{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,12,30]],"date-time":"2024-12-30T18:18:04Z","timestamp":1735582684552},"reference-count":4,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2009,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>Genotyping of single-nucleotide polymorphisms (SNPs) is a fundamental technology in modern genetics. The SNPlex\u2122 mid-throughput genotyping system (Applied Biosystems, Foster City, CA, USA) enables the multiplexed genotyping of up to 48 SNPs simultaneously in a single DNA sample. The high level of automation and the large amount of data produced in a high-throughput laboratory require advanced software tools for quality control and workflow management.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>We have developed two programs, which address two main aspects of quality control in a SNPlex\u2122 genotyping environment: GMFilter improves the analysis of SNPlex\u2122 plates by removing wells with a low overall signal intensity. It enables scientists to automatically process the raw data in a standardized way before analyzing a plate with the proprietary GeneMapper software from Applied Biosystems. SXTestPlate examines the genotype concordance of a SNPlex\u2122 test plate, which was typed with a control SNP set. This program allows for regular quality control checks of a SNPlex\u2122 genotyping platform. It is compatible to other genotyping methods as well.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusion<\/jats:title>\n            <jats:p>GMFilter and SXTestPlate provide a valuable tool set for laboratories engaged in genotyping based on the SNPlex\u2122 system. The programs enhance the analysis of SNPlex\u2122 plates with the GeneMapper software and enable scientists to evaluate the performance of their genotyping platform.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-10-81","type":"journal-article","created":{"date-parts":[[2009,3,10]],"date-time":"2009-03-10T07:13:30Z","timestamp":1236669210000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":12,"title":["GMFilter and SXTestPlate: software tools for improving the SNPlex\u2122 genotyping system"],"prefix":"10.1186","volume":"10","author":[{"given":"Markus","family":"Teuber","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael H","family":"Wenz","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Stefan","family":"Schreiber","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andre","family":"Franke","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2009,3,9]]},"reference":[{"key":"2811_CR1","doi-asserted-by":"publisher","first-page":"111","DOI":"10.1016\/j.mrfmmm.2005.01.008","volume":"573","author":"FM De la Vega","year":"2005","unstructured":"De la Vega FM, Lazaruk KD, Rhodes MD, Wenz MH: Assessment of two flexible and compatible SNP genotyping platforms: TaqMan SNP Genotyping Assays and the SNPlex Genotyping System. Mutat Res 2005, 573: 111\u2013135.","journal-title":"Mutat Res"},{"key":"2811_CR2","first-page":"398","volume":"16","author":"AR Tobler","year":"2005","unstructured":"Tobler AR, Short S, Andersen MR, Paner TM, Briggs JC, Lambert SM, Wu PP, Wang Y, Spoonde AY, Koehler RT, Peyret N, Chen C, Broomer AJ, Ridzon DA, Zhou H, Hoo BS, Hayashibara KC, Leong LN, Ma CN, Rosenblum BB, Day JP, Ziegle JS, De La Vega FM, Rhodes MD, Hennessy KM, Wenz HM: The SNPlex genotyping system: a flexible and scalable platform for SNP genotyping. J Biomol Tech 2005, 16: 398\u2013406.","journal-title":"J Biomol Tech"},{"key":"2811_CR3","doi-asserted-by":"publisher","first-page":"847","DOI":"10.1038\/nrg1707","volume":"6","author":"F Pompanon","year":"2005","unstructured":"Pompanon F, Bonin A, Bellemain E, Taberlet P: Genotyping errors: causes, consequences and solutions. Nat Rev Genet 2005, 6: 847\u2013859. 10.1038\/nrg1707","journal-title":"Nat Rev Genet"},{"key":"2811_CR4","unstructured":"GMFilter[http:\/\/www.ikmb.uni-kiel.de\/gmfilter\/]"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-10-81.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,8,31]],"date-time":"2021-08-31T21:30:04Z","timestamp":1630445404000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-10-81"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,3,9]]},"references-count":4,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2009,12]]}},"alternative-id":["2811"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-10-81","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2009,3,9]]},"assertion":[{"value":"21 October 2008","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"9 March 2009","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"9 March 2009","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"81"}}