New APEX diagnostic for hereditary sensorineural hearing loss

DESCRIPTION (provided by applicant): In developed countries, approximately 1:1000 children are born deaf and approximately 1:300 children are born with some lesser degree of hearing loss. At least 50% of the deafness and hearing impairment is likely to be attributable to genetic factors, with a large number of genes involved in the pathogenesis. The molecular genetic basis for the majority of cases remains obscure, however, due to the lack of associated clinical features in -70% of cases (i.e. non-syndromic hearing loss) and due to the lack of molecular genetic tests that can evaluate a large number of mutations across multiple genes. With the advent of mandatory newborn hearing screening programs in all U.S. states, coupled with identification of many genes involved in the complex biology of hearing, demand for accurate molecular genetic analysis of hearing loss is growing rapidly. To that end, Drs. Gardner and Schrijver have invented a comprehensive diagnostic panel with 199 mutations underlying sensorineural (mostly nonsyndromic) hearing loss. It is an inexpensive microarray, capable of simultaneous evaluation of multiple mutations in eight genes (GJB2, GJB6, GJB3, GJA1, SCL26A4, SCL26A5 and the mitochondria! genes 12S rRNA and tRNA Ser). By use of Arrayed single Primer Extension (APEX), the diagnostic test combines the sequencing accuracy of single primer extension with the high throughput of the microarray format. The purpose of this proposal is further develop and fully validate this microarray for both research and diagnostic uses. With the provided budget, we can optimize the oligonucleotide primers on the chip for proper sample hybridization, optimize the DMA amplification and purification protocols, and screen the chip with several hundred patient DNA samples from hearing loss patients. We will test -100 patients with known mutations and -100 with no, or only one, known mutation. Molecular genetic testing is expected, by some, to eventually become the first step in determining the cause of hearing loss in patients of any age. Such molecular analysis may diminish the need for expensive and invasive testing or deep sedation required to perform hearing tests in young children. Early identification of molecular causes of hearing loss will also allow for proper intervention to prevent developmental delay in prelingual hearing impaired children. Research results from multiple patient samples will add to our body of knowledge about the genetic basis for hearing loss and specific genotype/phenotype correlations. In summary, if our assay proves to provide accurate results, then rapid, much more comprehensive, and relatively inexpensive genetic testing for sensorineural hearing loss becomes possible, enabling in turn prompt medical management for affected individuals and genetic counseling for their families.