Expression-based genetic/physical maps of Single-Nucleotide Polymorphisms identified by the Cancer Genome Anatomy Project

R. Clifford, M. Edmonson, Y. Hu, C. Nguyen, T. Scherpbier, Kenneth Buetow

Research output: Contribution to journalArticle

36 Citations (Scopus)

Abstract

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.hih.gov/GAI/). Our SNP detection tools are available to the public for noncommercial use.

Original languageEnglish (US)
Pages (from-to)1259-1265
Number of pages7
JournalGenome Research
Volume10
Issue number8
DOIs
StatePublished - 2000
Externally publishedYes

Fingerprint

Single Nucleotide Polymorphism
Anatomy
Genome
Neoplasms
Expressed Sequence Tags
Genes
Search Engine
Inborn Genetic Diseases
National Cancer Institute (U.S.)
Organism Cloning
Prostate
Colon
Breast
Kidney
Lung
Liver
DNA
Growth

ASJC Scopus subject areas

  • Genetics

Cite this

Expression-based genetic/physical maps of Single-Nucleotide Polymorphisms identified by the Cancer Genome Anatomy Project. / Clifford, R.; Edmonson, M.; Hu, Y.; Nguyen, C.; Scherpbier, T.; Buetow, Kenneth.

In: Genome Research, Vol. 10, No. 8, 2000, p. 1259-1265.

Research output: Contribution to journalArticle

Clifford, R. ; Edmonson, M. ; Hu, Y. ; Nguyen, C. ; Scherpbier, T. ; Buetow, Kenneth. / Expression-based genetic/physical maps of Single-Nucleotide Polymorphisms identified by the Cancer Genome Anatomy Project. In: Genome Research. 2000 ; Vol. 10, No. 8. pp. 1259-1265.
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