TRACERx Renal dataset

[jjgao]

Three papers on the TRACERx Renal dataset:

• https://www.cell.com/cell/fulltext/S0092-8674(18)30389-1
• https://www.cell.com/cell/fulltext/S0092-8674(18)30375-1
• https://www.cell.com/cell/fulltext/S0092-8674(18)30164-8

Maybe we only need to curate one dataset for these three studies: ccrcc_tracerx_2018?

• [ ] create a issue on datahub before curating a study (one issue per study) and copy this checklist to the issue tracker
• [ ] List information of the dataset/paper in the issue, e.g. pmid, paper link, suppl file link
• [ ] Document the curation process, e.g. how and by whom the data was transformed
• [ ] Follow the data checklist
• [ ] Create a pull request to datahub once the data is curated
• [ ] Push to triage portal
• [ ] Import into msk and public portal database
• [ ] Update cBioPortal news

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This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

[stale[bot]]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

[yichaoS]

3 papers share the same ~100 patient pool. All data needs merging.

Question: do we merge the 3 panels into one?

For paper 1 - https://www.cell.com/cell/fulltext/S0092-8674(18)30389-1 Driver panels: Table S6 tab "Driver panels" ("∼110 putative ccRCC driver genes") Mutation data: Table S6 tab "SNV_INDEL_DNV" Arm-level somatic CNA: Table S6 "Arm-level SCNA" Clinical: Table S1A, Table S1D, Table S1E

For paper 2 - https://www.cell.com/cell/fulltext/S0092-8674(18)30375-1 Clinical - Table S1A, S1B Driver panels: Table S2 tab "Driver panels" Mutation data: Table S2 tab "SNV_INDEL_DNV" (this mutation data seems to include all the samples of paper 1 already and using the same sample - didn't confirm if the mutations are totally overlapped as well, need double checking) Arm-level somatic CNA: Table S2 "Arm-level SCNA" *there's further WES/WGS for a subset of samples, but the data is not available - don't think we need to ask for that data, seems like it's more for validation purpose?

For paper 3 - https://www.cell.com/cell/fulltext/S0092-8674(18)30164-8 Clinical - Table S1,S2 *they discovered "Novel hotspot of driver mutations in 5′-UTR repressor of TERT" (data not available tho), but since portal don't include those mutations, guess we don't need to ask for that data for now?

[stale[bot]]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.