Date
Attendees
| Committee Member | Present | Absent |
|---|---|---|
| X | ||
| X | ||
| X | ||
| X | ||
| Elaine Ostrander | X | |
| Deborah Knapp | X | |
| Jeff Trent | X | |
| Dawn Duval | X | |
| Amy Leblanc | X | |
| Heather Gardner | X | |
| Cheryl London | X | |
| Christina Mazcko | X | |
| Paula Jacobs | X | |
| Renee Chambers | X | |
| Shaying Zhao | X | |
| Sunetra Das | X |
Outstanding Action Items
- Toby to reach out to Connie about extending invite to new PRECINCT members.
- Cheryl London to write abstract and also update the paper to include the new
- Cheryl London to add acknowledgement sections to the manuscripts.
Agenda
| Agenda Item | Who | Notes |
|---|---|---|
| BPSC Review Article: Tools & Resources for the Canine Genomic Landscape | Group Discussion |
|
Meeting Minutes (Not Verbatim)
TH - Let's think about repurposing this committee or augmenting the scope of this committee
CL - Issues with integrity of RNA and frozen specimens just as an example, perhaps protocol and data analysis standardizations.
AL - Beginning with nucleic acid extraction, dependent on tissue type, getting a single nuclei out of a real bone tumor, easy to do in mouse and simple tissues, but there are not standard protocols in dog.
TH - Would there be a place in the ICDC for SOPs pertaining to RNA isolation, nucleic acid extraction, library preparation, sequencing methods?
TH - Highlighting differences between human and dog, maybe differences in assay prep could contribute to differences in data
HG - Moving away from bulk RNA-Seq and whole exome, instead working with liquid biopsy and microRNA-Seq. It would be nice to have a community that has been working in parallel on some of these things, obtaining samples and QC of samples, library prep, and data analysis (no input on the canine side since most tools are developed for human).
AL - Methylation is a good example, doing this in Osteo right now, low pass whole genome helps to interpret methylation results computationally, this was something that was not known initially.
CL - A roadmap for people that don't always work with canine samples would be helpful so that they are not discouraged.
HG - Availability of analysis pipelines even for working locally.
SZ - Some discussion around canFam4 and annotation
AL - Sample procurement and processing is a good place to start as well as the buckets for analysis mentioned by Heather.
DD - There is talk of a Pan canFam genome
SZ - Genome annotation cannot be done by a single lab, this needs to be a community effort
CL - We can start with simple things such as sample requisition and sample preservation, OCT blocks cannot be used because the RNA is degraded.
HG - Challenges are around RNA quality and it is not high enough to perform 10X spatial transcriptomics. My understanding is that NCBI was going to handle annotations for canFam4, but instead they did the ROS version of the genome instead.
TH - Elaine may be a good contact for reaching out to NCBI
AL - We gained a ton of experience with NanoString from FFPE and how to approach these type of samples for the canine IO profiling assay, garbage in garbage out.
HG - QC has changed for the nCounter
AL - Having a pathologist involved is very important when assessing the integrity of samples, it is no longer RIN
Contacts from Dawn Duval regarding canFam4
Kerstin Lindblad-toh gave me these indivivduals as potential contacts to pressure for annotation of the GSD genome.ENSEMBLE
NCBI
Action items
Kuffel, Gina (NIH/NCI) [C] to start 2 docs, 1 for items to tack for standardization, 1 for the letter to move the needle on canFam4 annotations.
