{"@context":{"@vocab":"https://cir.nii.ac.jp/schema/1.0/","rdfs":"http://www.w3.org/2000/01/rdf-schema#","dc":"http://purl.org/dc/elements/1.1/","dcterms":"http://purl.org/dc/terms/","foaf":"http://xmlns.com/foaf/0.1/","prism":"http://prismstandard.org/namespaces/basic/2.0/","cinii":"http://ci.nii.ac.jp/ns/1.0/","datacite":"https://schema.datacite.org/meta/kernel-4/","ndl":"http://ndl.go.jp/dcndl/terms/","jpcoar":"https://github.com/JPCOAR/schema/blob/master/2.0/"},"@id":"https://cir.nii.ac.jp/crid/1363670319038616448.json","@type":"Article","productIdentifier":[{"identifier":{"@type":"DOI","@value":"10.1186/gb-2013-14-8-r90"}},{"identifier":{"@type":"URI","@value":"https://link.springer.com/content/pdf/10.1186/gb-2013-14-8-r90.pdf"}},{"identifier":{"@type":"URI","@value":"https://link.springer.com/article/10.1186/gb-2013-14-8-r90/fulltext.html"}}],"dc:title":[{"@value":"Virmid: accurate detection of somatic mutations with sample impurity inference"}],"description":[{"type":"abstract","notation":[{"@value":"<jats:title>Abstract</jats:title><jats:p>Detection of somatic variation using sequence from disease-control matched data sets is a critical first step. In many cases including cancer, however, it is hard to isolate pure disease tissue, and the impurity hinders accurate mutation analysis by disrupting overall allele frequencies. Here, we propose a new method, Virmid, that explicitly determines the level of impurity in the sample, and uses it for improved detection of somatic variation. Extensive tests on simulated and real sequencing data from breast cancer and hemimegalencephaly demonstrate the power of our model. A software implementation of our method is available at <jats:ext-link xmlns:xlink=\"http://www.w3.org/1999/xlink\" ext-link-type=\"uri\" xlink:href=\"http://sourceforge.net/projects/virmid/\">http://sourceforge.net/projects/virmid/</jats:ext-link>.</jats:p>"}]}],"creator":[{"@id":"https://cir.nii.ac.jp/crid/1383670319038616449","@type":"Researcher","foaf:name":[{"@value":"Sangwoo Kim"}]},{"@id":"https://cir.nii.ac.jp/crid/1383670319038616448","@type":"Researcher","foaf:name":[{"@value":"Kyowon Jeong"}]},{"@id":"https://cir.nii.ac.jp/crid/1383670319038616455","@type":"Researcher","foaf:name":[{"@value":"Kunal Bhutani"}]},{"@id":"https://cir.nii.ac.jp/crid/1380865125400885120","@type":"Researcher","foaf:name":[{"@value":"Jeong Ho Lee"}]},{"@id":"https://cir.nii.ac.jp/crid/1383670319038616454","@type":"Researcher","foaf:name":[{"@value":"Anand Patel"}]},{"@id":"https://cir.nii.ac.jp/crid/1383670319038616450","@type":"Researcher","foaf:name":[{"@value":"Eric Scott"}]},{"@id":"https://cir.nii.ac.jp/crid/1383670319038616451","@type":"Researcher","foaf:name":[{"@value":"Hojung Nam"}]},{"@id":"https://cir.nii.ac.jp/crid/1383670319038616457","@type":"Researcher","foaf:name":[{"@value":"Joseph G Gleeson"}]},{"@id":"https://cir.nii.ac.jp/crid/1383670319038616453","@type":"Researcher","foaf:name":[{"@value":"Vineet Bafna"}]},{"@id":"https://cir.nii.ac.jp/crid/1383670319038616452","@type":"Researcher","foaf:name":[{"@value":"Hayan Lee"}]}],"publication":{"publicationIdentifier":[{"@type":"EISSN","@value":"1474760X"}],"prism:publicationName":[{"@value":"Genome Biology"}],"dc:publisher":[{"@value":"Springer Science and Business Media LLC"}],"prism:publicationDate":"2013-08-29","prism:volume":"14","prism:number":"8","prism:startingPage":"R90"},"reviewed":"false","dc:rights":["http://creativecommons.org/licenses/by/2.0/","http://creativecommons.org/licenses/by/2.0/"],"url":[{"@id":"https://link.springer.com/content/pdf/10.1186/gb-2013-14-8-r90.pdf"},{"@id":"https://link.springer.com/article/10.1186/gb-2013-14-8-r90/fulltext.html"}],"createdAt":"2013-08-29","modifiedAt":"2024-10-08","relatedProduct":[{"@id":"https://cir.nii.ac.jp/crid/1360004236376823296","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"Activation of the Mitochondrial Apoptotic Pathway Produces Reactive Oxygen Species and Oxidative Damage in Hepatocytes That Contribute to Liver Tumorigenesis"}]},{"@id":"https://cir.nii.ac.jp/crid/1360857593672217728","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"Highly immunogenic cancer cells require activation of the WNT pathway for immunological escape"}]}],"dataSourceIdentifier":[{"@type":"CROSSREF","@value":"10.1186/gb-2013-14-8-r90"},{"@type":"CROSSREF","@value":"10.1158/1940-6207.capr-15-0022-t_references_DOI_FO2QIrmhBHZZaYWz5er5eR65Ug7"},{"@type":"CROSSREF","@value":"10.1126/sciimmunol.abc6424_references_DOI_FO2QIrmhBHZZaYWz5er5eR65Ug7"}]}