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Page History
This is the wiki for the Integrated Canine Data Commons (ICDC) project. This is a joint project between FNL's ADRD and BIDS Directorates to develop the ICDC for NCI's DCTD group, with Toby Hecht as the Federal Lead. The project was initiated via Task Order- HNC17V-12 - Integrated Canine Data Commons. The first phase of the project is to develop and deploy a prototype in two years. There are two option phases, create a production version and then operation and maintenance of Production version.
The ICDC will be part of NCI's CRDC and will be developed using Gen3 technology stack on Amazon AWS. The ICDC will contain canine clinical trial data consisting of many data types such as images, clinical data and sequencing.
Charter:
Anticipated Baseline Period of Performance: 9/24/18-9/23/20
Funding: Non-Severable
PIDs:
400.041.0076.001.001.002 – BIDS
400.041.0076.001.001.001 - ADRD
COR: Toby Hecht, PhD - DCTD
FNL Project Leads:
Matthew Beyers - BIDS
John Otridge - BIDS
Ralph Parchment - ADRD
Kickoff meeting: Will be scheduled with the government.
High Level Scope:
To create a new, dynamic data commons for canine cancer data, including not only clinical outcomes and genomics findings from canine clinical trials being conducted by the Comparative Oncology Program (COP) in collaboration with DCTD, but also the trials’ molecular, pharmacological, microenvironment, medical imaging and other study data.
Build a cloud-based prototype Canine Data Commons using Gen3 architecture. Follow CBIIT EPLC process. Linked to the Cancer Research Data Commons suite of projects (e.g., Expand Data Commons). A low number of concurrent users is expected for the prototype. Staffing will be internal FNL as well as external sub-contracts for SMEs. Stand-up and run a Steering Committee and incorporate their feedback into system design. Import existing data into developed system and provide mechanism for future data incorporation.
Success Criteria:
Technical Success:
e.g., stand up of system, ability to search, ability to load data, ability to login, etc.
Collaborative Success:
e.g., number and results of steering committee meetings, use cases defined, relationships developed with public, hits on the website.
Scientific Success:
e.g., papers developed based on data contained in the system, new ideas sparked by data or system collaboration, mentions at scientific meetings, new studies proposed/developed as a result of this system being publicly available.
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Websites of Interest to ICDC:
In the News:
How are dogs helping us cure cancer in people - US News and World Report: 2018
Papers of Interest:
Phylogenetic Reconstruction of Orthology, Paralogy, and Conserved Synteny for Dog and Human: 2006
Canine Cancer Genomics: Lessons for Canine and Human Health: 2019
"BREED-SPECIFIC CANCER RISK Cancer is the leading cause of disease-associated death in dogs, affecting one in four individuals, with 50% of dogs >10 years old developing the disease (65–67). Studies indicate that the genes and pathways involved in canine cancer development are similar to those found in humans (68, 69). The compressed life span of dogs means that cancers that take 15–20 years to mature in humans can be studied in the dog in 2–3 years (7, 70). Perhaps most importantly, canine cancers are spontaneous, distinguishing the dog from other mammalian cancer models such as the mouse, in which many cancers must be induced (reviewed in 3, 11, 13–15). Overall, this rationale argues that genetic studies of canine disease are a powerful way to advance our understanding of cancer in humans and companion animals alike (3, 11, 13, 71)."
...
"Perhaps most importantly, comparative genome hybridization arrays have the potential to yield information regarding ancestral mechanisms of cancer development by identifying common rearrangements in comparable human cancers. Examples include formation of the BCR-ABL fusion (Philadelphia chromosome) in canine chronic myelogenous leukemia in dogs, the translocation of the MYC gene to the immunoglobulin heavy-chain enhancer region in canine lymphoma, and deletion of the RB-1 locus in chronic lymphocytic leukemia (85)."
...
"In 2015, in an effort led by the National Human Genome Research Institute, we revealed the first comprehensive analysis of dog genome sequences, releasing data on 186 canine WGS (152), a data set composed of 102 purebred dogs, 12 wild canids, and 72 semiferal village dogs. This initial analysis revealed 28.01 million single-nucleotide variants (SNVs), 12.62 million indels, and 31,613 structural variants (SVs) (https://research.nhgri.nih.gov/dog_genome/). Canine dbSNP contains only SNVs and includes less than one-third of the variants found in the average canid WGS, while we found that a mean of 99.55% of SNVs, 99.57% of indels, and 95.63% of SVs from any single canid were present in at least one other individual in our WGS catalog. All data are available through the National Center for Biotechnology Information Sequence Read Archive or database of structural variation." (color emphasis added)
