{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,7]],"date-time":"2026-07-07T00:38:59Z","timestamp":1783384739735,"version":"3.54.6"},"reference-count":18,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":480,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,6,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: \u00a0CYP2D6 is highly polymorphic gene which encodes the (CYP2D6) enzyme, involved in the metabolism of 20\u201325% of all clinically prescribed drugs and other xenobiotics in the human body. CYP2D6 genotyping is recommended prior to treatment decisions involving one or more of the numerous drugs sensitive to CYP2D6 allelic composition. In this context, high-throughput sequencing (HTS) technologies provide a promising time-efficient and cost-effective alternative to currently used genotyping techniques. To achieve accurate interpretation of HTS data, however, one needs to overcome several obstacles such as high sequence similarity and genetic recombinations between CYP2D6 and evolutionarily related pseudogenes CYP2D7 and CYP2D8, high copy number variation among individuals and short read lengths generated by HTS technologies.<\/jats:p>\n               <jats:p>Results: In this work, we present the first algorithm to computationally infer CYP2D6 genotype at basepair resolution from HTS data. Our algorithm is able to resolve complex genotypes, including alleles that are the products of duplication, deletion and fusion events involving CYP2D6 and its evolutionarily related cousin CYP2D7. Through extensive experiments using simulated and real datasets, we show that our algorithm accurately solves this important problem with potential clinical implications.<\/jats:p>\n               <jats:p>Availability and implementation: Cypiripi is available at http:\/\/sfu-compbio.github.io\/cypiripi.<\/jats:p>\n               <jats:p>Contact: \u00a0cenk@sfu.ca.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv232","type":"journal-article","created":{"date-parts":[[2015,6,13]],"date-time":"2015-06-13T17:12:36Z","timestamp":1434215556000},"page":"i27-i34","source":"Crossref","is-referenced-by-count":44,"title":["Cypiripi: exact genotyping of <i>CYP2D6<\/i> using high-throughput sequencing data"],"prefix":"10.1093","volume":"31","author":[{"given":"Ibrahim","family":"Numanagi\u0107","sequence":"first","affiliation":[{"name":"1 School of Computing Science, Simon Fraser University, Burnaby, BC V5A 1S6, Canada, 2Department of Medicine, Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, IN 46202, USA and 3School of Informatics and Computing, Indiana University, Bloomington, IN 47401, USA"},{"name":"1 School of Computing Science, Simon Fraser University, Burnaby, BC V5A 1S6, Canada, 2Department of Medicine, Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, IN 46202, USA and 3School of Informatics and Computing, Indiana University, Bloomington, IN 47401, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Salem","family":"Maliki\u0107","sequence":"additional","affiliation":[{"name":"1 School of Computing Science, Simon Fraser University, Burnaby, BC V5A 1S6, Canada, 2Department of Medicine, Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, IN 46202, USA and 3School of Informatics and Computing, Indiana University, Bloomington, IN 47401, USA"},{"name":"1 School of Computing Science, Simon Fraser University, Burnaby, BC V5A 1S6, Canada, 2Department of Medicine, Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, IN 46202, USA and 3School of Informatics and Computing, Indiana University, Bloomington, IN 47401, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Victoria M.","family":"Pratt","sequence":"additional","affiliation":[{"name":"1 School of Computing Science, Simon Fraser University, Burnaby, BC V5A 1S6, Canada, 2Department of Medicine, Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, IN 46202, USA and 3School of Informatics and Computing, Indiana University, Bloomington, IN 47401, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Todd C.","family":"Skaar","sequence":"additional","affiliation":[{"name":"1 School of Computing Science, Simon Fraser University, Burnaby, BC V5A 1S6, Canada, 2Department of Medicine, Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, IN 46202, USA and 3School of Informatics and Computing, Indiana University, Bloomington, IN 47401, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David A.","family":"Flockhart","sequence":"additional","affiliation":[{"name":"1 School of Computing Science, Simon Fraser University, Burnaby, BC V5A 1S6, Canada, 2Department of Medicine, Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, IN 46202, USA and 3School of Informatics and Computing, Indiana University, Bloomington, IN 47401, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"S. Cenk","family":"Sahinalp","sequence":"additional","affiliation":[{"name":"1 School of Computing Science, Simon Fraser University, Burnaby, BC V5A 1S6, Canada, 2Department of Medicine, Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, IN 46202, USA and 3School of Informatics and Computing, Indiana University, Bloomington, IN 47401, USA"},{"name":"1 School of Computing Science, Simon Fraser University, Burnaby, BC V5A 1S6, Canada, 2Department of Medicine, Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, IN 46202, USA and 3School of Informatics and Computing, Indiana University, Bloomington, IN 47401, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2015,6,10]]},"reference":[{"key":"2023020115440626200_btv232-B1","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1038\/nature11632","article-title":"An integrated map of genetic variation from 1 092 human genomes","volume":"491","author":"Genomes Project Consortium","year":"2012","journal-title":"Nature"},{"key":"2023020115440626200_btv232-B2","doi-asserted-by":"crossref","first-page":"1061","DOI":"10.1038\/ng.437","article-title":"Personalized copy number and segmental duplication maps using next-generation sequencing","volume":"41","author":"Alkan","year":"2009","journal-title":"Nat. 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