Page History

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• Kuffel, Gina (NIH/NCI) [C]

• Debbie Knapp

• Dawn Duval
• Cheryl London

Goals

• 2 papers Publish a paper 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.

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1. Available tools for canine cancer genomics, immunotherapeutics
   • Standard pipelines
   • Examples of how tools are used
2. Cloud Resources 
   • Discussion on background of available resources to interrogate the data
     
     
3. Data repositories
   • where is the data being stored
   • how can data be accessed
   • highlight ICDC
     
     
4. Challenges of newly released CanFam genome versions (CanFam 4 is not yet fully annotated)
   
   
5. Emerging Technologies & Resources
   • Single Cell
   • nCounter Assay
   • Dependency Mapping - Genome wide CRISPR within canine cell lines to identify critical dependencies of those cell lines
   • Spatial Transcriptomics - targeted sequencing approach, NanoString enabled, markers and antibodies are identified to label regions of interest (macrophages, tumor cells, etc.), a probe set is used to pull out transcripts and measure expression
   • Liquid Biopsy

Action items