A systematic benchmark of copy number variation detection tools for high density SNP genotyping arrays

IF 3.4 2区生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Genomics Pub Date : 2024-11-01 DOI:10.1016/j.ygeno.2024.110962

M.N. van Baardwijk , L.S.E.M. Heijnen , H. Zhao , M. Baudis , A.P. Stubbs

引用次数: 0

Abstract

Copy Number Variations (CNVs) are crucial in various diseases, especially cancer, but detecting them accurately from SNP genotyping arrays remains challenging. Therefore, this study benchmarked five CNV detection tools—PennCNV, QuantiSNP, iPattern, EnsembleCNV, and R-GADA—using SNP array and WGS data from 2002 individuals of the DRAGEN re-analysis of the 1000 Genomes project. Results showed significant variability in tool performance. R-GADA had the highest recall but low precision, while PennCNV was the most reliable in terms of precision and F1 score. EnsembleCNV improved recall by combining multiple callers but increased false positives. Overall, current tools, including new methods, do not outperform PennCNV in precise CNV detection. Improved reference data and consensus on true positive CNV calls are necessary. This study provides valuable insights and scalable workflows for researchers selecting CNV detection methods in future studies.

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高密度 SNP 基因分型阵列拷贝数变异检测工具的系统基准。

拷贝数变异（CNV）在各种疾病尤其是癌症中至关重要，但从 SNP 基因分型阵列中准确检测 CNV 仍是一项挑战。因此，本研究利用千人基因组计划 DRAGEN 再分析 2002 个个体的 SNP 阵列和 WGS 数据，对五种 CNV 检测工具--PennCNV、QuantiSNP、iPattern、EnsembleCNV 和 R-GADA 进行了基准测试。结果显示，工具性能存在很大差异。R-GADA 的召回率最高，但精确度较低，而 PennCNV 在精确度和 F1 分数方面最为可靠。EnsembleCNV 通过结合多个调用者提高了召回率，但增加了假阳性。总体而言，包括新方法在内的现有工具在精确 CNV 检测方面并没有超过 PennCNV。有必要改进参考数据并就真阳性 CNV 调用达成共识。这项研究为研究人员在未来的研究中选择 CNV 检测方法提供了宝贵的见解和可扩展的工作流程。

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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来源期刊

Genomics 生物-生物工程与应用微生物

CiteScore

9.60

自引率

2.30%

发文量

260

审稿时长

60 days

期刊介绍： Genomics is a forum for describing the development of genome-scale technologies and their application to all areas of biological investigation. As a journal that has evolved with the field that carries its name, Genomics focuses on the development and application of cutting-edge methods, addressing fundamental questions with potential interest to a wide audience. Our aim is to publish the highest quality research and to provide authors with rapid, fair and accurate review and publication of manuscripts falling within our scope.