Question: Does the ALT phenotype co-occur with an enrichment in mutations in certain genes?
What methods do you plan to use to accomplish the scientific goals?
As in panel B below, assess number of patients (not samples) with mutations in the following genes (to reproduce pedcbio panel): TP53, ATRX, H3F3A, NF1, TTN, PPMD1, RYR1, BCOR, PIK3CA, CRK.
I am assuming this gene list was not pre-defined and instead is a survey of all genes mutated, so it is possible after changing our sample list, and jenny redoes this in pedcbio, there might be a new gene list.
Update: use TP53, ATRX, H3F3A, NF1 only.
Another thought I had is to run mutational co-occurrence using HGAT ALT+ and HGAT ALT- as two separate histologies. This asks a different question, though - are there any differences in the co-occurring or mutually exclusive genes across these two groups? This can probably be run here quickly (using OpenPBTA methods).
jharenza
commented
2 years ago
What are the scientific goals of the analysis?
Question: Does the ALT phenotype co-occur with an enrichment in mutations in certain genes?
What methods do you plan to use to accomplish the scientific goals?
As in panel B below, assess number of patients (not samples) with mutations in the following genes (to reproduce pedcbio panel): TP53, ATRX, H3F3A, NF1, TTN, PPMD1, RYR1, BCOR, PIK3CA, CRK.
I am assuming this gene list was not pre-defined and instead is a survey of all genes mutated, so it is possible after changing our sample list, and jenny redoes this in pedcbio, there might be a new gene list.
Update: use TP53, ATRX, H3F3A, NF1 only.
Another thought I had is to run mutational co-occurrence using HGAT ALT+ and HGAT ALT- as two separate histologies. This asks a different question, though - are there any differences in the co-occurring or mutually exclusive genes across these two groups? This can probably be run here quickly (using OpenPBTA methods).
What input data are required for this analysis?
https://github.com/d3b-center/Cole-telomere-analysis/blob/f655ac13e4d383de4cba18dd3365b14b767b0d04/analyses/oncoplot/plot_oncoplot.R#L19
meta file
How long do you expect is needed to complete the analysis? Will it be a multi-step analysis?
by april 15?
Who will complete the analysis (please add a GitHub handle here if relevant)?
@runjin326
What relevant scientific literature relates to this analysis?