{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,12]],"date-time":"2026-03-12T00:11:43Z","timestamp":1773274303739,"version":"3.50.1"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"14","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,7,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Sequencing by hybridization to oligonucleotides has evolved into an inexpensive, reliable and fast technology for targeted sequencing. Hundreds of human genes can now be sequenced within a day using a single hybridization to a resequencing microarray. However, several issues inherent to these arrays (e.g. cross-hybridization, variable probe\/target affinity) cause sequencing errors and have prevented more widespread applications. We developed an R package for resequencing microarray data analysis that integrates a novel statistical algorithm, sequence robust multi-array analysis (SRMA), for rare variant detection with high sensitivity (false negative rate, FNR 5%) and accuracy (false positive rate, FPR 1\u00d710\u22125). The SRMA package consists of five modules for quality control, data normalization, single array analysis, multi-array analysis and output analysis. The entire workflow is efficient and identifies rare DNA single nucleotide variations and structural changes such as gene deletions with high accuracy and sensitivity.<\/jats:p>\n               <jats:p>Availability: \u00a0http:\/\/cran.r-project.org\/, http:\/\/odin.mdacc.tmc.edu\/~wwang7\/SRMAIndex.html<\/jats:p>\n               <jats:p>Contact: \u00a0wwang7@mdanderson.org<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts286","type":"journal-article","created":{"date-parts":[[2012,5,12]],"date-time":"2012-05-12T01:02:48Z","timestamp":1336784568000},"page":"1928-1930","source":"Crossref","is-referenced-by-count":2,"title":["SRMA: an R package for resequencing array data analysis"],"prefix":"10.1093","volume":"28","author":[{"given":"Nianxiang","family":"Zhang","sequence":"first","affiliation":[{"name":"1 Department of Bioinformatics and Computational Biology, UT MD Anderson Cancer Center, Houston, TX 77030, 2Stanford Genome Technology Center, Stanford University, Palo Alto, CA 94304, USA, 3Bioinformatics Division, Walter & Eliza Hall Institute, Parkville, VIC 3052, Australia and 4Department of Statistics, University of California, Berkeley, CA 94720, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yan","family":"Xu","sequence":"additional","affiliation":[{"name":"1 Department of Bioinformatics and Computational Biology, UT MD Anderson Cancer Center, Houston, TX 77030, 2Stanford Genome Technology Center, Stanford University, Palo Alto, CA 94304, USA, 3Bioinformatics Division, Walter & Eliza Hall Institute, Parkville, VIC 3052, Australia and 4Department of Statistics, University of California, Berkeley, CA 94720, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Martin","family":"O'Hely","sequence":"additional","affiliation":[{"name":"1 Department of Bioinformatics and Computational Biology, UT MD Anderson Cancer Center, Houston, TX 77030, 2Stanford Genome Technology Center, Stanford University, Palo Alto, CA 94304, USA, 3Bioinformatics Division, Walter & Eliza Hall Institute, Parkville, VIC 3052, Australia and 4Department of Statistics, University of California, Berkeley, CA 94720, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Terence P.","family":"Speed","sequence":"additional","affiliation":[{"name":"1 Department of Bioinformatics and Computational Biology, UT MD Anderson Cancer Center, Houston, TX 77030, 2Stanford Genome Technology Center, Stanford University, Palo Alto, CA 94304, USA, 3Bioinformatics Division, Walter & Eliza Hall Institute, Parkville, VIC 3052, Australia and 4Department of Statistics, University of California, Berkeley, CA 94720, USA"},{"name":"1 Department of Bioinformatics and Computational Biology, UT MD Anderson Cancer Center, Houston, TX 77030, 2Stanford Genome Technology Center, Stanford University, Palo Alto, CA 94304, USA, 3Bioinformatics Division, Walter & Eliza Hall Institute, Parkville, VIC 3052, Australia and 4Department of Statistics, University of California, Berkeley, CA 94720, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Curt","family":"Scharfe","sequence":"additional","affiliation":[{"name":"1 Department of Bioinformatics and Computational Biology, UT MD Anderson Cancer Center, Houston, TX 77030, 2Stanford Genome Technology Center, Stanford University, Palo Alto, CA 94304, USA, 3Bioinformatics Division, Walter & Eliza Hall Institute, Parkville, VIC 3052, Australia and 4Department of Statistics, University of California, Berkeley, CA 94720, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wenyi","family":"Wang","sequence":"additional","affiliation":[{"name":"1 Department of Bioinformatics and Computational Biology, UT MD Anderson Cancer Center, Houston, TX 77030, 2Stanford Genome Technology Center, Stanford University, Palo Alto, CA 94304, USA, 3Bioinformatics Division, Walter & Eliza Hall Institute, Parkville, VIC 3052, Australia and 4Department of Statistics, University of California, Berkeley, CA 94720, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2012,5,10]]},"reference":[{"key":"2023012512431428500_B1","volume-title":"aroma.affymetrix: A generic framework in R for analyzing small to very large Affymetrix data sets in bounded memory.","author":"Bengtsson","year":"2008"},{"key":"2023012512431428500_B2","doi-asserted-by":"crossref","first-page":"695","DOI":"10.1038\/ng.f.136","article-title":"Common and rare variants in multifactorial susceptibility to common diseases","volume":"40","author":"Bodmer","year":"2008","journal-title":"Nat. Genet."},{"key":"2023012512431428500_B3","doi-asserted-by":"crossref","first-page":"2156","DOI":"10.1093\/bioinformatics\/btr330","article-title":"The variant call format and VCFtools","volume":"27","author":"Danecek","year":"2011","journal-title":"Bioinformatics"},{"key":"2023012512431428500_B4","doi-asserted-by":"crossref","first-page":"611","DOI":"10.1198\/016214502760047131","article-title":"Model-based clustering, discriminant analysis, and density estimation","volume":"97","author":"Fraley","year":"2002","journal-title":"J. Am. Stat. Assoc."},{"key":"2023012512431428500_B5","volume-title":"R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing","author":"R Development Core Team.","year":"2010"},{"key":"2023012512431428500_B6","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1016\/0377-0427(87)90125-7","article-title":"Silhouettes: a graphical aid to the interpretation and validation of cluster analysis","volume":"20","author":"Rousseeuw","year":"1987","journal-title":"J. Comput. Appl. Math."},{"key":"2023012512431428500_B7","doi-asserted-by":"crossref","first-page":"6549","DOI":"10.1073\/pnas.1018981108","article-title":"High-quality DNA sequence capture of 524 disease candidate genes","volume":"108","author":"Shen","year":"2011","journal-title":"Proc. Natl Acad. Sci. USA."},{"key":"2023012512431428500_B8","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1093\/nar\/gkq750","article-title":"Identification of rare DNA variants in mitochondrial disorders with improved array-based sequencing","volume":"39","author":"Wang","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"2023012512431428500_B9","doi-asserted-by":"crossref","DOI":"10.1016\/j.parkreldis.2011.12.012","article-title":"A DNA Resequencing Array for Genes Involved in Parkinson's Disease","author":"Wilkins","year":"2012","journal-title":"Parkinsonism Rel. Disord."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/14\/1928\/48870371\/bioinformatics_28_14_1928.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/14\/1928\/48870371\/bioinformatics_28_14_1928.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T16:49:36Z","timestamp":1674665376000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/28\/14\/1928\/219173"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,5,10]]},"references-count":9,"journal-issue":{"issue":"14","published-print":{"date-parts":[[2012,7,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bts286","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2012,7,15]]},"published":{"date-parts":[[2012,5,10]]}}}