Integrative Omics data set

What is BBMRI-NL’s Omics data set? 

Use the Explorer to view the data available for analysis.

The BBMRI-Omics data set has been created to study the relations between different omics levels and develop omics signatures of health and disease. The data set is publicly available and has proven to facilitate researchers in their discovery of novel biological mechanisms and biomarkers for health and disease. The BBMRI-Omics data set consists of 3,500 samples with integrative data (genome, epigenome, transcriptome and metabolome) with an extension of the metabolome in 30,000 extra individuals and whole genome sequences of a selective group of 700 individuals. 

The table below shows an overview of the techniques used and number of samples available for the different Omics measures present in the data set.

Why BBMRI-NL’s Omics data set?

With the BBMRI-Omics Explorer, designed to query the Omics dataset, you can explore the number of samples per selected set of omics data types, and check the distribution of sex, age and smoking status of the selected data set. You could also explore the number of individuals with a certain age range of interest having multiple omics levels available.
Intended users
The Omics data set and Explorer are meant for researchers investigating the relation between different genomic levels, and researchers investigating multilevel omics classifiers for disease risk.

Using BBMRI’s Omics data set

All data shared by participating biobanks including genome-wide SNP data, phenotypes, RNA-sequences, DNA methylation, and metabolomics on all individuals can be analyzed on centralized computational facilities, namely a 64-core virtual machine in the SURFsara High Performance Computing cloud. Here, BBMRI-Omics data are readily accessible through the dedicated R package BBMRIomics.

Access to BBMRI-Omics data using a centralized computational facility

In the near future we will have one data access procedure, but currently you still have to follow the separate data access procedures:

• For access to the Whole Genome Sequencing data, please go to the GoNL page.
• For access to Gene Expression or DNA methylation data, please go to the BIOS consortium page.
• For access to the Metabolomics data, please go to the Metabolomics Consortium page.

Wiki

The BBMRI BIOS consortium has in parallel with the Metabolomics Consortium generated DNA Methylation and Gene expression data. At the wiki, created by the BBMRI BIOS consortium, you can also find all the information concerning data requests, access and processing.

Support for BBMRI-NL’s Omics data set

For support on using the Omics dataset, contact Leon Mei, Molecular Epidemiology, Leiden University Medical Center.

BBMRI-Omics Management Team

Marian Beekman¹, Bastiaan T. Heijmans¹, Joyce van Meurs², Lude Franke³, Marleen van Greevenbroek⁴, Arfan Ikram⁵, Dorret I. Boomsma⁶, P. Eline Slagboom¹

1.Molecular Epidemiology, LUMC, Leiden

2.Internal Medicine, Erasmus University Medical Center, Rotterdam

3.Genetics, University Medical Center Groningen, University of Groningen, Groningen

4.Internal Medicine, School for Cardiovascular Diseases, Fac. Health, Medicine and Life Sciences, Maastricht University, Maastricht

5.Epidemiology, Erasmus University Medical Center Rotterdam, Rotterdam

6.Biological Psychology, Vrije Universiteit, Amsterdam