2020-04-03 Executive Team Meeting Notes

Date

03 Apr 2020

Attendees

• Kim, Erika (NIH/NCI) [E]Unknown User (hechtt)Otridge, John (NIH/NCI) [C]Singh, Anju (NIH/NCI) [E]Sommers, Connie (NIH/NCI) [E]Unknown User (leblancak)Unknown User (knappd@purdue.edu.commons)Unknown User (parchmentr)Mazcko, Christina (NIH/NCI) [E]Beyers, Matthew (NIH/NCI) [C]

Goals

• Breed-specific reference genomes – Debbie

  • Ask Elaine Ostrander if her lab would provide breed specific genome information - sequencing out of white blood cells (Normal).  Might need to do some spot checks of the sequences.  Debbie thinks there might be 800 sequences across different breeds.    Is there a specific genotyping that can be done to identify breeds? and how that determination was made?  Maybe she has enough data to share the AKC registered dog data.  Elinor Karlsson (Broad) has been working on genotyping different breeds.  Should we have a conversation with Elaine and Elinor together?  Debbie will talk to Elaine first and get her take.  John will reach out to Elinor to get some of her time sooner rather than later.  Broad has a reference genome that may be an aggregate across normal dogs.  They might have access to normal tissue and blood sequences.  Got samples from CCOG.  Difference between tissue and blood sequencing?  Only relevant difference if tissue has any relation to tumor tissue.  Would we accept tumor sequence without normal (blood) sequence as well?  The tumor sequence alone is not useful without a breed-specific reference genome.  These reference standards could really assist analysis for studies that do not provide a normal sequence.  Question: are we asking for raw data or variant calls from Elinor/Elaine?  Variant call file (from Elaine's reference genomes) can be used as a filtering mechanism.  Raw data files will require a variant processing pipeline in the cloud.  Could have variant call files for the different breeds.  Need to gain insight as to how Elaine/Elinor would expect someone to use the data.  Raw data files could lead to lack of standardization without a standard pipeline.  Suggestion is to use variant call files.

• ICDC Communications plan – Erika

  • OCPL/CBIIT/DCTD communications teams worked on a communication plan that was shared with everyone via email.  Erika will be drafting a paragraph describing the ICDC and requesting additional data sets and will distribute to the Executive Committee.

  • Request for data - from all submitters, regardless of publication status.  Start with NCI grantees (Anju is collating this list) and then reach out to wider list of organizations.

  • Potentially want to submit ICDC to this list of registries: https://www.nlm.nih.gov/NIHbmic/domain_specific_repositories.html.  General thought is that we need more clarity around data submission process first.

• Other - All 

  • Ralph discussed the draft minutes.  Approved to go out to the SC.

Action items

• Unknown User (knappd@purdue.edu.commons) to talk to Elaine about breed specific reference genomes
• Otridge, John (NIH/NCI) [C]  to talk to Elinor about potential for collaboration with Elaine
• Singh, Anju (NIH/NCI) [E]  to provide list of NCI grantees doing canine research to reach out to them to submit data
• Unknown User (parchmentr) to send out the draft minutes to the SC.
• Kim, Erika (NIH/NCI) [E] to write paragraph about ICDC and requesting additional data sets.