| | 1 | = The BIOS Consortium (Biobank-based Integrative Omics Studies) = |
| | 2 | '''Welcome to the Wiki of the BIOS Consortium.''' |
| | 3 | |
| | 4 | The mission of the BIOS Consortium is to create a large-scale data infrastructure and to bring together BBMRI researchers focusing on integrative omics studies in Dutch Biobanks. |
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| | 6 | The advent of the genome-wide association study (GWAS) led to the successful identification of thousands of variants that are robustly associated with complex disease phenotypes. Dutch biobanks played a substantial role in these discoveries. For most of these variants, however, the mechanisms through which they contribute to these phenotypes remain unknown. The BIOS Consortium applies a functional genomics approach that integrates genome-wide genetic data with data on the epigenome and transcriptome to elucidate these mechanisms. Over 4000 samples from BBMRI-NL biobanks with in-depth information on disease phenotypes and GWAS data are being enriched with RNA-sequencing and genome-wide DNA methylation data. The same is true for samples with whole-genome sequencing data from GoNL. This unique data infrastructure provides a powerful platform to evaluate key questions in integrative omics from establishing comprehensive eQTL and meQTL catalogues to linking molecular pathways across omics levels to phenotypic outcomes. |
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| | 8 | See also [https://www.bbmri.nl/on_offer/bios/ our BBMRI website] |
| | 9 | |
| | 10 | '''Note:''' Read [wiki:FgWiki Using this wiki] before making changes to these pages. |
| | 11 | |
| | 12 | = Table of contents = |
| | 13 | |
| | 14 | * '''BIOS data accessibility and locations''' |
| | 15 | * [wiki:FgVirtualMachine Accessing the BIOS Virtual Machine and Grid SRM] |
| | 16 | * [wiki:FgPreparedData Recommended BIOS datasets for downstream analysis] - One page overview of all BIOS datasets available on the BIOS VM. |
| | 17 | * [wiki:FgMetadatabase Metadatabase] - Description of the metadatabase where all BIOS metadata are stored. |
| | 18 | * [wiki:FgDataInfrastructure Grid data infrastructure] - Descriptions and locations regarding data storage on Grid. |
| | 19 | * [wiki:FgBIOSRutils BIOSRutils package] - Using BIOS data from R. |
| | 20 | |
| | 21 | * '''Infrastructure and data on Groningen Cluster''' |
| | 22 | * [wiki:FgUMCGFileStructure UMCG file structure] - Descriptions and locations regarding computation resources and project datasets on the Groningen Cluster. |
| | 23 | |
| | 24 | |
| | 25 | * '''Main BIOS Papers''' |
| | 26 | * [wiki:FgFirstPaper First eQTL paper] - 'Hypothesis-free identification of modulators of genetic risk factors' (in revision at Nature Genetics http://biorxiv.org/content/early/2015/11/30/033217) |
| | 27 | * [wiki:FgFirstmeQTLPaper First meQTL paper] - 'Disease variants alter transcription factor levels and methylation of their binding sites' (in revision at Nature Genetics, http://biorxiv.org/content/early/2015/12/01/033084.1) |
| | 28 | |
| | 29 | * '''Organisation''' |
| | 30 | * [wiki:FgWiki Using this wiki] - Notes on editing and structuring our wiki pages. |
| | 31 | * [wiki:FgMeetingMinutes Meeting minutes] - Minutes of our meetings. |
| | 32 | * [wiki:FgPresentations Presentations and Materials] - Presentations of the project plus templates, logos. |
| | 33 | |
| | 34 | * '''[wiki:FgPrivate Private] ''' |
