MAF threshold in The Cancer Genome Atlas (TCGA) and Personal Genome Project (PGP)

Question

[fatmasayed93]

I am studying the minor allele frequency (MAF) over different datasets. Geneticists used to exclude SNPs with MAF under certain small values. In big databases and projects like 1000 genome-project (MAF=0.01) and HapMap-project (MAF=0.05), they've mentioned the value of the MAF threshold. I want to know the values of the MAF threshold adopted in The Cancer Genome Atlas (TCGA) and Personal Genome Project (PGP).

Answer 1

[Kevin Blighe]

For PGP, please inquire direct to the UK team at UCL: https://www.personalgenomes.org.uk/

For the TCGA, I am not sure that minor allele frequency was used for the purpose of filtering somatic variants. Please check the materials and methods of the published works relating to TCGA data.

Kevin