ASCAT

ASCAT (allele-specific copy number analysis of tumors) is an R tool to dissect genome-wide allele-specific copy numbers in tumors using Affymetrix and Illumina single nucleotide (SNP) array data that may or may not include germline samples. The ASCAT algorithm differentiates typical cell admixture and tumor aneuploidy.

Topic

Oncology;Genomics;Human genetics

Detail

  • Operation: Genome visualisation;Copy number estimation

  • Software interface: Command-line user interface

  • Language: R

  • License: GNU General Public License v3

  • Cost: Free

  • Version name: 3.0.0/3.1

  • Credit: Norwegian Research Council, Functional Genomics-Norsk Forskningsråd (Norwegian Research Council) (FUGE-NFR) FUGE-NFR, Swizz Bridge Award, Research Foundation–Flanders (FWO), Institute for Cancer Research supported, the European Association for Cancer Research, Lillemor Grobstoks Legacy for Cancer Research, National Cancer Institute Breast Specialized Program of Research Excellence, the Breast Cancer Research Foundation, the V Foundation for Cancer Research.

  • Input: txt, .bc, .gg

  • Output: -

  • Contact: Tom Lesluyes tom.lesluyes@crick.ac.uk, Vessela N. Kristensen Vessela.N.Kristensen@rr-research.no, info@crick.ac.uk

  • Collection: -

  • Maturity: Stable

Publications

  • Allele-specific copy number analysis of tumors.
  • Van Loo P, Nordgard SH, Lingjærde OC, Russnes HG, Rye IH, Sun W, Weigman VJ, Marynen P, Zetterberg A, Naume B, Perou CM, Børresen-Dale AL, Kristensen VN. Allele-specific copy number analysis of tumors. Proc Natl Acad Sci U S A. 2010 Sep 28;107(39):16910-5. doi: 10.1073/pnas.1009843107. Epub 2010 Sep 13. PMID: 20837533; PMCID: PMC2947907.
  • https://doi.org/10.1073/pnas.1009843107
  • PMID: 20837533
  • PMC: PMC2947907

Download and documentation

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