The BIOS Consortium (Biobank-based Integrative Omics Studies)

Welcome to the Wiki of the BIOS Consortium.

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.

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.

See also ​our BBMRI website

Note: Read Using this wiki before making changes to these pages.

Table of contents

• BIOS data accessibility and locations
  • Getting access to BIOS data - Instructions on how to request access to the BIOS datasets.
  • Accessing the BIOS Virtual Machine and Grid SRM - Description of the various methods to connect to BIOS resources.
  • Recommended BIOS datasets for downstream analysis - One page overview of all BIOS datasets available on the BIOS VM.
  • Metadatabase - Description of the metadatabase where all BIOS metadata are stored.
  • Grid data infrastructure - Descriptions and locations regarding data storage on Grid.
  • ​BIOSRutils - Using BIOS data from R.

• Infrastructure and data on Groningen Cluster
  • UMCG file structure - Descriptions and locations regarding computation resources and project datasets on the Groningen Cluster.

• Main BIOS Papers
  • 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), see attached file for RNA seq QC and processing.
  • 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). See also ​Methylation QC and processing.

• Organisation
  • The BIOS team
  • Using this wiki - Notes on editing and structuring our wiki pages.
  • Meeting minutes? - Minutes of our meetings.
  • Presentations and Materials? - Presentations of the project plus templates, logos.

• Private?