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d3b-center / OpenPedCan-analysis

The analysis repository for the Open Pediatric Cancer Project
https://d3b-center.github.io/OpenPedCan-analysis/
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Updated analysis: Update LGG FGFR1 mutations for FGFR subtype #614

Open jharenza opened 5 days ago

jharenza commented 5 days ago

What analysis module should be updated and why?

molecular subtyping LGAT

What changes need to be made? Please provide enough detail for another participant to make the update.

Ensure all of the following FGFR1 mutations are included, per the Ryall et al paper, and possibly pull just K656 amino acid since we are seeing many more changes at this site, per https://pedcbioportal.kidsfirstdrc.org/results/mutations?plots_horz_selection=%7B%7D&plots_vert_selection=%7B%7D&plots_coloring_selection=%7B%7D&tab_index=tab_visualize&Action=Submit&session_id=670e889cafce6a1f957f0944

FGFR1 p.N546K
FGFR1 p.K656E 
FGFR1 p.N546K
FGFR1 p.K654D
FGFR1 p.K654E
FGFR1 p.N544K
FGFR1 p.V559M
FGFR1 p.N544K
FGFR1 p.R659L
FGFR1 p.K687E

What input data should be used? Which data were used in the version being updated?

When do you expect the revised analysis will be completed?

Who will complete the updated analysis?

jharenza commented 5 days ago

@sangeetashukla table S3 in the pub here has these mutations I listed above.