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. 2006 Jan 1;34(Database issue):D617-21.
doi: 10.1093/nar/gkj151.

SNP500Cancer: a public resource for sequence validation, assay development, and frequency analysis for genetic variation in candidate genes

Bernice R Packer  1 , Meredith Yeager, Laura Burdett, Robert Welch, Michael Beerman, Liqun Qi, Hugues Sicotte, Brian Staats, Mekhala Acharya, Andrew Crenshaw, Andrew Eckert, Vinita Puri, Daniela S Gerhard, Stephen J Chanock
Affiliations

SNP500Cancer: a public resource for sequence validation, assay development, and frequency analysis for genetic variation in candidate genes

Bernice R Packer et al. Nucleic Acids Res. .

Abstract

The SNP500Cancer database provides sequence and genotype assay information for candidate SNPs useful in mapping complex diseases, such as cancer. The database is an integral component of the NCI Cancer Genome Anatomy Project (http://cgap.nci.nih.gov). SNP500Cancer reports sequence analysis of anonymized control DNA samples (n = 102 Coriell samples representing four self-described ethnic groups: African/African-American, Caucasian, Hispanic and Pacific Rim). The website is searchable by gene, chromosome, gene ontology pathway, dbSNP ID and SNP500Cancer SNP ID. As of October 2005, the database contains >13 400 SNPs, 9124 of which have been sequenced in the SNP500Cancer population. For each analysed SNP, gene location and >200 bp of surrounding annotated sequence (including nearby SNPs) are provided, with frequency information in total and per subpopulation as well as calculation of Hardy-Weinberg equilibrium for each subpopulation. The website provides the conditions for validated sequencing and genotyping assays, as well as genotype results for the 102 samples, in both viewable and downloadable formats. A subset of sequence validated SNPs with minor allele frequency >5% are entered into a high-throughput pipeline for genotyping analysis to determine concordance for the same 102 samples. In addition, the results of genotype analysis for select validated SNP assays (defined as 100% concordance between sequence analysis and genotype results) are posted for an additional 280 samples drawn from the Human Diversity Panel (HDP). SNP500Cancer provides an invaluable resource for investigators to select SNPs for analysis, design genotyping assays using validated sequence data, choose selected assays already validated on one or more genotyping platforms, and select reference standards for genotyping assays. The SNP500Cancer database is freely accessible via the web page at http://snp500cancer.nci.nih.gov.

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Figures

Figure 1
Figure 1
The SNP page for a typical SNP from the SNP500Cancer website, showing links to external resources, the SNP within flanking sequence, frequency data and links to assay information.
Figure 2
Figure 2
The distribution of 13.437 SNPs in SNP500Cancer—those already in dbSNP, those not yet in dbSNP (submitted for next build). Almost 10% of SNP500Cancer SNPs were found to have no variation in the set of 102 individuals of the SNP500Cancer population overall, even though they are in dbSNP.
See this image and copyright information in PMC

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