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.
- BBBMRIomcis - Accessing and analyzing BIOS (RP4 metabolomics and RP2 GoNL) data using the R programming language (https://cran.r-project.org/).
- Post your questions about BIOS datasets here https://www.biostars.org/t/bbmri-nl-bios/ using bbmri-nl-bios as tag, and we'll get back to you shortly. See Forum for more instructions on how to post questions on BioStars?.
- Main BIOS Papers
- First eQTL paper - 'Hypothesis-free identification of modulators of genetic risk factors' (accepted 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' (accepted at Nature Genetics, http://biorxiv.org/content/early/2015/12/01/033084.1).
- BIOS QTL browser