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 humans, represent a valuable resource for the genetic analysis of cancer and other illnesses. These markers may be used in a variety of ways to investigate the genetic underpinnings of disease. In gene-based studies, the correlat...

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Bibliographic Details
Published in:Genome research 2000-08, Vol.10 (8), p.1259-1265
Main Authors: Clifford, R, Edmonson, M, Hu, Y, Nguyen, C, Scherpbier, T, Buetow, K H
Format: Article
Language:English
Subjects:
Chromosome Mapping - methods
Chromosome Mapping - trends
Databases, Factual
Gene Expression
Gene Library
Genetic Linkage
Human Genome Project
Humans
Information Storage and Retrieval
Internet
Neoplasms - genetics
Physical Chromosome Mapping - methods
Physical Chromosome Mapping - trends
Polymorphism, Single Nucleotide - genetics
Reproducibility of Results
Resource
Software
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Summary:SNPs (Single-Nucleotide Polymorphisms), the most common DNA variant in humans, represent a valuable resource for the genetic analysis of cancer and other illnesses. These markers may be used in a variety of ways to investigate the genetic underpinnings of disease. In gene-based studies, the correlations between allelic variants of genes of interest and particular disease states are assessed. An extensive collection of SNP markers may enable entire 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 cloning. The National Cancer Institute's CGAP-GAI (Cancer Genome Anatomy Project Genetic Annotation Initiative) group has identified 10,243 SNPs by examining publicly available EST (Expressed Sequence Tag) chromatograms. More than 6800 of these polymorphisms have been placed on expression-based integrated genetic/physical maps. In addition to a set of comprehensive SNP maps, we have produced maps containing single nucleotide polymorphisms in genes expressed in breast, colon, kidney, liver, lung, or prostate tissue. The integrated maps, a SNP search engine, and a Java-based tool for viewing candidate SNPs in the context of EST assemblies can be accessed via the CGAP-GAI web site (http://cgap.nci.nih.gov/GAI/). Our SNP detection tools are available to the public for noncommercial use.
ISSN:1088-9051
1549-5469
DOI:10.1101/gr.10.8.1259