News

Evidence for 28 genetic disorders discovered by combining healthcare and research data

A  collaboration between X-omics partner Radboudumc, GeneDx and the Wellcome Sanger Institute has discovered 28 genes that can be linked to developmental disorders.

Exome-sequence datasets from the three different institutes were combined into a cohort of 31,058 patients in order to have more statistical power. It became the largest statistical study of these mutations to date.

The approach and results of this work have been published in the scientific journal Nature. See the link below for the full article.

X-omics consortium member Christian Gilissen jointly supervised this great work and several other consortium members were involved.

View article

Summary X-omics festival 2020

On September 28th, X-omics organized the second edition of the X-omics festival “the future of X-omics research is now!”.

The event contained a keynote lecture about the 100,000 Genomes Project, lectures from young investigators, lectures with reference to several application areas and technology pitches.

The second X-omics festival was a success and we thank all the speakers, the sponsors and the participants.

An overview of the highlights, key take home messages, presentations and a link to the festival recordings has been compiled and can be found at our festival page.

We hope to see you again during future X-omics events.

Recap festival 2020

UMC Utrecht one of the first GeoMx Premier Access sites

We are excited to announce that our X-omics Genomics core UMC Utrecht has been selected as one of the eight global GeoMx Premier Access Sites. Under this agreement, Edwin Cuppen, Ies Nijman and their team will enable a broader user base to try the Cancer Transcriptome Atlas and evaluate the applicability of GeoMX Digital Spatial Profiler in their research.

NanoString Technologies, a leading provider of life science tools for discovery and translational research, announced the establishment of the GeoMx Premier Access Sites, a global service network that will provide access to the GeoMx Cancer Transcriptome Atlas and future GeoMx commercial assays. The company also announced the availability of the new GeoMx Whole Transcriptome Atlas through the Technology Access Program for the GeoMx Digital Spatial Profiler (DSP). Together these initiatives provide expanded access to next generation sequencing readout on GeoMx DSP.

More information

Cancelation X-omics workshop

Cancelation X-omics workshop “Strategies to overcome your challenges in X-omics data integration” (September 29th 2020)

As a result of the current coronavirus measures, the maximum number of participants that could join the workshop in person is limited. Therefore, we have decided to cancel this workshop 

An alternative online workshop series will be organized later this year.

We will provide you with further details about this online workshop series in September.

We hope you understand the decision we had to make and that you all will join us during the online workshop series instead.

HUPO webinar

HUPO Connect 2020 will organize a series of 60 minute webinars as a prelude to the main Congress sessions.

On Thursday 24 September 2020, 16:00 CEST, our leader of the innovation core Proteomics, Albert Heck will participate in the webinar “New Innovations in Proteomics” and talk about “Fishing Within the Proteome with Phosphate and Phosphonate Handles”.

Attendees will be able to submit questions via a text chat or live Q&A directly after the presentations.

Go register yourself for this amazing webinar and receive a discount for the main congress registration.

More information and registration

New collaboration between our proteomics innovation core Utrecht University and Bruker

Our partner Utrecht University and Bruker announce a collaboration to advance the study of the 3-D structures and interactions of proteins by mass spectrometry. The laboratory of Albert Heck at Utrecht University has been a leader in proteomics and the study of protein structure and interactions by mass spectrometry for over two decades. Richard Scheltema recently joined Utrecht University as group leader to focus on crosslinking mass spectrometry (XL-MS) for structural and interaction proteomics.

The collaborative work will focus on the development of TIMS (Trapped Ion Mobility Spectrometry) and PASEF (Parallel Accumulation Serial Fragmentation) methods, along with crosslinkers and XL-MS software for the timsTOF Pro 4D-Proteomics mass spectrometer, in order to take advantage of its unique large-scale, accurate CCS workflows.

Combining the novel, enrichable PhoX crosslinker, developed by Heck and Scheltema, with the extreme speed and sensitivity of PASEF methods on the timsTOF Pro platform, enables the discovery of more crosslinked products which yield more information about protein structures and interactions.


More information about this research

New COVID-19 genetic factor discovered at X-omics partner Radboud university medical center

Corona Radboudumc

A new COVID-19 genetic factor has been discovered by the Radboud university medical center. A multidisciplinary team of immunologists, geneticists and various experts from other disciplines collaborated to achieve this important finding. The genomics facility of X-omics, located at the Radboud university medical center, was used for this research.

The approach and results of this work have been published in a Preliminary Communication of JAMA network. See the link below for the full article.

Preliminary Communication:
fullarticle @ jamanetwork.com

In the youtube video below, X-omics consortium member, Alexander Hoischen, explains the discovery in more detail together with members of the multidisciplinary team involved, Caspar van der Made and Frank van de Veerdonk. The video features the genomics facility of X-omics used in this research and its new equipment.

Watch on Youtube

PMID: 32706371

Summary X-omics online workshop series “Strategies to Overcome Your Challenges in Multi-omics Data Integration”

In June, X-omics organized its first online workshop series. Different aspects of challenges and solutions related to multi-omics data integration were addressed in four workshops:

#1 Data standards and multi-omics data integration
#2 Linked data in practice: An RDF based-approach with SPARQLing-genomics
#3 Showcases of multi-omics data integration
#4 Pitch your own multi-omics project

The workshop series was a  success and we want to thank all those who participated, the speakers, the invited experts and the workshop organizing committee.

An overview of all workshop highlights, key take-home messages, presentations and a link to the workshop recordings has been compiled and can be found in the training schools section

We hope to see you again during future X-omics events.

Workshop series

Big data in the fight against Covid-19 – Podcast

Peter-Bram ‘t Hoen, our core team member and leader of the data pillar was invited to give his opinion on the use of big data in the fight against the Covid-19 pandemic. 

On Tuesday 19th May he talked about the Personal Health Train project as an efficient way of making health data accessible In the NPO podcast “De Dag” 

Interested in what he has to say? Listen to the podcast:

NPO podcast "De Dag" (In Dutch only)

High-Resolution mRNA and Secretome Atlas of Human Enteroendocrine Cells

Researchers from our partner institution Utrecht University have worked together with researchers from the Hubrecht Institute and in collaboration with other research teams and generated an in-depth description of the hormone-producing cells in the human gut. 

These are very rare and unique cells to different species of animals which makes them difficult to study. An extensive toolbox has been developed by the researchers to study human hormone-producing cells in tiny versions of the gut grown in the lab (organoids). These tools allowed them to uncover secrets of the human gut.

More information about this research

The study findings and results are presented in the scientific journal Cell.

PMID: 32407674

Training schools

X-omics online workshop series “Strategies to Overcome Your Challenges in Multi-omics Data Integration”

June 2020

In June 2020, X-omics organized the first online workshop series. Different aspects of challenges and solutions related to multi-omics data integration were addressed in four workshops.

Workshop series

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