Eliot Shearer - Non-Syndromic Deafness

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My project focuses on applying new high-throughput sequencing technologies for determination of genetic causes of hearing loss. Sanger sequencing was developed in 1977 and is the current gold standard for genetic testing. The primary limiting factors in this method of genetic sequencing are in generating the amplicons via PCR to sequence and the method of sequencing by chain-termination. For example, traditionally, a person diagnosed with autosomal recessive non-syndromic hearing loss (ARNSHL) is initially screened for mutations in GJB2, which may be the cause of hearing loss in 50% of individuals.  However, if the deafness-causing mutation were not found in the GJB2 gene, to screen all 28 genes implicated in ARNSHL would require sequence analysis of at least 1000 exons and over 300,000 base pairs.  Screening this number of exons in one patient would be expensive (thousands of dollars) and require several weeks for sequencing alone, with significant data analysis by trained individuals also required. Screening for autosomal dominant non-syndromic hearing loss is similarly time consuming and expensive.

However, new high-throughput sequencing technologies, including pyrosequencing, overcome the limitations of Sanger sequencing, as they can sequence millions of base pairs in a single run, thus overcoming the hurdle of base-by-base Sanger sequencing. In addition, new custom-made sequence capture technology allows targeted capture of millions of desired base pairs, further streamlining sequencing. Although these technologies have been used experimentally with promising results, to date, no studies have validated the use of high-throughput sequencing technologies for the use of determination of deafness causing mutations in affected individuals. Non-syndromic hearing loss is uniquely suited to the use of these new technologies due to the large number of genes involved, which could theoretically be sequenced simultaneously. The goal of my project is to validate high-throughput sequencing and sequence capture technologies in the context of hereditary hearing loss to improve clinical diagnostics as well as for research use.