ASCAT

Allele-Specific Copy number Analysis of Tumors

Welcome to the ASCAT web site

ASCAT is a tool for accurate dissection of genome-wide allele-specific copy number in tumors. ASCAT accounts for normal cell admixture and tumor aneuploidy in the analysis of SNP array data from cancer samples. ASCAT allows analysis of Illumina and Affymetrix SNP array data of tumor samples (with or without matching germline samples).

Here you can find the ASCAT software suite, as well as example SNP array data to try out ASCAT and Illumina 109k SNP array data of 112 matched breast carcinomas.

ASCAT 2.1

ASCAT 2.1 is the latest version (January 2012) of the previously published ASCAT software. The main improvements over version 1.0 are:

All the software is now available in an easy-to-use and coherent R software suite (2.0).

There are major improvements in computational speed (2.0).

The new version works for all SNP-array platforms (2.0).

The core algorithm is updated for better performance (2.0).

A new option is available to perform analysis of tumor samples without matched normal data (2.0).

The segmentation algorithm has been adapted to increase sensitivity in samples with low noise and to increase robustness in more noisy samples (2.1).

Click here to download a zip-file containing the R script for ASCAT 2.1, the ASPCF segmentation algorithm and the plug-in for running ASCAT on tumor samples without matching germline data.

To use ASCAT 2.1 with matched normal data:

   source("ascat.R")
   ascat.bc = ascat.loadData("Tumor_LogR.txt","Tumor_BAF.txt","Germline_LogR.txt","Germline_BAF.txt")
   ascat.plotRawData(ascat.bc)
   ascat.bc = ascat.aspcf(ascat.bc)
   ascat.plotSegmentedData(ascat.bc)
   ascat.output = ascat.runAscat(ascat.bc)

To use ASCAT 2.1 without matched normal data:

   source("ascat.R")
   ascat.bc = ascat.loadData("Tumor_LogR.txt","Tumor_BAF.txt")
   ascat.plotRawData(ascat.bc)
   source("predictGG.R")
   platform = "AffySNP6"
   ascat.gg = ascat.predictGermlineGenotypes(ascat.bc, platform)
   ascat.bc = ascat.aspcf(ascat.bc,ascat.gg=ascat.gg)
   ascat.plotSegmentedData(ascat.bc)
   ascat.output = ascat.runAscat(ascat.bc)

Platforms currently supported are: "Affy100k", "Affy250k_sty", "Affy250k_nsp", "Affy500k", "AffySNP6", "AffyOncoScan", "Illumina109k", "IlluminaCytoSNP", "Illumina610k", "Illumina660k", "Illumina700k", "Illumina1M" and "Illumina2.5M". For the example data below, a "Custom10k" platform is also included. If you would like to run ASCAT without matched normal data on another platform, and are prepared to send over some sample data, please contact us.

Example data

A zip-file with simulated example data to try out ASCAT can be found here. The data simulates 100 samples of a custom made 10k array.

Data

Breast carcinoma SNP array data are available. The data consists of the Log R values and B-Allele frequencies for the germline SNP array data, as well as Log R values and B-Allele frequencies for the tumor (breast carcinoma) SNP array data. We also include tumor LogR data after adjustment for GC bias using the method described in Diskin et al. Nucleic Acids Research, 36:e126, 2008, as we find that this significantly improves the performance of ASCAT.
Due to privacy regulations, the data are password protected. Please contact us to obtain access.

Older ASCAT versions

ASCAT 1.0

ASCAT 1.0 is the original version of the ASCAT software, as published in Allele-specific copy number analysis of tumors by Peter Van Loo, Silje H. Nordgard, Ole Christian Lingjærde, Hege G. Russnes, Inga H. Rye, Wei Sun, Victor J. Weigman, Peter Marynen, Anders Zetterberg, Bjørn Naume, Charles M. Perou, Anne-Lise Børresen-Dale, and Vessela N. Kristensen. Proceedings of the National Academy of Sciences of the USA, 107:16910-16915, 2010. Click here to download the ASPCF algorithm written in Matlab used to segment the data prior to running ASCAT. The main function is aspcf.m. Click here to download the ASCAT 1.0 algorithm written in R. The main function is runASCAT. You can also download a script in R used to apply ASCAT 1.0 to the breast carcinoma data, which demonstrates how ASCAT may be applied to data in practice.

Breast carcinoma SNP array results using ASCAT 1.0 may be downloaded and consists of results of applying the ASPCF algorithm to the breast carcinoma SNP array data and allelic skewness estimates, including counts, skewness percentage and p-values.

ASCAT 2.0

Click here to download a zip-file containing the R script for ASCAT 2.0 (June 2011), the ASPCF segmentation algorithm and the plug-in for running ASCAT on tumor samples without matching germline data.

Which ASCAT version should I use?

We recommend to always use the latest ASCAT version. For exact reproduction of the findings in our original study (ASCAT version 1.0) or in other published studies, other ASCAT versions may however by useful.

How to cite ASCAT?

Allele-specific copy number analysis of tumors by Peter Van Loo, Silje H. Nordgard, Ole Christian Lingjærde, Hege G. Russnes, Inga H. Rye, Wei Sun, Victor J. Weigman, Peter Marynen, Anders Zetterberg, Bjørn Naume, Charles M. Perou, Anne-Lise Børresen-Dale, and Vessela N. Kristensen. Proceedings of the National Academy of Sciences of the USA, 107:16910-16915, 2010.