{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,15]],"date-time":"2026-07-15T07:06:39Z","timestamp":1784099199920,"version":"3.55.0"},"reference-count":23,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2025,9,17]],"date-time":"2025-09-17T00:00:00Z","timestamp":1758067200000},"content-version":"vor","delay-in-days":16,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000057","name":"NIGMS","doi-asserted-by":"publisher","award":["R35 GM155298"],"award-info":[{"award-number":["R35 GM155298"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000054","name":"NCI","doi-asserted-by":"publisher","award":["R01 CA268973"],"award-info":[{"award-number":["R01 CA268973"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Biostatistics and Bioinformatics Shared Resource"},{"name":"Moffitt Cancer Center by NCI","award":["P30 CA076292"],"award-info":[{"award-number":["P30 CA076292"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Clonal hematopoiesis (CH) is a molecular biomarker associated with various adverse outcomes in both healthy individuals and those with underlying conditions, including cancer. Detecting CH usually involves genomic sequencing of individual blood samples followed by robust bioinformatics data filtering. We report an R package, qcCHIP, a bioinformatics pipeline that implements permutation-based parameter optimization to guide quality control filtering and cohort-specific CH identification. We benchmark qcCHIP under various data settings, including different sequencing depths, ranges of cohort sizes, with and without normal-tumor paired samples, and across different cancer types. We show that qcCHIP allows users to customize analysis needs to generate CH calls based on cohort-specific data characteristics.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>qcCHIP R package is freely accessible at GitHub https:\/\/github.com\/tenglab\/qcCHIP and DOI: 10.5281\/zenodo.16421861.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf522","type":"journal-article","created":{"date-parts":[[2025,9,19]],"date-time":"2025-09-19T23:17:57Z","timestamp":1758323877000},"source":"Crossref","is-referenced-by-count":1,"title":["qcCHIP: an R package to identify clonal hematopoiesis variants using cohort-specific data characteristics"],"prefix":"10.1093","volume":"41","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7081-3694","authenticated-orcid":false,"given":"Xiang","family":"Liu","sequence":"first","affiliation":[{"name":"Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute , Tampa, FL 33612,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yi-Han","family":"Tang","sequence":"additional","affiliation":[{"name":"Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute , Tampa, FL 33612,","place":["United States"]},{"name":"Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute , Tampa, FL 33612,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James","family":"Blachly","sequence":"additional","affiliation":[{"name":"The Ohio State University Comprehensive Cancer Center , Columbus, OH 43210,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephen","family":"Edge","sequence":"additional","affiliation":[{"name":"Roswell Park Comprehensive Cancer Center , Buffalo, NY 14203,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yasminka A","family":"Jakubek","sequence":"additional","affiliation":[{"name":"University of Kentucky Markey Cancer Center , Lexington, KY 40536,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Martin","family":"McCarter","sequence":"additional","affiliation":[{"name":"University of Colorado Cancer Center , Aurora, CO 80045,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Abdul Rafeh","family":"Naqash","sequence":"additional","affiliation":[{"name":"University of Oklahoma Stephenson Cancer Center , Oklahoma City, OK 73104,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kenneth G","family":"Nepple","sequence":"additional","affiliation":[{"name":"University of Iowa Holden Comprehensive Cancer Center , Iowa City, IA 52242,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Afaf","family":"Osman","sequence":"additional","affiliation":[{"name":"University of Utah Huntsman Cancer Institute , Salt Lake City, UT 84112,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthew J","family":"Reilley","sequence":"additional","affiliation":[{"name":"University of Virginia Comprehensive Cancer Center , Charlottesville, VA 22903,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gregory","family":"Riedlinger","sequence":"additional","affiliation":[{"name":"Rutgers Cancer Institute , New Brunswick, NJ 08901,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bodour","family":"Salhia","sequence":"additional","affiliation":[{"name":"Norris Comprehensive Cancer Center, University of Southern California , Los Angeles, CA 90089,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bryan P","family":"Schneider","sequence":"additional","affiliation":[{"name":"Indiana University Simon Comprehensive Cancer Center , Indianapolis, IN 46202,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Craig","family":"Shriver","sequence":"additional","affiliation":[{"name":"Murtha Cancer Center , Bethesda, MD 20814,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michelle L","family":"Churchman","sequence":"additional","affiliation":[{"name":"Aster Insights , Hudson, FL 34667,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Robert J","family":"Rounbehler","sequence":"additional","affiliation":[{"name":"Aster Insights , Hudson, FL 34667,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4513-0282","authenticated-orcid":false,"given":"Jamie K","family":"Teer","sequence":"additional","affiliation":[{"name":"Department of Biostatistics and Bioinformatics, H. 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