qcCHIP: An R package to identify clonal hematopoiesis variants using cohort-specific data characteristics

Xiang Liu; Yi-Han Tang; James Blachly; Stephen Edge; Yasminka A Jakubek; Martin McCarter; Abdul Rafeh Naqash; Kenneth G Nepple; Afaf Osman; Matthew J Reilley; Gregory Riedlinger; Bodour Salhia; Bryan P Schneider; Craig Shriver; Michelle L Churchman; Robert J Rounbehler; Jamie K Teer; Nancy Gillis; Mingxiang Teng

doi:10.1093/bioinformatics/btaf522

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qcCHIP: An R package to identify clonal hematopoiesis variants using cohort-specific data characteristics

Journal article

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qcCHIP: An R package to identify clonal hematopoiesis variants using cohort-specific data characteristics

Xiang Liu, Yi-Han Tang, James Blachly, Stephen Edge, Yasminka A Jakubek, Martin McCarter, Abdul Rafeh Naqash, Kenneth G Nepple, Afaf Osman, Matthew J Reilley, …

Bioinformatics (Oxford, England), Vol.41(9), btaf522

09/01/2025

DOI: 10.1093/bioinformatics/btaf522

PMCID: PMC12466928

PMID: 40973027

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Abstract

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. qcCHIP R package is freely accessible at GitHub https://github.com/tenglab/qcCHIP and DOI: 10.5281/zenodo.16421861. Supplementary data are available at Bioinformatics online.

Details

Title: Subtitle: qcCHIP: An R package to identify clonal hematopoiesis variants using cohort-specific data characteristics
Creators: Xiang Liu - Moffitt Cancer Center
Yi-Han Tang - Moffitt Cancer Center
James Blachly - The Ohio State University
Stephen Edge - Roswell Park Comprehensive Cancer Center
Yasminka A Jakubek - Markey Cancer Center
Martin McCarter - University of Colorado Denver
Abdul Rafeh Naqash - Oklahoma State University Oklahoma City
Kenneth G Nepple - University of Iowa
Afaf Osman - University of Utah
Matthew J Reilley - University of Virginia
Gregory Riedlinger - Rutgers, The State University of New Jersey
Bodour Salhia - University of Southern California
Bryan P Schneider - Indiana University Health
Craig Shriver - Murtha Cancer Center, Bethesda, MD 20814, United States
Michelle L Churchman
Robert J Rounbehler - Aster Insights, Hudson, FL 34667, United States
Jamie K Teer - Moffitt Cancer Center
Nancy Gillis - Moffitt Cancer Center
Mingxiang Teng - Moffitt Cancer Center
Resource Type: Journal article
Publication Details: Bioinformatics (Oxford, England), Vol.41(9), btaf522
DOI: 10.1093/bioinformatics/btaf522
PMID: 40973027
PMCID: PMC12466928
NLM abbreviation: Bioinformatics
ISSN: 1367-4811
eISSN: 1367-4811
Publisher: Oxford University Press
Grant note: NIGMS: R35 GM155298 NCI: R01 CA268973 Biostatistics and Bioinformatics Shared Resource at the Moffitt Cancer Center: NCI P30 CA076292
This work was supported in part by NIGMS R35 GM155298, NCI R01 CA268973, and the Biostatistics and Bioinformatics Shared Resource at the Moffitt Cancer Center by NCI P30 CA076292.
Language: English
Electronic publication date: 09/17/2025
Date published: 09/01/2025
Academic Unit: Urology
Record Identifier: 9984963625702771

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