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

被引：3

作者：

Antonello, Alice ^{[2
]}

Bergamin, Riccardo ^{[2
]}

Calonaci, Nicola ^{[2
]}

Househam, Jacob ^{[1
]}

Milite, Salvatore ^{[2
,3
]}

Williams, Marc J. ^{[4
]}

Anselmi, Fabio ^{[2
]}

d'Onofrio, Alberto ^{[2
]}

Sundaram, Vasavi ^{[6
]}

Sosinsky, Alona ^{[6
]}

Cross, William C. H. ^{[5
]}

Caravagna, Giulio ^{[2
,7
]}

机构：

[1] Queen Mary Univ London, Evolut & Canc Lab, Ctr Genom & Computat Biol, Barts Canc Inst,Barts & London Sch Med & Dent, London, England

[2] Univ Trieste, Dept Math Informat & Geosci MIGe, Trieste, Italy

[3] Human Technopole, Ctr Computat Biol, Milan, Italy

[4] Mem Sloan Kettering, Dept Computat Oncol, New York, NY USA

[5] UCL, UCL Canc Inst, Dept Res Pathol, London, England

[6] Genom England, London, England

[7] Inst Canc Res, Ctr Evolut & Canc, Evolutionary Genom & Modelling Team, London, England

来源：

GENOME BIOLOGY | 2024年 / 25卷 / 01期

基金：

英国惠康基金;

关键词：

INTRATUMOR HETEROGENEITY; EVOLUTIONARY HISTORY; CANCER; RECONSTRUCTION; MUTATIONS; INFERENCE; TRACKING; IMPACT;

D O I：

10.1186/s13059-024-03170-5

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

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.

引用

页数：40

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