Reddy et al., Diffuse Large B Cell Lymphoma, Cell 2017 (SEPTEMBER RELEASE)

[rmadupuri]

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

[rmadupuri]

Study identifier: dlbcl_duke_2017 PMID: 28985567

Curation Process:

Datatype	Source	Comments
Clinical	Table S1 (Sheet 1, 2)	1,001 patients
Mutation	Table S1 (Sheet 4)	WES
CNA	Table S1 (Sheet 5)	log2CNA

The Mutation table did not follow MAF file format. It was converted to MAF format programmatically based on the info given in the supporting sheet that 0 indicates absence and 1 indicates the presence of the variant.

NOTE: Only mutations in 150 genes identified as driver genes were released with this manuscript. All 1001 samples were sequenced and only 972 samples had atleast 1 mutation.

Checklist:

• [x] Does study name and study ID follow our convention? e.g. Tumor_Type (Institue, Journal Year); brca_mskcc_2015
• [x] Is study meta data complete? e.g. pmid, group of PUBLIC
• [x] Were all samples profiled with WES/WGS? If not, is gene panel file curated?
• [x] Are oncotree codes of all samples curated; Cancer Type and Cancer Type Detailed needs to be added in addition to Oncotree Code
• [x] Clinical sample and patient data with meta files
• [x] Mutations data with meta files
• [x] MAF is based on hg19
• [x] MAF with 2 isoforms: uniprot and mskcc
• [x] CNA data with meta files
• [ ] CNA segment data with meta files (NA)
• [ ] Expression data including z-scores with meta files (NA)
• [x] Case-lists for all profiles.
• [x] Passes Validation
• [x] Manual checking (Niki or JJ): Triage Portal