cBioPortal: Out of date mapping?

[Metitiri, Ediri E]

Hi cBioPortal,

 

How are you? I recently discovered cBioPortal and I am really impressed with its interactive format. However, I noticed today while investigating aspects of the TCGA-KIRC Firehouse results that the current IGV is incorrectly mapped to hg19 and not to the most updated hg38 (see attached).

 

Could the locations to detected SNPs via cBioPortal in fact have incorrect locations?

How do I update the IGV to display SNP locations mapped to the most current hg38 for the correct SNP locations?

 

Thanks, I look forward to your response.

 

Warm regards,

 

Ediri Metitiri, MSc

PhD Candidate – Rodriguez Lab

Department of Medical Education

Integrated Biomedical Sciences Program

UT Health San Antonio

8403 Floyd Curl Dr., Rm. 276

San Antonio, TX 78229

meti...@livemail.uthscsa.edu

 

 

[debr...@mskcc.org]

Hi Ediri,

 

Thanks for reaching out!

 

Although the cBioPortal software supports hg38 the currently available public datasets are all based on hg19. We unfortunately don’t provide any tools for on the fly remapping to hg38

 

There are some online tools like LiftOver to help with this if you need to remap a handful of variants:

 

https://genome.ucsc.edu/cgi-bin/hgLiftOver

 

As a workaround one can e.g. download the mutation table, put it in liftOver and open it in IGV.

 

That said the majority of the mutation, copy number and expression data is actually pretty concordant between hg19 and hg38 as described in Gao et al 2019. So it depends a bit on your use case how important the use of hg38 is

 

Let us know if you have any other questions or if you’d like us to clarify anything

 

Thanks!

Ino

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