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Page History
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| Committee Member | Present | Absent |
|---|---|---|
| X | ||
| X | ||
| X | ||
| X | ||
| X | ||
| X | ||
| Elaine Ostrander | X | |
| Deborah Knapp | X | |
| Jeff Trent | X | |
| Dawn Duval | X | |
| Anju Singh | X | |
| Amy Leblanc | X | |
| Heather Gardner | ||
| Cheryl London | X | |
| Christina Mazcko | X | |
| Paula Jacobs | X | |
| Renee Chambers | X | |
| Shaying Zhao | X | |
| William Hendricks | X |
Outstanding Action Items
- Elaine to Kuffel, Gina (NIH/NCI) [C] to schedule Reuben Buckley to present at a future meeting
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| Item | Who | Notes |
|---|---|---|
| Revisit Committee Goals | Group Discussion |
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| ICDC User Research | Gina |
Meeting Minutes (Not Verbatim)
DK - Paper for standards that can be followed...the topic is extremely broad and we have not been able to narrow it down. Elaine has offered to put together an outline and assigning sections to committee members. This publication is dependent on several other publications that are not yet in press, the suggestion is to wait on the other pubs.
EO - The dog 10K group has worked hard and all sequences have been released except a few from S. America. They are publicly available. The VCF file including all of this data has been generated and is being tested. The dog 10K paper is being written right now and is being submitted in March. Breed validation and duplicates are being handled. The deadline for contributors is end of February. These sequences have been aligned to new GSD CanFam 4.0, not 3.1, however our group has also done the alignment to 3.1.
CL - If you don't have the normal, how can you call the variants to generate the VCF file?
EO - All variants have been called, 2 datasets, 1 for the 2000 sequences identified in the paper with strict filtering requirements and the confidence is high. We have 15,000 other sequences that we will call variants for. The file generated will be a VCF reference file that can be personalized.
CL - How accessible will this file be through the ICDC?
EO - Maybe a user guide from the 10K folks that can be made available through the ICDC.
CL - Breed prediction algorithm usability?
EO - Use a breed prediction algorithm to detect breed and then overlay
CL - Could we simplify and instead publish a review paper of cancer genomics where we are and where we are going and not be too prescriptive about methodologies. Leverage data for some comparative analysis. That would be something that is easier for us to write and it is still novel.
TH - and what we could end up doing in the future, we can think about this.
RC - This is a whole new dimension
CL - Digging into some of the research findings, a few years ago we were not able to leverage therapeutics available because little was known of genomic landscape. Many canine mutations share somatic mutations. Now that the database is more robust we can ask better questions. Look at genomics and inform the precision medicine.
RC - I think we need to come up with 3 questions and see if we have the data to answer those questions.
CL - Don't always need huge cohorts of patients, small groups can be used to look for large signals and if we are trying to move the needle we should be looking for big signals.
DK- What should the timeline be in regards to the 10K data?
EO - 10K is going to Genome Biology
TH - This is a different approach and different group of interests.
CL - 2 papers to flank Dog 10K, first design and test methodologies and applicability to precision medicine, second would be an overview of how the tools and resources for analyzing genomic data is changing (here are datasets that can be used, basic resources, guides, the new reference genome, etc.) solves the issue of calling variants differently, there is not an overall blueprint for analysis best practices and the space is filled with differing interpretations. This paper would not be prescriptive, it would be a review of available tools and datasets. The paper would be a Best Practices paper.
EO - We would need to engage folks from the 10K to get a good summary, this is not cancer specific. The project is not funded so we should keep that in mind.
DK - Working on a study that would add true normals to ICDC (right now we only have adjacent normals).
| Panel | ||
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Email for ICDC User ResearchSubject: Help NCI improve the NCI Canine Data Commons Content: Dear colleagues, If you or your colleagues work with large, structured, queryable comparative oncology data sets and related tools, NCI’s Integrated Canine Data Commons (ICDC) would like to meet with you. As part of NCI’s Cancer Research Data Commons, the ICDC provides cloud-based access to data from spontaneously occurring cancer in dogs. No prior experience with the portal is required, however they are interested in speaking with:
For those interested, interviews will be held between January 31 and February 4. Each participant will work with a moderator in a one-on-one remote interview that will last an hour. Participants will receive an honorarium for their time. Due to federal regulations, NCI staff, contractors, trainees, interns, and fellows are not eligible for an incentive. If you would like to meet with the ICDC team, please complete our short survey to get started. Thank you, Signature ### |
Action items
- Elaine to reach out to the Dog 10K group about making a user guide accessible
- Elaine to identify a point person from 10K group to provide summary of best practices
- Unknown User (114973298126195513658) to reach out Eileen Resnick
- Kuffel, Gina (NIH/NCI) [C] to send out User Research email to BPSC
