biostudies-literatureLiu XNCI NIH HHSNIGMS NIH HHSBiostatistics and Bioinformatics Shared Resourcebtaf522https://www.ebi.ac.uk/biostudies/studies/S-EPMC12466928biostudies-literatureUnknown41(9)<h4>Summary</h4>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-sBioinformatics (Oxford, England)qcCHIP: an R package to identify clonal hematopoiesis variants using cohort-specific data characteristics.PMC12466928R01 CA268973P30 CA076292R35 GM155298Osman AMcCarter MSchneider BPNepple KGRiedlinger GTang YHReilley MJGillis NTeer JKTeng MBlachly JNaqash ARLiu XSalhia BShriver CJakubek YAChurchman MLRounbehler RJEdge SfalseqcCHIP: an R package to identify clonal hematopoiesis variants using cohort-specific data characteristics.<h4>Summary</h4>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-s2025-01-01T00:00:00Z2025 Sep2026-05-01T03:18:36.418Z2026-05-01T03:10:39.398ZS-EPMC124669284097302710.1093/bioinformatics/btaf522