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hCNV Implementation Studies

Beacon and Beyond — Implementation-driven standards and protocols for CNV discovery and data exchange

ELIXIR implementation study, 2021-2023

Lead: Michael Baudis

The initial 2019-2021 hCNV community implementation study employed a set of perceived needs to

  1. deliver first community standards and procedures
  2. identify intersections with other ELIXIR communities and stakeholders in ELIXIR connected organizations, such as GA4GH; and
  3. to streamline priorities for relevant, achievable deliveries of hCNV community projects.

This hCNV implementation study - approved by ELIXIR for the period of mid-2021 to 2023 - focuses on those potential high-value targets for data access and delivery, using reference resources and community stakeholder engagement to directly implement and test hCNV resources aligned with ELIXIR ecosystems. The main target here will be the empowerment of the Beacon protocol, to act as standard for federated hCNV discovery and data delivery, in conjunction with additional GA4GH derived standards.

Reference hCNV datasets, use-case workflows and benchmarking

ELIXIR implementation study, 2021-2023

Leads: Christophe Béroux & David Salgado

The ELIXIR human CNV Community (hCNV) was created in December 2018. In two years contributions to the field have been numerous (ELIXIR IS, Rare Diseases, Federated Human Data, Beacons, GA4GH, EJP-RD and Beyond 1 Million Genomes - B1MG). The Community now aims to address the major challenge of NGS data interpretation in the era of whole genome sequencing: Copy Number Variation.

During the first commissioned service offered as a starting grant, the Community has identified various gaps to proceed with CNV tools benchmarking and in particular for Exome and targeted sequencing, which are by far the most widely used technologies in diagnostic laboratories and in research. Within this implementation study we want to provide solutions and bioinformatic infrastructure solutions to fill identified gaps, and to make these biomedical reference materials available (i.e. via Open Science) to the various communities and platforms.

hCNV Community Study 2019-2021

Establishing th eh-CNV Community

Leads: Christophe Béroud, Michael Baudis & David Salgado

The human CNV community (h-CNV) has been officially created in December 2018. It aims to address some challenges of NGS data interpretation in the era of whole genome sequencing for the most frequent mutation type: Copy Number Variation. Seven topics have been identified during the kick-off meeting and further refined with all h-CNV partners. This ultimately led to the proposal described in this implementation study.

Selected deliverables

  • D2.n Reference Datasets / Publications [PDF]
  • D3.2 Improvement of community formats for CNV exchange [PDF]
  • D4.1 & 4.2 Enabling CNV data discovery in diagnostic and phenotypic context [PDF]
  • D5.1 ELIXIR hCNV Community: CNV annotations [PDF]