SNP in a specific loci

Question

[rob.costa1234]

I want to check presence of SNPS in a one particular loci in TCGA data a one specific cancer. I was wondering is there any online toll that can provide me such information relatively quickly. I dont think Cbioportal can do this

Thanks Rob

[Matteo Schiavinato]

This question has been asked already in two posts:

• How can I obtain SNP from TCGA?
• TCGA SNP arrays

In none of them there seems to be an answer but you could first ask there to write how they solved it, since a couple of years have passed by.

Can this be of help? https://genomebiology.biomedcentral.com/articles/10.1186/gb-2011-12-4-r41

Also, a grammar nazi note: it's locus, when it's singular, loci is plural!

Answer 1

[Sean Davis]

A new feature in the NCI Genomic Data Commons allows searching for a specific somatic mutation (but NOT snp). Here is an example of a search for BRAF V600E.

http://bit.ly/2DVYyre

If you are looking for germline SNPs, you'll need to apply for TCGA data access and then grab variant files.