Description
The analysis of somatic variation has become an essential part of biomedicine, mostly affecting cancer genomics. With the increasingaccessibility to whole-genome sequencing by research groups and the incorporation of genomics into healthcare, the demand for highquality ways of improving discovery.As a natural continuation of the previous project and in the context of international collaborative environments, such as the projectEUCANCan, or the Global Alliance for Genome and Health (GA4GH), our group aims at overcoming this situation by designing andimplementing a computing platform for the assessment and improvement of variant calling pipelines. Following our long research trajectorydeveloping genome analysis tools, we here propose to build a systems where users can stablish, assess and improve their analysispipelines. This platform is going to be based on an extensive comparison of a large number of samples and variant callers to generateintegrated evaluation models that inform about the weak and strong points. In addition, the system will also recommend ways to improvethese pipelines and reach quality thresholds adjusted to the specific research or clinical scenario. The possible incorporation andintegration of this benchmarking platform with other complementary benchmarking exercises, such as OpenEBench, and its use indifferent oncology research environments, ensures its visibility and impact in the community.In addition, and as a complementary effort towards the characterization of somatic structural variation, our group also aims at analysingand describing the landscape of somatic variation in healthy tissues. In particular, we plan to investigate the structural variation occurringduring neural development, and assess the role of the gene PGBD5, as a continuation of our previous work. This will constitute the first comprehensive characterization of somatic structural variation in healthy tissue, which can inform, not only of the new challenges on variant calling, but also on the potential mechanisms behind somatic variation and carcinogenesis.
El proyecto PID2020-119797RB-I00 de investigación está financiado por MICIU/AEI /10.13039/501100011033
