Pleasance et al. Pan-cancer analysis of advanced patient tumors reveals interactions between therapy and genomic landscapes. Nat Cancer, 2020.

[jjgao]

https://www.nature.com/articles/s43018-020-0050-6

This study contains the following data types:

• Mutations
• Copy number alterations
• Structural variants
• Gene expression
• Mutational signatures
• Survival
• Treatments
• Response to ICIs
• Any others?

To-do:

• [ ] create an 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 the default quick select study list see https://github.com/cBioPortal/cbioportal/issues/5831 (only for studies that are not overlapping with existing ones; only for human tumors, not cell lines)
• [ ] Update cBioPortal news

[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.

[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.

[rmadupuri]

Cohort Stats: 570 pats - profiled using whole-genome and transcriptome sequencing

Data Availability: Clinical data - Supp Table 1, 2 Mutation rates - Source Data Extended Data Fig. 2 Mutational Signatures - Source Data Extended Data Fig. 5 Germline variants - Source Data Extended Data Fig. 8

Genomic data available at: https://www.bcgsc.ca/downloads/POG570/ POG570_small_mutations.txt.gz - Complete list of somatic small mutations (SNVs and indels). POG570_TPM_expression.txt.gz: Expression by gene in TPM Table_S1_Demographics.xlsx - Cohort demographics Table_S2_Treatment.xlsx - Treatment and survival data Table_S7_Sequencing.xlsx - Sequencing parameters

Clinical and genomic data (MAF, CNA and Expression) split to multiple studies by cancer type is also available here: https://www.personalizedoncogenomics.org/cbioportal/. This studies can be downloaded & combined.

Status: Study can be curated from the supplemental data but I have also emailed the author (May 26, 2021) if they can share the combined dataset since it is already been transformed to portal formats in their local instance.

[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.

[rmadupuri]

The study is released at https://www.cbioportal.org/study/summary?id=pog570_bcgsc_2020.