qcCHIP: an R package to identify clonal hematopoiesis variants using cohort-specific data characteristics.
Where this comes from
- Record sourced from PubMed, PMID 40973027.
- Also identified by DOI 10.1093/bioinformatics/btaf522 and PMC identifier 12466928.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
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.
Medical subject headings
- Clonal Hematopoiesis
- Software
- Computational Biology