KOMP2-Phase 2 Production and Phenotyping by the DTCC Consortium

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KOMP2-Phase2 Production and Phenotyping by the DTCC Consortium ABSTRACT This application is to competitively renew funding for the DTCC Consortium’s Phase2 participation in the Knockout Mouse Production and Phenotyping (KOMP2) Project. Member centers of the DTCC Consortium include the University of California Davis (UCD; lead institution), The Centre for Phenogenomics (TCP) in Toronto, the Children’s Hospital Oakland Research Institute (CHORI), and Charles River Laboratories International Inc (CRL). We propose to leverage our experience and continue to use well-tested coordinated management, strategies, protocols, and processes successfully implemented for KOMP2-Phase1 to increase, expand, and enhance activities for KOMP2-Phase2. In KOMP2-Phase1, the DTCC completed (or is on track to complete by the end of Phase1) all established goals and achieve all metrics (e.g., accelerated microinjection of ES cell clones, increased production rate of germline mutants, early completion of production timeline, on- track for completion of phenotyping) that exceed objectives and goals required for the scope of work we propose by the DTCC in KOMP2-Phase2. In this renewal, the DTCC proposes to phenotype male and female cohorts for at least 1,500 mutant homozygous (HOM) or heterozygous (HET) mouse lines produced using Cas9 RNA-guided nuclease (Cas9 RGN) and corresponding age and sex –matched wildtype (WT) controls in 3 phenotyping pipelines (Embryo, Juvenile, and Adult) using all IMPC-required and several optional IMPReSS- established tests across multiple organ systems. After applying center-based quality assurance of processes, and quality control of products (mice and data), all data (including meta-data) will be uploaded without delay to the Data Coordination Center (DCC) and then the Mouse Phenotyping Informatics Infrastructure (MPI2) for public access through the IMPC web portal (www.impc.org). To enhance the efficiency of generating mouse lines and data, DTCC member Centers will conduct technology development projects to improve and increase efficiency of production (e.g. high-efficiency RGN-mediated targeting, lacZ knockin insertion) and pilot phenotyping tests (e.g. automated home cage monitoring and micronucleus [genome instability]) to establish their added-value, reproducibility, and cost-effectiveness in our Juvenile and Adult Pipelines. Phenotyping technology development activities will include a novel quantitative kit-based proteomic assay, and metabolomic profiling of mutant mouse lines that promise to add significant scientific value and increase research utility of phenotyping data. In addition, the DTCC will actively engage the scientific community by seeking nominations for genes to study (e.g., Adult Pipeline), prioritize responses to requests for KOMP2 mice while production and phenotyping is in progress and after deposition into the Mutant Mouse Resource and Research Center (www.mmrrc.org), and provide value-added services and collaborations (e.g., PAR-13-231 Phenotyping Embryo Lethals, histopathology support to the Baylor-Harwell KOMP2-Phase2 Consortium). In addition to input from NIH Program Officers, the DTCC will be guided by advice and recommendations of the DTCC Panel of Expert Advisors, the NIH KOMP2 Scientific Advisory Board, and the IMPC Panel of Scientific Consultants. The DTCC will participate in all KOMP2 and IMPC consortium activities, including monthly teleconferences, subcommittee working groups and meetings, national and international conferences, site visits, and other relevant activities. In order to maximize the scientific output and effect on biomedical research, the DTCC also commits to coordinate its efforts with those production, phenotyping, and research and development efforts by other KOMP2-funded participants. In summary, by the end of 5 years, the DTCC will have contributed genotype-confirmed mice and validated broad-based phenotyping data for at least 1,500 mutant mouse lines on time and within budget in support of the KOMP2 program and the IMPC effort to functionally annotate the mammalian genome.