Drug discovery projects at the Eisai AiM Institute are grounded in human biology and entrepreneurial collaboration. We enjoy strong scientific collaborations with groups focused on human genetics and other human data in academia, non-profit groups, and the biotech/pharma industry. In this spirit of collaboration, we are sharing a tool we have developed, Target Gene Notebook, with the broader scientific community.
Target Gene Notebook was developed to enable more efficient linking of genetic associations to functional biological information. This process is essential to translating genetic insights into therapeutic hypotheses and, eventually, drug discovery. While many browsers and databases provide access to unfiltered genome annotations and genetic results, there is currently no way to maintain group curation of all the relevant information and to integrate it with proprietary experimental data. Target Gene Notebook is an e-notebook to facilitate the organization of results, and we provide it freely here for the purposes of assisting therapeutic target evaluation and the creation of durable institutional or public knowledge bases.
With a gene or locus as the focal point, the software identifies candidate published associations and allows the user to review and store an assessment of each finding. Graphical displays utilize published LD patterns across global populations derived from public reference panels to derive ‘credible sets’ of variants representing published associations. Public resources of relevance to target evaluation (e.g., variation patterns in ExAC/Gnomad, expression patterns in GTEx) are also automatically included. In addition, eQTLs as defined from GTEx are included as associations (complete with credible set definition) for visual assessment of phenotype – eQTL overlaps. The notebook can be extended to include other eQTL sets and other association modalities (e.g., protein-QTLs).
This represents a beta version of Target Gene Notebook, and we are continuing its development and are open to feedback and collaboration. We encourage the development of this as a community resource across commercial and academic institutions. Users can try the software by downloading the zip file and following the installation instructions in the archive. Source code is available upon request.
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