{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,19]],"date-time":"2026-02-19T12:29:55Z","timestamp":1771504195310,"version":"3.50.1"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"18","license":[{"start":{"date-parts":[[2016,11,14]],"date-time":"2016-11-14T00:00:00Z","timestamp":1479081600000},"content-version":"vor","delay-in-days":900,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/3.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Exome sequencing (exome-seq) data, which are typically used for calling exonic mutations, have also been utilized in detecting DNA copy number variations (CNVs). Despite the existence of several CNV detection tools, there is still a great need for a sensitive and an accurate CNV-calling algorithm with built-in QC steps, and does not require a paired reference for each sample.<\/jats:p>\n               <jats:p>Results: We developed a novel method named PatternCNV, which (i) accounts for the read coverage variations between exons while leveraging the consistencies of this variability across different samples; (ii) reduces alignment BAM files to WIG format and therefore greatly accelerates computation; (iii) incorporates multiple QC measures designed to identify outlier samples and batch effects; and (iv) provides a variety of visualization options including chromosome, gene and exon-level views of CNVs, along with a tabular summarization of the exon-level CNVs. Compared with other CNV-calling algorithms using data from a lymphoma exome-seq study, PatternCNV has higher sensitivity and specificity.<\/jats:p>\n               <jats:p>Availability and implementation: The software for PatternCNV is implemented using Perl and R, and can be used in Mac or Linux environments. Software and user manual are available at http:\/\/bioinformaticstools.mayo.edu\/research\/patterncnv\/ , and R package at https:\/\/github.com\/topsoil\/patternCNV\/ .<\/jats:p>\n               <jats:p>Contact: \u00a0Asmann.Yan@mayo.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu363","type":"journal-article","created":{"date-parts":[[2014,5,30]],"date-time":"2014-05-30T02:31:57Z","timestamp":1401417117000},"page":"2678-2680","source":"Crossref","is-referenced-by-count":47,"title":["PatternCNV: a versatile tool for detecting copy number changes from exome sequencing data"],"prefix":"10.1093","volume":"30","author":[{"given":"Chen","family":"Wang","sequence":"first","affiliation":[{"name":"1 Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, 2 Division of Epidemiology, Department of Health Sciences Research, 3 Division of Hematology, Department of Internal Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN 55905 and 4 Department of Health Sciences Research, Mayo Clinic, 4500 San Pablo Road South, Jacksonville, FL 32224, USA"}]},{"given":"Jared M.","family":"Evans","sequence":"additional","affiliation":[{"name":"1 Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, 2 Division of Epidemiology, Department of Health Sciences Research, 3 Division of Hematology, Department of Internal Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN 55905 and 4 Department of Health Sciences Research, Mayo Clinic, 4500 San Pablo Road South, Jacksonville, FL 32224, USA"}]},{"given":"Aditya V.","family":"Bhagwate","sequence":"additional","affiliation":[{"name":"1 Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, 2 Division of Epidemiology, Department of Health Sciences Research, 3 Division of Hematology, Department of Internal Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN 55905 and 4 Department of Health Sciences Research, Mayo Clinic, 4500 San Pablo Road South, Jacksonville, FL 32224, USA"}]},{"given":"Naresh","family":"Prodduturi","sequence":"additional","affiliation":[{"name":"1 Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, 2 Division of Epidemiology, Department of Health Sciences Research, 3 Division of Hematology, Department of Internal Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN 55905 and 4 Department of Health Sciences Research, Mayo Clinic, 4500 San Pablo Road South, Jacksonville, FL 32224, USA"}]},{"given":"Vivekananda","family":"Sarangi","sequence":"additional","affiliation":[{"name":"1 Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, 2 Division of Epidemiology, Department of Health Sciences Research, 3 Division of Hematology, Department of Internal Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN 55905 and 4 Department of Health Sciences Research, Mayo Clinic, 4500 San Pablo Road South, Jacksonville, FL 32224, USA"}]},{"given":"Mridu","family":"Middha","sequence":"additional","affiliation":[{"name":"1 Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, 2 Division of Epidemiology, Department of Health Sciences Research, 3 Division of Hematology, Department of Internal Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN 55905 and 4 Department of Health Sciences Research, Mayo Clinic, 4500 San Pablo Road South, Jacksonville, FL 32224, USA"}]},{"given":"Hugues","family":"Sicotte","sequence":"additional","affiliation":[{"name":"1 Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, 2 Division of Epidemiology, Department of Health Sciences Research, 3 Division of Hematology, Department of Internal Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN 55905 and 4 Department of Health Sciences Research, Mayo Clinic, 4500 San Pablo Road South, Jacksonville, FL 32224, USA"}]},{"given":"Peter T.","family":"Vedell","sequence":"additional","affiliation":[{"name":"1 Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, 2 Division of Epidemiology, Department of Health Sciences Research, 3 Division of Hematology, Department of Internal Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN 55905 and 4 Department of Health Sciences Research, Mayo Clinic, 4500 San Pablo Road South, Jacksonville, FL 32224, USA"}]},{"given":"Steven N.","family":"Hart","sequence":"additional","affiliation":[{"name":"1 Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, 2 Division of Epidemiology, Department of Health Sciences Research, 3 Division of Hematology, Department of Internal Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN 55905 and 4 Department of Health Sciences Research, Mayo Clinic, 4500 San Pablo Road South, Jacksonville, FL 32224, USA"}]},{"given":"Gavin R.","family":"Oliver","sequence":"additional","affiliation":[{"name":"1 Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, 2 Division of Epidemiology, Department of Health Sciences Research, 3 Division of Hematology, Department of Internal Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN 55905 and 4 Department of Health Sciences Research, Mayo Clinic, 4500 San Pablo Road South, Jacksonville, FL 32224, USA"}]},{"given":"Jean-Pierre A.","family":"Kocher","sequence":"additional","affiliation":[{"name":"1 Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, 2 Division of Epidemiology, Department of Health Sciences Research, 3 Division of Hematology, Department of Internal Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN 55905 and 4 Department of Health Sciences Research, Mayo Clinic, 4500 San Pablo Road South, Jacksonville, FL 32224, USA"}]},{"given":"Matthew J.","family":"Maurer","sequence":"additional","affiliation":[{"name":"1 Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, 2 Division of Epidemiology, Department of Health Sciences Research, 3 Division of Hematology, Department of Internal Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN 55905 and 4 Department of Health Sciences Research, Mayo Clinic, 4500 San Pablo Road South, Jacksonville, FL 32224, USA"}]},{"given":"Anne J.","family":"Novak","sequence":"additional","affiliation":[{"name":"1 Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, 2 Division of Epidemiology, Department of Health Sciences Research, 3 Division of Hematology, Department of Internal Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN 55905 and 4 Department of Health Sciences Research, Mayo Clinic, 4500 San Pablo Road South, Jacksonville, FL 32224, USA"}]},{"given":"Susan L.","family":"Slager","sequence":"additional","affiliation":[{"name":"1 Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, 2 Division of Epidemiology, Department of Health Sciences Research, 3 Division of Hematology, Department of Internal Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN 55905 and 4 Department of Health Sciences Research, Mayo Clinic, 4500 San Pablo Road South, Jacksonville, FL 32224, USA"}]},{"given":"James R.","family":"Cerhan","sequence":"additional","affiliation":[{"name":"1 Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, 2 Division of Epidemiology, Department of Health Sciences Research, 3 Division of Hematology, Department of Internal Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN 55905 and 4 Department of Health Sciences Research, Mayo Clinic, 4500 San Pablo Road South, Jacksonville, FL 32224, USA"}]},{"given":"Yan W.","family":"Asmann","sequence":"additional","affiliation":[{"name":"1 Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, 2 Division of Epidemiology, Department of Health Sciences Research, 3 Division of Hematology, Department of Internal Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN 55905 and 4 Department of Health Sciences Research, Mayo Clinic, 4500 San Pablo Road South, Jacksonville, FL 32224, USA"}]}],"member":"286","published-online":{"date-parts":[[2014,5,29]]},"reference":[{"key":"2023012711554823400_btu363-B1","doi-asserted-by":"crossref","first-page":"551","DOI":"10.1038\/nrg2593","article-title":"Mechanisms of change in gene copy number","volume":"10","author":"Hastings","year":"2009","journal-title":"Nat. Rev. Genet."},{"key":"2023012711554823400_btu363-B2","doi-asserted-by":"crossref","first-page":"568","DOI":"10.1101\/gr.129684.111","article-title":"VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing","volume":"22","author":"Koboldt","year":"2012","journal-title":"Genome Res."},{"key":"2023012711554823400_btu363-B3","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":"2023012711554823400_btu363-B4","doi-asserted-by":"crossref","first-page":"3879","DOI":"10.1073\/pnas.1121343109","article-title":"Discovery and prioritization of somatic mutations in diffuse large B-cell lymphoma (DLBCL) by whole-exome sequencing","volume":"109","author":"Lohr","year":"2012","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012711554823400_btu363-B5","doi-asserted-by":"crossref","first-page":"557","DOI":"10.1093\/biostatistics\/kxh008","article-title":"Circular binary segmentation for the analysis of array-based DNA copy number data","volume":"5","author":"Olshen","year":"2004","journal-title":"Biostatistics"},{"key":"2023012711554823400_btu363-B6","doi-asserted-by":"crossref","first-page":"R97","DOI":"10.1186\/gb-2011-12-9-r97","article-title":"A comparative analysis of exome capture","volume":"12","author":"Parla","year":"2011","journal-title":"Genome Biol."},{"key":"2023012711554823400_btu363-B7","doi-asserted-by":"crossref","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","article-title":"BEDTools: a flexible suite of utilities for comparing genomic features","volume":"26","author":"Quinlan","year":"2010","journal-title":"Bioinformatics"},{"key":"2023012711554823400_btu363-B8","doi-asserted-by":"crossref","first-page":"2648","DOI":"10.1093\/bioinformatics\/btr462","article-title":"Exome sequencing-based copy-number variation and loss of heterozygosity detection: exomeCNV","volume":"27","author":"Sathirapongsasuti","year":"2011","journal-title":"Bioinformatics"},{"key":"2023012711554823400_btu363-B9","doi-asserted-by":"crossref","first-page":"1461","DOI":"10.1093\/bioinformatics\/btt151","article-title":"FishingCNV: a graphical software package for detecting rare copy number variations in exome-sequencing data","volume":"29","author":"Shi","year":"2013","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/18\/2678\/48929570\/bioinformatics_30_18_2678.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/18\/2678\/48929570\/bioinformatics_30_18_2678.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T12:43:05Z","timestamp":1674823385000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/30\/18\/2678\/2475632"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,5,29]]},"references-count":9,"journal-issue":{"issue":"18","published-print":{"date-parts":[[2014,9,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btu363","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2014,9,15]]},"published":{"date-parts":[[2014,5,29]]}}}