Are there downloadable DBs for hotspot mutations?

Question

[agicict]

I want to know whether detected variants are hotspot mutations in TCGA or not.

Though cBioportal provides hotspot site for each gene, it doesn't provide download function.

Are there sites that provide hotspot mutation list or table?

Thank you

[Titus]

may be you are looking for that : http://cancer.sanger.ac.uk/cosmic

Answer 1

[agicict]

I found two sites providing hotspot information used in cbioportal. http://cancerhotspots.org/#/home http://3dhotspots.org/3d/#/home They are downloadable.

[poisonAlien]

adding to the list:

1. database of curated mutations http://docm.genome.wustl.edu

2. civic (mostly clinically actionable) : https://civic.genome.wustl.edu/home

Answer 2

[Samuel Brady]

I don't know of a database. But you can ask whether your specific mutations are recurrent by querying cBio over the web, using Python.

import urllib2 

# get information on breast cancer "brca" mutations in gene PIK3CA
cBioUrl = "http://www.cbioportal.org/webservice.do?cmd=getMutationData&genetic_profile_id=brca_tcga_mutations&gene_list=PIK3CA"

# read cBio to find PIK3CA mutation info in breast cancer, which you can parse to find recurrent mutations
cBioFile = urllib2.urlopen(cBioUrl)
recurrenceData = cBioFile.read()   # parse through the recurrenceData string (column "amino_acid_change")

The recurrenceData variable contains a list of samples with PIK3CA mutations, and the "amino_acid_change" column will tell you sites at which TCGA samples have mutations.

To scale this up, you would just make a loop where you replace the "PIK3CA" in cBioUrl with your gene of interest, and replace "brca" with your cancer type of interest. You can also query 19 common cancer types by looping through the following list in Python.

pancan19_cancerIDs = ["ov", "ucec", "gbm", "brca", "luad",
                                        "prad", "skcm", "stad", "paad", "cesc",
                                        "blca", "hnsc", "kirp", "lgg", "laml",
                                        "kirc", "thca", "lusc", "coadread"]

[agicict]

Thank you. I found two sites providing hotspot information used in cbioportal. http://cancerhotspots.org/#/home http://3dhotspots.org/3d/#/home They are downloadable.