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ELIXIR Human Copy Number Variation community

Among the different types of inherited and acquired genomic variants, regional genomic copy number variations (CNV) contribute - if measured by affected genomic sequences - contribute by far the largest amount of genomic changes, contributing both to many syndromic diseases as well as the vast majority of human cancers. The website of the Human Copy Number Variation Community (hCNV) is a resource originated in ELIXIR's h-CNV Community Implementation Study (2019-2021) with the aim to provide a resource hub and knowledge exchange space for scientists and practitioners working with - or being interested in - genomic copy number variations in health and diseases. However, the scope of the community extends beyond CNVs and includes definition of and work with other types of genomic variations with a focus on structural variants.

CNV News and Announcements

Call for Papers BMC Molecular Cytogenetics

Computational Insights into Chromosomal Aberrations: Advancing Molecular Cytogenetics using Genomics Databases

Edited by Jeremy Squire, Federal University of São Paulo, Brazil

BMC logo image With potential interest for members of the CNV communities, BMC Molecular Cytogenetics is calling for submissions to a new Collection on Computational Insights into Chromosomal Aberrations: Advancing Molecular Cytogenetics using Genomics Databases.

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The ELIXIR hCNV Community - Making complex genomics accessible

ELIXIR Webcast

Michael Baudis, Antonio Rausell & Krzysztof Poterlowicz

Abstract Genomic copy number variants (CNV) are a major contributor to human genome variation and important factors in rare disease genetics and cancer genomics. However, the complexity of CNV detection technologies, the lack of standardised annotation formats and the fragmentation of cytogenetic and genomic communities so far has limited large scale utilization of CNV profiles in computational genomics. Continue reading

Beaconize this: Databases for Cancer Genomics and the Development of Open Data Standards

Seminar at the Bioinformatics club of the Centre de Recherche des Cordeliers (CRC)
Université Paris Cité

Michael Baudis

In this seminar at the Centre de Recherche des Cordeliers in Paris Michael presents the work of the group, with special emphasis on the role of the Progenetix oncogenomics resources and tools in the development, implementation and testing of the Beacon standard of the Global Alliance for Genomics and Health (GA4GH).

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hCNV Community Meeting 2023

A visit to the Hinxton motherlode...

biohackathon logo image On the last day of November 2023 members of the ELIXIR hCNV community meet on the Wellcome Trust Genome Campus in Hinxton for a hCNV community event. Main topics are the definition of achievable short term goals with intersecting interests and expertise, as well as how to aquire long term support for the community's activities.

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CNV Project at biohackathon23

Participating at #BioHackEU23 in Barcelona with a CNV reference resource project

biohackathon logo image Members of the hCNV community participate at this year's Biohackathon Europe event. The main project will address the creation of the template for a "beaconized" public resource for reference (i.e. not disease associated) copy number variation data, including the necessary tooling for the import from e.g. VCF or BED file variants into Beacon backends (such as our bycon environment).

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Progenetix as SIB and ELIXIR Resource

Recognizing the Progenetix platform as Swiss contribution to the European bioinformatics resources ecosystem

elixir logo The Progenetix resource has finally been recognized as an official contribution to the ELIXIR European bioinformatics informatics ecosystem. Besides Expasy Progenetix now is linked through ELIXIR's resource page. Or just go directly to (and its daughter project

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CNV Annotation Standards

New page dedicated to the documentation of CNV standards

We have updated an earlier page that linked to different cytogeneic & genomic annotation standards with an extensive table delineating CNV labeling in several file and API formats. The documentation itself is now linked from the main menue for easier access.

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GA4GH special interest group.

GA4GH special interest group working on Structural Varation Representation

GA4GH is seeking members to participate in new special interest group that would tackle the problem of representing structural variations in sequenced DNA

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ELIXIR All Hands 2022 - h-CNV Representation

Workshop proposals | Amsterdam 7-10 June 2022

The hCNV community has been invited to participate in 3 workshops:

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hCNV Implementation Studies Old and New

Michael Baudis @ ELIXIR Human Data Communities

This presentation provided an overview about the hCNV community, implementation studies and ongoing work, e.g. interaction with the GA4GH VRS standard group and Beacon development.

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CNV Ontology Proposal - Now Live at EFO

EFO Ontology contains now terms for (relative) CNV levels

EFO copy number assessment treeAs part of the hCNV-X work - related to "Workflows and Tools for hCNV Data Exchange Procedures" and to the intersection with Beacon and GA4GH VRS - we have now a new proposal for the creation of an ontology for the annotation of (relative) CNV events. The CNV representation ontology is targeted for adoption by Sequence Ontology (SO) and then to be used by an updated version of the VRS standard. Please see the discussions linked from the proposal page. However, we have also contributed the CNV proposal to EFO where it has gotten live on January 21.

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hCNV Site now at

The homepage of the hCNV community has now been mapped to the domain.

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The Progenetix oncogenomic resource in 2021

An article about current state and recent changes to th eProgenetix resource

Qingyao Huang, Paula Carrio Cordo, Bo Gao, Rahel Paloots, Michael Baudis

Database (Oxford). 2021 Jul 17;2021:baab043.

DATABASE logoThis article provides an overview of recent changes and additions to the Progenetix database and the services provided through the resource.

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hCNV Community and Implementation Studies

Presentation at ELIXIR All Hands 2021

At the ELIXIR All Hands 2021 Human Data Day Michael presents a very brief overview of the ending and upcoming ELIXIR hCNV implementation studies.

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CNV Beacon at Biohackathon Europe 2020

CNV detection software containerisation and benchmarking

For the Biohackathon Europe (Nov 08-22), the hCNV project participates with a "containerisation" project.

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PR: The ELIXIR hCNV Community publishes its programme

ELIXIR h-CNV press release

The ELIXIR Community on Human Copy Number Variations (hCNV) has presented its work programme. In a paper published in the ELIXIR F1000R gateway, the Community defines seven strategic objectives to support human CNV detection and interpretation ... (please read on

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The ELIXIR hCNV Community

White Paper Published @ F1000Research

The ELIXIR Human Copy Number Variations Community: building bioinformatics infrastructure for research

Salgado D, Armean IM, Baudis M et al.

F1000Research 2020, 9 (ELIXIR):1229


Copy number variations (CNVs) are major causative contributors both in the genesis of genetic diseases and human neoplasias. While “High-Throughput” sequencing technologies are increasingly becoming the primary choice for genomic screening analysis, their ability to efficiently detect CNVs is still heterogeneous and remains to be developed.

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HGVS 2019 Gothenburg

CNV Satellite Meeting @ Human Genome Variation Society - Gothenburg 2019

As a satellite meeting of the European Human Genetics Conference, the HGVS2019 meeting this year had a focus on human Copy Number Number Variations.

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h-CNV kick-off

h-CNV community kick-off meeting at ELIXIR All Hands in Lisbon

The h-CNV community had its kick-off meeting at the ELIXIR All Hands meeting in Lisbon, June 17-20 2019.

The meeting was used to present and discuss the different work packages and overall organisation of the project (slides attached).

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Launch of the ELIXIR h-CNV Community

A new ELIXIR community

The first h-CNV Community Implementation Study was officially launched on June 1st, 2019.

The project has an initial time span of two years. For further information please follow the link to the ELIXIR project page.

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