres enrolling children with global delay or hearing impairments were excluded, and two centres declined to participate. Approximately half of the children attending a language unit for at least 50% of the week were randomly sampled, yielding 242 children (185 males and 57 females) aged between 6 years and 2 months and 7 years and 10 months. These children were then reassessed at approximately 8 years and 11 years of age and also at 14 years of age when assessment was extended to first-degree relatives. Of the 124 (51%) families who agreed to take part in the study, 11 were not assessed because of alterations in family circumstances. From the 113 fully consenting and assessed families, 93 were selected for participation in the present study based on the following proband criteria [see "Other"]."

Genotyping Methods: 
"DNA was extracted using standard protocols and quantified with Pico Green (Molecular Probes, Eugene, OR, USA). If necessary, samples were pre-amplified using Genomiphi DNA amplification kits (GE Healthcare, Amersham, UK). Eight microsatellite markers were amplified across a 10.5-Mb region of chromosome 16q (16q23.1–16q24.2) and nine microsatellite markers from a 23.5-Mb region of chromosome 19 (19q12–19q13.42). DNA was amplified using fluorescently labelled primers (Applied Biosystems, MWG Biotech, Foster City, CA, USA). Polymerase chain reaction products were pooled allowing concurrent detection by ABI 3700 sequencers (Applied Biosystems). Data were extracted using GENESCAN (version 3.1) and GENOTYPER (version 2.0) software (Applied Biosystems), manually verified and checked for inconsistencies within GENETIC ANALYSIS software (version 2, A. Young). Marker haplotypes were generated within GENEHUNTER 2.0 (Kruglyak et al. 1996), and all chromosomes showing an excessive number of recombinations were re-examined at the genotype level. The Integrated Genotyping System (R. Mott) was used for the storage of genotypic data. Sex-averaged maps were taken from the deCODE (Iceland) company’s genetic map (Kong et al. 2002) supplemented with data from the human genome map (University of California, Santa Cruz). Markers were selected on average one every 10 cM."

Analysis Methods: 
Linkage analysis was performed both with a Tobit DeFries-Fulker model and with a standard Haseman-Elston (1972) model. "For the peaks of the LOD scores, we also computed empirical P values using Monte Carlo permutation testing."

Other Details: 
Diagnostic criteria:

Probands have "performance IQ of 80 or more and a minimum of one concurrent standardized language test score that fell at least 1 SD below the population mean at one of the longitudinal assessment stages." Tests included the non-word repetition (NWR) task, the past tense (PT) task, and expressive language scores on the CELF-R (Semel et al 1987).

Other criteria:

"No sensory neural hearing loss.
English as a first language.
No record of a medical condition likely to affect language.
No record of a co-morbid diagnosis of autism."

Markers: 

19q12-19q13.42 Expressive language impairment Falcaro et al 2008

Additional Phenotype Details: May be assessed using the expressive language scale of the Clinical Evaluation of Language Fundamentals (CELF-R) battery (Semel et al. 1992).

Reference

Semel EM, Wiig EH, Secord W (1992) Clinical evaluation of language fundamentals—revised. Phychological Corporation, San Antonio.

Basic Study Type:  Linkage study

Study Cohort: 
Summary:

"The sample considered in this paper consists. . .of 93 probands (68 males and 25 females) and their first-degree relatives, where the minimum age for participation was 6 years. Probands had a mean age of 14 years and 5 months (age range: 13 years and 1 months to 16 years and 2 months). There were 300 first-degree relatives: 93 fathers, 93 mothers, 35 male/24 female siblings over the age of 16 years and 26 male/29 female siblings between the ages of 6 and 16 years. The mean age was 44 years and 1 month for parents, 18 years and 8 months for older siblings and 12 years and 4 months for younger siblings."

Only 40 of the 93 families were genotyped, as "families with no full siblings (n = 27) or only non-consenting siblings (n = 16) or where the proband had co-occurring medical illness such as autism (n = 8), had non-Caucasian ancestry (n = 1) or contributed to a previous SLIC collection (n = 1) were excluded."

Details:

"Participants were originally part of the Manchester Language Study (Conti-Ramsden & Botting 1999a,b; Conti-Ramsden et al. 1997). Probands were recruited from 118 language units attached to English mainstream schools. All language units catering for primary school year 2 children were contacted. Centres enrolling children with global delay or hearing impairments were excluded, and two centres declined to participate. Approximately half of the children attending a language unit for at least 50% of the week were randomly sampled, yielding 242 children (185 males and 57 females) aged between 6 years and 2 months and 7 years and 10 months. These children were then reassessed at approximately 8 years and 11 years of age and also at 14 years of age when assessment was extended to first-degree relatives. Of the 124 (51%) families who agreed to take part in the study, 11 were not assessed because of alterations in family circumstances. From the 113 fully consenting and assessed families, 93 were selected for participation in the present study based on the following proband criteria [see "Other"]."

Genotyping Methods: 
"DNA was extracted using standard protocols and quantified with Pico Green (Molecular Probes, Eugene, OR, USA). If necessary, samples were pre-amplified using Genomiphi DNA amplification kits (GE Healthcare, Amersham, UK). Eight microsatellite markers were amplified across a 10.5-Mb region of chromosome 16q (16q23.1–16q24.2) and nine microsatellite markers from a 23.5-Mb region of chromosome 19 (19q12–19q13.42). DNA was amplified using fluorescently labelled primers (Applied Biosystems, MWG Biotech, Foster City, CA, USA). Polymerase chain reaction products were pooled allowing concurrent detection by ABI 3700 sequencers (Applied Biosystems). Data were extracted using GENESCAN (version 3.1) and GENOTYPER (version 2.0) software (Applied Biosystems), manually verified and checked for inconsistencies within GENETIC ANALYSIS software (version 2, A. Young). Marker haplotypes were generated within GENEHUNTER 2.0 (Kruglyak et al. 1996), and all chromosomes showing an excessive number of recombinations were re-examined at the genotype level. The Integrated Genotyping System (R. Mott) was used for the storage of genotypic data. Sex-averaged maps were taken from the deCODE (Iceland) company’s genetic map (Kong et al. 2002) supplemented with data from the human genome map (University of California, Santa Cruz). Markers were selected on average one every 10 cM."

Analysis Methods: 
Linkage analysis was performed both with a Tobit DeFries-Fulker model and with a standard Haseman-Elston (1972) model. "For the peaks of the LOD scores, we also computed empirical P values using Monte Carlo permutation testing."

Other Details: 
Diagnostic criteria:

Probands have "performance IQ of 80 or more and a minimum of one concurrent standardized language test score that fell at least 1 SD below the population mean at one of the longitudinal assessment stages." Tests included the non-word repetition (NWR) task, the past tense (PT) task, and expressive language scores on the CELF-R (Semel et al 1987).

Other criteria:

"No sensory neural hearing loss.
English as a first language.
No record of a medical condition likely to affect language.
No record of a co-morbid diagnosis of autism."

Markers: 

2p15-2p16 Dyslexia Susceptibility to developmental dyslexia Fisher et al 2002

Additional Phenotype Details: Typical diagnostic criteria for dyslexia include remarkable deviation from population mean on age-appropriate standardized reading and spelling tests, such as those in the Wechsler intelligence tests. Reading tests may include oral reading and non-word reading.

Usually, a Performance Intelligence Quotient (PIQ) of at least 70 or 80 on the age-appropriate Weschler test is also a criterion.

References (fourth editions of these tests are also now available):

Wechsler D. 1991. Wechsler intelligence scale for children- third edition (WISC-III). San Antonio: The Psychological Corporation.

Wechsler D. 1997. Wechsler Adult Intelligence Scale-III (WAIS-III). San Antonio: The Psychological Corporation.

Basic Study Type:  Linkage study

Study Cohort: 
"The UK sample consisted of 89 families (195 total sibling pairs), ascertained through a dyslexia clinic on the basis of one severely dyslexic child and reported reading problems in one or more siblings [7,14,15]. The US sample comprised 119 families (180 total sibling pairs) drawn from the Colorado twin study of reading disability [2]. In this epidemiological sample, twin-pairs in which at least one member had a positive school history of reading difficulty were systematically recruited from school districts [5,6,8]."

Genotyping Methods: 
"We genotyped 401 highly polymorphic markers, spanning all 22 autosomes and the X chromosome, in children and parents from each family. Thirty-nine US families included only one parent; the remaining 80 US families and all 89 UK families included both parents. The majority of markers came from the ABI PRISM LMS2-MD10 panels (Applied Biosystems). We took sex-averaged marker maps from CHLC (Co-operative Human Linkage Center) supplemented with data from Généthon [26], and verified these by comparison with maps estimated from our genome-screen marker data. We carried out semi-automated fluorescent genotyping using standard techniques as described [7]. We checked raw allele size data for consistent inheritance and converted them to LINKAGE format using the GAS software package (version 2.0; Alan Young, Oxford University). We used Discovery Manager (Genomica Corporation) for the storage of genotypic and phenotypic data and the creation of the appropriate files for statistical analysis. As a further check on genotyping quality, we generated marker haplotypes from the data using Genehunter2.0 (GH2.0; ref. 27) to identify any chromosomes showing an excessive number of recombination events. The statistical analyses also incorporated genotypic data, from 16 markers in the UK sample and eight in the US sample, which
had previously been generated for targeted studies of the 6p21.3 QTL [5–8]."

Analysis Methods: 
The authors performed variance components linkage analysis, a DeFries-Fulker
linkage analysis, and X-linked QTL analysis using the Haseman-Elston method.

Other Details: 
Phenotypic measures:

All children were assessed with tests of phoneme awareness (PA), phonological decoding (PD) and orthographic coding (OC). The authors describe the tests as follows:

PA: Spoonerism test (UK), "tests of phoneme transposition/deletion" (US)

PD: "Oral reading of non-words that lack real meaning (such as torlep)"

OC: "Forced-choice tasks that required rapid recognition of a target word compared with a phonologically identical non-word (such as rain versus rane)" (both samples); "oral reading of irregular words (such as yacht and colonel) that violate the standard letter-sound conventions of English" (UK only)

Also note: "Although the sample sizes investigated here may be sufficient for the detection of linkage to major QTLs, they are too small to yield reliable estimates of relative effect sizes for each hypothesized reading component at any particular QTL."

Markers:  D18S53

6p22.2 Dyslexia Single-word reading Francks et al 2004

Additional Phenotype Details: Possible measures include the single-word reading subtest of Wechsler Objective Reading Dimensions
(WORD), and the British Ability Scales (BAS) test of single-word reading.


References

Elliot CD, Murray DJ, Pearson LS (1979) The British ability scales. NFER, Slough, UK

Rust J, Golombok S, Trickey G (1993) Wechsler objective reading dimensions. Psychological Corporation, Sidcup.

Markers:  rs1061925rs1061925rs2143340rs3033236rs9467247

6p22.2 Dyslexia Orthographic coding of irregular words Francks et al 2004

Additional Phenotype Details: use of word-specific spelling patterns to recognize irregular words

Markers:  rs1061925rs2143340rs9467247

6p22.2 Dyslexia Spelling ability Francks et al 2004

Additional Phenotype Details: Possible measures include the spelling subtests of any of a number of intelligence and literacy tests, e.g.:

Peabody Individual Achievement Test (PIAT)
Western Australian Literacy and Numeracy Assessment (WALNA)
Wide Range Achievement Test (WRAT)

Markers:  rs2143340rs3033236

6p22.2 Dyslexia Orthographic coding in forced word choice Francks et al 2004

Additional Phenotype Details: assessed using a forced word choice test

Markers:  rs1061925rs2143340

2p11 Dyslexia Susceptibility to developmental dyslexia Kaminen et al 2003

Additional Phenotype Details: Typical diagnostic criteria for dyslexia include remarkable deviation from population mean on age-appropriate standardized reading and spelling tests, such as those in the Wechsler intelligence tests. Reading tests may include oral reading and non-word reading.

Usually, a Performance Intelligence Quotient (PIQ) of at least 70 or 80 on the age-appropriate Weschler test is also a criterion.

References (fourth editions of these tests are also now available):

Wechsler D. 1991. Wechsler intelligence scale for children- third edition (WISC-III). San Antonio: The Psychological Corporation.

Wechsler D. 1997. Wechsler Adult Intelligence Scale-III (WAIS-III). San Antonio: The Psychological Corporation.

Basic Study Type:  Linkage study

Study Cohort: 
"Eleven families with 97 subjects, of whom 70 were available for thorough testing for dyslexia, were studied. Nine families with 70 members altogether (28 dyslexic, 28 non-dyslexic, and 14 not tested) were recruited from the Department of Paediatric Neurology at the Hospital for Children and Adolescents (formerly Children’s Castle Hospital), University of Helsinki, Finland. These families were selected from about 14017 based on their informativeness for linkage. Two families with 27 members altogether (12 dyslexic, 11 non-dyslexic, and four uncertain) were recruited from the Central Hospital of Central Finland, Jyväskylä, Finland. In these two families, dyslexia testing, with normal results, was performed in three of the non-dyslexic subjects, and a further eight subjects reporting normal reading performance were also classified as unaffected."

Genotyping Methods: 
"Genome wide scan was carried out at the Finnish Genome Centre, University of Helsinki, using 376 microsatellite markers from the Applied Biosystems Linkage Mapping Set MD-10. The average distance between markers was 10 cM. DNA (20 ng) was dried on microtitre plates for each PCR assay. The PCRs were performed in 5 µl volumes in conditions recommended by the reagent manufacturer (Applied Biosystems). The fluorescence labelled PCR products were pooled (10-20 markers/pool), and separated on a MegaBace 1000 capillary electrophoresis instrument (Molecular Dynamics, Sunnyvale, CA). The alleles were visualised using Genetic Profiler 1.5 software (MolecularDynamics)."

Analysis Methods: 
The authors performed parametric analysis with both an autosomal dominant model and a recessive model, as well as non-parametric analysis.

Other Details: 
Diagnostic criteria:

"Remarkable deviation (depending on the age, at least two years) in reading skills compared to chronological age and normal performance intelligence quotient (IQ >85). The diagnosis of dyslexia was determined by Finnish reading and spelling tests designed for children under 13 years of age [18] and adults, [19] described elsewhere in detail. [20] The IQ was determined by WAIS-R21 or WISC-R22 and subjects with an IQ below 85 were excluded from this study. In order to determine whether dyslexia was the result of a deficit in one or more of phonological awareness, rapid naming, or verbal short term memory, reading related neurocognitive skills were assessed by neuropsychological tests. [23–26]"

Markers:  D2S2216

7q32 Dyslexia Susceptibility to developmental dyslexia Kaminen et al 2003

Additional Phenotype Details: Typical diagnostic criteria for dyslexia include remarkable deviation from population mean on age-appropriate standardized reading and spelling tests, such as those in the Wechsler intelligence tests. Reading tests may include oral reading and non-word reading.

Usually, a Performance Intelligence Quotient (PIQ) of at least 70 or 80 on the age-appropriate Weschler test is also a criterion.

References (fourth editions of these tests are also now available):

Wechsler D. 1991. Wechsler intelligence scale for children- third edition (WISC-III). San Antonio: The Psychological Corporation.

Wechsler D. 1997. Wechsler Adult Intelligence Scale-III (WAIS-III). San Antonio: The Psychological Corporation.

Basic Study Type:  Linkage study

Study Cohort: 
"Eleven families with 97 subjects, of whom 70 were available for thorough testing for dyslexia, were studied. Nine families with 70 members altogether (28 dyslexic, 28 non-dyslexic, and 14 not tested) were recruited from the Department of Paediatric Neurology at the Hospital for Children and Adolescents (formerly Children’s Castle Hospital), University of Helsinki, Finland. These families were selected from about 14017 based on their informativeness for linkage. Two families with 27 members altogether (12 dyslexic, 11 non-dyslexic, and four uncertain) were recruited from the Central Hospital of Central Finland, Jyväskylä, Finland. In these two families, dyslexia testing, with normal results, was performed in three of the non-dyslexic subjects, and a further eight subjects reporting normal reading performance were also classified as unaffected."

Genotyping Methods: 
"Genome wide scan was carried out at the Finnish Genome Centre, University of Helsinki, using 376 microsatellite markers from the Applied Biosystems Linkage Mapping Set MD-10. The average distance between markers was 10 cM. DNA (20 ng) was dried on microtitre plates for each PCR assay. The PCRs were performed in 5 µl volumes in conditions recommended by the reagent manufacturer (Applied Biosystems). The fluorescence labelled PCR products were pooled (10-20 markers/pool), and separated on a MegaBace 1000 capillary electrophoresis instrument (Molecular Dynamics, Sunnyvale, CA). The alleles were visualised using Genetic Profiler 1.5 software (MolecularDynamics)."

Analysis Methods: 
The authors performed parametric analysis with both an autosomal dominant model and a recessive model, as well as non-parametric analysis.

Other Details: 
Diagnostic criteria:

"Remarkable deviation (depending on the age, at least two years) in reading skills compared to chronological age and normal performance intelligence quotient (IQ >85). The diagnosis of dyslexia was determined by Finnish reading and spelling tests designed for children under 13 years of age [18] and adults, [19] described elsewhere in detail. [20] The IQ was determined by WAIS-R21 or WISC-R22 and subjects with an IQ below 85 were excluded from this study. In order to determine whether dyslexia was the result of a deficit in one or more of phonological awareness, rapid naming, or verbal short term memory, reading related neurocognitive skills were assessed by neuropsychological tests. [23–26]"

Markers:  D7S530

12q21-12q24 Stuttering Susceptibility to nonsyndromic stuttering Kang et al 2010

Additional Phenotype Details: Stuttering may be diagnosed using the Stuttering Severity Instrument (SSI). In some studies, subjects are asked to read a standardized text aloud and to engage in free speech for a certain amount of time, and the percentage of dysfluencies (out of all words, and/or out of all syllables) determines the diagnosis.

Reference

Riley, G. 2009. SSI-4: Stuttering severity instrument--Fourth edition; examiner's manual. Pro-Ed, Austin, TX (2009).

Basic Study Type:  - Linkage analysis - Candidate gene sequencing

Study Cohort: 
Summary:

(1) Members of Pakistani family PKST72
(2) 121 other Pakistani subjects with stuttering
(3) 270 affected subjects from the US and England, of a variety of ethnicities (see below)
(4) 96 Pakistani control subjects
(5) 276 white North American control subjects

"We analyzed families that had participated in previous linkage studies [12] and focused on the largest family, designated PKST72 (Fig. 1). In addition, we studied unrelated cases of stuttering in 46 Pakistani subjects (one from each of the previously studied families [12]) and 77 additional unrelated persons with stuttering from Pakistan, as well as 270 affected, unrelated persons from the United States and England. This last group was enrolled through public appeal."

"The ancestry of the Pakistani and North American–British participants was determined by self-report (see the Supplementary Appendix); all Pakistani participants were Asian in origin, and the affected North American–British participants described themselves as white (206 participants), black (25), Asian (16), Hispanic (13), Native American (1), and other or unknown (9). The mean (±SD) age in our sample of affected, unrelated subjects was 30.7±12.1 years (for the age distribution, see Fig. 2 in the Supplementary Appendix). The Pakistani control subjects consisted of 96 age-matched and sex-matched persons with normal speech from the same region of Pakistan. The control subjects consisted of 276 well-characterized, neurologically normal North American whites who were initially ascertained and evaluated as control subjects in a large study of Parkinson’s disease (Coriell Institute for Medical Research)."

Genotyping Methods: 
"Gene identification and bioinformatic analyses were based on the UCSC Genome Browser, March 2006 assembly. Comparative genomic hybridization [17] was performed with the use of a custom CGH 385K Array (NimbleGen), which was designed to query 10 megabase pairs centered on base pair 99,197,889 (i.e., base pair 94,220,151 to base pair 104,175,626) of the chromosome 12 sequence in seven affected and three unaffected Pakistani subjects. DNA sequencing was performed on genomic DNA that was purified with the use of standard methods. Genetic variants identified by sequencing were considered for further analysis if they met the following criteria: they had not previously been described as a common single-nucleotide polymorphism in the worldwide population (as indicated by an rs number); they altered a known functional protein motif or resulted in an amino acid insertion or deletion; they altered an amino acid that is perfectly conserved in mammals; and they produced a prominent physical alteration, such as a change in charge or polarity, in the amino acid.

"Protein-sequence alignments were performed with the use of MultAlin 5.4.1.[18] Clinical evaluations included a medical history interview and physical examination, a limited skeletal survey, an echocardiographic examination, evaluations of urine for excreted oligosaccharides and of blood for lysosomal hexosaminidase activity, and a dilated-pupil ophthalmologic examination."

Analysis Methods: 
Nonparametric and two-point linkage analyses.

Other Details: 
Inclusion criteria:

"Young children, in whom recovery from stuttering is common, were excluded from the study; also excluded were subjects who reported neurologic or psychiatric symptoms."

Diagnostic criteria:

"Age of 8 years or older; stuttering duration of 6 months or longer; evidence of a family history of stuttering; and speech characterized by more than 4% stuttering dysfluencies, as measured with the Stuttering Severity Instrument, 3rd edition (SSI-3) [15], or a well-characterized standard reading passage [16]."

Markers:  D12S1607

6p21.3-6p22 Dyslexia Orthographic choice Kaplan et al 2002

Basic Study Type:  Linkage and association

Study Cohort: 
Summary:

392 individuals from 104 families (parents and siblings)

Details:

"The sample used in the current study consisted of nuclear families collected by the Colorado Learning Disabilities Research Center (CLDRC) (DeFries et al. 1997). Subjects included members of MZ twin pairs (in which case, only one member of the MZ twin pair was used), DZ twin pairs, and nontwin siblings who have previously been reported in two papers that showed the original evidence for linkage in this region. The DZ twin sample studied by Cardon et al. (1994) showed linkage with a reading composite score, and the twin and sibling samples described by Gaya´n et al. (1999) showed linkage with several reading and language phenotypes. This current sample consisted of 127 families. However, a number of families were uninformative because of missing phenotypes and/or genotypes. Therefore, the sample included in the analyses reported here included 104 families and 392 individuals (parents and siblings), of whom 221 were siblings. There were 8 families with one offspring, 79 families with two offspring, 13 families with three offspring, and 4 families with four offspring. These offspring comprised a total of 142 sib pairs who were informative for linkage analyses, of whom 117 were independent sib pairs, computed as n - 1 per family of n offspring.

"Families were ascertained so that at least one sibling in each family had a school history of reading problems. Families were predominantly white middle-class families ascertained from school districts in the state of Colorado. Subjects for whom English was a second language were not included in the initial sample. Subjects with evidence of serious neurological, emotional, or uncorrected sensory deficits were excluded from the present analyses. The average age of the 221 siblings analyzed was 11.55 years, ranging from 8.02 to 18.53 years."

Genotyping Methods: 
"DNA was extracted from blood and buccal samples that were obtained from parents and offspring. Technicians were blinded through the assignment of random tracking numbers to the clinical samples and through predetermined PCR plate, pooling plate, and gel-lane assignments. Although all members of a single family were analyzed on the same gel, no two relatives were resolved in consecutive lanes. To avoid errors due to overflow, we staggered loading between consecutive lanes by 100 scans. In each gel, two external controls—CEPH1331-1 and CEPH1331-2—and two of nine unrelated internal controls chosen from the sample with RD were included. GeneScan and GenoTyper (ABI/Perkin-Elmer) were used to track and convert ABI377-fluorescent-chromatogram data to base-pair assignments. Two technicians independently scored the output of every gel, compared the consistency of base-pair assignments by use of a Microsoft Excel macro (Allele Comparison), and resolved conflicts or flagged alleles for regenotyping. The final base-pair assignments were then ported to Genetic Analysis System software package, version 2.0 (A. Young, Oxford University, 1993–95), for allele binning and for the identification of allele-inheritance inconsistencies within pedigrees."

Analysis Methods: 
"We performed Haseman-Elston and DeFries-Fulker linkage analyses, as well as transmission/disequilibrium, total-association, and variance-components analyses, on 11 quantitative reading and language phenotypes."

Other Details: 
Phenotypic measures:

"Quantitative-trait data were provided for the following 11 phenotypes: OC (1) is the ability to recognize words’ specific orthographic patterns and was measured here with our experimental tests for orthographic choice (OCH [2]) and homonym choice (HCH [3]); a composite score for both tests (i.e., OC composite) was created by averaging the z scores for both tasks. PD (4) is the oral reading of nonwords, which have straightforward pronunciations that are based on their spelling. PA (5) is the ability to isolate and manipulate abstract subsyllabic sounds in speech; for the present analyses, it was measured with our experimental phoneme-transposition (PTP [6]) and phoneme-deletion (PDL [7]) tasks, as well as with a composite score for both tests. WR (8) was measured with our experimental timed-word-recognition (TWR [9]) task and the untimed standardized PIAT word-recognition (PWR [10]) task, which required subjects to read words aloud; a composite score for both tests was also created. Finally, the discriminant score (DISC [11]) for reading was a weighted composite of the reading recognition, reading comprehension, and spelling subtests of the PIAT [Peabody Individual Achievement Test]."

Markers:  D6S461 ,  JA04

7q31 Dyspraxia Susceptibility to developmental verbal dyspraxia Lai et al 2000

Additional Phenotype Details: Impaired ability to sequence movements for speech.

Basic Study Type: - Candidate gene sequencing - FISH (fluorescent in situ hybridization)

Study Cohort: 

Summary:

Subjects were the KE family and two unrelated children with chromosome translocations, patients CS and BRD. The KE family includes many members with developmental verbal dyspraxia. Patient CS was a 5.5 year old male with language impairment and verbal dyspraxia. Patient BRD was an 8 year old male with "receptive and expressive language problems, accompanied by behavioral difficulties and low-range intellectual abilities, despite normal physical/motor development."

Details:

"In 1987, the KE family (see fig. 1) was referred for genetic counseling by the director of a school for children with speech and language problems, at which many family members had been pupils. The condition was characterized as a developmental verbal dyspraxia (Hurst et al. 1990)."

"CS is a 5.5-year-old boy with language impairment and verbal dyspraxia. He has a de novo balanced reciprocal translocation t(5;7)(q22;q31.2) which was identified prior to his birth via amniocentesis. Examination at birth showed no abnormalities, but he was referred back to the genetics team at age 2 years because of concerns of delayed speech and mild motor delay. Subsequent assessment at age 3 years 6 mo, performed by means of the Bailey scale, gave an overall mental development in the mildly delayed range. Although nonverbal skills were in the normal range, there was impairment in both understanding and expression of speech. A diagnosis was made of oral dyspraxia. By 4 years of age, CS was able to put two words together, and his understanding had progressed. Fine and gross motor development had also improved, although there was still evidence of mild impairment. There is no history of speech and language disorder in the family of CS, and none of his siblings (one full sibling and three half-siblings) have any language problems. His mother reports that he has never been able to laugh spontaneously or to sneeze."

"BRD is an 8-year-old boy with a history of receptive and expressive language problems, accompanied by behavioral difficulties and low-range intellectual abilities, despite normal physical/motor development. He continues to show difficulties following verbal instructions in school, and has word-finding and sequencing problems accompanied by poor articulation. An MRI scan at age 6 years 11 months detected a small dysembryoplastic neuroepithelial tumor in his right temporal lobe. A more detailed description of the clinical phenotype of BRD is given in Warburton et al. (2000). Cytogenetic analysis previously revealed a de novo balanced reciprocal translocation, t(2;7)(p23;q31.3) (Warburton et al. 2000)."

Genotyping Methods: 

"Construction of Human-Hamster Somatic Cell Hybrids:"

"The Chinese hamster mutant cell line a23, deficient in thymidine kinase, was cultured in 5% CO2 as a monolayer in Dulbecco’s modification of Eagle medium (DMEM, Life Technologies) supplemented with 10% fetal calf serum (FCS). White cells were separated from peripheral blood from three affected members of the KE family (II-2, II-9, and III-20) using Histopaque (Sigma). Each sample was combined in equal proportions with trypsinized a23 cells and was placed in serum-free medium. After the cells were spun down, the medium was aspirated. The cell mixture was resuspended in 50% polyethylene glycol (PEG, molecular weight 1450, Sigma), was washed, and was set up in culture with DMEM and 10% FCS at low cell density. After 24 h, the culture medium was replaced with the same medium containing hypoxanthine, aminopterin, and thymidine (HAT, Life Technologies). Once hybrid colonies reached 2–4 mm in diameter (14 d after fusion), they were picked into 24-well plates. DNA prepared from samples of 1 x 10^5–5 x 10^5 cells was tested by PCR for chromosome 7–specific markers."

Genotyping:

"Primers flanking novel polymorphic repeats were designed using the PRIMER program, accessed through the United Kingdom Human Genome Mapping Project resource center. Fluorescence-based semiautomated genotyping was performed as described (Fisher et al. 1998)."

FISH methods:

"PHA-stimulated T lymphocytes or lymphoblastoid cells lines were harvested by conventional techniques, and fixed suspensions were dropped onto slides. Slides were denatured at 70deg C in 70% formamide/2 x SSC for 2 min 30 s, were incubated in cold 2 x SSC, and were serially dehydrated in 70%, 90%, and 100% (twice) ethanol at room temperature. Probe DNA was labeled by nick translation with biotin (Gibco BRL BioNick Labeling System) or Digoxigenin (DIG; Roche) following
manufacturers’ protocols. FISH of BACs and PACs was performed as described (Millwood et al. 1997). Biotinylated probes were visualized with two layers of FITC-conjugated streptavidin (green; Vector Labs) and biotinylated goat anti-streptavidin (Vector Labs). DIG-labeled probes were visualized with mouse anti-DIG antibodies (Roche), followed by Cy5-conjugated rabbit anti-mouse and goat anti-rabbit antibodies (pseudocolored blue). Chromosomes were counterstained with Vectorshield containing propidium iodide (Vector Labs). The slides were viewed on a Nikon Optiphot, and images were captured with a Bio-Rad MRC 1024 laser-scanning confocal microscope and Lasersharp software."

"Determination of Genomic Organization of CAGH44:"

"Exon/intron boundaries for exons 1–2 of CAGH44 were identified by comparison of the reported mRNA sequence (accession U80741) to completed BAC sequence. Boundaries for exons 3–6 were determined using either long-range PCR or vectorette (Munroe et al. 1994). For the former, we amplified products from human genomic or BAC DNA, using the Expand Long Template System (Boehringer Mannheim), with primers designed from CAGH44 mRNA. Products were sequenced using BigDye Terminator Cycle Sequencing kits (PE Applied Biosystems). For the vectorette method, libraries were made by complete digestion of BAC DNA using frequent-cutting restriction enzymes followed by ligation to annealed vectorette bubble anchors. Fragments containing exon/intron boundary sequences were amplified from vectorette libraries by PCR with the NotI-A primer in combination with specific primers derived from available CAGH44 sequences."

Analysis Methods: 

"Linkage analyses were run under the assumption that the disorder in the KE pedigree is due to a single autosomal dominant locus with full penetrance, as described (Fisher et al. 1998)."

Markers: 

7q33 Dyslexia Susceptibility to developmental dyslexia Matsson et al 2011

Additional Phenotype Details: Typical diagnostic criteria for dyslexia include remarkable deviation from population mean on age-appropriate standardized reading and spelling tests, such as those in the Wechsler intelligence tests. Reading tests may include oral reading and non-word reading.

Usually, a Performance Intelligence Quotient (PIQ) of at least 70 or 80 on the age-appropriate Weschler test is also a criterion.

References (fourth editions of these tests are also now available):

Wechsler D. 1991. Wechsler intelligence scale for children- third edition (WISC-III). San Antonio: The Psychological Corporation.

Wechsler D. 1997. Wechsler Adult Intelligence Scale-III (WAIS-III). San Antonio: The Psychological Corporation.

Basic Study Type:  Linkage study

Study Cohort: 
"The original Finnish sample set was used in the fine-mapping stages 1 and 2 (FM1 and FM2) and consisted of 97 subjects from 11 families (40 affected, 39 healthy, 18 unknown) from the Helsinki region (Kaminen et al. 2003). The extended Finnish material, used in FM3, includes all individuals of the original Finnish sample set and additional families, including totally 457 individuals (of which 153 affected, 254 healthy and 50 unknown) from the Helsinki region and from the Jyva¨skyla¨ Longitudinal study of Dyslexia (JLD). The German sample set, used in FM1 and FM3, included 251 German dyslexia families (1050 individuals; 251 probands with dyslexia, 178 affected sibs, 119 healthy sibs and 502 parents with phenotype unknown) (Anthoni et al. 2007). For the German sample set, we also used trios classified according to severity of dyslexia in probands."

Genotyping Methods: 
"The microsatellite repeats used in fine-mapping stage 1 (FM1) and the 142 SNPs spanning 20 Mb of sequence on chromosome 7q31–q34 in FM2, were amplified and genotyped as previously reported (Anthoni et al. 2007). In both FM1 and FM2, we used the original Finnish sample set. In short, microsatellite markers were genotyped and scored with MegaBACE 1000 DNA Analyzer System (Molecular Dynamics/Amersham Life Sciences) and the Genetic Profiler software (Amersham Biosciences). The microsatellite markers used for genotyping the German sample set were: D7S1799, D7S496, D7S525, D7S650, D7S648, D7S2519, D7S649, D7S1804, D7S509 and D7S495. The positions of the markers used are according to Genome Build 36.3. Primer sequences for genotyping of microsatellite markers are available upon request. All SNP markers chosen for this study were present in phase 1 and 2 of HapMap release 24 and had a minor allele frequency (MAF)>0.1. Information regarding SNPs for mapping and gene tagging were gathered from The International HapMap consortium (http:\\www.hapmap.org/) using phase 1 and phase 2 Data Release 24 for CEU population and Entrez SNP (http:\\www.ncbi.nlm.nih.gov/sites/entrez). Marker positions and locations are according to NCBI (http:\\www.ncbi.nlm.nih.gov/) Mapviewer, Homo Sapiens Build 36.3 (http;\\www.ncbi.nlm.nih.gov/projects/mapview/). Database of Genomic Variants, (Genome Build 36) was used to locate any reported regions of copy number variations overlapping with genotyped SNPs in FM3 in the candidate gene region on chromosome 7q33–q34. D’ for visualizations of LD in German and Finnish sample sets as well as for the CEU population sample in HapMap was calculated using Haploview 4.1 with the confidence intervals option for LD block definition (Barrett et al. 2005).

"For SNP genotyping, we used a Sequenom (San Diego, CA) instrument with iPLEX Gold assay technology. Two investigators scored SNP genotypes independently. Before genotyping at stages FM2 and FM3, we validated all SNPs on DNA from 14 trios (42 individuals) of the CEPH population sample used in HapMap. In addition, all SNPs were re-genotyped on 5% of the samples and the concordance for FM2 and FM3 was 99.9% for both Finnish and German sample sets. In FM3, we successfully genotyped 52 SNPs in the extended Finnish sample set and 53 SNPs in the German sample set (Supplementary Table 1) with a success rate (SR) of[91 and[95%, respectively. The genotype call rate was at least 70% in all fine-mapping steps. Supplementary Table 1 summarizes all markers included in the genetic mapping approaches (FM1 to 3)."

Analysis Methods: 
Non-parametric linkage analysis (NPL), pedigree disequilibrium tests (PDT) for families, and transmission disequilibrium tests (TDT)for trios.

Other Details: 
Diagnostic criteria (from Kaminen et al 2003, "A genome scan for developmental dyslexia confirms linkage to chromosome p11 and suggests new locus on 7q32", J Med Genet 40(5):340–345):

"Remarkable deviation (depending on the age, at least two years) in reading skills compared to chronological age and normal performance intelligence quotient (IQ >85). The diagnosis of dyslexia was determined by Finnish reading and spelling tests designed for children under 13 years of age [18] and adults, [19] described elsewhere in detail. [20] The IQ was determined by WAIS-R21 or WISC-R22 and subjects with an IQ below 85 were excluded from this study. In order to determine whether dyslexia was the result of a deficit in one or more of phonological awareness, rapid naming, or verbal short term memory, reading related neurocognitive skills were assessed by neuropsychological tests. [23–26]"

Markers: 

7q31 SLI Discrete language phenotype O'Brien et al 2003

Basic Study Type:  Association and linkage studies

Study Cohort: 
Summary: 1608 individuals, 604 families

All subjects were genotyped. 96 probands were also "directly sequenced for the mutation in exon 14 of FOXP2."

Details:

"The participants of the present study consisted of probands identified in a population-based study of children with and without language impairment who are being followed during their school years. The probands were identified when they were in kindergarten from a sample of children enrolled in schools in Iowa and Illinois. All 7,218 children from the chosen communities were given a language-screening test. Those who failed and one-third of those who passed were sampled for a more complete language, speech, hearing, and IQ assessment. By use of this information, children were diagnosed with respect to their language status, in accordance with a system described by Tomblin et al. (1996). The results of the screening and diagnosis were published in a study that found a 7.4% incidence of SLI in that group (Tomblin et al. 1997). The parents of 1,744 participants who received the diagnostic evaluations were asked to participate in a registry for future research. From this registry, 604 children were sampled to participate in a longitudinal study. This sample consisted of all children who were language impaired and for whom assent was obtained, as well as a random sample of those children with assent who were developing typically. Phenotypic measures were obtained in second grade for all these children (table 1). Information was also collected on the language phenotype of the siblings of the probands through assessment with one of three language batteries, depending upon the siblings’ ages (table 2). High between-battery correlations had been obtained with these tests, indicating that they were testing the same traits in siblings and probands. Performance IQ (PIQ) was assessed by the performance battery of Wechsler Intelligence Scale for Children-Third Edition (Wechsler 1991). Only children with a PIQ >70 were included in the statistical analysis."

Genotyping Methods: 
"The samples were genotyped for microsatellite repeats in chromosome 7 by amplification of the region by PCR. The PCR product was run on denaturing 6% polyacrylamide gel, and bands were visualized via silver staining. All samples were genotyped for a tetranucleotide repeat (GATT) in the CFTR gene, a marker chosen for ease in genotyping on sequencing gels (Gasparini et al. 1991) as well as its location in the region of critical interest, 3 Mb distal to FOXP2 on 7q31. Next, two tetranucleotide repeat CHLC markers in 7q31, D7S1817 and D7S3052, located 5 Mb proximal to FOXP2, were used to genotype all samples using standard CHLC PCR conditions (Murray et al. 1994). Using a GATA repeat in intron 2 of FOXP2 with primers designed by Wassink et al. (2002), all samples—including those from affected individuals, their family members, and controls—were genotyped, for a total of 1,608 genotyped individuals. By use of the published sequence of FOXP2 available on the Human Genome Gateway Browser and Sequencher 4.1, six additional tetranucleotide repeats were found within the intronic regions of FOXP2, as described by Lai et al. (2001). Primers were designed to amplify these microsatellite repeats, and genotypes were generated for a subset of samples. These genotypes were used to calculate the degree of linkage disequilibrium between the seven markers in FOXP2 using the GOLD program (Abecasis and Cookson 2000). Two markers, both TTTA repeats within the intronic regions between exons 1 and 2 and exons 3a and 3b of FOXP2 (Lai et al. 2001; Bruce and Margolis 2002), were not in linkage disequilibrium with the GATA repeat and were used to genotype samples from families with siblings. A total of 781 samples were genotyped for all three markers. These genotypes were analyzed again to confirm that the additional markers were not in linkage disequilibrium with the GATA repeat and therefore would provide additional information to test for association. Primers and PCR conditions are available upon request."

Analysis Methods: 
The authors performed sib-pair linkage with both the discrete phenotype and the continuous test scores.

For the association analysis, "affected family–based controls (AFBAC) analysis and the extended transmission/disequilibrium test (ETDT) for multiple alleles were used with the discrete language phenotype, and the quantitative transmission/disequilibrium test (QTDT) was used with the continuous language scores."

Other Details: Diagnostic criterion:

Composite language score of 1.14 SDs below the mean for second grade.

Tests for probands:

PPVT-R, CREVET, CELF-III (Sentence structures, concepts and directions; listening to paragraphs; word structure, recalling sentences), and narrative generation (total clauses)

Tests for siblings:

Ages 4-6:
TOLD-2:P (picture vocabulary, oral vocabulary, grammatic understanding, sentence imitation, grammatic completion)
Ages 7-8:
PPVT-R and CELF-III (sentence structures, concepts and directions, word structures, recalling sentences, listening to paragraphs)
Ages 9-14:
PPVT-R and CELF-III (formulated sentences, concepts and directions, recalling sentences, listening to paragraphs)

Markers:  D7S3052

7q31.1-7q31.3 AOS Childhood apraxia of speech Palka et al 2012

Basic Study Type:  - aCGH analyses (array comparative genomic hybridization) - FISH (fluorescent in situ hybridization) study

Study Cohort: 
Summary:

10-year-old girl with childhood apraxia of speech (CAS) and mild mental retardation

Detail:

"The patient is a 10-year-old girl, the second child of healthy, nonconsanguineous parents. She was born at term, by caesarean section, after a pregnancy with intrauterine growth retardation identified by fetal ultrasound at 7 months. At birth, growth parameters were in the normal range. Developmental milestones were delayed. On physical examination, she had a high arched palate and lordosis (Fig 1a and 1b). The rest of the physical exam was normal. Brain MRI was normal. To define the phenotype more precisely, a detailed psychological evaluation was conducted at 12 years. Mild psychomotor retardation with a more severe language delay was noted."

IQ

"IQ test was performed with theWechsler Intelligence Scale for Children—Revised [37]. The total IQ was 71, indicating mild mental retardation. Verbal IQ (57) and performance IQ (88) were impaired with a significant difference between the 2 partial IQs."

Language

"Language was tested using the Peabody Picture Vocabulary Test (third edition) and the Italian test Batteria di Valutazione Neuropsicologica per l’Adolescenza [38,39]. The Peabody Picture Vocabulary Test was used to assess receptive vocabulary. Raw score was 84 with a standard score lower than 65, showing a delay compared with her chronological age. The Batteria di Valutazione Neuropsicologica per l’Adolescenza was organized in 3 subtests: 1 for the comprehensive language (Token Test) and 2 for the expressive language (Naming Ability and Spontaneous Language Production). The Token Test showed a delay; the patient was able to understand 30 of 36 sentences, showing a standard score of 35 based on a mean of 50. The expressive language result also showed impairment. The patient was able to name correctly 49 of 88 pictures but with dyslalia, several errors in semantic generalization and paraphrases for use (standard score 40); she was not always able to make syntactical and semantical correct sentences with the available words (standard score 59)."

Adaptive behavior (including communication)

"Adaptive behavior was assessed using the Italian form of the Vineland Adaptive Behavior Scales (Table 1) [40]. The interviews assessed up to 4 domains of adaptive behavior (communication, daily living skills, socialization, and motor skills). In the communication domain, verbal comprehension was restricted to simple actions in sequence, and expressive language was organized in very short sentences, without articles and using the infinite form of the verb. Phonological problems were also present. Written language was impaired: the patient was able to read but without prosody, and writing was mainly dictation. In the daily living skills domain, the patient had abilities necessary for daily living. The socialization domain assessment revealed that the girl was aware of her limits and thus was inhibited with unfamiliar people. In the motor field, she presented a mild hindrance with difficulties in fine praxis and balance problems."

Genotyping Methods: 
"The karyotype on cultured lymphocytes performed by 3 laboratories was 46,XX with a 550 G-band resolution. An aCGH analysis using the CytoChip 575-Kb resolution bacterial artificial chromosome (BAC) array (BlueGnome, Cambridge, United Kingdom) was performed according to the recommendations of the manufacturer. Data were analyzed using the BlueFuse for microarray software package (BlueGnome). . .
"The chromosomal abnormality was confirmed by fluorescence in situ hybridization analysis in 50% cells, using multicolor chromosome banding with a chromosome 7 specific probe set and with a commercially available probe for the FOXP2 region (RP11-328M22) according to the manufacturer’s instructions (Fig 1f)."

Other Details: 
"The analysis disclosed a deletion of ~14.8 Mb on chromosome 7q31, from BAC RP11-328M22 to BAC RP11-224A1 (Fig 1c). A repeated high-resolution cytogenetic analysis revealed a mosaic deletion of the segment between 7q31.1 and 7q31.3 (Fig 1d and 1e)."

After FISH:
". . .the chromosomal complement of the patient was reinterpreted as 46,XX [50%]/46,XX,del(7q (q31.1 -> 31P.3)[50%]. Parental karyotypes were normal."

Markers: 

6p22.1 Reduced expression of KIAA0319 Paracchini et al 2006

Markers:  rs4504469-rs2038137-rs2143340 112 haplotype

16q12.1-16q23.1 Stuttering Susceptibility to stuttering Raza et al 2012

Additional Phenotype Details: Stuttering may be diagnosed using the Stuttering Severity Instrument (SSI). In some studies, subjects are asked to read a standardized text aloud and to engage in free speech for a certain amount of time, and the percentage of dysfluencies (out of all words, and/or out of all syllables) determines the diagnosis.

Reference
Riley, G. 2009. SSI-4: Stuttering severity instrument--Fourth edition; examiner's manual. Pro-Ed, Austin, TX (2009).

Basic Study Type:  Linkage study

Study Cohort: 
"Research subjects were enrolled in Lahore and surrounding areas of Punjab, Pakistan. . .The pedigree of family PKST58 is shown in Fig. 1. DNA samples were obtained from 26 family members (starred) who were genotyped, 14 of whom were classified as affected."

Genotyping Methods: 
"A genome-wide linkage scan was performed on the Illumina Human Likage-24 Chip (containing 5913 SNPS, ftp://ftp.illumina.com, username and password available from Illumina). SNP genotypes were qualified using seven genotyping data analysis parameters (cluster separation, call frequency, AB R mean, AB T mean, Mendelian inheritance, heterozygote excess, and minor allele frequencies, http://www.illumina.com/Documents/products/technotes/technote_infinium_genotyping_data_analysis.pdf), after which 5448 SNPs met criteria for linkage analysis."

Follow-up genotyping in chromosomes 16, 6, 11, 9, and 21: "We selected microsatellite markers spanning these suggestive linkage loci from UCSC genome browser (hg18 assembly) for additional genotyping and fine mapping."

Analysis Methods: 
The authors performed an initial parametric linkage analysis for the genome-wide scan, followed by analyses under modified recessive, strict recessive, additive, and dominant models for the fine mapping. They also calculated simulated LOD scores.

Other Details: 
Diagnostic criteria:

At least 4% stuttering dysfluencies on the Stuttering Severity Index, 3rd edition (SSI-3). "All individuals scored as affected were persistent stutterers."

Markers: 

3q13.2-3q13.33 Stuttering Susceptibility to stuttering Raza et al 2010

Additional Phenotype Details: Stuttering may be diagnosed using the Stuttering Severity Instrument (SSI). In some studies, subjects are asked to read a standardized text aloud and to engage in free speech for a certain amount of time, and the percentage of dysfluencies (out of all words, and/or out of all syllables) determines the diagnosis.

Reference
Riley, G. 2009. SSI-4: Stuttering severity instrument--Fourth edition; examiner's manual. Pro-Ed, Austin, TX (2009).

Basic Study Type:  Linkage study

Study Cohort: 
"All the available individuals of a consanguineous [Pakistani] family (PKST77, Fig. 1)," n = 22.

Genotyping Methods: 
"A genome-wide linkage scan was performed using 6,090 SNPs assayed on the Illumina Human Linkage-12 Chip. . .The interval extending from markers D3S3044 (112.44 Mb) to D3S3636 (126.64 Mb) was genotyped with additional microsatellite and SNP markers."

Analysis Methods: 
The authors performed two-point and multipoint analysis under an autosomal recessive model.

Other Details: 
Diagnostic criteria:

A score >16 on the Stuttering Severity Instrument, 3rd edition (SSI-3). "All individuals scored as affected were persistent stutterers, aged eight years or above who have stuttered for more than 6 months."

Markers:  D3S1303 ,  D3S1310 ,  rs1317244rs7631540

12q22-12q24.2 Stuttering Susceptibility to stuttering Riaz et al 2005

Additional Phenotype Details: Stuttering may be diagnosed using the Stuttering Severity Instrument (SSI). In some studies, subjects are asked to read a standardized text aloud and to engage in free speech for a certain amount of time, and the percentage of dysfluencies (out of all words, and/or out of all syllables) determines the diagnosis.

Reference
Riley, G. 2009. SSI-4: Stuttering severity instrument--Fourth edition; examiner's manual. Pro-Ed, Austin, TX (2009).

Markers: 

7q31.2 AOS Childhood apraxia of speech Rice et al 2012

Basic Study Type:  aCGH (array comparative genomic hybridization)

Study Cohort: 
Summary:

4-year-old boy with childhood apraxia of speech (CAS) and Pervasive Developmental Disorder-Not Otherwise Specified (PDD-NOS)

His mother, age 24, diagnosed with persistent CAS, receptive and expressive language delay, PDD-NOS, and specific learning disabilities

See paper for detail.

Genotyping Methods: 
"aCGH analysis was performed using the Agilent 2 x 105 K custom array (Agilent Technologies, Inc., Santa Clara, CA), designed for clinical testing by the International Standards for Cytogenomic Arrays Consortium [ISCA: https://www.iscaconsortium.org/]. This array contains more than 105,000 oligonucleotide probes and provides high density coverage for clinically relevant deletion/ duplication syndromes and the telomere and pericentromeric regions, together with genome-wide coverage with an average probe spacing of ~35 kb. Preparation of test and control DNA, labeling, and hybridization were performed following the manufacturer’s protocols."

Markers: 

7q31 SLI General language skills Rice et al 2009

Additional Phenotype Details: 

The following are examples of standardized tests for various aspects of language ability:

Clinical Evaluation of Language Fundamentals (CELF)
Test of Language Development (TOLD)
Test of Early Grammatical Impairment (TEGI)
Comprehensive Test of Phonological Processing subtest (CTOPP)
Peabody Picture Vocabulary Test (PPVT)

Additional measures include utterance length and performance on a non-word repetition task (NWR).

Basic Study Type:  Linkage and association studies

Study Cohort: 
Summary:

322 subjects (86 probands, 134 siblings, 102 parents and other relatives)

Detail:

Participants "were drawn from an ongoing longitudinal study of Specific Language Impairment. . .There were 86 probands, mean ages 6;1 to 8;10 across variables, ascertained from school speech pathology caseloads followed by assessment to meet the requirements of the study. There were a total of 134 siblings: 77 males, mean age 8;6; 57 females, mean age 8;5. Previous studies report longitudinal outcomes for part of this sample, documenting that the children’s language impairments persist into adolescence [13, 69–72]."

Genotyping Methods: 
For linkage study:

"Several extended families were included, and some phenotypes were available for relatives besides siblings. The pair counts for each phenotype by the type of relative are shown in Table 3, and these data were included in the linkage analyses. . .Well-characterized microsatellite markers in the critical regions of linkage were identified through the NCBI UNISTS website, with intermarker centimorgan distances taken from the Rutgers Combined Linkage-Physical map v2 [89]. Markers were selected to be about 2 cM apart, particularly targeting the candidate genes. The positions and heterogeneity of each marker are shown in Table 4.

"Fluorescent labeled primers for the selected markers were obtained from Applied Biosystems (Foster City, CA) or IDT (Coralville, IA) and genotyping was done on an AB 3730 DNA Analyzer (Applied Biosystems, Foster City, CA). Allele calls were reviewed by two experienced technologists and were checked for inheritance and recombination errors using the programs GAS [90] and MERLIN [91]. Any markers with unresolvable genotypes were re-run and re-evaluated or eliminated from the analysis."

For association study:

"We genotyped 53 SNPs covering the candidate genes DCDC2 and KIAA0319 on chromosome 6p22 and the FOXP2 region of chromosome 7. SNPs were selected which tag regions of linkage disequilibrium using the Tagger function on HapMap (URL), along with SNPs selected to replicate previously reported associations and haplotypes with RD. In all, 36 SNPs were genotyped on chromosome six spanning the genes DCDC2, KIAA0319, and TTRAP. On chromosome 7, we genotyped 17 SNPs spanning FOXP2, including the region upstream of the gene. . .Genotyping was done on a Sequenom MassArray iPlex system."

Analysis Methods: 
Linkage analysis:

The authors performed linkage analysis with both quantitative and categorical measures, using MERLIN and verifying the results by running the same quantitative analysis using the DeFries-Fulker Augmented analysis.

Association analysis:

"Only quantitative traits were used in this analysis, and analysis was again done by two methods: QTDT and FBAT. The same quantitative measures were used as in the linkage analyses. "

Other Details: 
Inclusion criteria:

"Probands met four entrance screening criteria. The first was nonverbal intelligence above 85. For children ages 3;6 to 6;11 it was measured with the Columbia Mental Maturity Scales [73] and for children ages 7–17, the performance IQ scales from the Wechsler Intelligence Test for Children [74] were utilized. Parents and children ages 17 years and older were evaluated with the performance scales for the Wechsler Intelligence Test for Adults [75]. Probands met exclusionary criteria for nonverbal intelligence; this requirement was not met for parents and siblings whose intellectual status was an outcome of the study. The second criterion for the probands was normal hearing acuity. The third was no history of neurological disorders or diagnosis of autism. The fourth was intelligible speech sufficient for language transcription and production of target phonemes used in word final morphology, as in “goes” and “talks.” Probands were identified as SLI based on language performance one standard deviation or more below the mean on an age appropriate language test. All probands were screened for articulation to ensure they could produce the phonemes needed for morphological measurement and sufficient intelligibility for reliable spontaneous language transcription. Family members received age appropriate speech, language, and reading assessments. Siblings were recruited from age 2 years to adulthood. Within age levels, all participants received the same assessments. The probands and siblings received multiple times of measurement as part of the longitudinal study. For the phenotyping in this study, the lowest value of each variable of interest was selected. This is in keeping with the methods used in the SLI Consortium studies where past or current language performance was used to identify probands [3]. Further, the lowest performance estimate captures the late talker status of siblings."

Diagnostic criteria:

"Probands were identified as SLI based on language performance one standard deviation or more below the mean on an age appropriate language test."

Tests used:

Woodcock and GORT (reading)
GFTA (articulation)
MLU, TEGI, CTOPP, PPVT and the Omnibus language score ("facets of language").

Markers:  D7S2459

1p36 SLI General language skills Rice et al 2009

Additional Phenotype Details: 

The following are examples of standardized tests for various aspects of language ability:

Clinical Evaluation of Language Fundamentals (CELF)
Test of Language Development (TOLD)
Test of Early Grammatical Impairment (TEGI)
Comprehensive Test of Phonological Processing subtest (CTOPP)
Peabody Picture Vocabulary Test (PPVT)

Additional measures include utterance length and performance on a non-word repetition task (NWR).

Basic Study Type:  Linkage and association studies

Study Cohort: 
Summary:

322 subjects (86 probands, 134 siblings, 102 parents and other relatives)

Detail:

Participants "were drawn from an ongoing longitudinal study of Specific Language Impairment. . .There were 86 probands, mean ages 6;1 to 8;10 across variables, ascertained from school speech pathology caseloads followed by assessment to meet the requirements of the study. There were a total of 134 siblings: 77 males, mean age 8;6; 57 females, mean age 8;5. Previous studies report longitudinal outcomes for part of this sample, documenting that the children’s language impairments persist into adolescence [13, 69–72]."

Genotyping Methods: 
For linkage study:

"Several extended families were included, and some phenotypes were available for relatives besides siblings. The pair counts for each phenotype by the type of relative are shown in Table 3, and these data were included in the linkage analyses. . .Well-characterized microsatellite markers in the critical regions of linkage were identified through the NCBI UNISTS website, with intermarker centimorgan distances taken from the Rutgers Combined Linkage-Physical map v2 [89]. Markers were selected to be about 2 cM apart, particularly targeting the candidate genes. The positions and heterogeneity of each marker are shown in Table 4.

"Fluorescent labeled primers for the selected markers were obtained from Applied Biosystems (Foster City, CA) or IDT (Coralville, IA) and genotyping was done on an AB 3730 DNA Analyzer (Applied Biosystems, Foster City, CA). Allele calls were reviewed by two experienced technologists and were checked for inheritance and recombination errors using the programs GAS [90] and MERLIN [91]. Any markers with unresolvable genotypes were re-run and re-evaluated or eliminated from the analysis."

For association study:

"We genotyped 53 SNPs covering the candidate genes DCDC2 and KIAA0319 on chromosome 6p22 and the FOXP2 region of chromosome 7. SNPs were selected which tag regions of linkage disequilibrium using the Tagger function on HapMap (URL), along with SNPs selected to replicate previously reported associations and haplotypes with RD. In all, 36 SNPs were genotyped on chromosome six spanning the genes DCDC2, KIAA0319, and TTRAP. On chromosome 7, we genotyped 17 SNPs spanning FOXP2, including the region upstream of the gene. . .Genotyping was done on a Sequenom MassArray iPlex system."

Analysis Methods: 
Linkage analysis:

The authors performed linkage analysis with both quantitative and categorical measures, using MERLIN and verifying the results by running the same quantitative analysis using the DeFries-Fulker Augmented analysis.

Association analysis:

"Only quantitative traits were used in this analysis, and analysis was again done by two methods: QTDT and FBAT. The same quantitative measures were used as in the linkage analyses. "

Other Details: 
Inclusion criteria:

"Probands met four entrance screening criteria. The first was nonverbal intelligence above 85. For children ages 3;6 to 6;11 it was measured with the Columbia Mental Maturity Scales [73] and for children ages 7–17, the performance IQ scales from the Wechsler Intelligence Test for Children [74] were utilized. Parents and children ages 17 years and older were evaluated with the performance scales for the Wechsler Intelligence Test for Adults [75]. Probands met exclusionary criteria for nonverbal intelligence; this requirement was not met for parents and siblings whose intellectual status was an outcome of the study. The second criterion for the probands was normal hearing acuity. The third was no history of neurological disorders or diagnosis of autism. The fourth was intelligible speech sufficient for language transcription and production of target phonemes used in word final morphology, as in “goes” and “talks.” Probands were identified as SLI based on language performance one standard deviation or more below the mean on an age appropriate language test. All probands were screened for articulation to ensure they could produce the phonemes needed for morphological measurement and sufficient intelligibility for reliable spontaneous language transcription. Family members received age appropriate speech, language, and reading assessments. Siblings were recruited from age 2 years to adulthood. Within age levels, all participants received the same assessments. The probands and siblings received multiple times of measurement as part of the longitudinal study. For the phenotyping in this study, the lowest value of each variable of interest was selected. This is in keeping with the methods used in the SLI Consortium studies where past or current language performance was used to identify probands [3]. Further, the lowest performance estimate captures the late talker status of siblings."

Diagnostic criteria:

"Probands were identified as SLI based on language performance one standard deviation or more below the mean on an age appropriate language test."

Tests used:

Woodcock and GORT (reading)
GFTA (articulation)
MLU, TEGI, CTOPP, PPVT and the Omnibus language score ("facets of language").

Markers:  D1S1592

1p36 SLI Oral reading Rice et al 2009

Additional Phenotype Details: May be assessed using the Gray Oral Reading Test (GORT)

Basic Study Type:  Linkage and association studies

Study Cohort: 
Summary:

322 subjects (86 probands, 134 siblings, 102 parents and other relatives)

Detail:

Participants "were drawn from an ongoing longitudinal study of Specific Language Impairment. . .There were 86 probands, mean ages 6;1 to 8;10 across variables, ascertained from school speech pathology caseloads followed by assessment to meet the requirements of the study. There were a total of 134 siblings: 77 males, mean age 8;6; 57 females, mean age 8;5. Previous studies report longitudinal outcomes for part of this sample, documenting that the children’s language impairments persist into adolescence [13, 69–72]."

Genotyping Methods: 
For linkage study:

"Several extended families were included, and some phenotypes were available for relatives besides siblings. The pair counts for each phenotype by the type of relative are shown in Table 3, and these data were included in the linkage analyses. . .Well-characterized microsatellite markers in the critical regions of linkage were identified through the NCBI UNISTS website, with intermarker centimorgan distances taken from the Rutgers Combined Linkage-Physical map v2 [89]. Markers were selected to be about 2 cM apart, particularly targeting the candidate genes. The positions and heterogeneity of each marker are shown in Table 4.

"Fluorescent labeled primers for the selected markers were obtained from Applied Biosystems (Foster City, CA) or IDT (Coralville, IA) and genotyping was done on an AB 3730 DNA Analyzer (Applied Biosystems, Foster City, CA). Allele calls were reviewed by two experienced technologists and were checked for inheritance and recombination errors using the programs GAS [90] and MERLIN [91]. Any markers with unresolvable genotypes were re-run and re-evaluated or eliminated from the analysis."

For association study:

"We genotyped 53 SNPs covering the candidate genes DCDC2 and KIAA0319 on chromosome 6p22 and the FOXP2 region of chromosome 7. SNPs were selected which tag regions of linkage disequilibrium using the Tagger function on HapMap (URL), along with SNPs selected to replicate previously reported associations and haplotypes with RD. In all, 36 SNPs were genotyped on chromosome six spanning the genes DCDC2, KIAA0319, and TTRAP. On chromosome 7, we genotyped 17 SNPs spanning FOXP2, including the region upstream of the gene. . .Genotyping was done on a Sequenom MassArray iPlex system."

Analysis Methods: 
Linkage analysis:

The authors performed linkage analysis with both quantitative and categorical measures, using MERLIN and verifying the results by running the same quantitative analysis using the DeFries-Fulker Augmented analysis.

Association analysis:

"Only quantitative traits were used in this analysis, and analysis was again done by two methods: QTDT and FBAT. The same quantitative measures were used as in the linkage analyses. "

Other Details: 
Inclusion criteria:

"Probands met four entrance screening criteria. The first was nonverbal intelligence above 85. For children ages 3;6 to 6;11 it was measured with the Columbia Mental Maturity Scales [73] and for children ages 7–17, the performance IQ scales from the Wechsler Intelligence Test for Children [74] were utilized. Parents and children ages 17 years and older were evaluated with the performance scales for the Wechsler Intelligence Test for Adults [75]. Probands met exclusionary criteria for nonverbal intelligence; this requirement was not met for parents and siblings whose intellectual status was an outcome of the study. The second criterion for the probands was normal hearing acuity. The third was no history of neurological disorders or diagnosis of autism. The fourth was intelligible speech sufficient for language transcription and production of target phonemes used in word final morphology, as in “goes” and “talks.” Probands were identified as SLI based on language performance one standard deviation or more below the mean on an age appropriate language test. All probands were screened for articulation to ensure they could produce the phonemes needed for morphological measurement and sufficient intelligibility for reliable spontaneous language transcription. Family members received age appropriate speech, language, and reading assessments. Siblings were recruited from age 2 years to adulthood. Within age levels, all participants received the same assessments. The probands and siblings received multiple times of measurement as part of the longitudinal study. For the phenotyping in this study, the lowest value of each variable of interest was selected. This is in keeping with the methods used in the SLI Consortium studies where past or current language performance was used to identify probands [3]. Further, the lowest performance estimate captures the late talker status of siblings."

Diagnostic criteria:

"Probands were identified as SLI based on language performance one standard deviation or more below the mean on an age appropriate language test."

Tests used:

Woodcock and GORT (reading)
GFTA (articulation)
MLU, TEGI, CTOPP, PPVT and the Omnibus language score ("facets of language").

Markers:  D1S1592

1p36 SLI Speech articulation Rice et al 2009

Additional Phenotype Details: May be tested using the Goldman Fristoe Test of Articulation (GFTA).

Basic Study Type:  Linkage and association studies

Study Cohort: 
Summary:

322 subjects (86 probands, 134 siblings, 102 parents and other relatives)

Detail:

Participants "were drawn from an ongoing longitudinal study of Specific Language Impairment. . .There were 86 probands, mean ages 6;1 to 8;10 across variables, ascertained from school speech pathology caseloads followed by assessment to meet the requirements of the study. There were a total of 134 siblings: 77 males, mean age 8;6; 57 females, mean age 8;5. Previous studies report longitudinal outcomes for part of this sample, documenting that the children’s language impairments persist into adolescence [13, 69–72]."

Genotyping Methods: 
For linkage study:

"Several extended families were included, and some phenotypes were available for relatives besides siblings. The pair counts for each phenotype by the type of relative are shown in Table 3, and these data were included in the linkage analyses. . .Well-characterized microsatellite markers in the critical regions of linkage were identified through the NCBI UNISTS website, with intermarker centimorgan distances taken from the Rutgers Combined Linkage-Physical map v2 [89]. Markers were selected to be about 2 cM apart, particularly targeting the candidate genes. The positions and heterogeneity of each marker are shown in Table 4.

"Fluorescent labeled primers for the selected markers were obtained from Applied Biosystems (Foster City, CA) or IDT (Coralville, IA) and genotyping was done on an AB 3730 DNA Analyzer (Applied Biosystems, Foster City, CA). Allele calls were reviewed by two experienced technologists and were checked for inheritance and recombination errors using the programs GAS [90] and MERLIN [91]. Any markers with unresolvable genotypes were re-run and re-evaluated or eliminated from the analysis."

For association study:

"We genotyped 53 SNPs covering the candidate genes DCDC2 and KIAA0319 on chromosome 6p22 and the FOXP2 region of chromosome 7. SNPs were selected which tag regions of linkage disequilibrium using the Tagger function on HapMap (URL), along with SNPs selected to replicate previously reported associations and haplotypes with RD. In all, 36 SNPs were genotyped on chromosome six spanning the genes DCDC2, KIAA0319, and TTRAP. On chromosome 7, we genotyped 17 SNPs spanning FOXP2, including the region upstream of the gene. . .Genotyping was done on a Sequenom MassArray iPlex system."

Analysis Methods: 
Linkage analysis:

The authors performed linkage analysis with both quantitative and categorical measures, using MERLIN and verifying the results by running the same quantitative analysis using the DeFries-Fulker Augmented analysis.

Association analysis:

"Only quantitative traits were used in this analysis, and analysis was again done by two methods: QTDT and FBAT. The same quantitative measures were used as in the linkage analyses. "

Other Details: 
Inclusion criteria:

"Probands met four entrance screening criteria. The first was nonverbal intelligence above 85. For children ages 3;6 to 6;11 it was measured with the Columbia Mental Maturity Scales [73] and for children ages 7–17, the performance IQ scales from the Wechsler Intelligence Test for Children [74] were utilized. Parents and children ages 17 years and older were evaluated with the performance scales for the Wechsler Intelligence Test for Adults [75]. Probands met exclusionary criteria for nonverbal intelligence; this requirement was not met for parents and siblings whose intellectual status was an outcome of the study. The second criterion for the probands was normal hearing acuity. The third was no history of neurological disorders or diagnosis of autism. The fourth was intelligible speech sufficient for language transcription and production of target phonemes used in word final morphology, as in “goes” and “talks.” Probands were identified as SLI based on language performance one standard deviation or more below the mean on an age appropriate language test. All probands were screened for articulation to ensure they could produce the phonemes needed for morphological measurement and sufficient intelligibility for reliable spontaneous language transcription. Family members received age appropriate speech, language, and reading assessments. Siblings were recruited from age 2 years to adulthood. Within age levels, all participants received the same assessments. The probands and siblings received multiple times of measurement as part of the longitudinal study. For the phenotyping in this study, the lowest value of each variable of interest was selected. This is in keeping with the methods used in the SLI Consortium studies where past or current language performance was used to identify probands [3]. Further, the lowest performance estimate captures the late talker status of siblings."

Diagnostic criteria:

"Probands were identified as SLI based on language performance one standard deviation or more below the mean on an age appropriate language test."

Tests used:

Woodcock and GORT (reading)
GFTA (articulation)
MLU, TEGI, CTOPP, PPVT and the Omnibus language score ("facets of language").

Markers:  D1S1592

6p22 SLI Oral reading Rice et al 2009

Additional Phenotype Details: May be assessed using the Gray Oral Reading Test (GORT)

Basic Study Type:  Linkage and association studies

Study Cohort: 
Summary:

322 subjects (86 probands, 134 siblings, 102 parents and other relatives)

Detail:

Participants "were drawn from an ongoing longitudinal study of Specific Language Impairment. . .There were 86 probands, mean ages 6;1 to 8;10 across variables, ascertained from school speech pathology caseloads followed by assessment to meet the requirements of the study. There were a total of 134 siblings: 77 males, mean age 8;6; 57 females, mean age 8;5. Previous studies report longitudinal outcomes for part of this sample, documenting that the children’s language impairments persist into adolescence [13, 69–72]."

Genotyping Methods: 
For linkage study:

"Several extended families were included, and some phenotypes were available for relatives besides siblings. The pair counts for each phenotype by the type of relative are shown in Table 3, and these data were included in the linkage analyses. . .Well-characterized microsatellite markers in the critical regions of linkage were identified through the NCBI UNISTS website, with intermarker centimorgan distances taken from the Rutgers Combined Linkage-Physical map v2 [89]. Markers were selected to be about 2 cM apart, particularly targeting the candidate genes. The positions and heterogeneity of each marker are shown in Table 4.

"Fluorescent labeled primers for the selected markers were obtained from Applied Biosystems (Foster City, CA) or IDT (Coralville, IA) and genotyping was done on an AB 3730 DNA Analyzer (Applied Biosystems, Foster City, CA). Allele calls were reviewed by two experienced technologists and were checked for inheritance and recombination errors using the programs GAS [90] and MERLIN [91]. Any markers with unresolvable genotypes were re-run and re-evaluated or eliminated from the analysis."

For association study:

"We genotyped 53 SNPs covering the candidate genes DCDC2 and KIAA0319 on chromosome 6p22 and the FOXP2 region of chromosome 7. SNPs were selected which tag regions of linkage disequilibrium using the Tagger function on HapMap (URL), along with SNPs selected to replicate previously reported associations and haplotypes with RD. In all, 36 SNPs were genotyped on chromosome six spanning the genes DCDC2, KIAA0319, and TTRAP. On chromosome 7, we genotyped 17 SNPs spanning FOXP2, including the region upstream of the gene. . .Genotyping was done on a Sequenom MassArray iPlex system."

Analysis Methods: 
Linkage analysis:

The authors performed linkage analysis with both quantitative and categorical measures, using MERLIN and verifying the results by running the same quantitative analysis using the DeFries-Fulker Augmented analysis.

Association analysis:

"Only quantitative traits were used in this analysis, and analysis was again done by two methods: QTDT and FBAT. The same quantitative measures were used as in the linkage analyses. "

Other Details: 
Inclusion criteria:

"Probands met four entrance screening criteria. The first was nonverbal intelligence above 85. For children ages 3;6 to 6;11 it was measured with the Columbia Mental Maturity Scales [73] and for children ages 7–17, the performance IQ scales from the Wechsler Intelligence Test for Children [74] were utilized. Parents and children ages 17 years and older were evaluated with the performance scales for the Wechsler Intelligence Test for Adults [75]. Probands met exclusionary criteria for nonverbal intelligence; this requirement was not met for parents and siblings whose intellectual status was an outcome of the study. The second criterion for the probands was normal hearing acuity. The third was no history of neurological disorders or diagnosis of autism. The fourth was intelligible speech sufficient for language transcription and production of target phonemes used in word final morphology, as in “goes” and “talks.” Probands were identified as SLI based on language performance one standard deviation or more below the mean on an age appropriate language test. All probands were screened for articulation to ensure they could produce the phonemes needed for morphological measurement and sufficient intelligibility for reliable spontaneous language transcription. Family members received age appropriate speech, language, and reading assessments. Siblings were recruited from age 2 years to adulthood. Within age levels, all participants received the same assessments. The probands and siblings received multiple times of measurement as part of the longitudinal study. For the phenotyping in this study, the lowest value of each variable of interest was selected. This is in keeping with the methods used in the SLI Consortium studies where past or current language performance was used to identify probands [3]. Further, the lowest performance estimate captures the late talker status of siblings."

Diagnostic criteria:

"Probands were identified as SLI based on language performance one standard deviation or more below the mean on an age appropriate language test."

Tests used:

Woodcock and GORT (reading)
GFTA (articulation)
MLU, TEGI, CTOPP, PPVT and the Omnibus language score ("facets of language").

Markers: 

6p22 SLI General language skills Rice et al 2009

Additional Phenotype Details: 

The following are examples of standardized tests for various aspects of language ability:

Clinical Evaluation of Language Fundamentals (CELF)
Test of Language Development (TOLD)
Test of Early Grammatical Impairment (TEGI)
Comprehensive Test of Phonological Processing subtest (CTOPP)
Peabody Picture Vocabulary Test (PPVT)

Additional measures include utterance length and performance on a non-word repetition task (NWR).

Basic Study Type:  Linkage and association studies

Study Cohort: 
Summary:

322 subjects (86 probands, 134 siblings, 102 parents and other relatives)

Detail:

Participants "were drawn from an ongoing longitudinal study of Specific Language Impairment. . .There were 86 probands, mean ages 6;1 to 8;10 across variables, ascertained from school speech pathology caseloads followed by assessment to meet the requirements of the study. There were a total of 134 siblings: 77 males, mean age 8;6; 57 females, mean age 8;5. Previous studies report longitudinal outcomes for part of this sample, documenting that the children’s language impairments persist into adolescence [13, 69–72]."

Genotyping Methods: 
For linkage study:

"Several extended families were included, and some phenotypes were available for relatives besides siblings. The pair counts for each phenotype by the type of relative are shown in Table 3, and these data were included in the linkage analyses. . .Well-characterized microsatellite markers in the critical regions of linkage were identified through the NCBI UNISTS website, with intermarker centimorgan distances taken from the Rutgers Combined Linkage-Physical map v2 [89]. Markers were selected to be about 2 cM apart, particularly targeting the candidate genes. The positions and heterogeneity of each marker are shown in Table 4.

"Fluorescent labeled primers for the selected markers were obtained from Applied Biosystems (Foster City, CA) or IDT (Coralville, IA) and genotyping was done on an AB 3730 DNA Analyzer (Applied Biosystems, Foster City, CA). Allele calls were reviewed by two experienced technologists and were checked for inheritance and recombination errors using the programs GAS [90] and MERLIN [91]. Any markers with unresolvable genotypes were re-run and re-evaluated or eliminated from the analysis."

For association study:

"We genotyped 53 SNPs covering the candidate genes DCDC2 and KIAA0319 on chromosome 6p22 and the FOXP2 region of chromosome 7. SNPs were selected which tag regions of linkage disequilibrium using the Tagger function on HapMap (URL), along with SNPs selected to replicate previously reported associations and haplotypes with RD. In all, 36 SNPs were genotyped on chromosome six spanning the genes DCDC2, KIAA0319, and TTRAP. On chromosome 7, we genotyped 17 SNPs spanning FOXP2, including the region upstream of the gene. . .Genotyping was done on a Sequenom MassArray iPlex system."

Analysis Methods: 
Linkage analysis:

The authors performed linkage analysis with both quantitative and categorical measures, using MERLIN and verifying the results by running the same quantitative analysis using the DeFries-Fulker Augmented analysis.

Association analysis:

"Only quantitative traits were used in this analysis, and analysis was again done by two methods: QTDT and FBAT. The same quantitative measures were used as in the linkage analyses. "

Other Details: 
Inclusion criteria:

"Probands met four entrance screening criteria. The first was nonverbal intelligence above 85. For children ages 3;6 to 6;11 it was measured with the Columbia Mental Maturity Scales [73] and for children ages 7–17, the performance IQ scales from the Wechsler Intelligence Test for Children [74] were utilized. Parents and children ages 17 years and older were evaluated with the performance scales for the Wechsler Intelligence Test for Adults [75]. Probands met exclusionary criteria for nonverbal intelligence; this requirement was not met for parents and siblings whose intellectual status was an outcome of the study. The second criterion for the probands was normal hearing acuity. The third was no history of neurological disorders or diagnosis of autism. The fourth was intelligible speech sufficient for language transcription and production of target phonemes used in word final morphology, as in “goes” and “talks.” Probands were identified as SLI based on language performance one standard deviation or more below the mean on an age appropriate language test. All probands were screened for articulation to ensure they could produce the phonemes needed for morphological measurement and sufficient intelligibility for reliable spontaneous language transcription. Family members received age appropriate speech, language, and reading assessments. Siblings were recruited from age 2 years to adulthood. Within age levels, all participants received the same assessments. The probands and siblings received multiple times of measurement as part of the longitudinal study. For the phenotyping in this study, the lowest value of each variable of interest was selected. This is in keeping with the methods used in the SLI Consortium studies where past or current language performance was used to identify probands [3]. Further, the lowest performance estimate captures the late talker status of siblings."

Diagnostic criteria:

"Probands were identified as SLI based on language performance one standard deviation or more below the mean on an age appropriate language test."

Tests used:

Woodcock and GORT (reading)
GFTA (articulation)
MLU, TEGI, CTOPP, PPVT and the Omnibus language score ("facets of language").

Markers: 

15q21 SLI Speech articulation Rice et al 2009

Additional Phenotype Details: May be tested using the Goldman Fristoe Test of Articulation (GFTA).

Basic Study Type:  Linkage and association studies

Study Cohort: 
Summary:

322 subjects (86 probands, 134 siblings, 102 parents and other relatives)

Detail:

Participants "were drawn from an ongoing longitudinal study of Specific Language Impairment. . .There were 86 probands, mean ages 6;1 to 8;10 across variables, ascertained from school speech pathology caseloads followed by assessment to meet the requirements of the study. There were a total of 134 siblings: 77 males, mean age 8;6; 57 females, mean age 8;5. Previous studies report longitudinal outcomes for part of this sample, documenting that the children’s language impairments persist into adolescence [13, 69–72]."

Genotyping Methods: 
For linkage study:

"Several extended families were included, and some phenotypes were available for relatives besides siblings. The pair counts for each phenotype by the type of relative are shown in Table 3, and these data were included in the linkage analyses. . .Well-characterized microsatellite markers in the critical regions of linkage were identified through the NCBI UNISTS website, with intermarker centimorgan distances taken from the Rutgers Combined Linkage-Physical map v2 [89]. Markers were selected to be about 2 cM apart, particularly targeting the candidate genes. The positions and heterogeneity of each marker are shown in Table 4.

"Fluorescent labeled primers for the selected markers were obtained from Applied Biosystems (Foster City, CA) or IDT (Coralville, IA) and genotyping was done on an AB 3730 DNA Analyzer (Applied Biosystems, Foster City, CA). Allele calls were reviewed by two experienced technologists and were checked for inheritance and recombination errors using the programs GAS [90] and MERLIN [91]. Any markers with unresolvable genotypes were re-run and re-evaluated or eliminated from the analysis."

For association study:

"We genotyped 53 SNPs covering the candidate genes DCDC2 and KIAA0319 on chromosome 6p22 and the FOXP2 region of chromosome 7. SNPs were selected which tag regions of linkage disequilibrium using the Tagger function on HapMap (URL), along with SNPs selected to replicate previously reported associations and haplotypes with RD. In all, 36 SNPs were genotyped on chromosome six spanning the genes DCDC2, KIAA0319, and TTRAP. On chromosome 7, we genotyped 17 SNPs spanning FOXP2, including the region upstream of the gene. . .Genotyping was done on a Sequenom MassArray iPlex system."

Analysis Methods: 
Linkage analysis:

The authors performed linkage analysis with both quantitative and categorical measures, using MERLIN and verifying the results by running the same quantitative analysis using the DeFries-Fulker Augmented analysis.

Association analysis:

"Only quantitative traits were used in this analysis, and analysis was again done by two methods: QTDT and FBAT. The same quantitative measures were used as in the linkage analyses. "

Other Details: 
Inclusion criteria:

"Probands met four entrance screening criteria. The first was nonverbal intelligence above 85. For children ages 3;6 to 6;11 it was measured with the Columbia Mental Maturity Scales [73] and for children ages 7–17, the performance IQ scales from the Wechsler Intelligence Test for Children [74] were utilized. Parents and children ages 17 years and older were evaluated with the performance scales for the Wechsler Intelligence Test for Adults [75]. Probands met exclusionary criteria for nonverbal intelligence; this requirement was not met for parents and siblings whose intellectual status was an outcome of the study. The second criterion for the probands was normal hearing acuity. The third was no history of neurological disorders or diagnosis of autism. The fourth was intelligible speech sufficient for language transcription and production of target phonemes used in word final morphology, as in “goes” and “talks.” Probands were identified as SLI based on language performance one standard deviation or more below the mean on an age appropriate language test. All probands were screened for articulation to ensure they could produce the phonemes needed for morphological measurement and sufficient intelligibility for reliable spontaneous language transcription. Family members received age appropriate speech, language, and reading assessments. Siblings were recruited from age 2 years to adulthood. Within age levels, all participants received the same assessments. The probands and siblings received multiple times of measurement as part of the longitudinal study. For the phenotyping in this study, the lowest value of each variable of interest was selected. This is in keeping with the methods used in the SLI Consortium studies where past or current language performance was used to identify probands [3]. Further, the lowest performance estimate captures the late talker status of siblings."

Diagnostic criteria:

"Probands were identified as SLI based on language performance one standard deviation or more below the mean on an age appropriate language test."

Tests used:

Woodcock and GORT (reading)
GFTA (articulation)
MLU, TEGI, CTOPP, PPVT and the Omnibus language score ("facets of language").

Markers: 

15q21 SLI General language skills Rice et al 2009

Additional Phenotype Details: 

The following are examples of standardized tests for various aspects of language ability:

Clinical Evaluation of Language Fundamentals (CELF)
Test of Language Development (TOLD)
Test of Early Grammatical Impairment (TEGI)
Comprehensive Test of Phonological Processing subtest (CTOPP)
Peabody Picture Vocabulary Test (PPVT)

Additional measures include utterance length and performance on a non-word repetition task (NWR).

Basic Study Type:  Linkage and association studies

Study Cohort: 
Summary:

322 subjects (86 probands, 134 siblings, 102 parents and other relatives)

Detail:

Participants "were drawn from an ongoing longitudinal study of Specific Language Impairment. . .There were 86 probands, mean ages 6;1 to 8;10 across variables, ascertained from school speech pathology caseloads followed by assessment to meet the requirements of the study. There were a total of 134 siblings: 77 males, mean age 8;6; 57 females, mean age 8;5. Previous studies report longitudinal outcomes for part of this sample, documenting that the children’s language impairments persist into adolescence [13, 69–72]."

Genotyping Methods: 
For linkage study:

"Several extended families were included, and some phenotypes were available for relatives besides siblings. The pair counts for each phenotype by the type of relative are shown in Table 3, and these data were included in the linkage analyses. . .Well-characterized microsatellite markers in the critical regions of linkage were identified through the NCBI UNISTS website, with intermarker centimorgan distances taken from the Rutgers Combined Linkage-Physical map v2 [89]. Markers were selected to be about 2 cM apart, particularly targeting the candidate genes. The positions and heterogeneity of each marker are shown in Table 4.

"Fluorescent labeled primers for the selected markers were obtained from Applied Biosystems (Foster City, CA) or IDT (Coralville, IA) and genotyping was done on an AB 3730 DNA Analyzer (Applied Biosystems, Foster City, CA). Allele calls were reviewed by two experienced technologists and were checked for inheritance and recombination errors using the programs GAS [90] and MERLIN [91]. Any markers with unresolvable genotypes were re-run and re-evaluated or eliminated from the analysis."

For association study:

"We genotyped 53 SNPs covering the candidate genes DCDC2 and KIAA0319 on chromosome 6p22 and the FOXP2 region of chromosome 7. SNPs were selected which tag regions of linkage disequilibrium using the Tagger function on HapMap (URL), along with SNPs selected to replicate previously reported associations and haplotypes with RD. In all, 36 SNPs were genotyped on chromosome six spanning the genes DCDC2, KIAA0319, and TTRAP. On chromosome 7, we genotyped 17 SNPs spanning FOXP2, including the region upstream of the gene. . .Genotyping was done on a Sequenom MassArray iPlex system."

Analysis Methods: 
Linkage analysis:

The authors performed linkage analysis with both quantitative and categorical measures, using MERLIN and verifying the results by running the same quantitative analysis using the DeFries-Fulker Augmented analysis.

Association analysis:

"Only quantitative traits were used in this analysis, and analysis was again done by two methods: QTDT and FBAT. The same quantitative measures were used as in the linkage analyses. "

Other Details: 
Inclusion criteria:

"Probands met four entrance screening criteria. The first was nonverbal intelligence above 85. For children ages 3;6 to 6;11 it was measured with the Columbia Mental Maturity Scales [73] and for children ages 7–17, the performance IQ scales from the Wechsler Intelligence Test for Children [74] were utilized. Parents and children ages 17 years and older were evaluated with the performance scales for the Wechsler Intelligence Test for Adults [75]. Probands met exclusionary criteria for nonverbal intelligence; this requirement was not met for parents and siblings whose intellectual status was an outcome of the study. The second criterion for the probands was normal hearing acuity. The third was no history of neurological disorders or diagnosis of autism. The fourth was intelligible speech sufficient for language transcription and production of target phonemes used in word final morphology, as in “goes” and “talks.” Probands were identified as SLI based on language performance one standard deviation or more below the mean on an age appropriate language test. All probands were screened for articulation to ensure they could produce the phonemes needed for morphological measurement and sufficient intelligibility for reliable spontaneous language transcription. Family members received age appropriate speech, language, and reading assessments. Siblings were recruited from age 2 years to adulthood. Within age levels, all participants received the same assessments. The probands and siblings received multiple times of measurement as part of the longitudinal study. For the phenotyping in this study, the lowest value of each variable of interest was selected. This is in keeping with the methods used in the SLI Consortium studies where past or current language performance was used to identify probands [3]. Further, the lowest performance estimate captures the late talker status of siblings."

Diagnostic criteria:

"Probands were identified as SLI based on language performance one standard deviation or more below the mean on an age appropriate language test."

Tests used:

Woodcock and GORT (reading)
GFTA (articulation)
MLU, TEGI, CTOPP, PPVT and the Omnibus language score ("facets of language").

Markers:  D15S1012

15q21 SLI Oral reading Rice et al 2009

Additional Phenotype Details: May be assessed using the Gray Oral Reading Test (GORT)

Basic Study Type:  Linkage and association studies

Study Cohort: 
Summary:

322 subjects (86 probands, 134 siblings, 102 parents and other relatives)

Detail:

Participants "were drawn from an ongoing longitudinal study of Specific Language Impairment. . .There were 86 probands, mean ages 6;1 to 8;10 across variables, ascertained from school speech pathology caseloads followed by assessment to meet the requirements of the study. There were a total of 134 siblings: 77 males, mean age 8;6; 57 females, mean age 8;5. Previous studies report longitudinal outcomes for part of this sample, documenting that the children’s language impairments persist into adolescence [13, 69–72]."

Genotyping Methods: 
For linkage study:

"Several extended families were included, and some phenotypes were available for relatives besides siblings. The pair counts for each phenotype by the type of relative are shown in Table 3, and these data were included in the linkage analyses. . .Well-characterized microsatellite markers in the critical regions of linkage were identified through the NCBI UNISTS website, with intermarker centimorgan distances taken from the Rutgers Combined Linkage-Physical map v2 [89]. Markers were selected to be about 2 cM apart, particularly targeting the candidate genes. The positions and heterogeneity of each marker are shown in Table 4.

"Fluorescent labeled primers for the selected markers were obtained from Applied Biosystems (Foster City, CA) or IDT (Coralville, IA) and genotyping was done on an AB 3730 DNA Analyzer (Applied Biosystems, Foster City, CA). Allele calls were reviewed by two experienced technologists and were checked for inheritance and recombination errors using the programs GAS [90] and MERLIN [91]. Any markers with unresolvable genotypes were re-run and re-evaluated or eliminated from the analysis."

For association study:

"We genotyped 53 SNPs covering the candidate genes DCDC2 and KIAA0319 on chromosome 6p22 and the FOXP2 region of chromosome 7. SNPs were selected which tag regions of linkage disequilibrium using the Tagger function on HapMap (URL), along with SNPs selected to replicate previously reported associations and haplotypes with RD. In all, 36 SNPs were genotyped on chromosome six spanning the genes DCDC2, KIAA0319, and TTRAP. On chromosome 7, we genotyped 17 SNPs spanning FOXP2, including the region upstream of the gene. . .Genotyping was done on a Sequenom MassArray iPlex system."

Analysis Methods: 
Linkage analysis:

The authors performed linkage analysis with both quantitative and categorical measures, using MERLIN and verifying the results by running the same quantitative analysis using the DeFries-Fulker Augmented analysis.

Association analysis:

"Only quantitative traits were used in this analysis, and analysis was again done by two methods: QTDT and FBAT. The same quantitative measures were used as in the linkage analyses. "

Other Details: 
Inclusion criteria:

"Probands met four entrance screening criteria. The first was nonverbal intelligence above 85. For children ages 3;6 to 6;11 it was measured with the Columbia Mental Maturity Scales [73] and for children ages 7–17, the performance IQ scales from the Wechsler Intelligence Test for Children [74] were utilized. Parents and children ages 17 years and older were evaluated with the performance scales for the Wechsler Intelligence Test for Adults [75]. Probands met exclusionary criteria for nonverbal intelligence; this requirement was not met for parents and siblings whose intellectual status was an outcome of the study. The second criterion for the probands was normal hearing acuity. The third was no history of neurological disorders or diagnosis of autism. The fourth was intelligible speech sufficient for language transcription and production of target phonemes used in word final morphology, as in “goes” and “talks.” Probands were identified as SLI based on language performance one standard deviation or more below the mean on an age appropriate language test. All probands were screened for articulation to ensure they could produce the phonemes needed for morphological measurement and sufficient intelligibility for reliable spontaneous language transcription. Family members received age appropriate speech, language, and reading assessments. Siblings were recruited from age 2 years to adulthood. Within age levels, all participants received the same assessments. The probands and siblings received multiple times of measurement as part of the longitudinal study. For the phenotyping in this study, the lowest value of each variable of interest was selected. This is in keeping with the methods used in the SLI Consortium studies where past or current language performance was used to identify probands [3]. Further, the lowest performance estimate captures the late talker status of siblings."

Diagnostic criteria:

"Probands were identified as SLI based on language performance one standard deviation or more below the mean on an age appropriate language test."

Tests used:

Woodcock and GORT (reading)
GFTA (articulation)
MLU, TEGI, CTOPP, PPVT and the Omnibus language score ("facets of language").

Markers:  D15S1012 ,  D15S119

7q31.1 AOS Apraxia of speech with characteristics of spastic dysarthria Shriberg et al 2006

Basic Study Type: Case studies and comparison to cohort studies

Study Cohort: 
Summary:

Case studies: 50yo woman (B.) and her 18yo daughter (T.), both with a 7;13 translocation and "cognitive, language and speech challenges" (diagnosed with apraxia of speech, or AOS)
(Also see Tomblin et al 2009)

Comparison groups: 9 adults with spastic dysarthria (S_DYS) and 14 adults with acquired AOS

Case studies detail:

"The case study participants were a 50-year-old mother (B.) and her 18-year-old daughter (T.) referred to the third author by a geneticist (sixth author) in B. and T.’s home state. Clinical history obtained for these 2 speakers, termed the TB family, indicated that each had been diagnosed as having AOS associated with a de novo balanced 7;13 chromosomal translocation in the mother that was inherited by the daughter. The geneticist who made the referral suspected that the genotypes and phenotypes of these 2 individuals might be similar to those reported for affected members of the KE family. A review of their clinical records indicated that since early childhood, B. and, particularly, T., received extensive speech-language therapy, primarily in the public schools, for cognitive–language delays and severe AOS."

Comparison groups detail:

"To provide additional data on the questions addressed in this case study, we compared findings from B. and T. with data from two groups of adult speakers with acquired motor speech disorders. Odell and Shriberg (2001) reported data from 9 adults with S_DYS and 14 adults with acquired AOS. The conversational speech samples from all except 2 of the speakers with S_DYS met the prosody–voice coding requirement of 24 intelligible utterances, reducing to 7 the total number of participants in the present study with spastic or spastic-flaccid dysarthria. . .Table 3 is a summary of clinical information for the speakers in the comparison groups. All 21 participants were native speakers of American English, and with the exception of 1 speaker with cerebral palsy (described below), none had premorbid histories of speech or language disorders. As shown in Table 3, speakers in both groups were predominantly male (S_DYS: 7 of 7, 100%; AOS: 12 of 14, approximately 86%); a between-groups test of proportions was nonsignificant. The speakers’ ages ranged from 48 to 81 years; a t test for differences in mean age was nonsignificant. At assessment, participants in the two groups (excluding the participant with cerebral palsy) ranged from 1 to 180 months postonset of brain damage; a t test for differences inmeanmonths postonset was nonsignificant. . .
"Classification criteria for acquired apraxia and subtypes of dysarthria followed the guidelines in Wertz, LaPointe, and Rosenbek (1984) and Darley, Aronson, and Brown (1975), respectively. As described for the speakers with AOS in Odell and Shriberg (2001) and confirmed for the speakers with S_DYS, none of these participants had substantial hearing loss, less than low–normal cognitive performance, or dementia. The primary diagnosis for 18 of the 21 speakers was one or more strokes,most commonly resulting in a unilateral, left-hemisphere lesion as documented by radiological reports or physician comments in the medical records. . .The 21 speakers had only very mild or no aphasia.
"As indicated above, one of the speakers with S_DYS had cerebral palsy and was included in the present sample to allow for an inspection of developmental issues. This participant was within the same age range as the other speakers with S_DYS and approximately the same age as B. at the time his speech was assessed. Detailed inspection of this individual’s speech, prosody, and voice profiles indicated that, with one exception discussed later, he did not substantially differ in severity or error type from the other 6 speakers with S_DYS."

Genotyping Methods: 
See Tomblin et al 2009

Analysis Methods: 
Comparison of B. and T.'s speech, prosody, and voice characteristics with those of the two comparison groups.

Other Details: 
13 phenotypic measures:
(PVSP = Prosody–Voice Screening Profile (Shriberg, Kwiatkowski, & Rasmussen, 1990).)

Speech:

Severity of speech involvement
Percentage of Consonants Correct
Percentage of Vowels Correct
Percentage of Consonant Correct by Manner Feature
Intelligibility Index
Error consistency
Error target analysis
Error type analysis
Whole-word analysis
Summative analysis
Error type
SODA analysis using severity-adjusted indexes
Residual error analysis
Error typicality
EMA analysis

Prosody:

Phrasing
PVSP Codes 2–8
Rate
PVSP Codes 9–12
Sentential stress
PVSP Codes 13–16 and subcodes
Lexical stress
Lexical stress ratio
Emphatic stress
Emphatic stress ratio

Voice:

Loudness
PVSP Codes 17–18
Pitch
PVSP Codes 19–22
Laryngeal quality
PVSP Codes 23–29
Resonance
PVSP Codes 30–32

Markers: 

18p11 Stuttering Susceptibility to stuttering Shugart et al 2004

Additional Phenotype Details: Stuttering may be diagnosed using the Stuttering Severity Instrument (SSI). In some studies, subjects are asked to read a standardized text aloud and to engage in free speech for a certain amount of time, and the percentage of dysfluencies (out of all words, and/or out of all syllables) determines the diagnosis.

Reference
Riley, G. 2009. SSI-4: Stuttering severity instrument--Fourth edition; examiner's manual. Pro-Ed, Austin, TX (2009).

Basic Study Type:  Linkage study

Study Cohort: 
Summary:

226 individuals from 68 families (188 affected)

Details:

"Families were recruited from the general outbred population of North America and Great Britain via targeted appeals to stuttering interest groups and to the general public. Subjects were individuals over the age of 8 (mean age 31 years) who currently stuttered, and had done so for at least 6 months. . .A complete diagram of the pedigrees of all families included is available from the corresponding author. . .The sample consisted of 68 families; 23 of these families consisted of one generation, 33 contained two generations, and 12 contained three generations. Overall, the families contained an average of 2.72 affected individuals per family. The sample contained 48 sibships with 2 affected, 9 sibships with 3 affected, 2 shipships 4 affected, and one pair of affected half-sibs. Of the 48 sibships with 2 affected, 22 had zero parents, 13 had 1 parent, and 13 had 2 parents genotyped and included in the analysis."

Genotyping Methods: 
"Genotyping was performed by standard fluorescent methods on an ABI 3700. The markers used were a modification of the CHLC version 9 marker set (392 markers, average spacing 9 cM, average heterozygosity 0.76). See www.cidr.jhmi.edu for details on genotyping methods. The error rate for the genome scan, based on 2,993 paired genotypes from blind duplicate samples, was 0.15%. The overall missing data rate was 14.4%, largely due to failed genotyping reactions with buccal swab DNA in the high throughput system employed. After accounting for failed genotyping reactions, a total of 81,928 genotypes were generated and analyzed in the initial genome-wide scan. Marker allele frequencies were computed using data from one individual randomly chosen from each pedigree. Initial genome-wide linkage analysis was performed coding unaffected individuals as such. Because of diagnostic uncertainties in subsequently sampled individuals in pedigree 0006, high resolution analysis on chromosome 18 was performed in this family coding individuals as either affected or unknown. . .For fine mapping, we typed 12 additional markers spanning approximately 60 cM on chromosome 18 for all families, resulting in a final combined marker spacing of 3.3 cM in this region."

Analysis Methods: 
"Analysis was first performed using non-parametric methods implemented in GENEHUNTER."

For the fine mapping on chromosome 18: "We then performed both para-metric and non-parametric statistical analyses using ALLEGRO [Gudbjartsson et al., 2000]. For the parametric analysis, an incomplete dominant mode of inheritance model was assumed, based on the overall pattern of stuttering in our family sample. Specifically, the penetrance was set to be 0.9 and the disease frequency was set to be 0.001."

Other Details: 
Inclusion criteria

"We excluded families with documented or reported stuttering in both the maternal and paternal lineages, as such bilineal families can obscure non- parametric statistical analysis."

Diagnostic criteria

"For diagnostic consistency, stuttering was evaluated by a single clinician (J.M.), using a standardized reading text of 500 words containing balanced numbers of each class of speech sounds [Webster, 1978] plus 5 min of free conversation speech. Text of the standard reading passage can be obtained from the corresponding author at: drayna@nidcd.nih.gov. Speech samples were recorded and stuttering dysfluencies (repetitions, prolongations, and blocks) were counted and evaluated as both percent of words spoken and percent of syllables spoken. Individuals were classified as affected if they demonstrated >=4% word dysfluencies in either reading or free speech, a cut-off typically regarded as mild-to-moderate stuttering in clinical settings."

Markers:  D18S78 ,  D18S847

18q11.2-18q12 Stuttering Susceptibility to stuttering Shugart et al 2004

Additional Phenotype Details: Stuttering may be diagnosed using the Stuttering Severity Instrument (SSI). In some studies, subjects are asked to read a standardized text aloud and to engage in free speech for a certain amount of time, and the percentage of dysfluencies (out of all words, and/or out of all syllables) determines the diagnosis.

Reference
Riley, G. 2009. SSI-4: Stuttering severity instrument--Fourth edition; examiner's manual. Pro-Ed, Austin, TX (2009).

Basic Study Type:  Linkage study

Study Cohort: 
Summary:

226 individuals from 68 families (188 affected)

Details:

"Families were recruited from the general outbred population of North America and Great Britain via targeted appeals to stuttering interest groups and to the general public. Subjects were individuals over the age of 8 (mean age 31 years) who currently stuttered, and had done so for at least 6 months. . .A complete diagram of the pedigrees of all families included is available from the corresponding author. . .The sample consisted of 68 families; 23 of these families consisted of one generation, 33 contained two generations, and 12 contained three generations. Overall, the families contained an average of 2.72 affected individuals per family. The sample contained 48 sibships with 2 affected, 9 sibships with 3 affected, 2 shipships 4 affected, and one pair of affected half-sibs. Of the 48 sibships with 2 affected, 22 had zero parents, 13 had 1 parent, and 13 had 2 parents genotyped and included in the analysis."

Genotyping Methods: 
"Genotyping was performed by standard fluorescent methods on an ABI 3700. The markers used were a modification of the CHLC version 9 marker set (392 markers, average spacing 9 cM, average heterozygosity 0.76). See www.cidr.jhmi.edu for details on genotyping methods. The error rate for the genome scan, based on 2,993 paired genotypes from blind duplicate samples, was 0.15%. The overall missing data rate was 14.4%, largely due to failed genotyping reactions with buccal swab DNA in the high throughput system employed. After accounting for failed genotyping reactions, a total of 81,928 genotypes were generated and analyzed in the initial genome-wide scan. Marker allele frequencies were computed using data from one individual randomly chosen from each pedigree. Initial genome-wide linkage analysis was performed coding unaffected individuals as such. Because of diagnostic uncertainties in subsequently sampled individuals in pedigree 0006, high resolution analysis on chromosome 18 was performed in this family coding individuals as either affected or unknown. . .For fine mapping, we typed 12 additional markers spanning approximately 60 cM on chromosome 18 for all families, resulting in a final combined marker spacing of 3.3 cM in this region."

Analysis Methods: 
"Analysis was first performed using non-parametric methods implemented in GENEHUNTER."

For the fine mapping on chromosome 18: "We then performed both para-metric and non-parametric statistical analyses using ALLEGRO [Gudbjartsson et al., 2000]. For the parametric analysis, an incomplete dominant mode of inheritance model was assumed, based on the overall pattern of stuttering in our family sample. Specifically, the penetrance was set to be 0.9 and the disease frequency was set to be 0.001."

Other Details: 
Inclusion criteria

"We excluded families with documented or reported stuttering in both the maternal and paternal lineages, as such bilineal families can obscure non- parametric statistical analysis."

Diagnostic criteria

"For diagnostic consistency, stuttering was evaluated by a single clinician (J.M.), using a standardized reading text of 500 words containing balanced numbers of each class of speech sounds [Webster, 1978] plus 5 min of free conversation speech. Text of the standard reading passage can be obtained from the corresponding author at: drayna@nidcd.nih.gov. Speech samples were recorded and stuttering dysfluencies (repetitions, prolongations, and blocks) were counted and evaluated as both percent of words spoken and percent of syllables spoken. Individuals were classified as affected if they demonstrated >=4% word dysfluencies in either reading or free speech, a cut-off typically regarded as mild-to-moderate stuttering in clinical settings."

Markers: 

16q24 SLI Nonword repetition SLI Consortium 2002

Additional Phenotype Details: 
Standardized tests for nonword repetition (NWR) include the Children's Test of Nonword Repetition (CNRep, Gathercole et al 1994), the nonword repetition test (NRT, Dollaghan & Campbell 1998), and the Nonword Repetition subtest of the Comprehensive Test of Phonological Processing (Wagner et al. 1999).

References

Gathercole SE, Willis CS, Baddeley AD, Emslie H. The Children’s Test of Nonword Repetition: a test of phonological working memory. Memory 1994;2:103-27.

Dollaghan, C., & Campbell, T. F. (1998). Nonword repetition and child language impairment. Journal of Speech, Language, and Hearing Research, 41, 1136–1146

Wagner, R. K., Torgesen, J. K., & Rashotte, C. A. (1999). Comprehensive test of phonological processing. Austin, TX: PRO-ED.

Basic Study Type:  Linkage study

Study Cohort: 
Summary:

473 individuals from 98 families.

Genetic data was collected from all individuals. Phenotypic data was collected from "252 children (153 males and 99 females), ages 5–19 years (mean 9.4 years; SD 3.04 years)," including unaffected siblings.

Details:

"Two centers recruited 473 individuals (including a total of 219 sib pairs) from 98 families. The Newcomen Centre at Guy’s Hospital, London, diagnosed and referred a clinically based sample, and the Cambridge Language and Speech Project (CLASP) provided families drawn from an ongoing epidemiological study.

"The cases selected at Guy’s Hospital were identified through three special schools for language disorders and through Afasic, a support organization for people with developmental and language impairments; thus, these individuals can be considered as representing a self-referred sample of children with persistent language problems needing special schooling and are not representative of the total population in the community. . .

"CLASP is a community-based longitudinal investigation of speech and language difficulties. The children recruited into the study were initially ascertained during their 3d year of life. A three-stage procedure was employed for case identification, and a standard age design was used to control for divergence between developmental stage and chronological age. Accordingly, at age 36 mo, the population was first defined by means of a questionnaire; then, at age 39 mo, this sample was screened, in more detail, for language difficulties; and, finally, at age 45 mo, age screen–positive cases were assessed in depth. When the children reached 8 years of age, they and their siblings were assessed by the CELF-R and Wechsler Scales of Intelligence–Third UK Edition (WISC-III [Wechsler 1992]), and buccal-DNA samples were collected in families of SLI cases. A detailed description of the ascertainment procedure and sample is available from Stott et al. (in press)."

"In both the Guy’s Hospital sample and the Cambridge sample, probands were selected who, either currently or in the past, had language skills >=1.5 SD below the normative mean for their chronological age, on the receptive and/or expressive scales of the CELF-R battery (Semel et al. 1992)."

"Any proband or sibling found to have a PIQ <80 was excluded from the genome screen. Additional exclusion criteria included MZ twinning, chronic illness requiring multiple hospital visits or admissions, deafness, an ICD-10/DSM-IV diagnosis of childhood autism, English being a second language, care provision by local authorities, and known neurological disorders. In the Guy’s Hospital sample, those families with chromosome abnormalities, including fragile X, were excluded by cytogenetic testing."

Genotyping Methods: 
Collection and preamplification:

"DNA was extracted by means of standard protocols, and all buccal-swab DNA samples were preamplified by a preamplification extension protocol (PEP). The PEP technique involves the random amplification of genomic DNA, using a pool of random 15-mer primers, and results in a 50–100-fold increase in template DNA for subsequent microsatellite amplification (Zhang et al. 1992). Prior to the genome screen, this approach was verified, across 20 primers, in a series of 27 controls. All controls showed comparable amplification of both genomic DNA and PEP DNA, and no evidence of preferential preamplification of specific alleles was seen (data not shown)."

Genetic scan:

"All 473 individuals were genotyped for 400 highly polymorphic dinucleotide-repeat microsatellite markers, taken from the ABI PRISM LMS2-MD10 panels (Applied Biosystems). PCR reactions were performed in 96-well Costar (Thermowell) plates on MJ Research PTC-225 thermocyclers. The fluorescent labeling of primers, with 6-FAM, HEX, and NED phosphoramidites (Applied Biosystems), allowed both the pooling of panels of PCR products and, by means of ABI 373A and 377 sequencers (Applied Biosystems), their subsequent separation and detection on 5% polyacrylamide gels.
"Data were extracted from gels by GENESCAN software (version 3.1) and were passed into the GENOTYPER program (version 2.0) for automated allele calling and manual genotype verification (Reed et al. 1994). Raw allele-size data were checked for inconsistencies, by GAS software (version 2.0) (A. Young, personal communication). Marker-allele frequencies were estimated within RECODE (version 1.4) (D.Weeks, personal communication), and Mega2 (version 2.2) (Mukhopadhyay et al. 1999; also see the Division of Statistical Genetics, Department of Human Genetics, University of Pittsburgh web site) was used for the creation of linkage files in a GENEHUNTER 2.0 (Kruglyak et al. 1996; also see the Whitehead Institute for Biomedical Research/MIT Center for Genome Research “/pub/software/genehunter” web site) package. The Discovery Manager system (Genomica) was used for the storage of genotypic data.

"Prior to statistical analyses, two data-verification steps were performed. Marker haplotypes were generated in a GENEHUNTER 2.0 (Kruglyak et al. 1996; also see the Whitehead Institute for Biomedical Research/MIT Center for Genome Research “/pub/software/genehunter” web site) package, and all chromosomes showing an excessive number of recombination events were re-examined at the genotype level. Corrected data were then run through SIBMED (sibpair mutation and error detection) (Douglas et al. 2000; also see the Center for Statistical Genetics, University of Michigan web site), to identify possible genotyping errors or mutations. SIBMED uses a hidden Markov model to calculate posterior error probabilities for each sib-pair/marker combination, given all the available marker data, an assumed genotype-error rate (set at 1%), and a known genetic map. All genotypes highlighted by SIBMED were excluded from subsequent analyses. Sex-averaged marker maps were from the Cooperative Human Linkage Center (see the CHLC Genetics Maps web site) and were supplemented with data from Ge´ne´thon (Dib et al. 1996).

Increasing marker density:

"Information-content maps were produced for each chromosome, in a MAPMAKER/SIBS (version 2.0) (Kruglyak and Lander 1995; also see the Whitehead Institute for Biomedical Research/MIT Center for Genome Research “/distribution/software/sibs” web site) package and were used to determine the markers used in a second round of genotyping, involving 100 microsatellites taken from the Ge´ne´thon map (Dib et al. 1996) and from the ABI PRISM LMS2-HD5 panels (Applied Biosystems). This additional wave of markers allowed the elimination of gaps in both marker density and information. Final marker density was estimated as being <8 cM, for all chromosomes."

Analysis Methods: 
Linkage analysis included only probands and siblings.

"The Haseman-Elston (HE) method (Haseman and Elston 1972) and the VC method (Amos 1994; Pratt et al. 2000) were used. . .to calculate—by means of the ELStrans, RLStrans, and NWRtrans scores, as quantitative measures of language ability—both single-point and multipoint LOD scores for all autosomes. Additional multipoint HE and VC analyses were subsequently performed, with the WISC-III (Wechsler 1992) measure of PIQ, for all areas that showed suggestive linkage to a language trait. . .Empirical estimates of the significance of all VC results were derived by means of simulations. . .Regions of linkage were identified as those which, under all four types of analysis performed, exceeded thresholds for “suggestive” linkage that have been proposed by Lander and Kruglyak (1995)."

The authors also ran an analysis for linkage to the X-chromosome using the Haseman-Elston method.

Other Details: 
Phenotypic measures for QTL analysis (only probands and siblings):

-Expressive language score on the CELF-R

-Receptive language score on the CELF-R

-Nonword repetition

Markers:  D16S5160

19q13 SLI Expressive language skills SLI Consortium 2002

Additional Phenotype Details: May be assessed using the expressive language scale of the Clinical Evaluation of Language Fundamentals (CELF-R) battery (Semel et al. 1992).

Reference

Semel EM, Wiig EH, Secord W (1992) Clinical evaluation of language fundamentals—revised. Phychological Corporation, San Antonio.

Basic Study Type:  Linkage study

Study Cohort: 
Summary:

473 individuals from 98 families.

Genetic data was collected from all individuals. Phenotypic data was collected from "252 children (153 males and 99 females), ages 5–19 years (mean 9.4 years; SD 3.04 years)," including unaffected siblings.

Details:

"Two centers recruited 473 individuals (including a total of 219 sib pairs) from 98 families. The Newcomen Centre at Guy’s Hospital, London, diagnosed and referred a clinically based sample, and the Cambridge Language and Speech Project (CLASP) provided families drawn from an ongoing epidemiological study.

"The cases selected at Guy’s Hospital were identified through three special schools for language disorders and through Afasic, a support organization for people with developmental and language impairments; thus, these individuals can be considered as representing a self-referred sample of children with persistent language problems needing special schooling and are not representative of the total population in the community. . .

"CLASP is a community-based longitudinal investigation of speech and language difficulties. The children recruited into the study were initially ascertained during their 3d year of life. A three-stage procedure was employed for case identification, and a standard age design was used to control for divergence between developmental stage and chronological age. Accordingly, at age 36 mo, the population was first defined by means of a questionnaire; then, at age 39 mo, this sample was screened, in more detail, for language difficulties; and, finally, at age 45 mo, age screen–positive cases were assessed in depth. When the children reached 8 years of age, they and their siblings were assessed by the CELF-R and Wechsler Scales of Intelligence–Third UK Edition (WISC-III [Wechsler 1992]), and buccal-DNA samples were collected in families of SLI cases. A detailed description of the ascertainment procedure and sample is available from Stott et al. (in press)."

"In both the Guy’s Hospital sample and the Cambridge sample, probands were selected who, either currently or in the past, had language skills >=1.5 SD below the normative mean for their chronological age, on the receptive and/or expressive scales of the CELF-R battery (Semel et al. 1992)."

"Any proband or sibling found to have a PIQ <80 was excluded from the genome screen. Additional exclusion criteria included MZ twinning, chronic illness requiring multiple hospital visits or admissions, deafness, an ICD-10/DSM-IV diagnosis of childhood autism, English being a second language, care provision by local authorities, and known neurological disorders. In the Guy’s Hospital sample, those families with chromosome abnormalities, including fragile X, were excluded by cytogenetic testing."

Genotyping Methods: 
Collection and preamplification:

"DNA was extracted by means of standard protocols, and all buccal-swab DNA samples were preamplified by a preamplification extension protocol (PEP). The PEP technique involves the random amplification of genomic DNA, using a pool of random 15-mer primers, and results in a 50–100-fold increase in template DNA for subsequent microsatellite amplification (Zhang et al. 1992). Prior to the genome screen, this approach was verified, across 20 primers, in a series of 27 controls. All controls showed comparable amplification of both genomic DNA and PEP DNA, and no evidence of preferential preamplification of specific alleles was seen (data not shown)."

Genetic scan:

"All 473 individuals were genotyped for 400 highly polymorphic dinucleotide-repeat microsatellite markers, taken from the ABI PRISM LMS2-MD10 panels (Applied Biosystems). PCR reactions were performed in 96-well Costar (Thermowell) plates on MJ Research PTC-225 thermocyclers. The fluorescent labeling of primers, with 6-FAM, HEX, and NED phosphoramidites (Applied Biosystems), allowed both the pooling of panels of PCR products and, by means of ABI 373A and 377 sequencers (Applied Biosystems), their subsequent separation and detection on 5% polyacrylamide gels.
"Data were extracted from gels by GENESCAN software (version 3.1) and were passed into the GENOTYPER program (version 2.0) for automated allele calling and manual genotype verification (Reed et al. 1994). Raw allele-size data were checked for inconsistencies, by GAS software (version 2.0) (A. Young, personal communication). Marker-allele frequencies were estimated within RECODE (version 1.4) (D.Weeks, personal communication), and Mega2 (version 2.2) (Mukhopadhyay et al. 1999; also see the Division of Statistical Genetics, Department of Human Genetics, University of Pittsburgh web site) was used for the creation of linkage files in a GENEHUNTER 2.0 (Kruglyak et al. 1996; also see the Whitehead Institute for Biomedical Research/MIT Center for Genome Research “/pub/software/genehunter” web site) package. The Discovery Manager system (Genomica) was used for the storage of genotypic data.

"Prior to statistical analyses, two data-verification steps were performed. Marker haplotypes were generated in a GENEHUNTER 2.0 (Kruglyak et al. 1996; also see the Whitehead Institute for Biomedical Research/MIT Center for Genome Research “/pub/software/genehunter” web site) package, and all chromosomes showing an excessive number of recombination events were re-examined at the genotype level. Corrected data were then run through SIBMED (sibpair mutation and error detection) (Douglas et al. 2000; also see the Center for Statistical Genetics, University of Michigan web site), to identify possible genotyping errors or mutations. SIBMED uses a hidden Markov model to calculate posterior error probabilities for each sib-pair/marker combination, given all the available marker data, an assumed genotype-error rate (set at 1%), and a known genetic map. All genotypes highlighted by SIBMED were excluded from subsequent analyses. Sex-averaged marker maps were from the Cooperative Human Linkage Center (see the CHLC Genetics Maps web site) and were supplemented with data from Ge´ne´thon (Dib et al. 1996).

Increasing marker density:

"Information-content maps were produced for each chromosome, in a MAPMAKER/SIBS (version 2.0) (Kruglyak and Lander 1995; also see the Whitehead Institute for Biomedical Research/MIT Center for Genome Research “/distribution/software/sibs” web site) package and were used to determine the markers used in a second round of genotyping, involving 100 microsatellites taken from the Ge´ne´thon map (Dib et al. 1996) and from the ABI PRISM LMS2-HD5 panels (Applied Biosystems). This additional wave of markers allowed the elimination of gaps in both marker density and information. Final marker density was estimated as being <8 cM, for all chromosomes."

Analysis Methods: 
Linkage analysis included only probands and siblings.

"The Haseman-Elston (HE) method (Haseman and Elston 1972) and the VC method (Amos 1994; Pratt et al. 2000) were used. . .to calculate—by means of the ELStrans, RLStrans, and NWRtrans scores, as quantitative measures of language ability—both single-point and multipoint LOD scores for all autosomes. Additional multipoint HE and VC analyses were subsequently performed, with the WISC-III (Wechsler 1992) measure of PIQ, for all areas that showed suggestive linkage to a language trait. . .Empirical estimates of the significance of all VC results were derived by means of simulations. . .Regions of linkage were identified as those which, under all four types of analysis performed, exceeded thresholds for “suggestive” linkage that have been proposed by Lander and Kruglyak (1995)."

The authors also ran an analysis for linkage to the X-chromosome using the Haseman-Elston method.

Other Details: 
Phenotypic measures for QTL analysis (only probands and siblings):

-Expressive language score on the CELF-R

-Receptive language score on the CELF-R

-Nonword repetition

Markers:  D19S908

16q24 SLI Reading comprehension SLI Consortium (SLIC) 2004

Additional Phenotype Details: May be assessed with the reading comprehension test from the Wechsler Objective Reading Dimensions (WORD) (Rust et al. 1993).

Basic Study Type: Linkage study

Study Cohort: 

Summary:

840 individuals, 184 families

Details:

"A total of 840 subjects (393 sib pairs) were recruited from 184 families by four separate centers (table 1)—the Newcomen Centre at Guy’s Hospital, London; the Cambridge Language and Speech Project (CLASP); the Child Life and Health Department at the University of Edinburgh; and the Department of Child Health at the University of Aberdeen.

"The cases recruited by the University of Aberdeen were selected from specialist language units within the Aberdeen and Aberdeenshire areas. These individuals represent a self-referred sample of children with severe and persistent language difficulties. Ethical approval was granted by the Grampian local research ethic committee. The Aberdeen sample was small (10 families, 11 sib pairs) and, as such, was amalgamated with the Guys sample for all analyses. Both of these groups were selected from clinical samples of severely affected children and, therefore, were considered to be the most similar of the samples in terms of ascertainment and clinical presentation. This assumption was supported by the distributions of the phenotypes within the two cohorts (table 2).

"The cases referred by the University of Edinburgh were selected originally to participate in a study of children with severe receptive-language impairments. These individuals were recruited from eastern and central Scotland on a prospective basis through consultant pediatricians and speech and language therapists. All probands required specialist educational support and were selected to have a historical language comprehension score >2 SD below that expected for their age. Families were initially approached by letter, and those who expressed an interest in the study were visited at home by a trained speech and language therapist. A detailed family history was taken by this professional, and all children who did not meet the SLIC study criteria (see below) were excluded. The final sample consisted of 48 families (111 sib pairs). The research program at Edinburgh was approved by local ethic committees in East and Central Scotland.

"Both the Guys and the Cambridge cohorts have been described in detail elsewhere (Burden et al. 1996; SLIC 2002). In brief, the cases referred by Guy’s Hospital represent a clinical sample selected through specialist language schools and through Afasic, a support organization for people with developmental and language impairments. The Cambridge cases were identified through epidemiological screening and from a subset of a sample collected for a community-based longitudinal investigation of speech and language difficulties.

"The Guys and Cambridge samples consist of 98 families, included in the original SLIC genome screen (wave 1), plus an additional 28 families (18 from Guy’s Hospital and 10 from Cambridge) recruited since that point. Thus, the entire cohort can be considered in terms of two waves: wave 1, consisting of the original genome screen sample of 98 families (from Guys and Cambridge), and wave 2, consisting of a replication set of 86 families collected after the completion of the genome screen (from Guys, Cambridge, Edinburgh, and Aberdeen). Alternatively, each cohort can be studied as an independent sample, resulting in three separate groups: Cambridge, Edinburgh, and Guys/Aberdeen (table 1)."

Genotyping Methods: 

"All 871 individuals were genotyped for 40 polymorphic microsatellite markers spanning chromosome 16 (table B1 [online only]), in addition to 21 microsatellite markers across chromosome 19 (table B2 [online only]). The genotyping methods have been described in detail elsewhere (SLIC 2002). In brief, marker regions were amplified within a 10-µl PCR reaction using fluorescently labeled primers (Applied Biosystems). PCR products were pooled, allowing concurrent detection by ABI 3700 sequencers (Applied Biosystems). Data were extracted using Genescan (version 3.1) and Genotyper (version 2.0) (Applied Biosystems) and were checked using Genetic Analysis Software (GAS version 2.0) (A. Young). Marker haplotypes were generated within GENEHUNTER2.0 (Kruglyak et al. 1996), and all chromosomes showing an excessive number of recombination events were re-examined at the genotype level. Sex-averaged marker maps were taken from the deCODE map (Kong et al. 2002) and were supplemented with data from the human genome map (UCSC, April 2003 assembly). Final marker density was estimated at ~10 cM across the entire length of both chromosomes (tables B1 and B2 [online only])."

Analysis Methods: 

The authors calculated single-point and multi-point LOD scores using both Haseman-Elston and variance-components methods.

"Simulations indicated that, of the three analyses performed (HE, with and without weighting, and VC), the HE method with no weighting for multiple sib pairs provided the best possible fit to theoretical statistics within our data set (fig. 1). Results hereafter, therefore, are presented for unweighted HE analyses only."

Separate analyses were performed on the wave 2 replication set, on the pooled wave 1 and 2 datasets, and on each sample (Guys/Aberdeen, Cambridge, and Edingurgh). Also, "three measures of reading ability (BRtrans, SPtrans, and RCtrans) were analyzed for linkage to chromosomes 16 and 19, both in the combined sample and in the various subgroups."

Other Details: 

Inclusion criteria:

". . .All families were selected to include a proband with, either currently or in the past, language skills >=1.5 SD below the normative mean for their chronological age on the expressive and/or receptive scales of the CELF-R battery (Semel et al. 1992). Any child reported to have a nonverbal IQ <80 was excluded from the study. Additional exclusion criteria included MZ twinning, chronic illness requiring multiple hospital visits or admissions, deafness, a clinical diagnosis of autism, English as a second language, children with known neurological disorders, and children under local authority care."


Phenotypic measures:

Evidence of linkage to NWR, BR, RC, and SP was found for the 16q24 locus.

Expressive language score (ELS), CELF-R
Receptive language score (RLS), CELF-R
Basic reading (BR), WORD
Reading comprehension (RC), WORD
Spelling (SP), WORD
Nonword repetition (NWR), SE Gathercole, personal communication

WORD: Wechler Objective Reading Dimensions
CELF-R: Clinical Evaluation of Language Fundamentals, Revised

Markers: 

16q24 SLI Spelling ability SLI Consortium (SLIC) 2004

Additional Phenotype Details: Possible measures include the spelling subtests of any of a number of intelligence and literacy tests, e.g.:

Peabody Individual Achievement Test (PIAT)
Western Australian Literacy and Numeracy Assessment (WALNA)
Wide Range Achievement Test (WRAT)

Basic Study Type: Linkage study

Study Cohort: 

Summary:

840 individuals, 184 families

Details:

"A total of 840 subjects (393 sib pairs) were recruited from 184 families by four separate centers (table 1)—the Newcomen Centre at Guy’s Hospital, London; the Cambridge Language and Speech Project (CLASP); the Child Life and Health Department at the University of Edinburgh; and the Department of Child Health at the University of Aberdeen.

"The cases recruited by the University of Aberdeen were selected from specialist language units within the Aberdeen and Aberdeenshire areas. These individuals represent a self-referred sample of children with severe and persistent language difficulties. Ethical approval was granted by the Grampian local research ethic committee. The Aberdeen sample was small (10 families, 11 sib pairs) and, as such, was amalgamated with the Guys sample for all analyses. Both of these groups were selected from clinical samples of severely affected children and, therefore, were considered to be the most similar of the samples in terms of ascertainment and clinical presentation. This assumption was supported by the distributions of the phenotypes within the two cohorts (table 2).

"The cases referred by the University of Edinburgh were selected originally to participate in a study of children with severe receptive-language impairments. These individuals were recruited from eastern and central Scotland on a prospective basis through consultant pediatricians and speech and language therapists. All probands required specialist educational support and were selected to have a historical language comprehension score >2 SD below that expected for their age. Families were initially approached by letter, and those who expressed an interest in the study were visited at home by a trained speech and language therapist. A detailed family history was taken by this professional, and all children who did not meet the SLIC study criteria (see below) were excluded. The final sample consisted of 48 families (111 sib pairs). The research program at Edinburgh was approved by local ethic committees in East and Central Scotland.

"Both the Guys and the Cambridge cohorts have been described in detail elsewhere (Burden et al. 1996; SLIC 2002). In brief, the cases referred by Guy’s Hospital represent a clinical sample selected through specialist language schools and through Afasic, a support organization for people with developmental and language impairments. The Cambridge cases were identified through epidemiological screening and from a subset of a sample collected for a community-based longitudinal investigation of speech and language difficulties.

"The Guys and Cambridge samples consist of 98 families, included in the original SLIC genome screen (wave 1), plus an additional 28 families (18 from Guy’s Hospital and 10 from Cambridge) recruited since that point. Thus, the entire cohort can be considered in terms of two waves: wave 1, consisting of the original genome screen sample of 98 families (from Guys and Cambridge), and wave 2, consisting of a replication set of 86 families collected after the completion of the genome screen (from Guys, Cambridge, Edinburgh, and Aberdeen). Alternatively, each cohort can be studied as an independent sample, resulting in three separate groups: Cambridge, Edinburgh, and Guys/Aberdeen (table 1)."

Genotyping Methods: 

"All 871 individuals were genotyped for 40 polymorphic microsatellite markers spanning chromosome 16 (table B1 [online only]), in addition to 21 microsatellite markers across chromosome 19 (table B2 [online only]). The genotyping methods have been described in detail elsewhere (SLIC 2002). In brief, marker regions were amplified within a 10-µl PCR reaction using fluorescently labeled primers (Applied Biosystems). PCR products were pooled, allowing concurrent detection by ABI 3700 sequencers (Applied Biosystems). Data were extracted using Genescan (version 3.1) and Genotyper (version 2.0) (Applied Biosystems) and were checked using Genetic Analysis Software (GAS version 2.0) (A. Young). Marker haplotypes were generated within GENEHUNTER2.0 (Kruglyak et al. 1996), and all chromosomes showing an excessive number of recombination events were re-examined at the genotype level. Sex-averaged marker maps were taken from the deCODE map (Kong et al. 2002) and were supplemented with data from the human genome map (UCSC, April 2003 assembly). Final marker density was estimated at ~10 cM across the entire length of both chromosomes (tables B1 and B2 [online only])."

Analysis Methods: 

The authors calculated single-point and multi-point LOD scores using both Haseman-Elston and variance-components methods.

"Simulations indicated that, of the three analyses performed (HE, with and without weighting, and VC), the HE method with no weighting for multiple sib pairs provided the best possible fit to theoretical statistics within our data set (fig. 1). Results hereafter, therefore, are presented for unweighted HE analyses only."

Separate analyses were performed on the wave 2 replication set, on the pooled wave 1 and 2 datasets, and on each sample (Guys/Aberdeen, Cambridge, and Edingurgh). Also, "three measures of reading ability (BRtrans, SPtrans, and RCtrans) were analyzed for linkage to chromosomes 16 and 19, both in the combined sample and in the various subgroups."

Other Details: 

Inclusion criteria:

". . .All families were selected to include a proband with, either currently or in the past, language skills >=1.5 SD below the normative mean for their chronological age on the expressive and/or receptive scales of the CELF-R battery (Semel et al. 1992). Any child reported to have a nonverbal IQ <80 was excluded from the study. Additional exclusion criteria included MZ twinning, chronic illness requiring multiple hospital visits or admissions, deafness, a clinical diagnosis of autism, English as a second language, children with known neurological disorders, and children under local authority care."


Phenotypic measures:

Evidence of linkage to NWR, BR, RC, and SP was found for the 16q24 locus.

Expressive language score (ELS), CELF-R
Receptive language score (RLS), CELF-R
Basic reading (BR), WORD
Reading comprehension (RC), WORD
Spelling (SP), WORD
Nonword repetition (NWR), SE Gathercole, personal communication

WORD: Wechler Objective Reading Dimensions
CELF-R: Clinical Evaluation of Language Fundamentals, Revised

Markers: 

16q24 SLI Text reading SLI Consortium (SLIC) 2004

Basic Study Type: Linkage study

Study Cohort: 

Summary:

840 individuals, 184 families

Details:

"A total of 840 subjects (393 sib pairs) were recruited from 184 families by four separate centers (table 1)—the Newcomen Centre at Guy’s Hospital, London; the Cambridge Language and Speech Project (CLASP); the Child Life and Health Department at the University of Edinburgh; and the Department of Child Health at the University of Aberdeen.

"The cases recruited by the University of Aberdeen were selected from specialist language units within the Aberdeen and Aberdeenshire areas. These individuals represent a self-referred sample of children with severe and persistent language difficulties. Ethical approval was granted by the Grampian local research ethic committee. The Aberdeen sample was small (10 families, 11 sib pairs) and, as such, was amalgamated with the Guys sample for all analyses. Both of these groups were selected from clinical samples of severely affected children and, therefore, were considered to be the most similar of the samples in terms of ascertainment and clinical presentation. This assumption was supported by the distributions of the phenotypes within the two cohorts (table 2).

"The cases referred by the University of Edinburgh were selected originally to participate in a study of children with severe receptive-language impairments. These individuals were recruited from eastern and central Scotland on a prospective basis through consultant pediatricians and speech and language therapists. All probands required specialist educational support and were selected to have a historical language comprehension score >2 SD below that expected for their age. Families were initially approached by letter, and those who expressed an interest in the study were visited at home by a trained speech and language therapist. A detailed family history was taken by this professional, and all children who did not meet the SLIC study criteria (see below) were excluded. The final sample consisted of 48 families (111 sib pairs). The research program at Edinburgh was approved by local ethic committees in East and Central Scotland.

"Both the Guys and the Cambridge cohorts have been described in detail elsewhere (Burden et al. 1996; SLIC 2002). In brief, the cases referred by Guy’s Hospital represent a clinical sample selected through specialist language schools and through Afasic, a support organization for people with developmental and language impairments. The Cambridge cases were identified through epidemiological screening and from a subset of a sample collected for a community-based longitudinal investigation of speech and language difficulties.

"The Guys and Cambridge samples consist of 98 families, included in the original SLIC genome screen (wave 1), plus an additional 28 families (18 from Guy’s Hospital and 10 from Cambridge) recruited since that point. Thus, the entire cohort can be considered in terms of two waves: wave 1, consisting of the original genome screen sample of 98 families (from Guys and Cambridge), and wave 2, consisting of a replication set of 86 families collected after the completion of the genome screen (from Guys, Cambridge, Edinburgh, and Aberdeen). Alternatively, each cohort can be studied as an independent sample, resulting in three separate groups: Cambridge, Edinburgh, and Guys/Aberdeen (table 1)."

Genotyping Methods: 

"All 871 individuals were genotyped for 40 polymorphic microsatellite markers spanning chromosome 16 (table B1 [online only]), in addition to 21 microsatellite markers across chromosome 19 (table B2 [online only]). The genotyping methods have been described in detail elsewhere (SLIC 2002). In brief, marker regions were amplified within a 10-µl PCR reaction using fluorescently labeled primers (Applied Biosystems). PCR products were pooled, allowing concurrent detection by ABI 3700 sequencers (Applied Biosystems). Data were extracted using Genescan (version 3.1) and Genotyper (version 2.0) (Applied Biosystems) and were checked using Genetic Analysis Software (GAS version 2.0) (A. Young). Marker haplotypes were generated within GENEHUNTER2.0 (Kruglyak et al. 1996), and all chromosomes showing an excessive number of recombination events were re-examined at the genotype level. Sex-averaged marker maps were taken from the deCODE map (Kong et al. 2002) and were supplemented with data from the human genome map (UCSC, April 2003 assembly). Final marker density was estimated at ~10 cM across the entire length of both chromosomes (tables B1 and B2 [online only])."

Analysis Methods: 

The authors calculated single-point and multi-point LOD scores using both Haseman-Elston and variance-components methods.

"Simulations indicated that, of the three analyses performed (HE, with and without weighting, and VC), the HE method with no weighting for multiple sib pairs provided the best possible fit to theoretical statistics within our data set (fig. 1). Results hereafter, therefore, are presented for unweighted HE analyses only."

Separate analyses were performed on the wave 2 replication set, on the pooled wave 1 and 2 datasets, and on each sample (Guys/Aberdeen, Cambridge, and Edingurgh). Also, "three measures of reading ability (BRtrans, SPtrans, and RCtrans) were analyzed for linkage to chromosomes 16 and 19, both in the combined sample and in the various subgroups."

Other Details: 

Inclusion criteria:

". . .All families were selected to include a proband with, either currently or in the past, language skills >=1.5 SD below the normative mean for their chronological age on the expressive and/or receptive scales of the CELF-R battery (Semel et al. 1992). Any child reported to have a nonverbal IQ <80 was excluded from the study. Additional exclusion criteria included MZ twinning, chronic illness requiring multiple hospital visits or admissions, deafness, a clinical diagnosis of autism, English as a second language, children with known neurological disorders, and children under local authority care."


Phenotypic measures:

Evidence of linkage to NWR, BR, RC, and SP was found for the 16q24 locus.

Expressive language score (ELS), CELF-R
Receptive language score (RLS), CELF-R
Basic reading (BR), WORD
Reading comprehension (RC), WORD
Spelling (SP), WORD
Nonword repetition (NWR), SE Gathercole, personal communication

WORD: Wechler Objective Reading Dimensions
CELF-R: Clinical Evaluation of Language Fundamentals, Revised

Markers: 

16q24 SLI Nonword repetition SLI Consortium (SLIC) 2004

Additional Phenotype Details: 
Standardized tests for nonword repetition (NWR) include the Children's Test of Nonword Repetition (CNRep, Gathercole et al 1994), the nonword repetition test (NRT, Dollaghan & Campbell 1998), and the Nonword Repetition subtest of the Comprehensive Test of Phonological Processing (Wagner et al. 1999).

References

Gathercole SE, Willis CS, Baddeley AD, Emslie H. The Children’s Test of Nonword Repetition: a test of phonological working memory. Memory 1994;2:103-27.

Dollaghan, C., & Campbell, T. F. (1998). Nonword repetition and child language impairment. Journal of Speech, Language, and Hearing Research, 41, 1136–1146

Wagner, R. K., Torgesen, J. K., & Rashotte, C. A. (1999). Comprehensive test of phonological processing. Austin, TX: PRO-ED.

Basic Study Type: Linkage study

Study Cohort: 

Summary:

840 individuals, 184 families

Details:

"A total of 840 subjects (393 sib pairs) were recruited from 184 families by four separate centers (table 1)—the Newcomen Centre at Guy’s Hospital, London; the Cambridge Language and Speech Project (CLASP); the Child Life and Health Department at the University of Edinburgh; and the Department of Child Health at the University of Aberdeen.

"The cases recruited by the University of Aberdeen were selected from specialist language units within the Aberdeen and Aberdeenshire areas. These individuals represent a self-referred sample of children with severe and persistent language difficulties. Ethical approval was granted by the Grampian local research ethic committee. The Aberdeen sample was small (10 families, 11 sib pairs) and, as such, was amalgamated with the Guys sample for all analyses. Both of these groups were selected from clinical samples of severely affected children and, therefore, were considered to be the most similar of the samples in terms of ascertainment and clinical presentation. This assumption was supported by the distributions of the phenotypes within the two cohorts (table 2).

"The cases referred by the University of Edinburgh were selected originally to participate in a study of children with severe receptive-language impairments. These individuals were recruited from eastern and central Scotland on a prospective basis through consultant pediatricians and speech and language therapists. All probands required specialist educational support and were selected to have a historical language comprehension score >2 SD below that expected for their age. Families were initially approached by letter, and those who expressed an interest in the study were visited at home by a trained speech and language therapist. A detailed family history was taken by this professional, and all children who did not meet the SLIC study criteria (see below) were excluded. The final sample consisted of 48 families (111 sib pairs). The research program at Edinburgh was approved by local ethic committees in East and Central Scotland.

"Both the Guys and the Cambridge cohorts have been described in detail elsewhere (Burden et al. 1996; SLIC 2002). In brief, the cases referred by Guy’s Hospital represent a clinical sample selected through specialist language schools and through Afasic, a support organization for people with developmental and language impairments. The Cambridge cases were identified through epidemiological screening and from a subset of a sample collected for a community-based longitudinal investigation of speech and language difficulties.

"The Guys and Cambridge samples consist of 98 families, included in the original SLIC genome screen (wave 1), plus an additional 28 families (18 from Guy’s Hospital and 10 from Cambridge) recruited since that point. Thus, the entire cohort can be considered in terms of two waves: wave 1, consisting of the original genome screen sample of 98 families (from Guys and Cambridge), and wave 2, consisting of a replication set of 86 families collected after the completion of the genome screen (from Guys, Cambridge, Edinburgh, and Aberdeen). Alternatively, each cohort can be studied as an independent sample, resulting in three separate groups: Cambridge, Edinburgh, and Guys/Aberdeen (table 1)."

Genotyping Methods: 

"All 871 individuals were genotyped for 40 polymorphic microsatellite markers spanning chromosome 16 (table B1 [online only]), in addition to 21 microsatellite markers across chromosome 19 (table B2 [online only]). The genotyping methods have been described in detail elsewhere (SLIC 2002). In brief, marker regions were amplified within a 10-µl PCR reaction using fluorescently labeled primers (Applied Biosystems). PCR products were pooled, allowing concurrent detection by ABI 3700 sequencers (Applied Biosystems). Data were extracted using Genescan (version 3.1) and Genotyper (version 2.0) (Applied Biosystems) and were checked using Genetic Analysis Software (GAS version 2.0) (A. Young). Marker haplotypes were generated within GENEHUNTER2.0 (Kruglyak et al. 1996), and all chromosomes showing an excessive number of recombination events were re-examined at the genotype level. Sex-averaged marker maps were taken from the deCODE map (Kong et al. 2002) and were supplemented with data from the human genome map (UCSC, April 2003 assembly). Final marker density was estimated at ~10 cM across the entire length of both chromosomes (tables B1 and B2 [online only])."

Analysis Methods: 

The authors calculated single-point and multi-point LOD scores using both Haseman-Elston and variance-components methods.

"Simulations indicated that, of the three analyses performed (HE, with and without weighting, and VC), the HE method with no weighting for multiple sib pairs provided the best possible fit to theoretical statistics within our data set (fig. 1). Results hereafter, therefore, are presented for unweighted HE analyses only."

Separate analyses were performed on the wave 2 replication set, on the pooled wave 1 and 2 datasets, and on each sample (Guys/Aberdeen, Cambridge, and Edingurgh). Also, "three measures of reading ability (BRtrans, SPtrans, and RCtrans) were analyzed for linkage to chromosomes 16 and 19, both in the combined sample and in the various subgroups."

Other Details: 

Inclusion criteria:

". . .All families were selected to include a proband with, either currently or in the past, language skills >=1.5 SD below the normative mean for their chronological age on the expressive and/or receptive scales of the CELF-R battery (Semel et al. 1992). Any child reported to have a nonverbal IQ <80 was excluded from the study. Additional exclusion criteria included MZ twinning, chronic illness requiring multiple hospital visits or admissions, deafness, a clinical diagnosis of autism, English as a second language, children with known neurological disorders, and children under local authority care."


Phenotypic measures:

Evidence of linkage to NWR, BR, RC, and SP was found for the 16q24 locus.

Expressive language score (ELS), CELF-R
Receptive language score (RLS), CELF-R
Basic reading (BR), WORD
Reading comprehension (RC), WORD
Spelling (SP), WORD
Nonword repetition (NWR), SE Gathercole, personal communication

WORD: Wechler Objective Reading Dimensions
CELF-R: Clinical Evaluation of Language Fundamentals, Revised

Markers:  D16S3040

2q31-2q33 Stuttering Susceptibility to stuttering Suresh et al 2006

Additional Phenotype Details: Stuttering may be diagnosed using the Stuttering Severity Instrument (SSI). In some studies, subjects are asked to read a standardized text aloud and to engage in free speech for a certain amount of time, and the percentage of dysfluencies (out of all words, and/or out of all syllables) determines the diagnosis.

Reference
Riley, G. 2009. SSI-4: Stuttering severity instrument--Fourth edition; examiner's manual. Pro-Ed, Austin, TX (2009).

Basic Study Type:  Linkage study

Study Cohort: 
Summary:

110 families, including 252 affected individuals, 45 individuals recovered from stuttering, and 19 too young to classify.

Details:

"The sample comprised 110 families, each with at least two non–parent/offspring relatives affected with stuttering. The families were collected from the University of Illinois at Urbana-Champaign (nf = 76); the Tel Aviv University School of Medicine, Israel (nf = 16); and the Helsingborg Hospital, Sweden (nf = 18). All samples were collected with the approval of local institutional review boards and with informed consent. The primary group of American families were identified (1) from pedigrees of 180 children previously evaluated for stuttering through a longitudinal study (the Illinois Stuttering Research Program), (2) through a well-established, nationwide network of speech-language pathologists specializing in stuttering, and (3) through publications, announcements, and fliers at meetings of organizations geared to provide support and information for people who stutter. Families from the Swedish and Israeli centers were identified and recruited by specialists in stuttering. Since the families were referred through a broad network of pediatricians, day care centers, and speech-language pathologists and by word of mouth, they were considerably more representative of the population than a typical clinical sample. Blood samples from a total of 585 individuals were collected. There were 362 males, 233 adult and 129 minor, and 223 females, 182 adult and 41 minor. A total of 365 affected-relative pairs were identified."

Genotyping Methods: 
"DNA was extracted from 3 ml of blood by use of the PureGene DNA extraction kit (Gentra), and the remainder of the blood was frozen. The Affymetrix Mapping Array 10K set was used for genotyping as per the standard protocol described elsewhere (Matsuzaki et al. 2004). Three pairs of MZ twins available in the data set were used to assess the discordance of genotype calls, with only one from each of the twin sets used in subsequent linkage analyses. The observed level of genotype disagreement was low, at 0.00012–0.00037."

Analysis Methods: 
The authors performed linkage analysis for the broad and narrow phenotype definitions using both a nonparametric model (the exponential model) and a parametric model (for a LOD score for families under heterogeneity, HLOD), as well as for the sex-stratified datasets. Based on these results, "to assess potential interactions between linkage signals of interest and the rest of the genome, conditional analyses were performed."

Also, "the family-based association test (FBAT) (v.1.5.5) (Rabinowitz and Laird 2000) was used to test the null hypothesis of no association and no linkage for each marker with the persistent-stuttering phenotype under an additive genetic model."

Other Details: 
Diagnostic criteria for the persistent stuttering phenotype:

"The individual stuttered for a minimum of 4 years and continued to stutter into later childhood and adulthood.

Subjects who met one or more of the following criteria were classified as having "ever stuttered":

"(1) direct observation of stuttering by one of the speech investigators,
(2) diagnosis and/or treatment by speech-language pathologists, or
(3) detailed description by a participant of stuttering behaviors, judged sufficient to
positively identify the disorder by a speech-language pathologist with expertise in stuttering."

Also note:

"Particular care was taken to verify any cases of naturally recovered stuttering (see Yairi and Ambrose [1999] for full treatment of this issue). If evidence was vague or conflicting, the stuttering was classified as “status unknown.”"

Markers: 

7q34-7q36 Stuttering Susceptibility to stuttering Suresh et al 2006

Additional Phenotype Details: Stuttering may be diagnosed using the Stuttering Severity Instrument (SSI). In some studies, subjects are asked to read a standardized text aloud and to engage in free speech for a certain amount of time, and the percentage of dysfluencies (out of all words, and/or out of all syllables) determines the diagnosis.

Reference
Riley, G. 2009. SSI-4: Stuttering severity instrument--Fourth edition; examiner's manual. Pro-Ed, Austin, TX (2009).

Basic Study Type:  Linkage study

Study Cohort: 
Summary:

110 families, including 252 affected individuals, 45 individuals recovered from stuttering, and 19 too young to classify.

Details:

"The sample comprised 110 families, each with at least two non–parent/offspring relatives affected with stuttering. The families were collected from the University of Illinois at Urbana-Champaign (nf = 76); the Tel Aviv University School of Medicine, Israel (nf = 16); and the Helsingborg Hospital, Sweden (nf = 18). All samples were collected with the approval of local institutional review boards and with informed consent. The primary group of American families were identified (1) from pedigrees of 180 children previously evaluated for stuttering through a longitudinal study (the Illinois Stuttering Research Program), (2) through a well-established, nationwide network of speech-language pathologists specializing in stuttering, and (3) through publications, announcements, and fliers at meetings of organizations geared to provide support and information for people who stutter. Families from the Swedish and Israeli centers were identified and recruited by specialists in stuttering. Since the families were referred through a broad network of pediatricians, day care centers, and speech-language pathologists and by word of mouth, they were considerably more representative of the population than a typical clinical sample. Blood samples from a total of 585 individuals were collected. There were 362 males, 233 adult and 129 minor, and 223 females, 182 adult and 41 minor. A total of 365 affected-relative pairs were identified."

Genotyping Methods: 
"DNA was extracted from 3 ml of blood by use of the PureGene DNA extraction kit (Gentra), and the remainder of the blood was frozen. The Affymetrix Mapping Array 10K set was used for genotyping as per the standard protocol described elsewhere (Matsuzaki et al. 2004). Three pairs of MZ twins available in the data set were used to assess the discordance of genotype calls, with only one from each of the twin sets used in subsequent linkage analyses. The observed level of genotype disagreement was low, at 0.00012–0.00037."

Analysis Methods: 
The authors performed linkage analysis for the broad and narrow phenotype definitions using both a nonparametric model (the exponential model) and a parametric model (for a LOD score for families under heterogeneity, HLOD), as well as for the sex-stratified datasets. Based on these results, "to assess potential interactions between linkage signals of interest and the rest of the genome, conditional analyses were performed."

Also, "the family-based association test (FBAT) (v.1.5.5) (Rabinowitz and Laird 2000) was used to test the null hypothesis of no association and no linkage for each marker with the persistent-stuttering phenotype under an additive genetic model."

Other Details: 
Diagnostic criteria for the persistent stuttering phenotype:

"The individual stuttered for a minimum of 4 years and continued to stutter into later childhood and adulthood.

Subjects who met one or more of the following criteria were classified as having "ever stuttered":

"(1) direct observation of stuttering by one of the speech investigators,
(2) diagnosis and/or treatment by speech-language pathologists, or
(3) detailed description by a participant of stuttering behaviors, judged sufficient to
positively identify the disorder by a speech-language pathologist with expertise in stuttering."

Also note:

"Particular care was taken to verify any cases of naturally recovered stuttering (see Yairi and Ambrose [1999] for full treatment of this issue). If evidence was vague or conflicting, the stuttering was classified as “status unknown.”"

Markers: 

12q23-12q24 Stuttering Susceptibility to stuttering Suresh et al 2006

Additional Phenotype Details: Stuttering may be diagnosed using the Stuttering Severity Instrument (SSI). In some studies, subjects are asked to read a standardized text aloud and to engage in free speech for a certain amount of time, and the percentage of dysfluencies (out of all words, and/or out of all syllables) determines the diagnosis.

Reference
Riley, G. 2009. SSI-4: Stuttering severity instrument--Fourth edition; examiner's manual. Pro-Ed, Austin, TX (2009).

Basic Study Type:  Linkage study

Study Cohort: 
Summary:

110 families, including 252 affected individuals, 45 individuals recovered from stuttering, and 19 too young to classify.

Details:

"The sample comprised 110 families, each with at least two non–parent/offspring relatives affected with stuttering. The families were collected from the University of Illinois at Urbana-Champaign (nf = 76); the Tel Aviv University School of Medicine, Israel (nf = 16); and the Helsingborg Hospital, Sweden (nf = 18). All samples were collected with the approval of local institutional review boards and with informed consent. The primary group of American families were identified (1) from pedigrees of 180 children previously evaluated for stuttering through a longitudinal study (the Illinois Stuttering Research Program), (2) through a well-established, nationwide network of speech-language pathologists specializing in stuttering, and (3) through publications, announcements, and fliers at meetings of organizations geared to provide support and information for people who stutter. Families from the Swedish and Israeli centers were identified and recruited by specialists in stuttering. Since the families were referred through a broad network of pediatricians, day care centers, and speech-language pathologists and by word of mouth, they were considerably more representative of the population than a typical clinical sample. Blood samples from a total of 585 individuals were collected. There were 362 males, 233 adult and 129 minor, and 223 females, 182 adult and 41 minor. A total of 365 affected-relative pairs were identified."

Genotyping Methods: 
"DNA was extracted from 3 ml of blood by use of the PureGene DNA extraction kit (Gentra), and the remainder of the blood was frozen. The Affymetrix Mapping Array 10K set was used for genotyping as per the standard protocol described elsewhere (Matsuzaki et al. 2004). Three pairs of MZ twins available in the data set were used to assess the discordance of genotype calls, with only one from each of the twin sets used in subsequent linkage analyses. The observed level of genotype disagreement was low, at 0.00012–0.00037."

Analysis Methods: 
The authors performed linkage analysis for the broad and narrow phenotype definitions using both a nonparametric model (the exponential model) and a parametric model (for a LOD score for families under heterogeneity, HLOD), as well as for the sex-stratified datasets. Based on these results, "to assess potential interactions between linkage signals of interest and the rest of the genome, conditional analyses were performed."

Also, "the family-based association test (FBAT) (v.1.5.5) (Rabinowitz and Laird 2000) was used to test the null hypothesis of no association and no linkage for each marker with the persistent-stuttering phenotype under an additive genetic model."

Other Details: 
Diagnostic criteria for the persistent stuttering phenotype:

"The individual stuttered for a minimum of 4 years and continued to stutter into later childhood and adulthood.

Subjects who met one or more of the following criteria were classified as having "ever stuttered":

"(1) direct observation of stuttering by one of the speech investigators,
(2) diagnosis and/or treatment by speech-language pathologists, or
(3) detailed description by a participant of stuttering behaviors, judged sufficient to
positively identify the disorder by a speech-language pathologist with expertise in stuttering."

Also note:

"Particular care was taken to verify any cases of naturally recovered stuttering (see Yairi and Ambrose [1999] for full treatment of this issue). If evidence was vague or conflicting, the stuttering was classified as “status unknown.”"

Markers: 

7q31.1 AOS Long-term developmental speech and language problems Tomblin et al 2009

Basic Study Type:  - Fluorescent in situ hybridization (FISH) - DNA sequencing

Study Cohort: 
Summary:

Mother (B, 50-52yo) and daughter (T, 18-20yo), both with "long-term developmental speech and language problems"

Details:

"The mother (B) and daughter (T) were first referred to our team by a geneticist because (a) they were known to have a translocation involving the 7q31 region containing FOXP2 and (b) both had long-term developmental speech and language problems. Prior cytogenetic studies had shown that B’s parents had normal chromosomes. Therefore, we determined that the chromosomal rearrangement originated with B and, thus, T received both derived 7 and 13 chromosomes from B. T and B have been found—by history and examination by physicians of this research group—to be healthy individuals with no clinically significant dysmorphology or neurological signs other than marked speech sound impairment."

Genotyping Methods: 
Fluorescent in situ hybridization analysis

"The first step in localizing the breakpoint requires the use of cytogenetic methods that allow the region of the breakpoint to be visualized. Fluorescent in situ hybridization (FISH) involves creating a strand of DNA (clone) that is labeled with fluorescent dye; this strand is then allowed to hybridize with a specific complementary sequence of DNA in the region of interest on the chromosome. Specifically, we used G-banded metaphase spreads of the patient cell lines. Clones for FISH were selected using the genome map provided by the University of California Santa Cruz (UCSC) Genomics Bioinformatics Group [4]. Bacterial Artificial Chromosome (BAC) clones, from RP11 libraries, and fosmid clones were obtained (Children’s Hospital of Oakland Research Institute) and were directly labeled with SpectrumOrange-dUTP (Vysis, Inc.; Downers Grove, IL). The labeled probes were hybridized to metaphase cells, and the chromosomes were analyzed using an Olympus BX60 fluorescent microscope. The Applied Imaging System’s Cytovision computer program was used to digitize the images to visualize the signals."

Long-range PCR amplification across breakpoints

". . .Primers were designed to amplify a PCR product that contained the breakpoint. These primers were designed using a sequence obtained from the UCSC genome browser within the fosmids used for cytogenetic studies shown to have spanned the breakpoint for each respective chromosome. Primers were picked with a length of 27 bp and an optimal melting temperature (Tm) of 64 °C [5].
"In order to amplify a product on the mother and daughter’s derivative 7 and derivative 13 chromosomes, forward primers on chromosome 7 were paired with reverse primers on chromosome 13, and vice versa, until a product was amplified. This was continued until a ~800 bp product containing the break was amplified for both derivative chromosomes. Normal chromosome 7 and chromosome 13 primer pairs were also used to amplify the region surrounding the break on the normal chromosomes. These products served as controls against which the derivative chromosome sequences were compared. All reactions were performed in 25 µl final volume using the TaKaRa LA PCR kit, Version 2.1. Denaturation steps were performed at 94 °C, and annealing/extension took place at 68 °C. Extension times began at 10 min for the first 10 cycles and then were increased to 15 min + 15 s/cycle for the remaining 20 cycles. Extension times were initially calculated using 1 min/kb as a general guideline."

Sequence Verification

"Sequencing was performed on the derivative 7, derivative 13, normal 7, and normal 13 PCR products using the primers previously described as well as new primers designed from within the final long-range PCR products. This sequence was then analyzed in order to find the exact location of the translocation in each derivative chromosome. This was done by comparing the derivative chromosome
sequence to the UCSC sequence data as well as to the normal chromosome sequence obtained from the patient."

Analysis Methods: 
Comparison of B and T's language and cognitive skills to those of the KE family, and in some cases to B and T's age group norms.

Other Details: 
Phenotypic measures:

(Some available from previous studies in which the KE family participated; some from B and T in this study.)

Receptive and expressive vocabulary

KE: British Picture Vocabulary Scale (BPVS; Dunn, Dunn, Whetton, & Pintillie, 1982)
KE: Wechsler Adult Intelligence Scale–III (WAIS-III; Wechsler, 1997).
B&T: Peabody Picture Vocabulary Test–3 (PPVT-3; Dunn, 1997)
B&T: Expressive Vocabulary Test (EVT;Williams, 1997)
B&T: Vocabulary subtest of the WAIS-III (Wechsler, 1997)

Grammar

KE and B&T: The Test of Receptive Grammar (TROG; Bishop, 1982)

Sentence comprehension

B&T: Clinical Evaluation of Language Fundamentals–III: Concepts and Directions (CELF-III:
C&D; Semel,Wiig, & Secord, 1995)

Tense marking

KE & B&T: Ullman Grammatic Completion Task (UGCT; Ullman & Gopnik, 1999).

Narrative production

B&T: Method developed by Saffran, Berndt, and Schwartz (1989)

Markers: 

6p21.3-6p22 Dyslexia Susceptibility to developmental dyslexia Turic et al 2003

Additional Phenotype Details: Typical diagnostic criteria for dyslexia include remarkable deviation from population mean on age-appropriate standardized reading and spelling tests, such as those in the Wechsler intelligence tests. Reading tests may include oral reading and non-word reading.

Usually, a Performance Intelligence Quotient (PIQ) of at least 70 or 80 on the age-appropriate Weschler test is also a criterion.

References (fourth editions of these tests are also now available):

Wechsler D. 1991. Wechsler intelligence scale for children- third edition (WISC-III). San Antonio: The Psychological Corporation.

Wechsler D. 1997. Wechsler Adult Intelligence Scale-III (WAIS-III). San Antonio: The Psychological Corporation.

Basic Study Type:  Linkage study

Study Cohort: 
"We ascertained two samples comprising 101 and 77 parent–proband trios, through contacts with local education authorities across South Wales (Stage 1) and mainly English schools specialised in the education of children with reading difficulties (Stage 2, see Table 1 for sample description)."

Genotyping Methods: 
"The chromosomal interval used for LD mapping was selected on the basis of the four recent studies supporting linkage to 6p21.3, [12,18–22] a distance of approximately 18cM (Figure 1). Data on marker names, position of markers and distances between markers were extracted from the Genome Database (http:/www.gdb.org.gdb/). We identified a 2cM region from D6S1558 to MOG which showed greatest overlap of evidence between studies, in which we increased our marker density to one per 0.2 cM. Primer pairs were obtained from MWG Biotech (Germany) and Genset (France) with the forward primer of each pair labelled with FAM, TET or HEX fluorescent dyes. Polymerase chain reactions (PCRs) were performed in 12 µl reaction volumes containing 48 ng of genomic DNA, 5 pmol of each primer, 1.5mM MgCl2, 50mM KCl, 10mM Tris HCl (pH 8.3), 200 µM dNTPs and 0.1 units Taq polymerase (Qiagen). All PCRs were performed on Hybaid PCR Express thermocyclers or MJ Research PTC-100 thermocyclers with an initial denaturation stage at 94°C for 5 min followed by 30 cycles (30s at 94°C, 30s at 50–65°C, 30s at 72°C) and a final extension step at 72°C for 5 min. Reactions for each marker were performed separately, with products being multiplexed into size-specific sets prior to gel electrophoresis. TAMRA-labelled molecular weight markers were run in each lane. Markers were typed on ABI373 sequencers using the GenescanTM and GenotyperTM software (Applied Biosystems)."

Analysis Methods: 
Single-, double- and triple-marker association tests were carried out with a haplotype relative risk (HRR) method and extended transmission disequilibrium test (eTDT) method "with Monte Carlo simulation implemented to obtain empirical significance levels."

"Parents were tested for Hardy–Weinberg equilibrium for each marker at each stage. Tests for marker–marker association were carried out in the affected offspring (Stage 1 [the first sample]) using EHPLUS. [52] EHPLUS incorporates a likelihood ratio test to evaluate the strength of association and was used in conjunction with PMPLUS[53] to obtain empirical significance levels."

"All individual markers and combinations of two or three consecutive markers, which were significantly associated with RD at Stage 1 were tested for association at Stage 2 [the second sample]."

Other Details: 
Diagnostic criteria:

An IQ >=85, and reading level at least two and a half years behind chronological age. IQ was measured with the vocabulary, similarities, block design, and picture completion subtests of the WISC III UK40. Reading age was measured with the accuracy score of the Neale Analysis of Reading Ability.


Other phenotypic measures:

-Phonological awareness (phoneme deletion and rhyme oddity)
-Phonological decoding (nonword reading task)
-Phonlogical coding in working memory (nonword repetition task)
-Orthographic ability (pseudohomophone judgement task)
-Rapid automatised naming (picture naming and digit naming)
-Single-word reading and spelling, measured with the BAS reading test
-Attention-deficit-hyperactivity disorder, measured with the Abbreviated Connor’s Questionnaire
-Vocabulary, measured with standard scores from the WISC III

Markers:  D6S506

13q21 Stuttering Susceptibility to stuttering Wittke-Thompson et al 2007

Additional Phenotype Details: Stuttering may be diagnosed using the Stuttering Severity Instrument (SSI). In some studies, subjects are asked to read a standardized text aloud and to engage in free speech for a certain amount of time, and the percentage of dysfluencies (out of all words, and/or out of all syllables) determines the diagnosis.

Reference
Riley, G. 2009. SSI-4: Stuttering severity instrument--Fourth edition; examiner's manual. Pro-Ed, Austin, TX (2009).

Basic Study Type:  Association and linkage studies

Study Cohort: 
Summary:

1623 individuals from 13 generations of 1 pedigree (48 "ever stuttered", 36 stuttering at time of study, 12 recovered)

Genotype data available from 40 of those who evere stuttered (30 current), from 9 generations of 232-member minimal pedigree

Details:

"Our studies focus on the Hutterites, a religious isolate that left Europe in the late 1800s and settled in the northern United States. The Hutterites are ideal for genetic studies because of their large family sizes and communal lifestyle. The subjects included in this study are from 9 colonies in South Dakota. These individuals are related to each other within a 1,623-member, 13 generation pedigree traced back in time to 64 founders, some of whom may have been related (Abney, McPeek, & Ober, 2000)."

"Of the 1,623 individuals phenotyped for stuttering, 48 were reported as having ever stuttered. Of these, 36 were stuttering at the time of the study and 12 were reported to have recovered from stuttering. . . For the 48 individuals classified as ever stuttered, DNA was unavailable for 8 individuals because they were too young (under age 6) to have blood drawn at the time of data collection. The remaining 40 individuals who stutter (30 current, 10 recovered) are related to each other in a 232-member minimal pedigree comprising 9 generations. A point of interest is that of the 10 individuals who recovered from stuttering, 5 individuals have a first degree relative with persistent stuttering (4 individuals with siblings and 1 individual’s mother). The remaining individuals who have recovered either do not report any members of their nuclear family who have stuttered, or there is a sibling who has also recovered from stuttering. All individuals who currently stutter or had recovered from stuttering were included in our analyses in the phenotype of ever stuttering."

Genotyping Methods: 
"Currently, 1271 DNA markers have been genotyped in the Hutterites. Two genome screens have been completed by the Mammalian Genotyping Service of the National Heart, Lung and Blood Institute, using Marshfield screening sets 9 and 51. Marshfield screening sets are collections of microsatellite markers used for genotyping that were compiled by the Marshfield Clinic Research Foundation. This has yielded a map density of approximately one marker every 5 cM, denser than most genome screens with one marker every 10–15 cM. Several hundred single nucleotide polymorphisms (SNPs) have also been genotyped, primarily in genes related to asthma and cardiovascular disease (Bourgain et al., 2003; Ober, Tsalenko, Parry, & Cox, 2000; Newman et al., 2003). All marker orders and map distances for framework markers are based on the physical map created by deCode Genetics (http://www.decode.com).

"Mendelian errors were detected using PedCheck (O’Connell &Weeks, 1998). SNPs were also checked for departures from Hardy-Weinberg equilibrium (Bourgain, Abney, Schneider, Ober, & McPeek, 2004), and those showing any deviation were excluded from these analyses."

Analysis Methods: 
(1) Genome-wide linkage analysis using NPLall and NPLpairs statistics

(2) Single-point and two-point TDT. "Due to the lack of independence between members in a single family, the TDT cannot be used as a test of association in the Hutterites, but can be used as a test of linkage."

(3) Family-Based Association Test (FBAT) using an additive model of inheritance

(4) Meta-analysis of this study and Suresh et al (2006), "New complexities in the genetics of stuttering: Significant sex-specific linkage signals," American Journal of Human Genetics, 78, 554–563.

Markers: 

7q31.2-7q32.2 Severe communication disorder with evidence of oromotor dyspraxia Zeesman et al 2006

Additional Phenotype Details: Additionally, dysmorphic features and mild developmental delay; inability to spontaneously cough, laugh, or sneeze.

Markers: 

7q31.1-7q31.2 Pronunciation difficulties, poor vocabulary Zilina et al 2012

Markers: 

7q31.1-7q31.31 Low vocalization activity, poor vocabulary Zilina et al 2012

Markers: