2020-05-11 DGAB Meeting notes

Notes from today:
Reviewed current status of studies
-Glioma done from case point of view, migrating data from SRA to ICDC bucket.
-COTC007b reannotated and reloaded.
-NCATS resubmitting with annotations per new guidelines and getting BAM files to replace FASTA files.
-Vemurifinab - working on aligning data with guidelines. Coming along nicely. Sequences already in GEO - need to be transferred to ICDC.
-Knapp cross-sectional study - starting alignment with guidelines. Sequences already in GEO - need to be transferred to ICDC.
-Shaying - not started yet.

Maps nicely to existing data model. Uses existing annotations on sample level not previously used, but anticipated (primary tumor vs. metastatic tumor). WGS, WES and RNA-seq data for 59 dogs. Very like the Glioma study. Osteosarcoma.
Matthew Breen is interested in quality scores since Osteosarcoma is notoriously difficult to work with.
Do these samples come from CCOGC? Tawa/Breen. Ohio/Colorado - Canine Comparative Oncology Group Cortortium. $2M project to collect 7 types of cancer. Specimens submitted to Frederick repository. Samples given to Ohio/Colorado to analyze (P30 grantees). May be duplicated from multiple sites analyzing the same samples. Must icluded CCOGC identifiers to be able to track unique samples.
***Need to ask Heather if these are CCOGC samples.
Lymphoma, Melanoma, Osteosarcoma.
Loop in Amy/Christina to compare against who got what. Provide this list to submitters to compare against. Need to know from where the samples originated.
SRA does not show other identifiers.
***Ask Heather and Will if they know if these samples are from CCOGC. Matthew Breen will formulate question and email me.
Approved to entry.

publication: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6642146/

Does this jump Shaying's study?
Potential duplication in Osteosarcoma complicates the issues.

**Need to go back to previous projects and see if their samples could possible be in other repositories as well.
Maybe we should prioritize this to sort out the CCOGC issues (Tawa). Go back to other studies and request other identifiers (Kibbe).
Shaying may also have samples out of CCOGC.
Matthew Breen will contact Christina Mazcko and see if she can make available the CCB numbers for CCOGC. CCB numbers are supposed to be permanently attached to samples to be able to track.

Prioritization tabled until next meeting to give us time to answer the questions that came up today.

**Add question to submission questionairre - what is the source of these samples?