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Nucleic Acids Research 2006 34(Database Issue):D617-D621; doi:10.1093/nar/gkj151
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Nucleic Acids Research, 2006, Vol. 34, Database issue D617-D621
© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

Article

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

Bernice R. Packer1,2,*, Meredith Yeager1,2, Laura Burdett1,2, Robert Welch1,2, Michael Beerman1,2, Liqun Qi1,2, Hugues Sicotte1,2, Brian Staats1,2, Mekhala Acharya3, Andrew Crenshaw1,2, Andrew Eckert1,2, Vinita Puri1,2, Daniela S. Gerhard4 and Stephen J. Chanock2,5

1Intramural Research Support Program, SAIC-Frederick, NCI-FCRDC Frederick, MD, USA 2Division of Cancer Epidemiology and Genetics, National Cancer Institute Bethesda, MD, USA 3Department of Bioinformatics, George Mason University Manassas, VA, USA 4Office of Cancer Genomics, National Cancer Institute Bethesda, MD, USA 5Section on Genomic Variation, Pediatric Oncology Branch, National Cancer Institute, National Institutes of Health Gaithersburg, MD, USA

*To whom correspondence should be addressed. Tel: +1 301 496 6019; Fax: +1 301 402 3134; Email: packerb{at}mail.nih.gov

Received September 14, 2005. Revised October 28, 2005. Accepted October 28, 2005.

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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 Cancer Epidemiol. Biomarkers Prev.Home page
M. P. Purdue, L. C. Sakoda, B. I. Graubard, R. Welch, S. J. Chanock, I. A. Sesterhenn, M. V. Rubertone, R. L. Erickson, and K. A. McGlynn
A Case-Control Investigation of Immune Function Gene Polymorphisms and Risk of Testicular Germ Cell Tumors
Cancer Epidemiol. Biomarkers Prev., January 1, 2007; 16(1): 77 - 83.
[Abstract] [Full Text] [PDF]

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 CarcinogenesisHome page
L. Hou, E.M. El-Omar, J. Chen, P. Grillo, C.S. Rabkin, A. Baccarelli, M. Yeager, S.J. Chanock, W. Zatonski, L.H. Sobin, et al.
Polymorphisms in Th1-type cell-mediated response genes and risk of gastric cancer
Carcinogenesis, January 1, 2007; 28(1): 118 - 123.
[Abstract] [Full Text] [PDF]

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 Cancer Epidemiol. Biomarkers Prev.Home page
L. Wang, H. Liu, Z. Zhang, M. R. Spitz, and Q. Wei
Association of Genetic Variants of O6-Methylguanine-DNA Methyltransferase with Risk of Lung Cancer in Non-Hispanic Whites
Cancer Epidemiol. Biomarkers Prev., December 1, 2006; 15(12): 2364 - 2369.
[Abstract] [Full Text] [PDF]

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 BloodHome page
D. A. Hill, S. S. Wang, J. R. Cerhan, S. Davis, W. Cozen, R. K. Severson, P. Hartge, S. Wacholder, M. Yeager, S. J. Chanock, et al.
Risk of non-Hodgkin lymphoma (NHL) in relation to germline variation in DNA repair and related genes
Blood, November 1, 2006; 108(9): 3161 - 3167.
[Abstract] [Full Text] [PDF]

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 Cancer Res.Home page
M. M. Gaudet, S. Chanock, J. Lissowska, S. I. Berndt, B. Peplonska, L. A. Brinton, R. Welch, M. Yeager, A. Bardin-Mikolajczak, and M. Garcia-Closas
Comprehensive Assessment of Genetic Variation of Catechol-O-Methyltransferase and Breast Cancer Risk
Cancer Res., October 1, 2006; 66(19): 9781 - 9785.
[Abstract] [Full Text] [PDF]


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