CNAqc

CNAqc performs computational validation of clonal and subclonal copy number alterations detected from bulk DNA sequencing using an evolution-inspired method.

Key Features:

• Quality Control for Somatic Data: CNAqc supports automated quality control procedures for tumor somatic data validation.
• Single-Cell Validation: CNAqc is validated using single-cell data and simulations.
• Large-Scale Application: CNAqc is applied to over 4000 TCGA and PCAWG samples.
• Clinical Integration: CNAqc is incorporated into the validation process for the clinically accredited bioinformatics pipeline at Genomics England.

Scientific Applications:

• Copy Number Alteration Validation: CNAqc computationally validates clonal and subclonal copy number alterations from bulk tumor sequencing data.
• Cancer Genomics Research: CNAqc enables quality-controlled analysis of cancer sequencing data across large cohorts such as TCGA and PCAWG.
• Clinical Bioinformatics Pipeline Integration: CNAqc serves as a validation component in clinically accredited somatic variant detection workflows.

Methodology:

CNAqc uses an evolution-inspired method to perform computational validation of clonal and subclonal CNAs detected from bulk DNA sequencing, addressing challenges from unknown sample purity, tumor ploidy, and intra-tumor heterogeneity.