Tumor ploidy determination in low-pass whole genome sequencing and allelic copy number visualization using the Constellation Plot

IF 10.1 1区生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Genome Biology Pub Date : 2025-05-20 DOI:10.1186/s13059-025-03599-2

Sarah H. Johnson, James B. Smadbeck, Roman M. Zenka, Michael T. Barrett, Athanasios Gaitatzes, Arnav Solanki, Angela B. Florio, Mitesh J. Borad, John C. Cheville, George Vasmatzis

引用次数: 0

Abstract

Ploidy determination across the genome has been challenging for low-pass-WGS tumor-only samples. We present BACDAC, a method that calculates tumor ploidy down to 1.2X effective tumor coverage. Allele fraction patterns displayed in the Constellation Plot verify tumor ploidy and reveal subclonal populations. BACDAC outputs a metric, 2N+LOH, that when combined with ploidy better distinguishes near-diploid from high-ploidy tumors. Validated using TCGA, BACDAC had good agreement with other methods and 88% agreement with experimental methods. Discrepancies occur mainly when BACDAC predicts diploidy with subclones rather than high-ploidy. Applied to 653 low-pass-WGS samples spanning 12 cancer subtypes, BACDAC calls 40% as high-ploidy.

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低通全基因组测序中的肿瘤倍性测定和使用星座图的等位基因拷贝数可视化

对于低通wgs肿瘤样本，整个基因组的倍性测定一直具有挑战性。我们提出BACDAC，一种计算肿瘤倍性到1.2倍有效肿瘤覆盖率的方法。星座图中显示的等位基因分数模式证实了肿瘤的倍性，并揭示了亚克隆群体。BACDAC输出一个指标，2N+LOH，当与倍性结合时，可以更好地区分近二倍体和高倍性肿瘤。经TCGA验证，BACDAC与其他方法的一致性较好，与实验方法的一致性达88%。差异主要发生在BACDAC预测具有亚克隆的二倍体而不是高倍性时。BACDAC应用于653个低通wgs样本，涵盖12种癌症亚型，其中40%为高倍性。

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

Genome Biology Biochemistry, Genetics and Molecular Biology-Genetics

CiteScore

21.00

自引率

3.30%

发文量

241

审稿时长

2 months

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