DOE Human Genome Program Contractor-Grantee Workshop VIII
February 27-March 2, 2000  Santa Fe, NM

74. Identifying Single Nucleotide Polymorphisms (SNPs) in Human Candidate Genes

Deborah A. Nickerson, Scott L. Taylor, and Mark J. Rieder

Department of Molecular Biotechnology, Box 357730, University of Washington, Seattle, WA 98195

debnick@u.washington.edu

Single nucleotide substitutions and unique base insertions and deletions are the most common form of polymorphism and disease-causing mutation in the human genome. Based on the natural frequency of these variants, they are likely to be the underlying cause of most phenotypic differences in humans. Because of their functional importance, a number of methods have been developed to identify single nucleotide polymorphisms (SNPs). Among these, direct sequence analysis has many advantages because it provides complete information about the location and nature of any variants in a single pass, is automatable, widely available, and simple to apply. To further automate the detection of SNPs by direct sequence analysis we have developed PolyPhred which together with Phred, Phrap, and Consed identifies nucleotide substitutions within a target sequence. Over the past year, we have developed several approaches to increase the accuracy and selectivity of PolyPhred as well as a tool known as PolyPhred2db that simplifies the development of databases of SNPs using information obtained by PolyPhred. The application of these tools in analyzing the diversity of human candidate genes will be described. Our results suggest that the levels and patterns of sequence variation found in human genes could pose challenges in identifying the sites, or combination of sites, that influence variation in the risk of disease within and among human populations.