Expression-based genetic/physical maps of single-nucleotide polymorphisms identified by the cancer genome anatomy project

SNPs (Single-Nucleotide Polymorphisms), the most common DNA variant in huma ns, represent a valuable resource for the genetic analysis of cancer and ot her illnesses. These markers may be used in a variety of ways to investigat e the genetic underpinnings of disease. In gene-based studies, the correlat ions between allelic variants of genes of interest and particular disease s tates are assessed. An extensive collection of SNP markers may enable entir e molecular pathways regulating cell metabolism, growth, or differentiation to be analyzed by this approach. In addition, high-resolution genetic maps based on SNPs will greatly facilitate linkage analysis and positional clon ing. The National Cancer Institute's CGAP-GAI (Cancer Genome Anatomy Projec t Genetic Annotation Initiative) group has identified 10,243 SNPs by examin ing publicly available EST (Expressed Sequence Tag) chromatograms. More tha n 6800 of these polymorphisms have been placed on expression-based integrat ed genetic/physical maps. in addition to a set of comprehensive SNP maps, w e have produced maps containing single nucleotide polymorphisms in genes ex pressed in breast, colon, kidney, liver, lung, or prostate tissue. The inte grated maps, a SNP search engine, and a lava-based tool for viewing candida te SNPs in the context of EST assemblies can be accessed via the CGAP-GAI w eb site [http://cgap.nci.nih.gov/GAI/). Our SNP detection tools are availab le to the public for noncommercial use.