Targeted genomic capture and massively parallel sequencing to identify genes for hereditary hearing loss in middle eastern families

Abstract

BackgroundIdentification of genes responsible for medically important traits is a major challenge in human genetics. Due to the genetic heterogeneity of hearing loss, targeted DNA capture and massively parallel sequencing are ideal tools to address this challenge. Our subjects for genome analysis are Israeli Jewish and Palestinian Arab families with hearing loss that varies in mode of inheritance and severity.ResultsA custom 1.46 MB design of cRNA oligonucleotides was constructed containing 246 genes responsible for either human or mouse deafness. Paired-end libraries were prepared from 11 probands and bar-coded multiplexed samples were sequenced to high depth of coverage. Rare single base pair and indel variants were identified by filtering sequence reads against polymorphisms in dbSNP132 and the 1000 Genomes Project. We identified deleterious mutations in CDH23, MYO15A, TECTA, TMC1, and WFS1. Critical mutations of the probands co-segregated with hearing loss. Screening of additional families in a relevant population was performed. TMC1 p.S647P proved to be a founder allele, contributing to 34% of genetic hearing loss in the Moroccan Jewish population.ConclusionsCritical mutations were identified in 6 of the 11 original probands and their families, leading to the identification of causative alleles in 20 additional probands and their families. The integration of genomic analysis into early clinical diagnosis of hearing loss will enable prediction of related phenotypes and enhance rehabilitation. Characterization of the proteins encoded by these genes will enable an understanding of the biological mechanisms involved in hearing loss.

American College of Medical Genetics and Genomics guideline for the clinical evaluation and etiologic diagnosis of hearing loss

“…The main advantage of these tests is their ability to address the problem of genetic heterogeneity, wherein many different genes result in phenotypes that cannot be easily distinguished clinically. [92][93][94][95][96] Several NGS tests are now clinically available and can be found by querying the GeneTests and Genetic Testing Registry websites. 97,98 NGS tests that use disease-targeted exon-capture approaches restrict sequencing to specific genes, such as genes known to be associated with hearing loss.…”

Novel myosin mutations for hereditary hearing loss revealed by targeted genomic capture and massively parallel sequencing

“…2,3 Our goal is to utilize this method in order to help solve the molecular etiology of the deaf population in the Middle East. Routine diagnostic tests conducted in the clinic, most of which do not use MPS, have the disadvantage of overlooking known and novel mutations in known deafness genes, some of which are very common in other populations.…”

“…12,21 In the Middle Eastern Jewish and Arab populations, to date, eight mutations have been reported in myosins IIIA, 7 myosin VIIA 22 and myosin XVA. 3,22 The present study, using targeted capture and MPS, defines nine novel mutations in MYO6, MYO7A and MYO15A, doubling the number of myosin mutations present in the Middle East responsible for non-syndromic hearing loss.…”

“…These genes include GJB6, PCDH15, USH1C, MYO3A, SLC26A4, LOXHD1, CDH23, MYO15A, WFS1, TECTA, POU4F3 and the inverted duplication of TJP2. 3,[23][24][25] All known deafness-causing mutations in the Palestinian population were excluded, including mutations in CDH23, MYO7A, MYO15A, OTOF, PJVK, SLC26A4, TECTA, TMHS, TMPRSS3, OTOA, PTPRQ and GPSM2. 22,26,27 Massive parallel sequencing Capture libraries were created and MPS was performed, followed by bioinformatics analysis, as previously described.…”

“…The combination of targeted genomic capture and massive parallel sequencing (MPS) has become a promising tool for detecting novel and known mutations involved in hereditary hearing loss and for solving many deafness cases in a rapid and cost-effective manner. 2,3 In our study, we applied this genomic method to determine the causative genes and mutations in undiagnosed deaf individuals of 96 Israeli Jewish and Palestinian Arab families. Among the mutations detected, we identified nine novel mutations in the genes encoding myosin VI, myosin VIIA and myosin XVA.…”