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

IF 5.4

Bioinformatics (Oxford, England) Pub Date : 2025-09-01 DOI:10.1093/bioinformatics/btaf522

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

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Abstract

Summary: 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.

Availability and implementation: qcCHIP R package is freely accessible at GitHub https://github.com/tenglab/qcCHIP and DOI: 10.5281/zenodo.16421861.

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qcCHIP：一个R包，用于使用群体特异性数据特征识别克隆造血变异。

摘要：克隆造血（CH）是一种与健康个体和潜在疾病（包括癌症）患者的各种不良结局相关的分子生物标志物。检测CH通常涉及个体血液样本的基因组测序，然后进行强大的生物信息学数据过滤。我们报告了一个R包，qcCHIP，一个生物信息学管道，实现基于排列的参数优化，以指导质量控制过滤和特定队列的CH识别。我们在各种数据设置下对qcCHIP进行基准测试，包括不同的测序深度，队列大小范围，有和没有正常肿瘤配对样本，以及不同的癌症类型。我们表明，qcCHIP允许用户自定义分析需求，以基于队列特定数据特征生成CH调用。可用性：qcCHIP R包可在GitHub https://github.com/tenglab/qcCHIP和DOI: 10.5281/zenodo.16421861免费获得。补充信息：补充数据可在生物信息学在线获取。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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Bioinformatics (Oxford, England)

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