copy number annotation with SEG and MAF

Question

[yana]

Hi; Is it possible to obtain :

• minor allele copy number,
• major allele copy number
• total copy number of segmented chromosome
• tumor ploidy

from TCGA SEG and/or MAF files?

Thanks

Answer 1

[Kevin Blighe]

'MAF files', in this context, likely means Mutation Annotation Format files - correct?

You have mentioned multiple things that you want to obtain, yet, what background research have you conducted? The open access (Level 3) TCGA segment data is derived from Affymetrix SNP 6.0 arrays and contains segment means - I believe they used Circular Binary Segmentation (CBS) to derive these. Broad Institute then further processed this data using GISTIC 2.0 to derive copy number: http://firebrowse.org/

It sounds like you want to determine allele-specific copy number, in which case you should look at Allele-Specific Copy number Analysis of Tumours (ASCAT): https://www.crick.ac.uk/research/labs/peter-van-loo/software

Kevin