Date
Attendees
Sunetra Das, Matt Beyers, Ana Damljanovic, Heather Gardner, Dawn Duval, Will Hendricks, Jack DiGiovanna, Sai Lakshmi Subramanian, Shaying Zhao, Elaine Ostrander, Brandi, Allison Heath
Goals
1. Genomics Best Practices document (define who is doing what.)
2. approaches to data harmonization
3. connect data harmonization goals to SBG
Discussion items
Goal of Genomics Best Practices document - provide overview of NGS, establish best practices (identifying elements of what's out there and outlining tools needed). Need to add material on reference genomes and annotations (Elaine). Table of tools and parameterization (Shaying). Having people remove everything with an RSID from their list of variants? Recommend NOT doing this. Assume RSID is a germline variant and eliminates many potential somatic variants which are in Canine dbSNP database. Dawn to add something about this to the document. Hot-spot P53 mutations present in dbSNP database. +++ indicates needed material
Shaying and Elaine provide material by Oct. 23. Will will add guidelines by Oct. 30th and then circulate.
Genomic Data Harmonization Strategy -
Building a workflow on SBG could be really useful. Need: tools and parameters for human don't work for canine. Brandi states that there are many tools already available - suggests stating suggested parameters in tools on SBG. Will: two separate needs: 1) enabling users to have access to these tools with recommended parameters; 2) benchmarkingto understand best tools/parameters based on empirical data. Allison says there hasn't been a lot of benchmarking on the canine side. SBG is happy to help with benchmarking. Dawn has cell lines that can be put on ICDC. Cell lines allow experimentation whereas primary tumor does not. Will thinks cell line data is highly desirable. Can figure out how to leverage the cell lines to do benchmarking. Sunetra says to be careful about which version of Ensemble to use.
Recommendation - continue discussion. compile parameters for tools.
Should we bring Non-cancer WG into Genomic WG along with SBG and put it all together? Elaine agrees. Monthly meeting!
SBG can create workflow based on KidsFirst workflow. Add Genomics WG into Non-Cancer WG meeting on Nov. 4 at noon ET.
