Phase I: Translational Genomics Research Institute (TGen), Ethos Discovery, Tufts University and The Children’s Hospital of Philadelphia Participate in CCGP
The CCOGC biobank collection was transferred by ACF from holding at Tufts University to TGen.
The biobank includes 2974 items which may include frozen tumor/normal tissue, whole blood, serum, plasma, urine and formalin/OCT preserved tumor/normal tissue.
A comprehensive inventory was completed by TGen.
Histology slides were made for soft tissue sarcoma (STS), diffuse large B-cell lymphoma and osteosarcoma samples.
TGen, Ethos Discovery and Tufts University participating researchers met to discuss prioritization of samples based on pathologic review and sample information to make the most clinical and scientific impact. An effort has been made to focus on 32 soft tissue sarcoma (STS) specimens for histology and pathology review since this is an underserved area for canine and human cancer research. From these 32 initially chosen, 19 STS specimens including three sub-types (fibrosarcoma, FSA; hemangiopericytoma, HPCT; peripheral nerve sheath tumor, PNST) were selected for genomics and proteomics analysis at TGen. Illumina sequence reads were generated from the exome and RNA-seq libraries to identify germline and somatic mutations.
The diffuse large B-cell lymphoma and osteosarcoma samples have also undergone pathology review at Ethos Discovery. A set of 10 B-cell lymphoma and as many as 20 or more osteosarcoma cases will be included in proteomic analysis.
Upcoming Phase I Completion & Phase II Commences (2023)
Simultaneously, TGen and the Children’s Hospital of Philadelphia (CHOP) researchers are working to improve and develop existing canine data analysis workflow and platform for the identification and integration of canine cancer driver mutations with external and human dataset.
In addition, the Genomics Profiling and Proteomics Profiling teams of the CCGP are responsible for on-going development and management of the canine cancer multi-omics pipeline. The team will conduct analysis of the data and development of new bioinformatics tools that can facilitate use of these data by the broader research community. The work done by this team will transfer to the Data Integration Team which is responsible for regularly scheduled public release and integration into a canine and comparative cancer genomics data portal. The data team will also work to integrate existing processed institutional canine cancer data including those within the Integrated Canine Data Commons (ICDC) and other pediatric and adult cancer datasets.
-The TGen canine workflow and tools are being ported over to the CHOP cloud platforms
-Next, existing results will be compared to TGen results to ensure reproducibility
-Once the workflow is established, the team will re-harmonize defined public resources as well as new incoming samples.
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