Application of Next-Generation–Sequencing in Hearing Loss Diagnosis - Next Generation Sequencing Technologies in Medical Genetics - page 63

7.4 Importance of Hearing Loss Detection

and Genetic Testing

Early detection and intervention for children with hearing loss offers opportunities
for improving language and speech development, thereby facilitating the acquisi-
tion of normal social and cognitive skills. Elucidation of the genetic basis of hearing
loss is crucial for the clinical management of patients and their family. In addition,
determination of genetic etiology in a large cohort of patients will provide better
understanding of genotype-phenotype correlations, which could help developing
specifi c therapeutic interventions. For syndromic hearing loss, selection of caus-
ative genes to reach a molecular diagnosis are possible based on associated symp-
toms, whereas this approach is not feasible for nonsyndromic hearing loss because
phenotype caused by most of the genes is indistinguishable. Therefore, sequential
screening of all hearing loss genes has been widely applied to identify the genetic
cause. Currently, genetic testing for hearing loss is conducted using different diag-
nostic algorithms in several institutions worldwide. Mutation screening of coding
and fl anking intronic regions of the candidate genes using automated Sanger
sequencing is the most common approach in vast the majority of these laboratories.
However, the extreme genetic heterogeneity of nonsyndromic and syndromic hear-
ing loss makes this strategy unfavorable in terms of cost and time. NGS technology
offers the advantage of sequencing multiple genes in parallel with lower cost and
higher time-effi ciency.

7.5 Capture-Based Hearing Loss Panels

Shearer et al. developed a comprehensive diagnostic platform named as OtoSCOPE
that targeted the exons of 54 known NSHL genes including Usher syndrome genes
(Table 7.1 ; Shearer et al. 2010 ). In this study, two hybridization capture-based
enrichment approaches, NimbleGen solid-phase enrichment and Agilent SureSelect
(SS) solution-based capture enrichment, were paired with 454 GS FLX pyrose-
quencing and Illumina GAII cyclic reversible termination sequencing, respectively.
By comparing these two platforms, SS-Illumina was shown to be superior in terms
of scalability, cost, and increased sensitivity, generating a 13-fold higher average
depth of coverage on targeted bases (903x vs 71x), with 95.3 % of targeted hearing
loss genes covered at 40x threshold (Table 7.1 ). Highly heterozygous SNPs in the
target regions were confi rmed by Sanger sequencing to determine the sensitivity
and specifi city, which were both greater than 99 % for the SS-Illumina platform.
Besides the use of three patients as positive controls, NSHL mutations were found
in STRC , MYO6 , KCNQ4 , MYN14 , and CDH23 genes in fi ve out of six idiopathic
SNHL patients, including three novel mutations. However, the variants found in one
patient were ruled out as causative mutations by segregation analysis. Similarly, a
capture-based enrichment approach was used in another study that was designed to