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¶
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.
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).
Continue readinghCNV Community Meeting 2023
A visit to the Hinxton motherlode...
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.
CNV Project at biohackathon23
Participating at #BioHackEU23 in Barcelona with a CNV reference resource project
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).
Progenetix as SIB and ELIXIR Resource
Recognizing the Progenetix platform as Swiss contribution to the European bioinformatics resources ecosystem
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 progenetix.org (and its daughter project cancercelllines.org).
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.
Continue readingGA4GH 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
Continue readingELIXIR All Hands 2022 - h-CNV Representation
Workshop proposals | Amsterdam 7-10 June 2022
The hCNV community has been invited to participate in 3 workshops:
Continue readinghCNV 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.
Continue readingCNV Ontology Proposal - Now Live at EFO
EFO Ontology contains now terms for (relative) CNV levels
As 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.
hCNV Site now at cnvar.org
The homepage of the hCNV community has now been mapped to the cnvar.org domain.
Continue readingThe 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.¶
- doi: 10.1093/database/baab043.
- PMID: 34272855
- PMCID: PMC8285936.
- bioRxiv. doi: doi.org/10.1101/2021.02.15.428237
This article provides an overview of recent changes and additions to the Progenetix database and the services provided through the resource.
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.
Continue readingCNV 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.
Continue readingPR: 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 elixir-europe.org)
Continue readingThe 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¶
Abstract¶
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.
Continue readingHGVS 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.
Continue readingh-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).
Links¶
- presentation slides (PDF)
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.
Continue reading