Computational validation of clonal and subclonal copy number alterations from bulk tumor sequencing using CNAqc Journal Article
| Authors: | Antonello, A.; Bergamin, R.; Calonaci, N.; Househam, J.; Milite, S.; Williams, M. J.; Anselmi, F.; d’Onofrio, A.; Sundaram, V.; Sosinsky, A.; Cross, W. C. H.; Caravagna, G. |
| Article Title: | Computational validation of clonal and subclonal copy number alterations from bulk tumor sequencing using CNAqc |
| Abstract: | 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. © 2024, The Author(s). |
| Keywords: | single nucleotide polymorphism; genetics; polymorphism, single nucleotide; neoplasm; neoplasms; gene amplification; computational biology; pathology; validation study; mutational analysis; algorithms; automation; mathematical model; molecular evolution; clonal variation; algorithm; genomics; cell fractionation; heterozygosity loss; bioinformatics; mathematical computing; dna copy number variations; dna fragmentation; copy number variation; single cell analysis; procedures; dna sequencing; measurement accuracy; humans; human; article; oncogenomics; malignant neoplasm; measurement precision |
| Journal Title: | Genome Biology |
| Volume: | 25 |
| Issue: | 1 |
| ISSN: | 1465-6906 |
| Publisher: | Biomed Central Ltd |
| Date Published: | 2024-01-01 |
| Start Page: | 38 |
| Language: | English |
| DOI: | 10.1186/s13059-024-03170-5 |
| PUBMED: | 38297376 |
| PROVIDER: | scopus |
| PMCID: | PMC10832148 |
| DOI/URL: | |
| Notes: | Source: Scopus |
