{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,27]],"date-time":"2026-07-27T14:02:35Z","timestamp":1785160955222,"version":"3.55.0"},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"1","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Next-generation sequencing has become a valuable tool for detecting mutations involved in Mendelian diseases. However, it is a challenge to identify the small subset of functionally important mutations from tens of thousands of rare variants in a whole exome\/genome. Therefore, we developed a toolkit called PriVar, a systematic prioritization pipeline that takes into consideration calling quality of the variants, their predicted functional impact, known connection of the gene to the disease and the number of mutations in a gene, and inference from linkage analysis.<\/jats:p>\n               <jats:p>Availability: Executable jar package is available at http:\/\/paed.hku.hk\/uploadarea\/yangwl\/html\/software.html.<\/jats:p>\n               <jats:p>Contact: yangwl@hkucc.hku.hk<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts627","type":"journal-article","created":{"date-parts":[[2012,10,27]],"date-time":"2012-10-27T00:18:50Z","timestamp":1351297130000},"page":"124-125","source":"Crossref","is-referenced-by-count":40,"title":["PriVar: a toolkit for prioritizing SNVs and indels from next-generation sequencing data"],"prefix":"10.1093","volume":"29","author":[{"given":"Lu","family":"Zhang","sequence":"first","affiliation":[{"name":"Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Hong Kong"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jing","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Hong Kong"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jing","family":"Yang","sequence":"additional","affiliation":[{"name":"Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Hong Kong"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dingge","family":"Ying","sequence":"additional","affiliation":[{"name":"Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Hong Kong"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yu lung","family":"Lau","sequence":"additional","affiliation":[{"name":"Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Hong Kong"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wanling","family":"Yang","sequence":"additional","affiliation":[{"name":"Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Hong Kong"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2012,10,25]]},"reference":[{"key":"2023020303202378200_bts627-B1","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1186\/1471-2105-6-55","article-title":"Speeding disease gene discovery by sequence based candidate prioritization","volume":"6","author":"Adie","year":"2005","journal-title":"BMC bioinformatics"},{"key":"2023020303202378200_bts627-B2","doi-asserted-by":"crossref","first-page":"491","DOI":"10.1038\/ng.806","article-title":"A framework for variation discovery and genotyping using next-generation DNA sequencing data","volume":"43","author":"DePristo","year":"2011","journal-title":"Nat. Genet."},{"key":"2023020303202378200_bts627-B3","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with Burrows-Wheeler transform","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"2023020303202378200_bts627-B4","doi-asserted-by":"crossref","first-page":"894","DOI":"10.1002\/humu.21517","article-title":"dbNSFP: a lightweight database of human nonsynonymous SNPs and their functional predictions","volume":"32","author":"Liu","year":"2011","journal-title":"Hum. Mutat."},{"key":"2023020303202378200_bts627-B5","doi-asserted-by":"crossref","first-page":"437","DOI":"10.1038\/gene.2012.8","article-title":"Exome sequencing identifies novel compound heterozygous mutations of IL-10 receptor 1 in neonatal-onset Crohn\u2019s disease","volume":"13","author":"Mao","year":"2012","journal-title":"Genes Immun."},{"key":"2023020303202378200_bts627-B6","doi-asserted-by":"crossref","first-page":"124","DOI":"10.1038\/ng0208-124","article-title":"A navigator for human genome epidemiology","volume":"40","author":"Yu","year":"2008","journal-title":"Nat. Genet."},{"key":"2023020303202378200_bts627-B7","doi-asserted-by":"crossref","first-page":"345","DOI":"10.1002\/humu.21432","article-title":"Homozygosity mapping on a single patient: identification of homozygous regions of recent common ancestry by using population data","volume":"32","author":"Zhang","year":"2011","journal-title":"Hum. Mutat."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/29\/1\/124\/49060289\/bioinformatics_29_1_124.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/29\/1\/124\/49060289\/bioinformatics_29_1_124.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,3]],"date-time":"2023-02-03T03:21:26Z","timestamp":1675394486000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/29\/1\/124\/272319"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,10,25]]},"references-count":7,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2013,1,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bts627","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2013,1]]},"published":{"date-parts":[[2012,10,25]]}}}