Where Can I Find Mutation Databases Specialized In Cancer?

Question

[Ahlam Ahmed]

I need mutated breast cancer genes for my analysis. So I'm bit confused whether there is an existing database which consists of sequences having mutations in it. Is there any database to get the mutated & non-mutated gene sequence?

Answer 1

[Malachi Griffith]

Here are some related resources that are focused on somatic mutations in cancer:

DOCM - Database of Curated Mutations

CIViC - Clinical Interpretation of Variants in Cancer

BioStars post: CIViC - Clinical Interpretation of Variants in Cancer

BioStars post: Exploring cancer mutation data portals

Here is another generally relevant post: Database Of Tumor Suppressors And/Or Oncogenes

Answer 2

[Sean Davis]

I'd suggest starting with COSMIC and ICGC.

[Ahlam Ahmed]

Thank you SEAN but, it doesn't contain information for many other genes like BRCA1 & BRCA2

[Sean Davis]

The databases I noted above are about somatic mutation, not germline mutation. Were you looking for somatic mutation databases or germline variants?

[Chirag Nepal]

Hi Sean, Does COSMIC have the information about somatic mutation ? Can you please point to the URL. I only found information at the gene level (cancer consensus genes). Thank you !!

PS: The link is here: http://cancer.sanger.ac.uk/cosmic/download

Answer 3

[raunakms]

Here are few such databases:

• Sanger: Cancer Gene Census
• Sanger: COSMIC
• Somatic Mutations in Epidermal Growth Factor Receptor DataBase
• IARC TP53 Database
• Breast Cancer Information Core - An on-line breast cancer mutation database. This is an international collaboration hosted by the NIH National Human Genome Research Institute. The Web site includes the database (requires registration), laboratory methods, forum and resources.

[Ahlam Ahmed]

Thnaks RAUNAK, but I didn't find any database about 187_189delAG and 5382insC in BRCA1and 6174delT in BRCA2.

Answer 4

[sue.mockus]

Newly released: jax.org/ckb

Answer 5

[Sean Davis]

Perhaps not a direct answer, but take a look at:

https://github.com/seandavi/awesome-cancer-variant-databases

Answer 6

[Rashedul Islam]

cBioPortal has mutation data for different cancer types including breast.

http://www.cbioportal.org/