{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:46Z","timestamp":1772138086121,"version":"3.50.1"},"reference-count":35,"publisher":"Oxford University Press (OUP)","issue":"10","license":[{"start":{"date-parts":[[2018,1,8]],"date-time":"2018-01-08T00:00:00Z","timestamp":1515369600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01CA211878-01 and P30CA023074-36S2"],"award-info":[{"award-number":["R01CA211878-01 and P30CA023074-36S2"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,5,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Tumor genome sequencing offers great promise for guiding research and therapy, but spurious variant calls can arise from multiple sources. Mouse contamination can generate many spurious calls when sequencing patient-derived xenografts. Paralogous genome sequences can also generate spurious calls when sequencing any tumor. We developed a BLAST-based algorithm, Mouse And Paralog EXterminator (MAPEX), to identify and filter out spurious calls from both these sources.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>When calling variants from xenografts, MAPEX has similar sensitivity and specificity to more complex algorithms. When applied to any tumor, MAPEX also automatically flags calls that potentially arise from paralogous sequences. Our implementation, mapexr, runs quickly and easily on a desktop computer. MAPEX is thus a useful addition to almost any pipeline for calling genetic variants in tumors.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The mapexr package for R is available at https:\/\/github.com\/bmannakee\/mapexr under the MIT license.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty010","type":"journal-article","created":{"date-parts":[[2018,1,5]],"date-time":"2018-01-05T23:13:39Z","timestamp":1515194019000},"page":"1713-1718","source":"Crossref","is-referenced-by-count":4,"title":["Sensitive and specific post-call filtering of genetic variants in xenograft and primary tumors"],"prefix":"10.1093","volume":"34","author":[{"given":"Brian K","family":"Mannakee","sequence":"first","affiliation":[{"name":"Department of Epidemiology and Biostatistics, Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson, AZ, USA"},{"name":"University of Arizona Cancer Center, University of Arizona, Tucson, AZ, USA"}]},{"given":"Uthra","family":"Balaji","sequence":"additional","affiliation":[{"name":"McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, USA"}]},{"given":"Agnieszka K","family":"Witkiewicz","sequence":"additional","affiliation":[{"name":"University of Arizona Cancer Center, University of Arizona, Tucson, AZ, USA"},{"name":"Department of Medicine, University of Arizona, Tucson, AZ, USA"},{"name":"Department of Pathology, University of Arizona, Tucson, AZ, USA"}]},{"given":"Ryan N","family":"Gutenkunst","sequence":"additional","affiliation":[{"name":"Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, USA"}]},{"given":"Erik S","family":"Knudsen","sequence":"additional","affiliation":[{"name":"University of Arizona Cancer Center, University of Arizona, Tucson, AZ, USA"},{"name":"Department of Medicine, University of Arizona, Tucson, AZ, USA"}]}],"member":"286","published-online":{"date-parts":[[2018,1,8]]},"reference":[{"key":"2023012713431999900_bty010-B1","doi-asserted-by":"crossref","first-page":"415","DOI":"10.1038\/nature12477","article-title":"Signatures of mutational processes in human cancer","volume":"500","author":"Alexandrov","year":"2013","journal-title":"Nature"},{"key":"2023012713431999900_bty010-B2","doi-asserted-by":"crossref","first-page":"17087","DOI":"10.18632\/oncotarget.7718","article-title":"Genomic characterization of patient-derived xenograft models established from fine needle aspirate biopsies of a primary pancreatic ductal adenocarcinoma and from patient-matched metastatic sites","volume":"7","author":"Allaway","year":"2016","journal-title":"Oncotarget"},{"key":"2023012713431999900_bty010-B3","doi-asserted-by":"crossref","first-page":"4591","DOI":"10.1182\/blood.V124.21.4591.4591","article-title":"Exome sequencing of familial MDS reveals novel mutations and high rates of false positive mutations in MLL3 due to pseudogene effects","volume":"124","author":"Bowler","year":"2014","journal-title":"Blood"},{"key":"2023012713431999900_bty010-B4","doi-asserted-by":"crossref","first-page":"260","DOI":"10.1016\/j.cell.2016.08.041","article-title":"A biobank of breast cancer explants with preserved intra-tumor heterogeneity to screen anticancer compounds","volume":"167","author":"Bruna","year":"2016","journal-title":"Cell"},{"key":"2023012713431999900_bty010-B5","doi-asserted-by":"crossref","first-page":"413","DOI":"10.1038\/nbt.2203","article-title":"Absolute quantification of somatic DNA alterations in human cancer","volume":"30","author":"Carter","year":"2012","journal-title":"Nat. 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