{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,18]],"date-time":"2025-10-18T10:22:47Z","timestamp":1760782967115},"reference-count":6,"publisher":"Oxford University Press (OUP)","issue":"13","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2007,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The undertaking of large-scale DNA sequencing screens for somatic variants in human cancers requires accurate and rapid processing of traces for variants. Due to their often aneuploid nature and admixed normal tissue, heterozygous variants found in primary cancers are often subtle and difficult to detect. To address these issues, we have developed a mutation detection algorithm, AutoCSA, specifically optimized for the high throughput screening of cancer samples.<\/jats:p>\n               <jats:p>Availability: http:\/\/www.sanger.ac.uk\/genetics\/CGP\/Software\/AutoCSA.<\/jats:p>\n               <jats:p>Contact: mrs@sanger.ac.uk<\/jats:p>","DOI":"10.1093\/bioinformatics\/btm152","type":"journal-article","created":{"date-parts":[[2007,5,8]],"date-time":"2007-05-08T00:13:40Z","timestamp":1178583220000},"page":"1689-1691","source":"Crossref","is-referenced-by-count":14,"title":["AutoCSA, an algorithm for high throughput DNA sequence variant detection in cancer genomes"],"prefix":"10.1093","volume":"23","author":[{"given":"E.","family":"Dicks","sequence":"first","affiliation":[{"name":"1 Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK and 2NGRL (Wessex), Salisbury District Hospital, Salisbury, SP2 8BJ, UK"}]},{"given":"J. W.","family":"Teague","sequence":"additional","affiliation":[{"name":"1 Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK and 2NGRL (Wessex), Salisbury District Hospital, Salisbury, SP2 8BJ, UK"}]},{"given":"P.","family":"Stephens","sequence":"additional","affiliation":[{"name":"1 Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK and 2NGRL (Wessex), Salisbury District Hospital, Salisbury, SP2 8BJ, UK"}]},{"given":"K.","family":"Raine","sequence":"additional","affiliation":[{"name":"1 Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK and 2NGRL (Wessex), Salisbury District Hospital, Salisbury, SP2 8BJ, UK"}]},{"given":"A.","family":"Yates","sequence":"additional","affiliation":[{"name":"1 Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK and 2NGRL (Wessex), Salisbury District Hospital, Salisbury, SP2 8BJ, UK"}]},{"given":"C.","family":"Mattocks","sequence":"additional","affiliation":[{"name":"1 Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK and 2NGRL (Wessex), Salisbury District Hospital, Salisbury, SP2 8BJ, UK"}]},{"given":"P.","family":"Tarpey","sequence":"additional","affiliation":[{"name":"1 Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK and 2NGRL (Wessex), Salisbury District Hospital, Salisbury, SP2 8BJ, UK"}]},{"given":"A.","family":"Butler","sequence":"additional","affiliation":[{"name":"1 Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK and 2NGRL (Wessex), Salisbury District Hospital, Salisbury, SP2 8BJ, UK"}]},{"given":"A.","family":"Menzies","sequence":"additional","affiliation":[{"name":"1 Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK and 2NGRL (Wessex), Salisbury District Hospital, Salisbury, SP2 8BJ, UK"}]},{"given":"D.","family":"Richardson","sequence":"additional","affiliation":[{"name":"1 Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK and 2NGRL (Wessex), Salisbury District Hospital, Salisbury, SP2 8BJ, UK"}]},{"given":"A.","family":"Jenkinson","sequence":"additional","affiliation":[{"name":"1 Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK and 2NGRL (Wessex), Salisbury District Hospital, Salisbury, SP2 8BJ, UK"}]},{"given":"H.","family":"Davies","sequence":"additional","affiliation":[{"name":"1 Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK and 2NGRL (Wessex), Salisbury District Hospital, Salisbury, SP2 8BJ, UK"}]},{"given":"S.","family":"Edkins","sequence":"additional","affiliation":[{"name":"1 Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK and 2NGRL (Wessex), Salisbury District Hospital, Salisbury, SP2 8BJ, UK"}]},{"given":"S.","family":"Forbes","sequence":"additional","affiliation":[{"name":"1 Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK and 2NGRL (Wessex), Salisbury District Hospital, Salisbury, SP2 8BJ, UK"}]},{"given":"K.","family":"Gray","sequence":"additional","affiliation":[{"name":"1 Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK and 2NGRL (Wessex), Salisbury District Hospital, Salisbury, SP2 8BJ, UK"}]},{"given":"C.","family":"Greenman","sequence":"additional","affiliation":[{"name":"1 Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK and 2NGRL (Wessex), Salisbury District Hospital, Salisbury, SP2 8BJ, UK"}]},{"given":"R.","family":"Shepherd","sequence":"additional","affiliation":[{"name":"1 Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK and 2NGRL (Wessex), Salisbury District Hospital, Salisbury, SP2 8BJ, UK"}]},{"given":"M. R.","family":"Stratton","sequence":"additional","affiliation":[{"name":"1 Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK and 2NGRL (Wessex), Salisbury District Hospital, Salisbury, SP2 8BJ, UK"}]},{"given":"P. A.","family":"Futreal","sequence":"additional","affiliation":[{"name":"1 Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK and 2NGRL (Wessex), Salisbury District Hospital, Salisbury, SP2 8BJ, UK"}]},{"given":"R.","family":"Wooster","sequence":"additional","affiliation":[{"name":"1 Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK and 2NGRL (Wessex), Salisbury District Hospital, Salisbury, SP2 8BJ, UK"}]}],"member":"286","published-online":{"date-parts":[[2007,5,7]]},"reference":[{"key":"2023062708443804600_B1","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1002\/humu.20188","article-title":"InSNP: a tool for automated detection and visualization of SNPs and InDels","volume":"26","author":"Manaster","year":"2005","journal-title":"Hum. Mutat"},{"key":"2023062708443804600_B2","doi-asserted-by":"crossref","first-page":"437","DOI":"10.1002\/1098-1004(200011)16:5<437::AID-HUMU9>3.0.CO;2-Q","article-title":"Comparative sequence analysis (CSA): a new sequence-based method for the identification and characterization of mutations in DNA","volume":"16","author":"Mattocks","year":"2000","journal-title":"Hum. Mutat"},{"key":"2023062708443804600_B3","doi-asserted-by":"crossref","first-page":"2745","DOI":"10.1093\/nar\/25.14.2745","article-title":"PolyPhred: automating the detection and genotyping of single nucleotide substitutions using fluorescence-based resequencing","volume":"25","author":"Nickerson","year":"1997","journal-title":"Nucleic Acids Res"},{"key":"2023062708443804600_B4","doi-asserted-by":"crossref","first-page":"375","DOI":"10.1038\/ng1746","article-title":"Automating sequence-based detection and genotyping of SNPs from diploid samples","volume":"38","author":"Stephens","year":"2006","journal-title":"Nat. Genet"},{"key":"2023062708443804600_B5","doi-asserted-by":"crossref","first-page":"436","DOI":"10.1101\/gr.2754005","article-title":"novoSNP, a novel computational tool for sequence variation discovery","volume":"15","author":"Weckx","year":"2005","journal-title":"Genome Res"},{"key":"2023062708443804600_B6","doi-asserted-by":"crossref","first-page":"e53","DOI":"10.1371\/journal.pcbi.0010053","article-title":"SNPdetector: a software tool for sensitive and accurate SNP detection","volume":"1","author":"Zhang","year":"2005","journal-title":"PLoS Comput. Biol"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/23\/13\/1689\/50715481\/bioinformatics_23_13_1689.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/23\/13\/1689\/50715481\/bioinformatics_23_13_1689.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,27]],"date-time":"2023-06-27T08:45:35Z","timestamp":1687855535000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/23\/13\/1689\/222717"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2007,5,7]]},"references-count":6,"journal-issue":{"issue":"13","published-print":{"date-parts":[[2007,7,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btm152","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2007,7]]},"published":{"date-parts":[[2007,5,7]]}}}