This page provides links to the software used in the above paper to perform bivariate segmentation of SNP array data with the ASPCF algorithm and subsequent estimation of allele specific copy number aberrations in tumors with the ASCAT algorithm. In addition, links are provided to the breast carcinoma SNP array data analysed in the paper, in the format required by the software. For additional information about the data sets and algorithms, we refer to the paper.
Supplementary material for the paper:
Allele-specific copy number analysis of tumors
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#, Vessela N. Kristensen# (*,#: equal contribution).
PNAS, 2010 (www.pnas.org/cgi/doi/10.1073/pnas.1009843107)
The ASPCF algorithm is written in MatLab and the main function is aspcf.m. The ASCAT algorithm is written in R and the main function is runASCAT. You can also download a script in R used to apply ASCAT to the breast carcinoma data, which demonstrates how ASCAT may be applied to data in practice.
Breast carcinoma SNP array data are available below. However, due to privacy regulations, the data are protected by login/password. Please contact us to obtain access. 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.
Breast carcinoma SNP array results 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.