General introduction

The Netherlands X-omics Initiative is a  new facility as part of the National Roadmap for Large-Scale Research Infrastructures. It is partly funded by NWO with a total budget of 40 million euro. The project started on September 2018 and will last for ten years.

The project aims to establish a X-omics research infrastructure across the Netherlands consisting of several existing facilities with various expertise‚Äôs related to molecular biology research (genomics, proteomics, metabolomics and data integration & analysis).

Through the project, we will:
1. Advance X-omics technologies far beyond state-of-art,
2. Realize an integrated X-omics infrastructure in the Netherlands.

Access will be provided to these facilities to enable researchers to use the newest X-omics technologies in their projects and drive new insights in biology.

helpdesk will be created through which researchers can get into contact with our experts for advice on X-omics approaches in general or specific omics-related sample or data analysis challenges.

During the project, training schools will be set up with courses on X-omics approaches and several meetings will be organized to expand the Dutch X-omics community.

A proof of principle of the X-omics approach will be provided by starting 3 technological demonstrators on different levels (cellular, individual and population).

Dutch collaboration

The Netherlands X-omics Initiative will be organized as a distributed network, consisting of a set of innovation cores (that drive innovation in data integration and analysis, genomics, proteomics and metabolomics) and application nodes (research institutes that ensure scalable access and broad uptake of these innovative technologies), see also the figure below. These cores and nodes will actively reach out to other facilities in the same omics areas and with (inter)national life sciences and clinical users through symposia, interactive workshops and a consultancy helpdesk. 

Overview of the dutch partners involved and organizational structure. 

The four pillars of the Netherlands X-omics Initiative will each be spearheaded by innovation cores: UMCU for genomics, Utrecht University for proteomics, Leiden University for metabolomics and Radboudumc for data integration & analysis.
These cores will oversee and direct the technological progress, as well as safeguard the X-omics implementation. The innovation cores will closely interact and collaborate with the application nodes, represented by laboratories in University of Groningen, UMC Groningen, Netherlands Cancer Institute, Hubrecht Institute, Leiden UMC, Erasmus MC. Together, these institutes will contribute to the innovation of X-omics technologies and make sure they are implemented locally.

Project objectives

The Netherlands X-omics initiative has two main objectives:

(1) pushing the technological boundaries in each of the omics areas.
(2) realizing an  integrated X-omics infrastructure.

Pushing the technological boundaries

Over the last two decades the Dutch omics infrastructure has become globally competitive and recognized for its innovativeness and impact. Realizing new methods and technologies to increase the throughput and miniaturization of omics technologies is key to further develop novel insights and applications. We will do so by:

(1) higher throughput, lowering costs and sample needed to improve scaling of whole genome sequencing analysis and tag-based approaches. 
(2) higher accuracy and sensitivity for e.g. structural variant detection using long-read technology. 
(3) improve coverage of analysis towards more complete (human) genomes and transcriptomes.

(1) higher throughput, lowering costs and sample needed, aiming at assays to support clinical decision making and other applications.
(2) development of faster and more sensitive mass spectrometers to improve proteome coverage and separation of proteoforms. 
(3) development of more sensitive enrichment technologies to improve depth of analysis of post-translational protein modifications.
(4) development of novel cross-linking approaches and affinity-proteomics technologies to elucidate the structural organization of proteins in their natural cellular environment. 
(5) in-depth charting of the molecular interactions within the cell, and how they respond to external perturbations.

(1) higher throughput, lowering costs and sample needed to enable single cell and population-based metabolomics analyses.
(2) absolute quantitation for more metabolites enabling the combination of different studies and additional data analysis strategies such as fluxomics.
(3) studying the dynamics within and between cells and tissues and the human body.

Realizing an integrated X-omics infrastructure

To fully benefit from the combined X-omics approach, we will develop national integration at three levels:

1.   Building a Netherlands X-omics expert community and access portal to facilitate researchers in designing and performing smart X-omics experiments. This community will include experts in statistical study design, cell biology, translational and clinical sciences, sample isolation, handling and storage, specific omics technologies, data stewardship and bioinformatics.

2.   Developing high quality data stewardship procedures for the generation and management of genomics, proteomics and metabolomics data (FAIR at the source) and develop infrastructures to share and jointly analyse omics data, also connecting to other data such as imaging, epidemiological and clinical data.

3.   Realizing an innovative X-omics integrative data analysis framework to facilitate the translation of big omics data to biologically relevant information, driven by experts in statistics, chemometrics and bioinformatics.

This research was (partially) funded by NWO, project 184.034.019