First hCNV Community Implementation Study

This Study's work will address the following themes:

  1. 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.
  2. 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.
  3. 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)
  4. 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).
  5. Functional annotation of CNVs
  6. Combinatorial approaches to CNV interpretation
  7. Identification of landmark genes in regions of interest
  8. 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).
  9. Dissemination:
    1. Training materials
    2. Train actors, patients and the general public
    3. Capacity Building training events across certain ELIXIR Nodes

Platform/Community: 

People involved: 

Christophe Beroud
David Salgado
Marc Hanauer
Victoria Dominguez del Angel
Michael Baudis
Thomas Keane
Cristina Yenyxe Gonzalez Garcia
Fiona Cunningham
Joaquin Dopazo
Alfonso Valencia
Salvador Capella
Sergi Beltran
Steven Laurie
Laura Furlong
John Hancock
Gary Saunders
Katharina Lauer
Leyla Garcia
Bauke Ylstra
Leon Mei
Morris Swertz
LF Johansson
Eivind Hovig
Attila Gyenesei
Katalin Monostory
Brane Leskošek
Polonca Ferk
Marko Vidak
Krzysztof Poterlowicz
Jan Korbel
Gemma Bullich
Janet Piñero
Daoud Sie
Pubudu Samarakoon