This Study's work will address the following themes:
- Optimal CNV detection pipelines for research and diagnostics: to release a set of sensitive and reliable pipelines, optimized and validated to detect CNV from various high throughput datasets. These pipelines will be available either through the ELIXIR compute nodes and/or as stand-alone solutions.
- Definition of reference datasets: to provide open reference datasets of fully validated somatic and germline CNVs representing a wide range of samples types and experimental technologies.
- Improvement of community formats for CNV exchange: to improve the VCF format and identify other nomenclatures and widely used formats in other communities (in alignment with GA4GH and the ELIXIR Interoperability Platform)
- Enabling CNV data discovery in diagnostic and phenotypic context: The hCNV Community will work towards enabling the ELIXIR Beacon Project for the envisioned patient discovery, through the support of extended clinical descriptions including enabling and testing of relevant annotation standards (e.g. HPO, NCIt and additional ontologies).
- Functional annotation of CNVs
- Combinatorial approaches to CNV interpretation
- Identification of landmark genes in regions of interest
- FAIRification of hCNV databases and datasets: The FAIR principles (Findable, Accessible, Interoperable, Reusable) will be applied to those systems to demonstrate the feasibility and utility of distributed CNV databases in order to allow interoperability (including resource and data discovery).
- Training materials
- Train actors, patients and the general public
- Capacity Building training events across certain ELIXIR Nodes
1 June 2019 to 31 May 2021