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SNP500Cancer Background Information


Cancer Genome Anatomy Project (CGAP)

The SNP500Cancer is part of the Cancer Genome Anatomy Project and is specifically designed to generate resources for the identification and characterization of genetic variation in genes important in cancer. CGAP is dedicated to the development of technology, including both assays and utilization of technical platforms. Accordingly, data pertaining to genes and their variation are made available on a public web-site (http://cgap.nci.nih.gov). The SNP500Cancer data represents one of several initiatives within the Genetic Annotation Initiative, designed to characterize variation, as a resource for applying genetic approaches to understanding the etiology of different cancers as well as related phenotypes.


SNP500Cancer

Purpose:

The purpose of the SNP500Cancer project is to re-sequence 102 reference samples from four ethnically diverse groups using anonymized samples from the Coriell Biorepository (Camden, NJ). The effort seeks to validate known or newly discovered Single Nucleotide Polymorphisms (SNPs) and other important classes of genetic variants of potential importance to molecular epidemiology studies of cancer and other diseases.

Specifically, data on this web site can be used by molecular epidemiologists to:

  • Select SNPs for analysis.
  • Set up genotype assays using the validated sequence data.
  • Choose selected assays already validated on one or more platforms.
  • Identify and obtain DNA samples with sequence-verified genotypes of interest for use as quality control samples to establish the accuracy of genotyping platforms.
  • Estimate common haplotypes in selected genes.

Initial selection of SNPs for study has been based upon review of the literature and with input from intramural and extramural investigators. The bias has been to choose SNPs within or closely situated to candidate genes, implicated in one or more cancers. Thus, there is a heavy weighting towards non-synonymous SNPs (i.e., those that result in an amino acid substitution). In particular, we acknowledge the Genome Analysis Group at the International Agency for Research on Cancer, Lyon, France, which provided data on a substantial number of SNPs in the database.

As additional potentially informative SNPs are identified and characterized, they will be added to the database on a regular basis. We welcome suggestions for new SNPs to consider including in the project, particularly SNPs with known or suspected functional relevance.

Currently Available (updated daily):

  • List of Genes/SNPs
  • Validated sequence results
  • Genotype of each of the 102 samples
  • Genotype of each of the 210 samples
  • Summary of genotype data by subpopulations
  • Primers, probes, and conditions for genotyping assays
  • Links to assay ordering information
  • Instructions and link to order samples, either individually or as a set from Coriell Institute
 
 
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