High-throughput sequencing to decipher the genetic heterogeneity of deafness

Abstract

Identifying genes causing non-syndromic hearing loss has been challenging using traditional approaches. We describe the impact that high-throughput sequencing approaches are having in discovery of genes related to hearing loss and the implications for clinical diagnosis.

Figure 1

Schematic diagram of the human ear. (a) The ear is composed of three major parts, the outer, middle and inner ear. Mutations in genes encoded by proteins functioning primarily in the cochlear of the inner ear are known to lead to sensorineural hearing loss. Mutations in these genes often are associated with balance defects because of their expression in the vestibule of the inner ear. (b) The scala media, scala tympani and scala vestibule are visible in a cross-section of the cochlear duct. TM, tympanic membrane. (c) The organ of Corti is contained within the cochlear duct, and includes sensory hair cells and supporting cells. (d) An outer hair cell showing the staircase pattern of the stereocilia bundle on its apical surface. Reproduced with permission from [47].

Figure 2

Pipeline for identification of pathogenic variants by targeted capture and high-throughput sequencing of deaf individuals. The major steps required to identify mutations responsible for deafness are outlined. The first step begins with institutional review board or Helsinki Committee authorization to perform research on human subjects, followed by extraction of genomic DNA from blood. A series of experimental and computational steps follow, with variations according to the type of sequencing platform used.

Figure 3

Prioritization of variants to identify causative hearing loss mutations. A series of computational steps (blue background) are required to tackle the many variants that come out of the high-throughput sequencing. High-confidence candidates will be further tested (orange background) in the proband's family and ethnic group using Sanger sequencing or restriction enzyme assays. Confirmed pathogenic mutations will be tested for biological function (gray background). Websites of the tools shown are at: 1000 Genomes Project [48]; dbSNP [49]; EVS [50]; PhyloP [51]; PolyPhen2 [52]; SIFT [53]; ConSurf [54].