ASCAT

Overview

ASCAT (Allele-Specific Copy number Analysis of Tumors) is a computational method for deriving tumor-specific allele-specific copy-number profiles from SNP array or sequencing data. It models the total and allele-specific copy-number signal jointly with tumor purity (cellularity) and ploidy, producing locus-by-locus integer copy-number calls per allele. ASCAT explicitly accounts for the mixture of tumor and normal cells in a sample, enabling accurate estimation of loss of heterozygosity (LOH) and clonal copy-number changes.

Used by

  • Pereira et al. 2016 — METABRIC breast cancer landscape: Used to call LOH in 2,433 primary breast tumours from the METABRIC cohort; cancer-cell-fraction (CCF) estimates for clonality analysis relied on ASCAT purity/ploidy calls; the authors explicitly note that subclonal architecture is only approximated rather than directly reconstructed from ASCAT output PMID:27161491.
  • Used in TRACERx to derive copy number, purity, and ploidy from multi-region exome sequencing data of 327 primary NSCLC tumor regions PMID:28445469
  • Applied to SNP array data (175 CCA cases) to estimate allele-specific copy numbers; identified ERBB2 amplifications (average 14 copies in amplified cases) confirmed independently by FISH PMID:28667006

Notes

  • ASCAT is designed for matched tumor/normal pairs; accuracy depends on normal-sample purity for reference allele frequency estimation.
  • CCF estimates downstream of ASCAT are approximate — ASCAT provides purity/ploidy for CCF normalization but does not directly reconstruct subclonal trees.
  • ASCAT was originally developed for SNP-array data (Affymetrix SNP 6.0, Illumina Omni) and later extended to sequencing (ASCAT-seq, ASCAT-WGS).
  • Published by Van Loo et al. (2010, PNAS); widely applied across TCGA and PCAWG pan-cancer studies.

Sources

  • Van Loo P et al. (2010) Allele-specific copy number analysis of tumors. Proceedings of the National Academy of Sciences 107:16910–16915.
  • PMID:27161491

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