EpiVar Browser: advanced exploration of epigenomics data under controlled access
Abstract Motivation Human epigenomic data has been generated by large consortia for thousands of cell types to be used as a reference map of normal and disease chromatin states. Since epigenetic data contains potentially identifiable information, similarly to genetic data, most raw files generated by these consortia are stored in controlled-access databases. It is important to protect identifiable information, but this should not hinder secure sharing of these valuable datasets.Results Guided by theFramework for responsible sharing of genomic and health-related datafrom the Global Alliance for Genomics and Health (GA4GH), we have developed a tool to facilitate the exploration of epigenomics datasets’ aggregate results, while filtering out identifiable information. Specifically, the EpiVar Browser allows a user to navigate an epigenetic dataset from a cohort of individuals and enables direct exploration of genotype-chromatin phenotype relationships. Because the information about individual genotypes is not accessible and aggregated in the output that is made available, no identifiable data is released, yet the interface allows for dynamic genotype - epigenome interrogation. This approach has the potential to accelerate analyses that would otherwise require a lengthy multi-step approval process and provides a generalisable strategy to facilitate responsible access to sensitive epigenomics data.Availability and implementation Online portal instance:<jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="https://computationalgenomics.ca/tools/epivar">https://computationalgenomics.ca/tools/epivar</jats:ext-link>Source code:<jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="https://github.com/c3g/epivar-browser">https://github.com/c3g/epivar-browser</jats:ext-link>.
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Preprint| Erscheinungsjahr: |
2023 |
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| Erschienen: |
2023 |
| Enthalten in: |
bioRxiv.org - (2023) vom: 08. Aug. Zur Gesamtaufnahme - year:2023 |
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| Sprache: |
Englisch |
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| Beteiligte Personen: |
Lougheed, David R [VerfasserIn] |
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| Links: |
Volltext [kostenfrei] |
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| doi: |
10.1101/2023.08.03.551309 |
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| PPN (Katalog-ID): |
XBI040424898 |
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| 520 | |a Abstract Motivation Human epigenomic data has been generated by large consortia for thousands of cell types to be used as a reference map of normal and disease chromatin states. Since epigenetic data contains potentially identifiable information, similarly to genetic data, most raw files generated by these consortia are stored in controlled-access databases. It is important to protect identifiable information, but this should not hinder secure sharing of these valuable datasets.Results Guided by theFramework for responsible sharing of genomic and health-related datafrom the Global Alliance for Genomics and Health (GA4GH), we have developed a tool to facilitate the exploration of epigenomics datasets’ aggregate results, while filtering out identifiable information. Specifically, the EpiVar Browser allows a user to navigate an epigenetic dataset from a cohort of individuals and enables direct exploration of genotype-chromatin phenotype relationships. Because the information about individual genotypes is not accessible and aggregated in the output that is made available, no identifiable data is released, yet the interface allows for dynamic genotype - epigenome interrogation. This approach has the potential to accelerate analyses that would otherwise require a lengthy multi-step approval process and provides a generalisable strategy to facilitate responsible access to sensitive epigenomics data.Availability and implementation Online portal instance:<jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="https://computationalgenomics.ca/tools/epivar">https://computationalgenomics.ca/tools/epivar</jats:ext-link>Source code:<jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="https://github.com/c3g/epivar-browser">https://github.com/c3g/epivar-browser</jats:ext-link> | ||
| 650 | 4 | |a Biology |7 (dpeaa)DE-84 | |
| 650 | 4 | |a 570 |7 (dpeaa)DE-84 | |
| 700 | 1 | |a Liu, Hanshi |4 aut | |
| 700 | 1 | |a Aracena, Katherine A |0 (orcid)0000-0002-8830-904X |4 aut | |
| 700 | 1 | |a Grégoire, Romain |4 aut | |
| 700 | 1 | |a Pacis, Alain |0 (orcid)0000-0003-4883-6176 |4 aut | |
| 700 | 1 | |a Pastinen, Tomi |0 (orcid)0000-0003-4016-5021 |4 aut | |
| 700 | 1 | |a Barreiro, Luis B |0 (orcid)0000-0001-9456-367X |4 aut | |
| 700 | 1 | |a Joly, Yann |0 (orcid)0000-0002-8775-2322 |4 aut | |
| 700 | 1 | |a Bujold, David |0 (orcid)0000-0001-7860-3264 |4 aut | |
| 700 | 1 | |a Bourque, Guillaume |0 (orcid)0000-0002-3933-9656 |4 aut | |
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