|Title:||Application of Massively Parallel Sequencing to Genetic Diagnosis in Multiplex Families with Idiopathic Sensorineural Hearing Impairment||Authors:||Chen-Chi Wu
|Issue Date:||2013||Publisher:||Public Library of Science||Journal Volume:||8||Journal Issue:||2||Source:||PLoS ONE||Abstract:||
Despite the clinical utility of genetic diagnosis to address idiopathic sensorineural hearing impairment (SNHI), the current strategy for screening mutations via Sanger sequencing suffers from the limitation that only a limited number of DNA fragments associated with common deafness mutations can be genotyped. Consequently, a definitive genetic diagnosis cannot be achieved in many families with discernible family history. To investigate the diagnostic utility of massively parallel sequencing (MPS), we applied the MPS technique to 12 multiplex families with idiopathic SNHI in which common deafness mutations had previously been ruled out. NimbleGen sequence capture array was designed to target all protein coding sequences (CDSs) and 100 bp of the flanking sequence of 80 common deafness genes. We performed MPS on the Illumina HiSeq2000, and applied BWA, SAMtools, Picard, GATK, Variant Tools, ANNOVAR, and IGV for bioinformatics analyses. Initial data filtering with allele frequencies (<5% in the 1000 Genomes Project and 5400 NHLBI exomes) and PolyPhen2/SIFT scores (>0.95) prioritized 5 indels (insertions/deletions) and 36 missense variants in the 12 multiplex families. After further validation by Sanger sequencing, segregation pattern, and evolutionary conservation of amino acid residues, we identified 4 variants in 4 different genes, which might lead to SNHI in 4 families compatible with autosomal dominant inheritance. These included GJB2 p.R75Q, MYO7A p.T381M, KCNQ4 p.S680F, and MYH9 p.E1256K. Among them, KCNQ4 p.S680F and MYH9 p.E1256K were novel. In conclusion, MPS allows genetic diagnosis in multiplex families with idiopathic SNHI by detecting mutations in relatively uncommon deafness genes. ? 2013 Wu et al.
|ISSN:||1932-6203||DOI:||10.1371/journal.pone.0057369||SDG/Keyword:||connexin 26; myosin VIIa; potassium channel KCNQ4; adult; article; autosomal dominant inheritance; bioinformatics; child; cohort analysis; controlled study; diagnostic procedure; diagnostic value; family; family history; female; gene; gene frequency; gene sequence; genetic conservation; genetic diagnosis; genetic procedures; genetic variability; GJB2 gene; GJB4 gene; heterozygosity; human; idiopathic disease; indel mutation; KCNQ4 gene; male; massively parallel sequencing; missense mutation; mouse; multiplex family; mutational analysis; MYH9 gene; MYO7A gene; nonhuman; nucleotide sequence; perception deafness; phenotype; Sanger sequencing; school child; segregation analysis; validation process
|Appears in Collections:||醫學院附設醫院 (臺大醫院)|
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