Copy Number Analysis

Summary

The Cancer Genome Project is using current high throughput techniques to characterise a series of cancer cell lines including those most frequently used in biological and pharmaceutical research and drug discovery. These screens include exome sequence analysis of the coding genome using the Agilent 50Mb bait set, and copy number analysis using the Affymetrix SNP6.0 array.

Copy number data has now been integrated in the COSMIC website and the old Copy Number Mapping page at http://www.sanger.ac.uk/genetics/CGP/cghviewer will no longer available from the end of October 2013.

Data

For CGP data, copy number analysis was carried out using the Affymetrix SNP6.0 array in conjunction with a bespoke algorithm (PICNIC: Predicting Integral Copy Numbers In Cancer).

Where available, copy number data from TCGA and ICGC have been included in COSMIC (for samples already present in the database ie samples with mutations). All TCGA data included in COSMIC has been reanalysed using ASCAT.

Definition of Gain and Loss:

  • ICGC: Gain and Loss as defined in the original data.
  • CGP Cell Lines (cell line exomes analysed with PICNIC)
    • Gain: total copy number ≥ 5 and minor allele > 0
    • Loss: minor allele = 0
  • TCGA (reanalysed with ASCAT):
    • Gain: total copy number ≥ average genome ploidy + 0.6
    • Loss: total copy number ≤ average genome ploidy - 0.6

Copy Number Analysis Tool

CONAN: A data mining tool to extract copy number information for predefined or user defined loci. The dataset includes all samples analysed using PICNIC or ASCAT where the total copy number and minor allele copy number are known. This replaces the previous version of CONAN at http://www.sanger.ac.uk/genetics/CGP/conan which will no longer available from the end of October 2013. For more information please see the CONAN help page.

Data Access

Copy number data for the Cell Line Project can be downloaded from our ftp site.

* quick link - http://q.sanger.ac.uk/dsoz3noh