2021-10-18-21 Best Practices Meeting Notes

Date

18 Oct 2021

Attendees

Committee Member	Present	Absent
Kuffel, Gina (NIH/NCI) [C]	X
Musk, Philip (NIH/NCI) [C]	X
Pihl, Todd (NIH/NCI) [C]		X
Unknown User (hechtt)	X
Kim, Erika (NIH/NCI) [E]	X
Sommers, Connie (NIH/NCI) [E]		X
Elaine Ostrander	X
Deborah Knapp		X
Jeff Trent		X
Dawn Duval	X
Anju Singh		X
Amy Leblanc	X
Heather Gardner	X
Cheryl London	X
Christina Mazcko	X
Paula Jacobs	X
Renee Chambers	X
Shaying Zhao	X
William Hendricks		X

Outstanding Action Items

Jeff Trent to confirm that Elaine is willing to take the lead on generating an outline for amplifying the white paper in preparation for publication
Kuffel, Gina (NIH/NCI) [C]to add invitee to meeting Sunetra.Das@colostate.edu
Kuffel, Gina (NIH/NCI) [C] to send email to Jeff Trent about identifying a point person.

Discussion items

Item	Who	Notes
Welcome & Roll Call	Gina Kuffel
New imputation paper	Elaine Ostrander	Best practices for low pass sequencing Link to paper on Box: https://nih.box.com/s/e86q5cithio6tfsu63rhq1vu0spg3btc Expected allele frequencies are an important factor
Alignment status of 1500 dog10K	Elaine Ostrander	Community using new German Shepherd reference from the Broad
Timing of Variant Release	Elaine Ostrander
Canine Reference Genome from the Broad	Elaine Ostrander	Link to paper on Box: https://nih.box.com/s/esdgq1qukgqmeae55wjauvegfrmp5y6o Paper shared through email with BPSC on July 20th from Toby.
Pan Cancer Study	Shaying Zhao	Breed prediction pipeline The 15TB harmonized reads are generated from cases with matched tumor and normal samples both passing our comprehensive quality control measures, including breed validation and prediction using our software provided

Committee Goals	Gina	Variant filter file Some of the filters are not well understood by the group A discussion is needed to identify overlap and differences in variant calling filter files being using by various groups Dependent on genome best practices for calling germ-line mutations

Meeting Minutes (Not Verbatim)

EO- Link to Michigan pipeline will be available soon. I can share with group when I have it.

RC- About to do sequencing on a chunk of dogs, the imputation paper could be a great reference.

EO- Helpful with low-pass sequencing.

EO- There will be a release of all variants. Everything will be re-called since they aligned to the new GSD reference.

EO- We can have Reuben Buckley attend the meeting next time and give a Q & A. He is also in the alignment group.

Previous Meeting Minutes (Not Verbatim)

HG- This outline will be different than the one that was initially drafted, would it be worth it to hit the bullet points on the document, who can be the point person to send out email and reminders

TP- Revamp of outline would be a good idea. Someone from the committee needs to take point on communications. Elaine and Jeff had made progress on a standard genome, but that is not reflected here.

DD- Reach out to Elaine through email and determine if she is willing to take the lead.

Action items

Elaine to send link to new GSD reference genome.
Kuffel, Gina (NIH/NCI) [C] to send out Buckley paper.
Kuffel, Gina (NIH/NCI) [C] to set up presentation with Shaying's group for next meeting.

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