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The initial 2019-2021 hCNV community implementation study employed a set of perceived needs to a) deliver first community standards and procedures; b) identify intersections with other ELIXIR communities and stakeholders in ELIXIR connected organizations, such as GA4GH; and c) to streamline priorities for relevant, achievable deliveries of hCNV community projects. This project for an hCNV implementation study 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.

The initial 2019-2021 hCNV community implementation study employed a set of perceived needs to a) deliver first community standards and procedures; b) identify intersections with other ELIXIR communities and stakeholders in ELIXIR connected organizations, such as GA4GH; and c) to streamline priorities for relevant, achievable deliveries of hCNV community projects. This project for an hCNV implementation study 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.

The initial 2019-2021 hCNV community implementation study employed a set of perceived needs to a) deliver first community standards and procedures; b) identify intersections with other ELIXIR communities and stakeholders in ELIXIR connected organizations, such as GA4GH; and c) to streamline priorities for relevant, achievable deliveries of hCNV community projects. This project for an hCNV implementation study 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.

The initial 2019-2021 hCNV community implementation study employed a set of perceived needs to a) deliver first community standards and procedures; b) identify intersections with other ELIXIR communities and stakeholders in ELIXIR connected organizations, such as GA4GH; and c) to streamline priorities for relevant, achievable deliveries of hCNV community projects. This project for an hCNV implementation study 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.

The initial 2019-2021 hCNV community implementation study employed a set of perceived needs to a) deliver first community standards and procedures; b) identify intersections with other ELIXIR communities and stakeholders in ELIXIR connected organizations, such as GA4GH; and c) to streamline priorities for relevant, achievable deliveries of hCNV community projects. This project for an hCNV implementation study 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.

The initial 2019-2021 hCNV community implementation study employed a set of perceived needs to a) deliver first community standards and procedures; b) identify intersections with other ELIXIR communities and stakeholders in ELIXIR connected organizations, such as GA4GH; and c) to streamline priorities for relevant, achievable deliveries of hCNV community projects. This project for an hCNV implementation study 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.

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

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

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

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

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

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

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

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

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

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

The ELIXIR human Copy Number Variation 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.

The ELIXIR human Copy Number Variation 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.

The ELIXIR human Copy Number Variation 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.

The ELIXIR human Copy Number Variation 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.

The ELIXIR human Copy Number Variation 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.