{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,9,16]],"date-time":"2024-09-16T06:32:12Z","timestamp":1726468332219},"reference-count":16,"publisher":"Oxford University Press (OUP)","issue":"1","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2005,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: SNP Chart is a Java application for the visualization and interpretation of microarray genotyping data primarily derived from arrayed primer extension-based chemistries. Spot intensity output files from microarray analysis tools are imported into SNP Chart, together with a multi-channel TIFF image of the original array experiment and a list of the actual single nucleotide polymorphisms (SNPs) being tested. Data from different and\/or replicate probes that interrogate the same SNP, but that are scattered across the array grid, can be reassembled into a single chart format, specific for the SNP. This allows a quick and very effective \u2018visualization\u2019\/\u2018quality control\u2019 of the data from multiple probes for the same SNP that can be easily interpreted and manually scored as a genotype.<\/jats:p>\n               <jats:p>Availability: \u00a0http:\/\/www.snpchart.ca<\/jats:p>\n               <jats:p>Contact: \u00a0stebbutt@mrl.ubc.ca<\/jats:p>\n               <jats:p>Supplementary information: A comprehensive manual describing SNP Chart is available at the above website, together with sample data files.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bth470","type":"journal-article","created":{"date-parts":[[2004,8,13]],"date-time":"2004-08-13T00:15:36Z","timestamp":1092356136000},"page":"124-127","source":"Crossref","is-referenced-by-count":18,"title":["SNP Chart: an integrated platform for visualization and interpretation of microarray genotyping data"],"prefix":"10.1093","volume":"21","author":[{"given":"Scott J.","family":"Tebbutt","sequence":"first","affiliation":[{"name":"James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research, St Paul's Hospital, University of British Columbia Vancouver, Canada V6Z 1Y6"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Igor V.","family":"Opushnyev","sequence":"additional","affiliation":[{"name":"James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research, St Paul's Hospital, University of British Columbia Vancouver, Canada V6Z 1Y6"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ben W.","family":"Tripp","sequence":"additional","affiliation":[{"name":"James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research, St Paul's Hospital, University of British Columbia Vancouver, Canada V6Z 1Y6"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ayaz M.","family":"Kassamali","sequence":"additional","affiliation":[{"name":"James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research, St Paul's Hospital, University of British Columbia Vancouver, Canada V6Z 1Y6"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wendy L.","family":"Alexander","sequence":"additional","affiliation":[{"name":"James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research, St Paul's Hospital, University of British Columbia Vancouver, Canada V6Z 1Y6"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marilyn I.","family":"Andersen","sequence":"additional","affiliation":[{"name":"James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research, St Paul's Hospital, University of British Columbia Vancouver, Canada V6Z 1Y6"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2004,8,12]]},"reference":[{"key":"2023013107190429800_B1","doi-asserted-by":"crossref","unstructured":"Ahmadian, A., Gharizadeh, B., Gustafsson, A.C., Sterky, F., Nyren, P., Uhlen, M., Lundeberg, J. 2000Single-nucleotide polymorphism analysis by pyrosequencing. Anal. Biochem.280103\u2013110","DOI":"10.1006\/abio.2000.4493"},{"key":"2023013107190429800_B2","doi-asserted-by":"crossref","unstructured":"Buetow, K.H., Edmonson, M., MacDonald, R., Clifford, R., Yip, P., Kelley, J., Little, D.P., Strausberg, R., Koester, H., Cantor, C.R., Braun, A. 2001High-throughput development and characterization of a genomewide collection of gene-based single nucleotide polymorphism markers by chip-based matrix-assisted laser desorption\/ionization time-of-flight mass spectrometry. Proc. Natl Acad. Sci. USA98581\u2013584","DOI":"10.1073\/pnas.98.2.581"},{"key":"2023013107190429800_B3","unstructured":"Chan, K., Wong, M.S., Chan, T.K., Chan, V. 2004A thalassaemia array for Southeast Asia. Br. J. Haematol.124232\u2013239"},{"key":"2023013107190429800_B4","doi-asserted-by":"crossref","unstructured":"Dawson, E., Abecasis, G.R., Bumpstead, S., Chen, Y., Hunt, S., Beare, D.M., Pabial, J., Dibling, T., Tinsley, E., Kirby, S., et al. 2002A first-generation linkage disequilibrium map of human chromosome 22. Nature418544\u2013548","DOI":"10.1038\/nature00864"},{"key":"2023013107190429800_B5","doi-asserted-by":"crossref","unstructured":"Gemignani, F., Perra, C., Landi, S., Canzian, F., Kurg, A., Tonisson, N., Galanello, R., Cao, A., Metspalu, A., Romeo, G. 2002Reliable detection of beta-thalassemia and G6PD mutations by a DNA microarray. Clin. Chem.482051\u20132054","DOI":"10.1093\/clinchem\/48.11.2051"},{"key":"2023013107190429800_B6","doi-asserted-by":"crossref","unstructured":"Hirschhorn, J.N., Sklar, P., Lindblad-Toh, K., Lim, Y.M., Ruiz-Gutierrez, M., Bolk, S., Langhorst, B., Schaffner, S., Winchester, E., Lander, E.S. 2000SBE-TAGS: an array-based method for efficient single-nucleotide polymorphism genotyping. Proc. Natl Acad. Sci. USA9712164\u201312169","DOI":"10.1073\/pnas.210394597"},{"key":"2023013107190429800_B7","unstructured":"Kennedy, G.C., Matsuzaki, H., Dong, S., Liu, W.M., Huang, J., Liu, G., Su, X., Cao, M., Chen, W., Zhang, J., et al. 2003Large-scale genotyping of complex DNA. Nat. Biotechnol.211233\u20131237"},{"key":"2023013107190429800_B8","doi-asserted-by":"crossref","unstructured":"Kurg, A., Tonisson, N., Georgiou, I., Shumaker, J., Tollett, J., Metspalu, A. 2000Arrayed primer extension: solid-phase four-color DNA resequencing and mutation detection technology. Genet. Test41\u20137","DOI":"10.1089\/109065700316408"},{"key":"2023013107190429800_B9","unstructured":"Landi, S., Gemignani, F., Gioia-Patricola, L., Chabrier, A., Canzian, F. 2003Evaluation of a microarray for genotyping polymorphisms related to xenobiotic metabolism and DNA repair. BioTechniques35816\u2013820 822, 824\u2013817"},{"key":"2023013107190429800_B10","doi-asserted-by":"crossref","unstructured":"Livak, K.J., Flood, S.J., Marmaro, J., Giusti, W., Deetz, K. 1995Oligonucleotides with fluorescent dyes at opposite ends provide a quenched probe system useful for detecting PCR product and nucleic acid hybridization. PCR Methods Appl.4357\u2013362","DOI":"10.1101\/gr.4.6.357"},{"key":"2023013107190429800_B11","doi-asserted-by":"crossref","unstructured":"Oliphant, A., Barker, D.L., Stuelpnagel, J.R., Chee, M.S. 2002BeadArray technology: enabling an accurate, cost-effective approach to high-throughput genotyping. BioTechniques Suppl.,56\u201358 60\u201351","DOI":"10.2144\/jun0207"},{"key":"2023013107190429800_B12","unstructured":"Risch, N. and Merikangas, K. 1996The future of genetic studies of complex human diseases. Science2731516\u20131517"},{"key":"2023013107190429800_B13","doi-asserted-by":"crossref","unstructured":"Sanger, F., Nicklen, S., Coulson, A.R. 1977DNA sequencing with chain-terminating inhibitors. Proc. Natl Acad. Sci. USA745463\u20135467","DOI":"10.1073\/pnas.74.12.5463"},{"key":"2023013107190429800_B14","doi-asserted-by":"crossref","unstructured":"Shumaker, J.M., Metspalu, A., Caskey, C.T. 1996Mutation detection by solid phase primer extension. Hum. Mutat.7346\u2013354","DOI":"10.1002\/(SICI)1098-1004(1996)7:4<346::AID-HUMU9>3.3.CO;2-9"},{"key":"2023013107190429800_B15","doi-asserted-by":"crossref","unstructured":"Tebbutt, S.J., Burkett, K.M., He, J-Q, Ruan, J., Opushnyev, I.V., Tripp, B.W., Zeznik, J.A., Abara, C.O., Nelson, C.C., Walley, K.R. 2004A microarray genotyping resource to determine population stratification in genetic association studies of complex disease. Bio Techniques  in press","DOI":"10.2144\/04376RR02"},{"key":"2023013107190429800_B16","unstructured":"Wang, D.G., Fan, J.B., Siao, C.J., Berno, A., Young, P., Sapolsky, R., Ghandour, G., Perkins, N., Winchester, E., Spencer, J., et al. 1998Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. Science2801077\u20131082"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/21\/1\/124\/48961863\/bioinformatics_21_1_124.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/21\/1\/124\/48961863\/bioinformatics_21_1_124.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T09:54:29Z","timestamp":1675158869000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/21\/1\/124\/212590"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2004,8,12]]},"references-count":16,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2005,1,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bth470","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2005,1,1]]},"published":{"date-parts":[[2004,8,12]]}}}