{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,26]],"date-time":"2025-11-26T04:57:28Z","timestamp":1764133048494},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"15","license":[{"start":{"date-parts":[[2017,4,8]],"date-time":"2017-04-08T00:00:00Z","timestamp":1491609600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,8,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>After the introduction of high-throughput sequencing, genotyping arrays continue to be a viable source for conducting large-scale genetic studies. Currently, Illumina is one of the largest genotyping array manufacturers. One technical issue that has always plagued the post-processing of Illumina genotyping array data is the strand definition. Against convention, Illumina uses their own definition of strand, which is inconsistent with the standard reference forward and reverse definition. This issue has been a major obstacle in the consistency of reporting, meta-analysis and correct interpretation of phenotype association results. To date, the strand issue has not been adequately addressed, prompting us to develop StrandScript, a tool that can convert all genotyping data generated from Illumina genotyping arrays to the reference forward strand. StrandScript works independently of the Illumina array version and is future proof for newer Illumina array designs. Furthermore, StrandScript can examine an Illumina genotyping array manifest file and can detect all problematic SNPs, including SNPs with wrong RS ID and SNPs with mismatched probe sequences. Here, we introduce StrandScript\u2019s design and development, and demonstrate its effectiveness using real genotyping data.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and Implementation<\/jats:title>\n                  <jats:p>https:\/\/github.com\/seasky002002\/Strandscript<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx186","type":"journal-article","created":{"date-parts":[[2017,4,5]],"date-time":"2017-04-05T07:24:43Z","timestamp":1491377083000},"page":"2399-2401","source":"Crossref","is-referenced-by-count":10,"title":["StrandScript: evaluation of Illumina genotyping array design and strand correction"],"prefix":"10.1093","volume":"33","author":[{"given":"Jing","family":"Wang","sequence":"first","affiliation":[{"name":"Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville TN, USA"}]},{"given":"David C","family":"Samuels","sequence":"additional","affiliation":[{"name":"Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville TN, USA"}]},{"given":"Yu","family":"Shyr","sequence":"additional","affiliation":[{"name":"Department of Biostatistics, Vanderbilt University Medical Center, Nashville TN, USA"}]},{"given":"Yan","family":"Guo","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville TN, USA"}]}],"member":"286","published-online":{"date-parts":[[2017,4,8]]},"reference":[{"key":"2023063012500321200_btx186-B1","doi-asserted-by":"crossref","first-page":"789","DOI":"10.1038\/nature02168","article-title":"The International HapMap Project","volume":"426","author":"HapMap","year":"2003","journal-title":"Nature"},{"key":"2023063012500321200_btx186-B2","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1038\/nature11632","article-title":"An integrated map of genetic variation from 1,092 human genomes","volume":"491","author":"Abecasis","year":"2012","journal-title":"Nature"},{"key":"2023063012500321200_btx186-B3","doi-asserted-by":"crossref","first-page":"2643","DOI":"10.1038\/nprot.2014.174","article-title":"Illumina human exome genotyping array clustering and quality control","volume":"9","author":"Guo","year":"2014","journal-title":"Nat. Protoc"},{"key":"2023063012500321200_btx186-B4","doi-asserted-by":"crossref","first-page":"1124","DOI":"10.1038\/ejhg.2013.304","article-title":"Coverage and efficiency in current SNP chips","volume":"22","author":"Ha","year":"2014","journal-title":"Eur. J. Hum. Genet"},{"key":"2023063012500321200_btx186-B5","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1534\/g3.112.004069","article-title":"Comparison of the performance of two commercial genome-wide association study genotyping platforms in Han Chinese samples","volume":"3","author":"Jiang","year":"2013","journal-title":"G3"},{"key":"2023063012500321200_btx186-B6","doi-asserted-by":"crossref","first-page":"4181","DOI":"10.1093\/nar\/gkp552","article-title":"Single nucleotide polymorphism arrays: a decade of biological, computational and technological advances","volume":"37","author":"LaFramboise","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"2023063012500321200_btx186-B7","author":"Nelson","year":"2014"},{"key":"2023063012500321200_btx186-B8","doi-asserted-by":"crossref","first-page":"361","DOI":"10.1016\/j.tig.2012.05.002","article-title":"Is \u2018forward\u2019 the same as \u2018plus\u2019? \u2026 and other adventures in SNP allele nomenclature","volume":"28","author":"Nelson","year":"2012","journal-title":"Trends Genet"},{"key":"2023063012500321200_btx186-B9","article-title":"Strategies for processing and quality control of Illumina genotyping arrays","author":"Zhao","year":"2017","journal-title":"Brief. Bioinform"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/15\/2399\/50756478\/bioinformatics_33_15_2399.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/15\/2399\/50756478\/bioinformatics_33_15_2399.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,30]],"date-time":"2023-06-30T12:50:18Z","timestamp":1688129418000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/33\/15\/2399\/3204987"}},"subtitle":[],"editor":[{"given":"John","family":"Hancock","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2017,4,8]]},"references-count":9,"journal-issue":{"issue":"15","published-print":{"date-parts":[[2017,8,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btx186","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2017,8,1]]},"published":{"date-parts":[[2017,4,8]]}}}