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Genetic Candidate Variants in Two Multigenerational Families with Childhood Apraxia of Speech.

ABSTRACT: Childhood apraxia of speech (CAS) is a severe and socially debilitating form of speech sound disorder with suspected genetic involvement, but the genetic etiology is not yet well understood. Very few known or putative causal genes have been identified to date, e.g., FOXP2 and BCL11A. Building a knowledge base of the genetic etiology of CAS will make it possible to identify infants at genetic risk and motivate the development of effective very early intervention programs. We investigated the genetic etiology of CAS in two large multigenerational families with familial CAS. Complementary genomic methods included Markov chain Monte Carlo linkage analysis, copy-number analysis, identity-by-descent sharing, and exome sequencing with variant filtering. No overlaps in regions with positive evidence of linkage between the two families were found. In one family, linkage analysis detected two chromosomal regions of interest, 5p15.1-p14.1, and 17p13.1-q11.1, inherited separately from the two founders. Single-point linkage analysis of selected variants identified CDH18 as a primary gene of interest and additionally, MYO10, NIPBL, GLP2R, NCOR1, FLCN, SMCR8, NEK8, and ANKRD12, possibly with additive effects. Linkage analysis in the second family detected five regions with LOD scores approaching the highest values possible in the family. A gene of interest was C4orf21 (ZGRF1) on 4q25-q28.2. Evidence for previously described causal copy-number variations and validated or suspected genes was not found. Results are consistent with a heterogeneous CAS etiology, as is expected in many neurogenic disorders. Future studies will investigate genome variants in these and other families with CAS.

SUBMITTER: Peter B

PROVIDER: S-EPMC4847873 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

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Genetic Candidate Variants in Two Multigenerational Families with Childhood Apraxia of Speech.

Peter Beate B Wijsman Ellen M EM Nato Alejandro Q AQ Matsushita Mark M MM Chapman Kathy L KL Stanaway Ian B IB Wolff John J Oda Kaori K Gabo Virginia B VB Raskind Wendy H WH

PloS one 20160427 4

Childhood apraxia of speech (CAS) is a severe and socially debilitating form of speech sound disorder with suspected genetic involvement, but the genetic etiology is not yet well understood. Very few known or putative causal genes have been identified to date, e.g., FOXP2 and BCL11A. Building a knowledge base of the genetic etiology of CAS will make it possible to identify infants at genetic risk and motivate the development of effective very early intervention programs. We investigated the gene ...[more]

PMID: 27120335

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Project description:Childhood apraxia of speech (CAS) is a rare, severe, persistent pediatric motor speech disorder with associated deficits in sensorimotor, cognitive, language, learning and affective processes. Among other neurogenetic origins, CAS is the disorder segregating with a mutation in FOXP2 in a widely studied, multigenerational London family. We report the first whole-exome sequencing (WES) findings from a cohort of 10 unrelated participants, ages 3 to 19 years, with well-characterized CAS.As part of a larger study of children and youth with motor speech sound disorders, 32 participants were classified as positive for CAS on the basis of a behavioral classification marker using auditory-perceptual and acoustic methods that quantify the competence, precision and stability of a speaker's speech, prosody and voice. WES of 10 randomly selected participants was completed using the Illumina Genome Analyzer IIx Sequencing System. Image analysis, base calling, demultiplexing, read mapping, and variant calling were performed using Illumina software. Software developed in-house was used for variant annotation, prioritization and interpretation to identify those variants likely to be deleterious to neurodevelopmental substrates of speech-language development.Among potentially deleterious variants, clinically reportable findings of interest occurred on a total of five chromosomes (Chr3, Chr6, Chr7, Chr9 and Chr17), which included six genes either strongly associated with CAS (FOXP1 and CNTNAP2) or associated with disorders with phenotypes overlapping CAS (ATP13A4, CNTNAP1, KIAA0319 and SETX). A total of 8 (80%) of the 10 participants had clinically reportable variants in one or two of the six genes, with variants in ATP13A4, KIAA0319 and CNTNAP2 being the most prevalent.Similar to the results reported in emerging WES studies of other complex neurodevelopmental disorders, our findings from this first WES study of CAS are interpreted as support for heterogeneous genetic origins of this pediatric motor speech disorder with multiple genes, pathways and complex interactions. We also submit that our findings illustrate the potential use of WES for both gene identification and case-by-case clinical diagnostics in pediatric motor speech disorders.

Project description:PurposeThe purpose of this study was to investigate the association between perceived single-word speech severity and intelligibility in children with childhood apraxia of speech (CAS), with and without comorbid language impairment (LI), and to investigate the contribution of different CAS signs to perceived single-word speech severity and single-word intelligibility.MethodThirty children with CAS, 18 with comorbid LI, completed the Goldman-Fristoe Test of Articulation-Second Edition (GFTA-2). Trained judges coded children's responses for signs of CAS and percent phonemes correct. Nine listeners, blind to diagnoses, rated speech severity using a visual analog scale. Intelligibility was assessed by comparing listeners' orthographic transcriptions of children's responses to target responses.ResultsMeasures of speech severity (GFTA-2 standard score, number of unique CAS signs, total CAS signs, and mean severity rating) were significantly correlated with measures of intelligibility (GFTA-2 raw score, percent phonemes correct, and mean intelligibility score). Speech severity and intelligibility did not differ significantly between children with and without LI. Only consonant errors contributed significant variability to speech severity. Consonant errors and stress errors contributed significant variability to intelligibility.ConclusionsFindings suggest that visual analog scale ratings are a valid and convenient measure of single-word speech severity and that GFTA-2 raw score is an equally convenient measure of single-word intelligibility. The result that consonant errors were by far the major contributor to single-word speech severity and intelligibility in children with CAS, with stress errors also making a small contribution to intelligibility, suggests that consonant accuracy and appropriate lexical stress should be prime therapeutic targets for these children in the context of treatment addressing motor planning/programming, self-monitoring, and self-correcting.Supplemental materialhttps://doi.org/10.23641/asha.19119350.

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Genetic Candidate Variants in Two Multigenerational Families with Childhood Apraxia of Speech.

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Genetic Candidate Variants in Two Multigenerational Families with Childhood Apraxia of Speech.

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