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Open Access Methodology article

Predicting candidate genes for human deafness disorders: a bioinformatics approach

Rami Alsaber, Christopher J Tabone and Raj P Kandpal*

Author Affiliations

Department of Biological Sciences, Fordham University Bronx, NY 10458, USA

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BMC Genomics 2006, 7:180  doi:10.1186/1471-2164-7-180

Published: 19 July 2006

Abstract

Background

There are more than 50 genes for autosomal dominant and autosomal recessive nonsyndromic hereditary deafness that are yet to be cloned. The human genome sequence and expression profiles of transcripts in the inner ear have aided positional cloning approaches. The knowledge of protein interactions offers additional advantages in selecting candidate genes within a mapped region.

Results

We have employed a bioinformatic approach to assemble the genes encoded by genomic regions that harbor various deafness loci. The genes were then in silico analyzed for their candidacy by expression pattern and ability to interact with other proteins. Such analyses have narrowed a list of 2400 genes from suspected regions of the genome to a manageable number of about 140 for further analysis.

Conclusion

We have established a list of strong candidate genes encoded by the regions linked to various nonsyndromic hereditary hearing loss phenotypes by using a novel bioinformatic approach. The candidates presented here provide a starting point for mutational analysis in well-characterized families along with genetic linkage to refine the loci. The advantages and shortcomings of this bioinformatic approach are discussed.