{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,30]],"date-time":"2025-10-30T22:28:23Z","timestamp":1761863303773},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"17","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,9,1]]},"abstract":"<jats:p>Summary: Recent advances in high-throughput sequencing technologies have enabled us to sequence large number of cancer samples to reveal novel insights into oncogenetic mechanisms. However, the presence of intratumoral heterogeneity, normal cell contamination and insufficient sequencing depth, together pose a challenge for detecting somatic mutations. Here we propose a fast and an accurate somatic single-nucleotide variations (SNVs) detection program, FaSD-somatic. The performance of FaSD-somatic is extensively assessed on various types of cancer against several state-of-the-art somatic SNV detection programs. Benchmarked by somatic SNVs from either existing databases or de novo higher-depth sequencing data, FaSD-somatic has the best overall performance. Furthermore, FaSD-somatic is efficient, it finishes somatic SNV calling within 14 h on 50X whole genome sequencing data in paired samples.<\/jats:p>\n               <jats:p>Availability and implementation: The program, datasets and supplementary files are available at http:\/\/jjwanglab.org\/FaSD-somatic\/.<\/jats:p>\n               <jats:p>Contact: \u00a0wangdatou2009@gmail.com.<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary Data are available at Bioinformatics online<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu338","type":"journal-article","created":{"date-parts":[[2014,5,16]],"date-time":"2014-05-16T01:21:59Z","timestamp":1400203319000},"page":"2498-2500","source":"Crossref","is-referenced-by-count":16,"title":["FaSD-somatic: a fast and accurate somatic SNV detection algorithm for cancer genome sequencing data"],"prefix":"10.1093","volume":"30","author":[{"given":"Weixin","family":"Wang","sequence":"first","affiliation":[{"name":"1 \u00a01Department of Biochemistry, LKS Faculty of Medicine, Hong Kong SAR, 2Shenzhen Institute of Research and Innovation, The University of Hong Kong, Shenzhen, Guangdong 518057, 3HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory, 4Department of Computer Science, 5Department of Pathology and 6Centre for Genomic Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China"}]},{"given":"Panwen","family":"Wang","sequence":"additional","affiliation":[{"name":"1 \u00a01Department of Biochemistry, LKS Faculty of Medicine, Hong Kong SAR, 2Shenzhen Institute of Research and Innovation, The University of Hong Kong, Shenzhen, Guangdong 518057, 3HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory, 4Department of Computer Science, 5Department of Pathology and 6Centre for Genomic Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China"}]},{"given":"Feng","family":"Xu","sequence":"additional","affiliation":[{"name":"1 \u00a01Department of Biochemistry, LKS Faculty of Medicine, Hong Kong SAR, 2Shenzhen Institute of Research and Innovation, The University of Hong Kong, Shenzhen, Guangdong 518057, 3HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory, 4Department of Computer Science, 5Department of Pathology and 6Centre for Genomic Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China"}]},{"given":"Ruibang","family":"Luo","sequence":"additional","affiliation":[{"name":"1 \u00a01Department of Biochemistry, LKS Faculty of Medicine, Hong Kong SAR, 2Shenzhen Institute of Research and Innovation, The University of Hong Kong, Shenzhen, Guangdong 518057, 3HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory, 4Department of Computer Science, 5Department of Pathology and 6Centre for Genomic Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China"}]},{"given":"Maria Pik","family":"Wong","sequence":"additional","affiliation":[{"name":"1 \u00a01Department of Biochemistry, LKS Faculty of Medicine, Hong Kong SAR, 2Shenzhen Institute of Research and Innovation, The University of Hong Kong, Shenzhen, Guangdong 518057, 3HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory, 4Department of Computer Science, 5Department of Pathology and 6Centre for Genomic Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China"}]},{"given":"Tak-Wah","family":"Lam","sequence":"additional","affiliation":[{"name":"1 \u00a01Department of Biochemistry, LKS Faculty of Medicine, Hong Kong SAR, 2Shenzhen Institute of Research and Innovation, The University of Hong Kong, Shenzhen, Guangdong 518057, 3HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory, 4Department of Computer Science, 5Department of Pathology and 6Centre for Genomic Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China"}]},{"given":"Junwen","family":"Wang","sequence":"additional","affiliation":[{"name":"1 \u00a01Department of Biochemistry, LKS Faculty of Medicine, Hong Kong SAR, 2Shenzhen Institute of Research and Innovation, The University of Hong Kong, Shenzhen, Guangdong 518057, 3HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory, 4Department of Computer Science, 5Department of Pathology and 6Centre for Genomic Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China"}]}],"member":"286","published-online":{"date-parts":[[2014,5,14]]},"reference":[{"key":"2023012711530369900_btu338-B1","doi-asserted-by":"crossref","first-page":"D945","DOI":"10.1093\/nar\/gkq929","article-title":"COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer","volume":"39","author":"Forbes","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"2023012711530369900_btu338-B2","doi-asserted-by":"crossref","first-page":"883","DOI":"10.1056\/NEJMoa1113205","article-title":"Intratumor heterogeneity and branched evolution revealed by multiregion sequencing","volume":"366","author":"Gerlinger","year":"2012","journal-title":"N. Engl. J. Med."},{"key":"2023012711530369900_btu338-B3","doi-asserted-by":"crossref","first-page":"439","DOI":"10.1016\/j.ajhg.2013.07.003","article-title":"DrGaP: a powerful tool for identifying driver genes and pathways in cancer sequencing studies","volume":"93","author":"Hua","year":"2013","journal-title":"Am. J. Hum. Genet."},{"key":"2023012711530369900_btu338-B4","doi-asserted-by":"crossref","first-page":"311","DOI":"10.1093\/bioinformatics\/btr665","article-title":"SomaticSniper: identification of somatic point mutations in whole genome sequencing data","volume":"28","author":"Larson","year":"2012","journal-title":"Bioinformatics"},{"key":"2023012711530369900_btu338-B5","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The Sequence Alignment\/Map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012711530369900_btu338-B6","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1038\/nature08658","article-title":"A comprehensive catalogue of somatic mutations from a human cancer genome","volume":"463","author":"Pleasance","year":"2010","journal-title":"Nature"},{"key":"2023012711530369900_btu338-B7","doi-asserted-by":"crossref","first-page":"719","DOI":"10.1038\/nature07943","article-title":"The cancer genome","volume":"458","author":"Stratton","year":"2009","journal-title":"Nature"},{"key":"2023012711530369900_btu338-B8","doi-asserted-by":"crossref","first-page":"4875","DOI":"10.1158\/0008-5472.CAN-12-2217","article-title":"Intratumor heterogeneity: evolution through space and time","volume":"72","author":"Swanton","year":"2012","journal-title":"Cancer Res."},{"key":"2023012711530369900_btu338-B9","doi-asserted-by":"crossref","first-page":"301","DOI":"10.1007\/978-1-4614-7645-0_15","article-title":"Assessment of mapping and SNP-detection algorithms for next-generation sequencing data in Cancer Genomics","volume-title":"Next Generation Sequencing in Cancer Research","author":"Wang","year":"2013"},{"key":"2023012711530369900_btu338-B10","doi-asserted-by":"crossref","first-page":"1258","DOI":"10.1038\/ncomms2256","article-title":"A fast and accurate SNP detection algorithm for next-generation sequencing data","volume":"3","author":"Xu","year":"2012","journal-title":"Nat. Commun."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/17\/2498\/48927411\/bioinformatics_30_17_2498.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/17\/2498\/48927411\/bioinformatics_30_17_2498.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T12:16:55Z","timestamp":1674821815000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/30\/17\/2498\/2748238"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,5,14]]},"references-count":10,"journal-issue":{"issue":"17","published-print":{"date-parts":[[2014,9,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btu338","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,5,14]]}}}