genome version in cbioportal

Question

[Arnaud Ceol]

Hi,

Anyone knows on which version of the human genome the data in the cbioportal is associated? I've downloaded mutations for several genes, but I've no idea whether they refer to hg18, hg19 or hg38, and didn't found any indication neither on the website nor on the forum.

thanks!

Answer 1

[Cyriac Kandoth]

Sorry that this isn't explicit on the portal. All variants in all studies use GRCh37.p13 loci and alleles. The autosomes and sex chromosome sequences are equivalent to hg19, but the mitochondrial DNA sequence is newer. Click here for details.

The effect of each variant is mapped to canonical isoforms per gene (as defined by Uniprot) in Gencode 19 using Ensembl's VEP with the vcf2maf and maf2maf wrappers that live here.

[echen1]

Hi Cyriac,

Your last post on this chat seemed to imply that TCGA mitochondrial DNA sequence mutations are available via cBioportal. But each time I enter in an mtDNA encoded gene (e.g. "MT-ND1" or "MTND1" or "ND1") in the cBioportal search box, the gene symbol pops up as invalid. Nuclear encoded mitochondrial genes (e.g. "SDHA") are searchable in the cBioportal search box for TCGA data. Thoughts? (is there another way to search, or does cBioportal just not have mtDNA encoded TCGA mutations?). Also, do you know if cBioportal offers the normal matched controls? And if we have permission/access to the private TCGA data, can we get it through cBioportal (I've downloaded the private data from CGHub, but I'm not a computer whiz, so I'd love to use the user-friendly cBioportal tools).

Thanks.

[khaimanij]

CGHub Database, as given in the paper (Database URL: https://cghub.ucsc.edu OR https://gdc.nci.nih.gov/) is unavailable. Any idea?