GDC TCGA: distinguishing samples that are not sequenced vs have no mutation calls

[Joshua Lau]

I’m working with the GDC TCGA LUAD dataset via the UCSC Xena Browser.

I noticed that there are 721 samples with phenotypic information, while the Ensemble Somatic Variant (WXS) file is a 194,731 × 12 table containing 577 unique samples. However, it is not clear whether 577 samples were successfully sequenced via WXS or if more were sequenced but do not appear in this table due to lacking somatic variants. 

Could you clarify how to distinguish between:
1. Samples that did not have WXS successfully performed, and
2. Samples for which WXS was performed but no somatic variants were detected?

For example, if gene X is altered in 100 patients, I’m unsure whether the appropriate denominator should be 577 (assuming all sequenced samples appear in the WXS file), or a larger number if some sequenced samples have no reported variants.

Thank you very much for your help!

Best regards,
Joshua Lau

[Mary Goldman]

Hi Joshua,

Great question! For all data from the GDC, the number of samples is the number of samples that successfully underwent WXS sequencing. There are no samples that were successfully sequenced but are not included in the .tsv file. So in this case, there are 577 samples that successfully underwent WXS sequencing.

Please let us know if you have any questions.

Best,

Mary

-----

Mary Goldman (she/her), Design and Outreach Engineer 

UCSC Xena

UC Santa Cruz Genomics Institute

Revealing life's code

--
You received this message because you are subscribed to the Google Groups "UCSC Xena and Cancer Genomics Browser" group.
To unsubscribe from this group and stop receiving emails from it, send an email to ucsc-cancer-genomics...@googlegroups.com.
To view this discussion visit https://groups.google.com/d/msgid/ucsc-cancer-genomics-browser/de66ab62-082c-4931-a6de-a75eba47b93dn%40googlegroups.com.