Single residue and in-frame indel mutation hotspots identified in 24,592 tumor samples by the algorithm described in [Chang et al. 2017] and [Chang et al. 2016] ->
Caution: this is a beta portal showing unvetted single residue mutation hotspot results. The hotspots have been identified in 40K MSK-IMPACT sequenced samples using the algorithm described in [Chang et al. 2017] and [Chang et al. 2016]
[ ] Show that this is V3 instead of V2 in the download tab. Ideally we can host both V2 and V3
[ ] The default ordering of hotspots does not list NRAS first. Seems like cancerhotspots.org sorts first by type of mutation (single residue vs inframe del), then q-value, but not entirely sure. According to Onur it probably uses the sorting from the data file
Other ideas:
[ ] add some columns to indicate in which cohort it was identified, (v1, v2 & v3)
[ ] add column that shows median number of mutations in samples with that hotspot (even better maybe small distribution lineplot)
[ ] add some icon (e.g. + or ) or column so we can see new genes (e.g. +) and old genes with new hotspots (e.g. ). This would allow us to easily search for them
[ ] Add a graphical representation of the tumor type distribution. In addition to the number, add a stacked bar chart with color coded tumor types adding up to 100%, just like what we have for the variants column.
Data updates:
[ ] We are missing the individual organ composition count for each variant (somehow some do show up, but that's maybe b/c of merging in the published results in some way?)
[ ] Make separate categories for missense, splice, nonsense and inframe-indel
[ ] add inframe indel mutations
[x] some issue with the counts for KRAS G12 (6012 lung vs 5520 total?)
[x] Tumor type count is off
[x] maybe do a run with excluding TMB > 50 (removed hypermutants)
[x] Add more info
Single residue and in-frame indel mutation hotspots identified in 24,592 tumor samples by the algorithm described in [Chang et al. 2017] and [Chang et al. 2016]->Caution: this is a beta portal showing unvetted single residue mutation hotspot results. The hotspots have been identified in 40K MSK-IMPACT sequenced samples using the algorithm described in [Chang et al. 2017] and [Chang et al. 2016][ ] Show that this is V3 instead of V2 in the download tab. Ideally we can host both V2 and V3
[ ] The default ordering of hotspots does not list NRAS first. Seems like cancerhotspots.org sorts first by type of mutation (single residue vs inframe del), then q-value, but not entirely sure. According to Onur it probably uses the sorting from the data file
Other ideas:
Data updates:
[ ] We are missing the individual organ composition count for each variant (somehow some do show up, but that's maybe b/c of merging in the published results in some way?)
[ ] Make separate categories for missense, splice, nonsense and inframe-indel
[ ] add inframe indel mutations
[x] some issue with the counts for KRAS G12 (6012 lung vs 5520 total?)
[x] Tumor type count is off
[x]
maybe do a run with excluding TMB > 50(removed hypermutants)[ ] Too many ALK mutations
[ ] ACVR1 very low counts