SNP500Cancer: a public resource for sequence validation, assay development, and frequency analysis for genetic variation in candidate genes
Identifieur interne : 000242 ( Istex/Corpus ); précédent : 000241; suivant : 000243SNP500Cancer: a public resource for sequence validation, assay development, and frequency analysis for genetic variation in candidate genes
Auteurs : Bernice R. Packer ; 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. ChanockSource :
- Nucleic Acids Research [ 0305-1048 ] ; 2006-01.
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.
Url:
DOI: 10.1093/nar/gkj151
Links to Exploration step
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Chanock</name><affiliation><mods:affiliation>Division of Cancer Epidemiology and Genetics, National Cancer Institute Bethesda, MD, USA</mods:affiliation></affiliation><affiliation><mods:affiliation>Section on Genomic Variation, Pediatric Oncology Branch, National Cancer Institute, National Institutes of Health Gaithersburg, MD, USA</mods:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">ISTEX</idno><idno type="RBID">ISTEX:89CF57E7454C0D81DB579D135BDDC14F2A9AD855</idno><date when="2006" year="2006">2006</date><idno type="doi">10.1093/nar/gkj151</idno><idno type="url">https://api.istex.fr/document/89CF57E7454C0D81DB579D135BDDC14F2A9AD855/fulltext/pdf</idno><idno type="wicri:Area/Istex/Corpus">000242</idno></publicationStmt><sourceDesc><biblStruct><analytic><title level="a" type="main" xml:lang="en">SNP500Cancer: a public resource for sequence validation, assay development, and frequency analysis for genetic variation in candidate genes</title><author><name sortKey="Packer, Bernice R" sort="Packer, Bernice R" uniqKey="Packer B" first="Bernice R." last="Packer">Bernice R. Packer</name><affiliation><mods:affiliation>Intramural Research Support Program, SAIC-Frederick, NCI-FCRDC Frederick, MD, USA</mods:affiliation></affiliation><affiliation><mods:affiliation>Division of Cancer Epidemiology and Genetics, National Cancer Institute Bethesda, MD, USA</mods:affiliation></affiliation><affiliation><mods:affiliation>To whom correspondence should be addressed. Tel: +1 301 496 6019; Fax: +1 301 402 3134; Email: packerb@mail.nih.gov</mods:affiliation></affiliation><affiliation><mods:affiliation>E-mail: packerb@mail.nih.gov</mods:affiliation></affiliation></author><author><name sortKey="Yeager, Meredith" sort="Yeager, Meredith" uniqKey="Yeager M" first="Meredith" last="Yeager">Meredith Yeager</name><affiliation><mods:affiliation>Intramural Research Support Program, SAIC-Frederick, NCI-FCRDC Frederick, MD, USA</mods:affiliation></affiliation><affiliation><mods:affiliation>Division of Cancer Epidemiology and Genetics, National Cancer Institute Bethesda, MD, USA</mods:affiliation></affiliation></author><author><name sortKey="Burdett, Laura" sort="Burdett, Laura" uniqKey="Burdett L" first="Laura" last="Burdett">Laura Burdett</name><affiliation><mods:affiliation>Intramural Research Support Program, SAIC-Frederick, NCI-FCRDC Frederick, MD, USA</mods:affiliation></affiliation><affiliation><mods:affiliation>Division of Cancer Epidemiology and Genetics, National Cancer Institute Bethesda, MD, USA</mods:affiliation></affiliation></author><author><name sortKey="Welch, Robert" sort="Welch, Robert" uniqKey="Welch R" first="Robert" last="Welch">Robert Welch</name><affiliation><mods:affiliation>Intramural Research Support Program, SAIC-Frederick, NCI-FCRDC Frederick, MD, USA</mods:affiliation></affiliation><affiliation><mods:affiliation>Division of Cancer Epidemiology and Genetics, National Cancer Institute Bethesda, MD, USA</mods:affiliation></affiliation></author><author><name sortKey="Beerman, Michael" sort="Beerman, Michael" uniqKey="Beerman M" first="Michael" last="Beerman">Michael Beerman</name><affiliation><mods:affiliation>Intramural Research Support Program, SAIC-Frederick, NCI-FCRDC Frederick, MD, USA</mods:affiliation></affiliation><affiliation><mods:affiliation>Division of Cancer Epidemiology and Genetics, National Cancer Institute Bethesda, MD, USA</mods:affiliation></affiliation></author><author><name sortKey="Qi, Liqun" sort="Qi, Liqun" uniqKey="Qi L" first="Liqun" last="Qi">Liqun Qi</name><affiliation><mods:affiliation>Intramural Research Support Program, SAIC-Frederick, NCI-FCRDC Frederick, MD, USA</mods:affiliation></affiliation><affiliation><mods:affiliation>Division of Cancer Epidemiology and Genetics, National Cancer Institute Bethesda, MD, USA</mods:affiliation></affiliation></author><author><name sortKey="Sicotte, Hugues" sort="Sicotte, Hugues" uniqKey="Sicotte H" first="Hugues" last="Sicotte">Hugues Sicotte</name><affiliation><mods:affiliation>Intramural Research Support Program, SAIC-Frederick, NCI-FCRDC Frederick, MD, USA</mods:affiliation></affiliation><affiliation><mods:affiliation>Division of Cancer Epidemiology and Genetics, National Cancer Institute Bethesda, MD, USA</mods:affiliation></affiliation></author><author><name sortKey="Staats, Brian" sort="Staats, Brian" uniqKey="Staats B" first="Brian" last="Staats">Brian Staats</name><affiliation><mods:affiliation>Intramural Research Support Program, SAIC-Frederick, NCI-FCRDC Frederick, MD, USA</mods:affiliation></affiliation><affiliation><mods:affiliation>Division of Cancer Epidemiology and Genetics, National Cancer Institute Bethesda, MD, USA</mods:affiliation></affiliation></author><author><name sortKey="Acharya, Mekhala" sort="Acharya, Mekhala" uniqKey="Acharya M" first="Mekhala" last="Acharya">Mekhala Acharya</name><affiliation><mods:affiliation>Department of Bioinformatics, George Mason University Manassas, VA, USA</mods:affiliation></affiliation></author><author><name sortKey="Crenshaw, Andrew" sort="Crenshaw, Andrew" uniqKey="Crenshaw A" first="Andrew" last="Crenshaw">Andrew Crenshaw</name><affiliation><mods:affiliation>Intramural Research Support Program, SAIC-Frederick, NCI-FCRDC Frederick, MD, USA</mods:affiliation></affiliation><affiliation><mods:affiliation>Division of Cancer Epidemiology and Genetics, National Cancer Institute Bethesda, MD, USA</mods:affiliation></affiliation></author><author><name sortKey="Eckert, Andrew" sort="Eckert, Andrew" uniqKey="Eckert A" first="Andrew" last="Eckert">Andrew Eckert</name><affiliation><mods:affiliation>Intramural Research Support Program, SAIC-Frederick, NCI-FCRDC Frederick, MD, USA</mods:affiliation></affiliation><affiliation><mods:affiliation>Division of Cancer Epidemiology and Genetics, National Cancer Institute Bethesda, MD, USA</mods:affiliation></affiliation></author><author><name sortKey="Puri, Vinita" sort="Puri, Vinita" uniqKey="Puri V" first="Vinita" last="Puri">Vinita Puri</name><affiliation><mods:affiliation>Intramural Research Support Program, SAIC-Frederick, NCI-FCRDC Frederick, MD, USA</mods:affiliation></affiliation><affiliation><mods:affiliation>Division of Cancer Epidemiology and Genetics, National Cancer Institute Bethesda, MD, USA</mods:affiliation></affiliation></author><author><name sortKey="Gerhard, Daniela S" sort="Gerhard, Daniela S" uniqKey="Gerhard D" first="Daniela S." last="Gerhard">Daniela S. Gerhard</name><affiliation><mods:affiliation>Office of Cancer Genomics, National Cancer Institute Bethesda, MD, USA</mods:affiliation></affiliation></author><author><name sortKey="Chanock, Stephen J" sort="Chanock, Stephen J" uniqKey="Chanock S" first="Stephen J." last="Chanock">Stephen J. Chanock</name><affiliation><mods:affiliation>Division of Cancer Epidemiology and Genetics, National Cancer Institute Bethesda, MD, USA</mods:affiliation></affiliation><affiliation><mods:affiliation>Section on Genomic Variation, Pediatric Oncology Branch, National Cancer Institute, National Institutes of Health Gaithersburg, MD, USA</mods:affiliation></affiliation></author></analytic><monogr></monogr><series><title level="j">Nucleic Acids Research</title><title level="j" type="abbrev">Nucl. Acids Res.</title><idno type="ISSN">0305-1048</idno><idno type="eISSN">1362-4962</idno><imprint><publisher>Oxford University Press</publisher><date type="published" when="2006-01">2006-01</date><biblScope unit="volume">34</biblScope><biblScope unit="supplement">suppl_1</biblScope><biblScope unit="page" from="D617">D617</biblScope><biblScope unit="page" to="D621">D621</biblScope></imprint><idno type="ISSN">0305-1048</idno></series><idno type="istex">89CF57E7454C0D81DB579D135BDDC14F2A9AD855</idno><idno type="DOI">10.1093/nar/gkj151</idno><idno type="local">gkj151</idno></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">0305-1048</idno></seriesStmt></fileDesc><profileDesc><textClass></textClass><langUsage><language ident="en">en</language></langUsage></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">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.</div></front></TEI><istex><corpusName>oup</corpusName><author><json:item><name>Bernice R. Packer</name><affiliations><json:string>Intramural Research Support Program, SAIC-Frederick, NCI-FCRDC Frederick, MD, USA</json:string><json:string>Division of Cancer Epidemiology and Genetics, National Cancer Institute Bethesda, MD, USA</json:string><json:string>To whom correspondence should be addressed. Tel: +1 301 496 6019; Fax: +1 301 402 3134; Email: packerb@mail.nih.gov</json:string><json:string>E-mail: packerb@mail.nih.gov</json:string></affiliations></json:item><json:item><name>Meredith Yeager</name><affiliations><json:string>Intramural Research Support Program, SAIC-Frederick, NCI-FCRDC Frederick, MD, USA</json:string><json:string>Division of Cancer Epidemiology and Genetics, National Cancer Institute Bethesda, MD, USA</json:string></affiliations></json:item><json:item><name>Laura Burdett</name><affiliations><json:string>Intramural Research Support Program, SAIC-Frederick, NCI-FCRDC Frederick, MD, USA</json:string><json:string>Division of Cancer Epidemiology and Genetics, National Cancer Institute Bethesda, MD, USA</json:string></affiliations></json:item><json:item><name>Robert Welch</name><affiliations><json:string>Intramural Research Support Program, SAIC-Frederick, NCI-FCRDC Frederick, MD, USA</json:string><json:string>Division of Cancer Epidemiology and Genetics, National Cancer Institute Bethesda, MD, USA</json:string></affiliations></json:item><json:item><name>Michael Beerman</name><affiliations><json:string>Intramural Research Support Program, SAIC-Frederick, NCI-FCRDC Frederick, MD, USA</json:string><json:string>Division of Cancer Epidemiology and Genetics, National Cancer Institute Bethesda, MD, USA</json:string></affiliations></json:item><json:item><name>Liqun Qi</name><affiliations><json:string>Intramural Research Support Program, SAIC-Frederick, NCI-FCRDC Frederick, MD, USA</json:string><json:string>Division of Cancer Epidemiology and Genetics, National Cancer Institute Bethesda, MD, USA</json:string></affiliations></json:item><json:item><name>Hugues Sicotte</name><affiliations><json:string>Intramural Research Support Program, SAIC-Frederick, NCI-FCRDC Frederick, MD, USA</json:string><json:string>Division of Cancer Epidemiology and Genetics, National Cancer Institute Bethesda, MD, USA</json:string></affiliations></json:item><json:item><name>Brian Staats</name><affiliations><json:string>Intramural Research Support Program, SAIC-Frederick, NCI-FCRDC Frederick, MD, USA</json:string><json:string>Division of Cancer Epidemiology and Genetics, National Cancer Institute Bethesda, MD, USA</json:string></affiliations></json:item><json:item><name>Mekhala Acharya</name><affiliations><json:string>Department of Bioinformatics, George Mason University Manassas, VA, USA</json:string></affiliations></json:item><json:item><name>Andrew Crenshaw</name><affiliations><json:string>Intramural Research Support Program, SAIC-Frederick, NCI-FCRDC Frederick, MD, USA</json:string><json:string>Division of Cancer Epidemiology and Genetics, National Cancer Institute Bethesda, MD, USA</json:string></affiliations></json:item><json:item><name>Andrew Eckert</name><affiliations><json:string>Intramural Research Support Program, SAIC-Frederick, NCI-FCRDC Frederick, MD, USA</json:string><json:string>Division of Cancer Epidemiology and Genetics, National Cancer Institute Bethesda, MD, USA</json:string></affiliations></json:item><json:item><name>Vinita Puri</name><affiliations><json:string>Intramural Research Support Program, SAIC-Frederick, NCI-FCRDC Frederick, MD, USA</json:string><json:string>Division of Cancer Epidemiology and Genetics, National Cancer Institute Bethesda, MD, USA</json:string></affiliations></json:item><json:item><name>Daniela S. Gerhard</name><affiliations><json:string>Office of Cancer Genomics, National Cancer Institute Bethesda, MD, USA</json:string></affiliations></json:item><json:item><name>Stephen J. Chanock</name><affiliations><json:string>Division of Cancer Epidemiology and Genetics, National Cancer Institute Bethesda, MD, USA</json:string><json:string>Section on Genomic Variation, Pediatric Oncology Branch, National Cancer Institute, National Institutes of Health Gaithersburg, MD, USA</json:string></affiliations></json:item></author><language><json:string>eng</json:string></language><originalGenre><json:string>other</json:string></originalGenre><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.</abstract><qualityIndicators><score>5.735</score><pdfVersion>1.2</pdfVersion><pdfPageSize>612 x 794 pts</pdfPageSize><refBibsNative>false</refBibsNative><keywordCount>0</keywordCount><abstractCharCount>1926</abstractCharCount><pdfWordCount>2735</pdfWordCount><pdfCharCount>18589</pdfCharCount><pdfPageCount>5</pdfPageCount><abstractWordCount>269</abstractWordCount></qualityIndicators><title>SNP500Cancer: a public resource for sequence validation, assay development, and frequency analysis for genetic variation in candidate genes</title><genre><json:string>other</json:string></genre><host><volume>34</volume><publisherId><json:string>nar</json:string></publisherId><pages><last>D621</last><first>D617</first></pages><issn><json:string>0305-1048</json:string></issn><genre><json:string>journal</json:string></genre><language><json:string>unknown</json:string></language><eissn><json:string>1362-4962</json:string></eissn><title>Nucleic Acids Research</title></host><categories><wos><json:string>BIOCHEMISTRY & MOLECULAR BIOLOGY</json:string></wos></categories><publicationDate>2006</publicationDate><copyrightDate>2006</copyrightDate><doi><json:string>10.1093/nar/gkj151</json:string></doi><id>89CF57E7454C0D81DB579D135BDDC14F2A9AD855</id><score>0.23141252</score><fulltext><json:item><original>true</original><mimetype>application/pdf</mimetype><extension>pdf</extension><uri>https://api.istex.fr/document/89CF57E7454C0D81DB579D135BDDC14F2A9AD855/fulltext/pdf</uri></json:item><json:item><original>false</original><mimetype>application/zip</mimetype><extension>zip</extension><uri>https://api.istex.fr/document/89CF57E7454C0D81DB579D135BDDC14F2A9AD855/fulltext/zip</uri></json:item><istex:fulltextTEI uri="https://api.istex.fr/document/89CF57E7454C0D81DB579D135BDDC14F2A9AD855/fulltext/tei"><teiHeader><fileDesc><titleStmt><title level="a" type="main" xml:lang="en">SNP500Cancer: a public resource for sequence validation, assay development, and frequency analysis for genetic variation in candidate genes</title><respStmt xml:id="ISTEX-API" resp="Références bibliographiques récupérées via GROBID" name="ISTEX-API (INIST-CNRS)"></respStmt><respStmt xml:id="ISTEX-API" resp="Références bibliographiques récupérées via GROBID" name="ISTEX-API (INIST-CNRS)"></respStmt><respStmt><resp>Références bibliographiques récupérées via GROBID</resp><name resp="ISTEX-API">ISTEX-API (INIST-CNRS)</name></respStmt></titleStmt><publicationStmt><authority>ISTEX</authority><publisher>Oxford University Press</publisher><availability><p>OUP</p></availability><date>2006</date></publicationStmt><notesStmt><note>*To whom correspondence should be addressed. Tel: +1 301 496 6019; Fax: +1 301 402 3134; Email: packerb@mail.nih.gov</note></notesStmt><sourceDesc><biblStruct type="inbook"><analytic><title level="a" type="main" xml:lang="en">SNP500Cancer: a public resource for sequence validation, assay development, and frequency analysis for genetic variation in candidate genes</title><author><persName><forename type="first">Bernice R.</forename><surname>Packer</surname></persName><email>packerb@mail.nih.gov</email><affiliation>Intramural Research Support Program, SAIC-Frederick, NCI-FCRDC Frederick, MD, USA</affiliation><affiliation>Division of Cancer Epidemiology and Genetics, National Cancer Institute Bethesda, MD, USA</affiliation><affiliation>To whom correspondence should be addressed. Tel: +1 301 496 6019; Fax: +1 301 402 3134; Email: packerb@mail.nih.gov</affiliation></author><author><persName><forename type="first">Meredith</forename><surname>Yeager</surname></persName><affiliation>Intramural Research Support Program, SAIC-Frederick, NCI-FCRDC Frederick, MD, USA</affiliation><affiliation>Division of Cancer Epidemiology and Genetics, National Cancer Institute Bethesda, MD, USA</affiliation></author><author><persName><forename type="first">Laura</forename><surname>Burdett</surname></persName><affiliation>Intramural Research Support Program, SAIC-Frederick, NCI-FCRDC Frederick, MD, USA</affiliation><affiliation>Division of Cancer Epidemiology and Genetics, National Cancer Institute Bethesda, MD, USA</affiliation></author><author><persName><forename type="first">Robert</forename><surname>Welch</surname></persName><affiliation>Intramural Research Support Program, SAIC-Frederick, NCI-FCRDC Frederick, MD, USA</affiliation><affiliation>Division of Cancer Epidemiology and Genetics, National Cancer Institute Bethesda, MD, USA</affiliation></author><author><persName><forename type="first">Michael</forename><surname>Beerman</surname></persName><affiliation>Intramural Research Support Program, SAIC-Frederick, NCI-FCRDC Frederick, MD, USA</affiliation><affiliation>Division of Cancer Epidemiology and Genetics, National Cancer Institute Bethesda, MD, USA</affiliation></author><author><persName><forename type="first">Liqun</forename><surname>Qi</surname></persName><affiliation>Intramural Research Support Program, SAIC-Frederick, NCI-FCRDC Frederick, MD, USA</affiliation><affiliation>Division of Cancer Epidemiology and Genetics, National Cancer Institute Bethesda, MD, USA</affiliation></author><author><persName><forename type="first">Hugues</forename><surname>Sicotte</surname></persName><affiliation>Intramural Research Support Program, SAIC-Frederick, NCI-FCRDC Frederick, MD, USA</affiliation><affiliation>Division of Cancer Epidemiology and Genetics, National Cancer Institute Bethesda, MD, USA</affiliation></author><author><persName><forename type="first">Brian</forename><surname>Staats</surname></persName><affiliation>Intramural Research Support Program, SAIC-Frederick, NCI-FCRDC Frederick, MD, USA</affiliation><affiliation>Division of Cancer Epidemiology and Genetics, National Cancer Institute Bethesda, MD, USA</affiliation></author><author><persName><forename type="first">Mekhala</forename><surname>Acharya</surname></persName><affiliation>Department of Bioinformatics, George Mason University Manassas, VA, USA</affiliation></author><author><persName><forename type="first">Andrew</forename><surname>Crenshaw</surname></persName><affiliation>Intramural Research Support Program, SAIC-Frederick, NCI-FCRDC Frederick, MD, USA</affiliation><affiliation>Division of Cancer Epidemiology and Genetics, National Cancer Institute Bethesda, MD, USA</affiliation></author><author><persName><forename type="first">Andrew</forename><surname>Eckert</surname></persName><affiliation>Intramural Research Support Program, SAIC-Frederick, NCI-FCRDC Frederick, MD, USA</affiliation><affiliation>Division of Cancer Epidemiology and Genetics, National Cancer Institute Bethesda, MD, USA</affiliation></author><author><persName><forename type="first">Vinita</forename><surname>Puri</surname></persName><affiliation>Intramural Research Support Program, SAIC-Frederick, NCI-FCRDC Frederick, MD, USA</affiliation><affiliation>Division of Cancer Epidemiology and Genetics, National Cancer Institute Bethesda, MD, USA</affiliation></author><author><persName><forename type="first">Daniela S.</forename><surname>Gerhard</surname></persName><affiliation>Office of Cancer Genomics, National Cancer Institute Bethesda, MD, USA</affiliation></author><author><persName><forename type="first">Stephen J.</forename><surname>Chanock</surname></persName><affiliation>Division of Cancer Epidemiology and Genetics, National Cancer Institute Bethesda, MD, USA</affiliation><affiliation>Section on Genomic Variation, Pediatric Oncology Branch, National Cancer Institute, National Institutes of Health Gaithersburg, MD, USA</affiliation></author></analytic><monogr><title level="j">Nucleic Acids Research</title><title level="j" type="abbrev">Nucl. Acids Res.</title><idno type="pISSN">0305-1048</idno><idno type="eISSN">1362-4962</idno><imprint><publisher>Oxford University Press</publisher><date type="published" when="2006-01"></date><biblScope unit="volume">34</biblScope><biblScope unit="supplement">suppl_1</biblScope><biblScope unit="page" from="D617">D617</biblScope><biblScope unit="page" to="D621">D621</biblScope></imprint></monogr><idno type="istex">89CF57E7454C0D81DB579D135BDDC14F2A9AD855</idno><idno type="DOI">10.1093/nar/gkj151</idno><idno type="local">gkj151</idno></biblStruct></sourceDesc></fileDesc><profileDesc><creation><date>2006</date></creation><langUsage><language ident="en">en</language></langUsage><abstract xml:lang="en"><p>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.</p></abstract></profileDesc><revisionDesc><change when="2006-01">Published</change><change xml:id="refBibs-istex" who="#ISTEX-API" when="2016-3-15">References added</change><change xml:id="refBibs-istex" who="#ISTEX-API" when="2016-3-21">References added</change><change xml:id="refBibs-istex" who="#ISTEX-API" when="2016-07-27">References added</change></revisionDesc></teiHeader></istex:fulltextTEI><json:item><original>false</original><mimetype>text/plain</mimetype><extension>txt</extension><uri>https://api.istex.fr/document/89CF57E7454C0D81DB579D135BDDC14F2A9AD855/fulltext/txt</uri></json:item></fulltext><metadata><istex:metadataXml wicri:clean="corpus oup" wicri:toSee="no header"><istex:xmlDeclaration>version="1.0" encoding="US-ASCII"</istex:xmlDeclaration><istex:docType PUBLIC="-//NLM//DTD Journal Publishing DTD v2.3 20070202//EN" URI="journalpublishing.dtd" name="istex:docType"></istex:docType><istex:document><article xml:lang="en" article-type="other"><front><journal-meta><journal-id journal-id-type="hwp">nar</journal-id><journal-id journal-id-type="nlm-ta">Nucleic Acids Res</journal-id><journal-id journal-id-type="publisher-id">nar</journal-id><journal-title>Nucleic Acids Research</journal-title><abbrev-journal-title abbrev-type="publisher">Nucl. Acids Res.</abbrev-journal-title><issn pub-type="ppub">0305-1048</issn><issn pub-type="epub">1362-4962</issn><publisher><publisher-name>Oxford University Press</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="other">gkj151</article-id><article-id pub-id-type="doi">10.1093/nar/gkj151</article-id><article-categories><subj-group subj-group-type="heading"><subject>Article</subject></subj-group></article-categories><title-group><article-title>SNP500Cancer: a public resource for sequence validation, assay development, and frequency analysis for genetic variation in candidate genes</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Packer</surname><given-names>Bernice R.</given-names></name><xref rid="AU1">1</xref><xref rid="AU2">2</xref><xref rid="COR1">*</xref></contrib><contrib contrib-type="author"><name><surname>Yeager</surname><given-names>Meredith</given-names></name><xref rid="AU1">1</xref><xref rid="AU2">2</xref></contrib><contrib contrib-type="author"><name><surname>Burdett</surname><given-names>Laura</given-names></name><xref rid="AU1">1</xref><xref rid="AU2">2</xref></contrib><contrib contrib-type="author"><name><surname>Welch</surname><given-names>Robert</given-names></name><xref rid="AU1">1</xref><xref rid="AU2">2</xref></contrib><contrib contrib-type="author"><name><surname>Beerman</surname><given-names>Michael</given-names></name><xref rid="AU1">1</xref><xref rid="AU2">2</xref></contrib><contrib contrib-type="author"><name><surname>Qi</surname><given-names>Liqun</given-names></name><xref rid="AU1">1</xref><xref rid="AU2">2</xref></contrib><contrib contrib-type="author"><name><surname>Sicotte</surname><given-names>Hugues</given-names></name><xref rid="AU1">1</xref><xref rid="AU2">2</xref></contrib><contrib contrib-type="author"><name><surname>Staats</surname><given-names>Brian</given-names></name><xref rid="AU1">1</xref><xref rid="AU2">2</xref></contrib><contrib contrib-type="author"><name><surname>Acharya</surname><given-names>Mekhala</given-names></name><xref rid="AU3">3</xref></contrib><contrib contrib-type="author"><name><surname>Crenshaw</surname><given-names>Andrew</given-names></name><xref rid="AU1">1</xref><xref rid="AU2">2</xref></contrib><contrib contrib-type="author"><name><surname>Eckert</surname><given-names>Andrew</given-names></name><xref rid="AU1">1</xref><xref rid="AU2">2</xref></contrib><contrib contrib-type="author"><name><surname>Puri</surname><given-names>Vinita</given-names></name><xref rid="AU1">1</xref><xref rid="AU2">2</xref></contrib><contrib contrib-type="author"><name><surname>Gerhard</surname><given-names>Daniela S.</given-names></name><xref rid="AU4">4</xref></contrib><contrib contrib-type="author"><name><surname>Chanock</surname><given-names>Stephen J.</given-names></name><xref rid="AU2">2</xref><xref rid="AU5">5</xref></contrib><aff id="AU1"><sup>1</sup>Intramural Research Support Program, SAIC-Frederick, NCI-FCRDC Frederick, MD, USA</aff><aff id="AU2"><sup>2</sup>Division of Cancer Epidemiology and Genetics, National Cancer Institute Bethesda, MD, USA</aff><aff id="AU3"><sup>3</sup>Department of Bioinformatics, George Mason University Manassas, VA, USA</aff><aff id="AU4"><sup>4</sup>Office of Cancer Genomics, National Cancer Institute Bethesda, MD, USA</aff><aff id="AU5"><sup>5</sup>Section on Genomic Variation, Pediatric Oncology Branch, National Cancer Institute, National Institutes of Health Gaithersburg, MD, USA</aff></contrib-group><author-notes><corresp id="COR1"><sup>*</sup>To whom correspondence should be addressed. Tel: +1 301 496 6019; Fax: +1 301 402 3134; Email: <ext-link xlink:href="packerb@mail.nih.gov" ext-link-type="email">packerb@mail.nih.gov</ext-link></corresp></author-notes><pub-date pub-type="ppub"><day>1</day><year>2006</year></pub-date><volume>34</volume><issue>suppl_1</issue><fpage>D617</fpage><lpage>D621</lpage><history><date date-type="accepted"><day>28</day><month>10</month><year>2005</year></date><date date-type="received"><day>14</day><month>9</month><year>2005</year></date><date date-type="rev-recd"><day>28</day><month>10</month><year>2005</year></date></history><permissions><copyright-statement>© 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 <ext-link xlink:href="journals.permissions@oxfordjournals.org" ext-link-type="email">journals.permissions@oxfordjournals.org</ext-link></copyright-statement><copyright-year>2006</copyright-year><license license-type="open-access"><p></p></license></permissions><abstract xml:lang="en"><p>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 (<ext-link xlink:href="http://cgap.nci.nih.gov" ext-link-type="url">http://cgap.nci.nih.gov</ext-link>). SNP500Cancer reports sequence analysis of anonymized control DNA samples (<italic>n</italic> = 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 <ext-link xlink:href="http://snp500cancer.nci.nih.gov" ext-link-type="url">http://snp500cancer.nci.nih.gov</ext-link>.</p></abstract><custom-meta-wrap><custom-meta><meta-name>hwp-legacy-fpage</meta-name><meta-value>D617</meta-value></custom-meta><custom-meta><meta-name>cover-date</meta-name><meta-value></meta-value></custom-meta><custom-meta><meta-name>hwp-legacy-dochead</meta-name><meta-value>research-article</meta-value></custom-meta></custom-meta-wrap></article-meta></front></article></istex:document></istex:metadataXml><mods version="3.6"><titleInfo lang="en"><title>SNP500Cancer: a public resource for sequence validation, assay development, and frequency analysis for genetic variation in candidate genes</title></titleInfo><titleInfo type="alternative" lang="en" contentType="CDATA"><title>SNP500Cancer: a public resource for sequence validation, assay development, and frequency analysis for genetic variation in candidate genes</title></titleInfo><name type="personal"><namePart type="given">Bernice R.</namePart><namePart type="family">Packer</namePart><affiliation>Intramural Research Support Program, SAIC-Frederick, NCI-FCRDC Frederick, MD, USA</affiliation><affiliation>Division of Cancer Epidemiology and Genetics, National Cancer Institute Bethesda, MD, USA</affiliation><affiliation>To whom correspondence should be addressed. Tel: +1 301 496 6019; Fax: +1 301 402 3134; Email: packerb@mail.nih.gov</affiliation><affiliation>E-mail: packerb@mail.nih.gov</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Meredith</namePart><namePart type="family">Yeager</namePart><affiliation>Intramural Research Support Program, SAIC-Frederick, NCI-FCRDC Frederick, MD, USA</affiliation><affiliation>Division of Cancer Epidemiology and Genetics, National Cancer Institute Bethesda, MD, USA</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Laura</namePart><namePart type="family">Burdett</namePart><affiliation>Intramural Research Support Program, SAIC-Frederick, NCI-FCRDC Frederick, MD, USA</affiliation><affiliation>Division of Cancer Epidemiology and Genetics, National Cancer Institute Bethesda, MD, USA</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Robert</namePart><namePart type="family">Welch</namePart><affiliation>Intramural Research Support Program, SAIC-Frederick, NCI-FCRDC Frederick, MD, USA</affiliation><affiliation>Division of Cancer Epidemiology and Genetics, National Cancer Institute Bethesda, MD, USA</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Michael</namePart><namePart type="family">Beerman</namePart><affiliation>Intramural Research Support Program, SAIC-Frederick, NCI-FCRDC Frederick, MD, USA</affiliation><affiliation>Division of Cancer Epidemiology and Genetics, National Cancer Institute Bethesda, MD, USA</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Liqun</namePart><namePart type="family">Qi</namePart><affiliation>Intramural Research Support Program, SAIC-Frederick, NCI-FCRDC Frederick, MD, USA</affiliation><affiliation>Division of Cancer Epidemiology and Genetics, National Cancer Institute Bethesda, MD, USA</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Hugues</namePart><namePart type="family">Sicotte</namePart><affiliation>Intramural Research Support Program, SAIC-Frederick, NCI-FCRDC Frederick, MD, USA</affiliation><affiliation>Division of Cancer Epidemiology and Genetics, National Cancer Institute Bethesda, MD, USA</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Brian</namePart><namePart type="family">Staats</namePart><affiliation>Intramural Research Support Program, SAIC-Frederick, NCI-FCRDC Frederick, MD, USA</affiliation><affiliation>Division of Cancer Epidemiology and Genetics, National Cancer Institute Bethesda, MD, USA</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Mekhala</namePart><namePart type="family">Acharya</namePart><affiliation>Department of Bioinformatics, George Mason University Manassas, VA, USA</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Andrew</namePart><namePart type="family">Crenshaw</namePart><affiliation>Intramural Research Support Program, SAIC-Frederick, NCI-FCRDC Frederick, MD, USA</affiliation><affiliation>Division of Cancer Epidemiology and Genetics, National Cancer Institute Bethesda, MD, USA</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Andrew</namePart><namePart type="family">Eckert</namePart><affiliation>Intramural Research Support Program, SAIC-Frederick, NCI-FCRDC Frederick, MD, USA</affiliation><affiliation>Division of Cancer Epidemiology and Genetics, National Cancer Institute Bethesda, MD, USA</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Vinita</namePart><namePart type="family">Puri</namePart><affiliation>Intramural Research Support Program, SAIC-Frederick, NCI-FCRDC Frederick, MD, USA</affiliation><affiliation>Division of Cancer Epidemiology and Genetics, National Cancer Institute Bethesda, MD, USA</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Daniela S.</namePart><namePart type="family">Gerhard</namePart><affiliation>Office of Cancer Genomics, National Cancer Institute Bethesda, MD, USA</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Stephen J.</namePart><namePart type="family">Chanock</namePart><affiliation>Division of Cancer Epidemiology and Genetics, National Cancer Institute Bethesda, MD, USA</affiliation><affiliation>Section on Genomic Variation, Pediatric Oncology Branch, National Cancer Institute, National Institutes of Health Gaithersburg, MD, USA</affiliation><role><roleTerm type="text">author</roleTerm></role></name><typeOfResource>text</typeOfResource><genre type="other" displayLabel="other"></genre><originInfo><publisher>Oxford University Press</publisher><dateIssued encoding="w3cdtf">2006-01</dateIssued><copyrightDate encoding="w3cdtf">2006</copyrightDate></originInfo><language><languageTerm type="code" authority="iso639-2b">eng</languageTerm><languageTerm type="code" authority="rfc3066">en</languageTerm></language><physicalDescription><internetMediaType>text/html</internetMediaType></physicalDescription><abstract lang="en">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.</abstract><note type="author-notes">*To whom correspondence should be addressed. Tel: +1 301 496 6019; Fax: +1 301 402 3134; Email: packerb@mail.nih.gov</note><relatedItem type="host"><titleInfo><title>Nucleic Acids Research</title></titleInfo><titleInfo type="abbreviated"><title>Nucl. Acids Res.</title></titleInfo><genre type="journal">journal</genre><identifier type="ISSN">0305-1048</identifier><identifier type="eISSN">1362-4962</identifier><identifier type="PublisherID">nar</identifier><identifier type="PublisherID-hwp">nar</identifier><identifier type="PublisherID-nlm-ta">Nucleic Acids Res</identifier><part><date>2006</date><detail type="volume"><caption>vol.</caption><number>34</number></detail><detail type="supplement"><number>suppl_1</number></detail><extent unit="pages"><start>D617</start><end>D621</end></extent></part></relatedItem><identifier type="istex">89CF57E7454C0D81DB579D135BDDC14F2A9AD855</identifier><identifier type="DOI">10.1093/nar/gkj151</identifier><identifier type="local">gkj151</identifier><accessCondition type="use and reproduction" contentType="copyright">© The Author 2006. Published by Oxford University Press. All rights reserved
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