Groups keyboard shortcuts have been updated
Dismiss
See shortcuts

IMPACT panel sizes

27 views
Skip to first unread message

Joris Vos

unread,
Sep 26, 2024, 8:33:54 AM9/26/24
to cBioPortal for Cancer Genomics Discussion Group
Hello!

I'm working with the TMB scores generated by cbioportal and am trying to figure out the panel sizes of the different iterations of MSK IMPACT. In other words, the denominator cbioportal uses to calculate the TMB scores. Could you tell me the size (in bases) of the following panels:
- IMPACT410
- IMPACT468
- IMPACT505

Thanks! Best wishes,

Joris Vos
Research Fellow, Luc Morris Lab



jagn...@gmail.com

unread,
Sep 27, 2024, 11:04:22 AM9/27/24
to cBioPortal for Cancer Genomics Discussion Group
Hi Jorios,

This information is available on cbioportal github.


Each gene panel has a separate file called data_gene_panel_***.txt. 
Inside the gene panel file, the data is available in the field number_of_profiled_coding_base_pairs

The values are
IMPACT410: 1021743 
IMPACT468: 1156473 
IMPACT505: 1218996

thanks
Jag

Joris Vos

unread,
Sep 28, 2024, 4:03:33 PM9/28/24
to cBioPortal for Cancer Genomics Discussion Group
Hi Jag,

Thanks! That's very helpful.

Have a great day,

Joris

Reply all
Reply to author
Forward
0 new messages