Posted: March 18, 2020

Letter of Intent due 30 days prior to application; Application due June 5, 2020

A tiered triage approach to the phenotyping of embryonic lethal KO strains to facilitate flexibility in experimental design and economize on breeding strategies is in place. Primary tier screening begins with a careful evaluation of genotype ratios during breeding to generate adult cohorts for the adult phenotyping pipeline. A mid-gestation stage of E12.5 is the initial reference time point for a "first look" at strains deemed embryonic lethal or subviable and for assessment of developmental anomalies. Based on the E12.5 analysis, embryos are triaged for further analyses at either earlier or later time points (e.g., E9.5 or E14.5 in KOMP2 or E18.5 across other IMPC centers) as recommended by the Bloomsbury Report. The established phenotyping pipeline includes collection of robust, three-dimensional imaging datasets that are accessible and free to be mined through the IMPC data portal (http://www.mousephenotype.org/data/embryo). In addition to the embryonic lethal KO strains, it is important to note two other cohorts of interest: the estimated 15% of perinatal lethal KO strains and 10% of subviable KO strains. These represent cohorts for further study as these are likely to represent models of human structural birth defects as well.

Depending upon the data available from the embryonic lethal pipeline primary tier screening being performed by the IMPC centers, investigators may consider three options when applying for funding through this FOA:

  • Pursue non-hypothesis-driven, non-mechanistic secondary- and/or tertiary tier screening on a select cohort of IMPC-generated KO strains using various approaches. 1) Studies could focus upon the acquisition of more detailed morphological information with any of a variety of 3D imaging modalities (e.g., magnetic resonance, µCT, high resolution epifluorescence microscopy, OPT, and optical coherence tomography). It is impossible to dictate the "best" stage or modality for imaging to discover novel phenotypes as developmental processes vary by embryonic stage and the interests of the investigators should dictate these aspects. The IMPC will continue to play a leadership role in standardizing operating procedures for 3D imaging of embryos in the same manner that they have developed the common protocols for adult phenotyping. Potential applicants are encouraged to visit the IMPC website for updated information [http://www.mousephenotype.org/data/embryo]. 2) An optional approach for characterization of gene function would be to perform mRNA expression profiling using RNA sequencing (RNAseq) of embryonic tissues to measure global perturbations caused by the KO. Sequencing technologies are continuously evolving; therefore, it is conceivable that this could be applied to embryonic mouse screening, too. 3)Tertiary tier screening would involve more focused phenotyping of strains of interest to individual investigators. These types of analyses could include, but are not limited to, more detailed immunohistochemistry, laser capture micro-dissection, or the development of cell-based assays.

    • It is anticipated that secondary and tertiary level phenotyping will involve collaborations between the IMPC production centers and investigators interested in advancing their research agendas by pursuing analyses of focused sets of mutants. An important aspect of secondary and tertiary tier screening will be the integration of phenotypic data into the existing database supported by the IMPC. Phenotypic data generated through this initiative are required to be deposited in the IMPC database as noted in Section IV.2. Resource Sharing Plan. The applicant must contact the IMPC data coordinating center at the European Bioinformatics Institute (the EBI-KOMP2 Mouse Phenotyping Informatics Infrastructure Consortium; Ann-Marie Mallon at a.mallon@har.mrc.ac.uk) to develop a data sharing strategy and to request a supporting letter of agreement for deposition of phenotypic data to IMPC. Please use "NIH PAR-20-137" as the subject line of your email. The letter of support should specify the negotiated cost of data deposition and the cost should be included in the requested budget.

  • Pursue a combination of non-hypothesis-driven, non-mechanistic secondary tier screening on a select cohort of IMPC-generated KO strains and hypothesis-driven aim(s) on selected strains. As the KOMP2 phenotyping effort continues (current phase, 2017-2021) it is clear that there will be a significant increase in phenotypic data available on embryonic lethal, perinatal lethal, and subviable KO strains. In an effort to encourage the further use of these data and strains, applications that make use of these IMPC-generated strains, further the phenotyping effort, and incorporate hypothesis-driven research aim(s) willedw be considered under this FOA. For these studies applicants can use a combination of IMPC and other resources to address their hypothesis.
  • Pursue strictly hypothesis-driven research on a select cohort of KOMP-IMPC-generated embryonic lethal, perinatal lethal, and/or subviable KO strains. Applications that have hypothesis-driven aim(s) to study the underlying mechanisms resulting in embryonic lethality, and/or perinatal lethality and/or subviability will also be considered under this FOA. For these studies applicants can use a combination of IMPC and other resources to address their hypothesis.

Read full solicitation here

Office of Grants and Contracts

Address

107 Ag Administration Building
University Park, PA 16802