database of genetic alternations for inherited cancer

Question

[J.F.Jiang]

Hi all,

We are going to start up a project to investigate the possibility of get inherited cancer by screening genetic alternations of genes, e.g., BRCA1/BRCA2 for breast cancer.

However, how to annotate these SNVs might be quite difficult.

One convenient way is to compare the results with those published data to check whether the SNV might drive the cancer.

I know one comercial database is HGMD, is there any public database that I can check in terms of cancer type, such as breast cancer, colorectal cancer, ovarian cancer ...

Thanks

[wangjq]

Have you found the database?

Answer 1

[Giovanni M Dall'Olio]

Look at the International Cancer Genome Consortium's data portal. You can click on a cancer type and get the list of most frequently mutated genes. If you then click on the # of Mutations column to get the list of most frequent mutations.

[J.F.Jiang]

The ICGC is a large portal offering collected data from other large projects, such as TCGA.

However, what I am looking for is the genetic variation for cancer, not the somatic ones.

So either TCGA or ICGC is a good source for investigation.

Thanks.

Answer 2

[Mary]

Just today I was looking around COSMIC for something else, and found myself on their tabs variation data for a gene I happened to be looking into. They have a number of ways you can explore the data and you might find some useful things in there.

COSMIC main site: http://cancer.sanger.ac.uk

Recent paper about their project: http://nar.oxfordjournals.org/content/43/D1/D805.full

[J.F.Jiang]

Thanks, Mary.

The COSMIC database is a large complex union for cancer variation detection. However, it is also collected from those somatic mutations, but not the variants inherited.