De La Vega Francisco M, Irvine Sean A, Anur Pavana, Potts Kelly, Kraft Lewis, Torres Raul, Kang Peter, Truong Sean, Lee Yeonghun, Han Shunhua, Onuchic Vitor, Han James
Tempus AI, Inc., Chicago, IL 60654, United States.
Department of Biomedical Data Sciences, Stanford University School of Medicine, Palo Alto, CA 94304, United States.
Bioinform Adv. 2025 Apr 10;5(1):vbaf071. doi: 10.1093/bioadv/vbaf071. eCollection 2025.
Whole-genome sequencing (WGS) is increasingly preferred for clinical applications due to its comprehensive coverage, effectiveness in detecting copy number variants (CNVs), and declining costs. However, systematic evaluations of WGS CNV callers tailored to germline clinical testing-where high sensitivity and confirmation of reported CNVs are essential-remain necessary. Clinical reporting typically emphasizes CNVs affecting coding regions over precise breakpoint detection. This study benchmarks several short-read WGS CNV detection tools using reference cell lines to inform their clinical use.
While tools vary in sensitivity (7%-83%) and precision (1%-76%), few meet the sensitivity needed for clinical testing. Callers generally perform better for deletions (up to 88% sensitivity) than duplications (up to 47% sensitivity), with poor detection of duplications under 5 kb. Notably, for CNVs in genes commonly included in clinical panels, significantly improved sensitivity and precision were observed when benchmarking against 25 cell lines with known CNVs. DRAGEN v4.2 high-sensitivity CNV calls, post-processed with custom filters, achieved 100% sensitivity and 77% precision on the optimized gene panel after excluding recurring artifacts. This level of performance may support clinical use with orthogonal confirmation of reportable CNVs, pending validation on laboratory-specific samples.
The data underlying this article are available in the European Nucleo-tide Archive under project accession PRJEB87628.
全基因组测序（WGS）因其全面的覆盖范围、检测拷贝数变异（CNV）的有效性以及成本的下降，在临床应用中越来越受到青睐。然而，针对种系临床检测量身定制的WGS CNV调用者的系统评估仍然是必要的，在种系临床检测中，高灵敏度和对报告的CNV的确认至关重要。临床报告通常更强调影响编码区域的CNV，而不是精确的断点检测。本研究使用参考细胞系对几种短读长WGS CNV检测工具进行了基准测试，以指导它们的临床应用。
虽然各工具在灵敏度（7%-83%）和精度（1%-76%）方面存在差异，但很少有工具能满足临床检测所需的灵敏度。调用者对缺失的检测通常比对重复的检测表现更好（灵敏度高达88%），对小于5 kb的重复检测效果较差。值得注意的是，对于临床检测板中通常包含的基因中的CNV，在对25个已知CNV的细胞系进行基准测试时，观察到灵敏度和精度有显著提高。使用定制过滤器进行后处理的DRAGEN v4.2高灵敏度CNV调用，在排除重复伪影后，在优化的基因检测板上实现了100%的灵敏度和77%的精度。在实验室特定样本上进行验证之前，这种性能水平可能支持在对可报告的CNV进行正交确认的情况下用于临床。
本文所依据的数据可在欧洲核苷酸档案馆获取，项目登录号为PRJEB87628。
