TCGA people, you were too slow ;-) , the group wanting to use PGS to find polygenic risk scores for mortality in breast cancer took over this Friday

PGS

https://github.com/episphere/pgs

Notebook: https://observablehq.com/@episphere/pgs <-- start here

https://maialab.org/quincunx/articles/pgs-scoring-file.html

[1:44 PM] Breeze, Charles (NIH/NCI) [F]
SNP Effect_Allele Beta CHR POS EAF Other_Allele YREF YALT
1:218615451 C 0.0344 1 218615451 0.276873171 A A C
2:183219101 C 0.0166 2 183219101 0.575386521 A C A
4:123835656 C 0.0196 4 123835656 0.737956739 A C A
5:42436916 C 0.0382 5 42436916 0.0848 A A C
5:127696022 C 0.0234 5 127696022 0.367268678 A A C
7:137611566 C 0.0189 7 137611566 0.572721566 A A C
9:94258836 C 0.0159 9 94258836 0.272151476 A A C
9:100482976 C 0.0185 9 100482976 0.249428883 A C A

​

[1:46 PM] Breeze, Charles (NIH/NCI) [F]
SNP Effect_Allele Beta CHR POS EAF Other_Allele YREF YALT

--- original TCGA plan : being moved to a different Friday ---

(going over list of elected APIs, see initial session for links to github and observable notebooks)The Cancer Genome Atlas (TCGA) / Genomic Data Commons (GDC)

TCGA

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Genomic Data Commons (GDC)

The heir of all things TCGA, with a GraphQL API.

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FireBrowse

Directly from the Broad Institute: http://firebrowse.org. This is an hackathon favorite , after you set a proxy to handle lack of SLA (we set one at DCEG) ...

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cBio

Cancer Bio Portal provides access to TCGA data extended to other studies and datasets. We are set to have a full session dedicated to cBio. It probably offers the simplest REST APIs to access TCGA data.

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