利用 CNAqc 计算验证来自肿瘤大样本测序的克隆和亚克隆拷贝数改变。

IF 12.3 1区生物学 Q1 Agricultural and Biological Sciences

Genome Biology Pub Date : 2024-01-31 DOI:10.1186/s13059-024-03170-5

Alice Antonello, Riccardo Bergamin, Nicola Calonaci, Jacob Househam, Salvatore Milite, Marc J Williams, Fabio Anselmi, Alberto d'Onofrio, Vasavi Sundaram, Alona Sosinsky, William C H Cross, Giulio Caravagna

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引用次数: 0

摘要

拷贝数改变（CNA）是癌症中最重要的遗传事件之一，但由于样本纯度、肿瘤倍性和肿瘤内异质性未知，从测序数据中检测CNA具有挑战性。在此，我们介绍一种受进化启发的方法--CNAqc，该方法可对从批量 DNA 测序中检测到的克隆和亚克隆 CNA 进行计算验证。CNAqc 利用单细胞数据和模拟进行了验证，已应用于 4000 多个 TCGA 和 PCAWG 样本，并已纳入英格兰基因组研究所临床认可的生物信息学管道的验证流程。CNAqc 设计用于支持肿瘤体细胞数据验证的自动质量控制程序。

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Computational validation of clonal and subclonal copy number alterations from bulk tumor sequencing using CNAqc.

Copy number alterations (CNAs) are among the most important genetic events in cancer, but their detection from sequencing data is challenging because of unknown sample purity, tumor ploidy, and general intra-tumor heterogeneity. Here, we present CNAqc, an evolution-inspired method to perform the computational validation of clonal and subclonal CNAs detected from bulk DNA sequencing. CNAqc is validated using single-cell data and simulations, is applied to over 4000 TCGA and PCAWG samples, and is incorporated into the validation process for the clinically accredited bioinformatics pipeline at Genomics England. CNAqc is designed to support automated quality control procedures for tumor somatic data validation.

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来源期刊

Genome Biology BIOTECHNOLOGY & APPLIED MICROBIOLOGY-GENETICS & HEREDITY

CiteScore

25.50

自引率

3.30%

发文量

审稿时长

14 weeks

期刊介绍： Genome Biology is a leading research journal that focuses on the study of biology and biomedicine from a genomic and post-genomic standpoint. The journal consistently publishes outstanding research across various areas within these fields. With an impressive impact factor of 12.3 (2022), Genome Biology has earned its place as the 3rd highest-ranked research journal in the Genetics and Heredity category, according to Thomson Reuters. Additionally, it is ranked 2nd among research journals in the Biotechnology and Applied Microbiology category. It is important to note that Genome Biology is the top-ranking open access journal in this category. In summary, Genome Biology sets a high standard for scientific publications in the field, showcasing cutting-edge research and earning recognition among its peers.