Handling of donors with multiple specimens or samples in donor-centric ICGC cohort

[David Wissel]

Dear UCSC Xena Team,

first of all, a big thank you for making this amazing resource available!

I have a question related to the handling of multiple specimens or samples in the donor-centric cohort of ICGC, specifically for copy number somatic mutation and somatic coding mutations. 

As far as I can tell from the "raw" data available from the ICGC data portal, for specific projects, some donors had multiple specimens and/or samples taken which in turn lead to duplicates in the somatic mutation and/or copy number data. I am finding these somewhat tricky to handle since it is not always apparent whether two specimens were taken at the same time or not.

I noticed that you only report donor id in your files in the donor-centric cohort, thus I was wondering how you dealt with these replicates?

Thank you very much in advance and best

David

[Mary Goldman]

Hi David,

So glad Xena works well for you!

I added some help text to better explain how we combine data across specimens to the page https://xenabrowser.net/datapages/?cohort=ICGC%20(donor%20centric). The short is that we didn't take into account different collection time points. Here is the text:

-------------

The genomic data in this cohort was combined for all specimens from a donor. For the segmented copy number data, all segments were put into one file and then displayed. All averaging happens in the display. For the mutation data, all mutations were put into a single file and then displayed. All mutations from all specimens are displayed together. The gene expression and -protein expression is for US projects only and hence no combining was needed.

------------

If there is other information I can provide, let me know.

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 on the web visit https://groups.google.com/d/msgid/ucsc-cancer-genomics-browser/71c67cd0-5f68-4310-bdd2-ba546528be12n%40googlegroups.com.