The Netherlands X-omics Initiative will have a strong focus on training and outreach and in this respect, will organize different types of events & activities in the coming 5 years. You can register for these events and activities at this website.

News

In our news section you will find interesting news and information related to x-omics technologies, research and its activities.

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

X-omics online Festival 2020

festival poster

As a result of the current coronavirus measures, the maximum number of participants that could join the festival in person is limited.

Therefore, X-omics has decided to organize this year’s festival as an online event on the same date: September 28th 2020.

If you would like to participate in this online edition of the X-omics festival then please register yourself again, so you will receive the new details including a link to participate. Registration is open via the button below.

The program has slightly changed. Here you can find the adapted version. Unfortunately, we no longer offer the possibility to display scientific posters.

We hope to see you all during the online edition of our X-omics festival on September 28th 2020.

Events

In our event section we will keep you updated on all events organized by x-omics and other organizations that relate to one of X-omics pillars (Genomics, Proteomics, Metabolomics, Data Analysis, Integration & Stewardship) or a combination of these fields.

X-omics online Festival 2020 

festival poster

Where Where icon Online
When  Calendar icon   September 28

HUPO Webinar

New innovations in Proteomics

HUPO Connect 2020

Where Where icon Online
When  Calendar icon   September 24

Visit hupo2020.org

Highlights

In our highlight section we will keep you posted about the purchase of new equipment, publications created with the help of the X-omics infrastructure and we will provide a platform to young investigators to introduce themselves.

Yanick Hagemeijer

Anna NiehuesI’m a PhD student at the University of Groningen (UG), where I work at the European Research Institute for the Biology of Ageing (ERIBA) and at Groningen Research Institute of Pharmacy (GRIP), my 2 promoters are Peter Horvatovich, from the department of Analytical Biochemistry at the UG and Victor Guryev from the Group of Genome Structure and Ageing (University Medical Center Groningen, UMCG) are both part of X-omics Netherlands Infrastructure Consortium as well. Currently, I am involved in the X-omics project with the goal of making a ‘portable’ pipeline to perform proteogenomics analysis from start to end.

I previously studied Bioinformatics at the Hogeschool van Arnhem & Nijmegen. During my Bsc I did an internship at the bacterial genomics group at the Center for Molecular and Biomolecular Informatics (CMBI). Following this research experience, I did another at the Hubrecht institute in Utrecht where Victor Guryev was my supervisor. After I graduated I went to Wageningen University & Research centre (WUR). Here, I did my master theses at the departments of Animal Breeding and Genetics (ABG) and Systems & Synthetic Biology (SSB). After finishing I applied for a job at the department of Experimental Cardiology at the UMCG. During my research there, I was working as a data-analyst/bioinformatician focused on performing GWAS analysis in the context of medical/cardiac phenotypes.

I regretted focusing solely on genomics and transcriptomics and not learning more about proteomics and other omics layers. This PhD within the X-omics Consortium allows me to work at the crossroads of sequencing and mass spectrometry data as part of the data integration and stewardship pillar. I’m interested in bringing the complexities of genomics and transcriptomics to the proteomics field. The integration of the patient specific protein variants to create personalized protein sequence databases, which can be used for database searching large LC-MS/MS datasets and to identify patient specific variants that have implications in complex diseases such as cancer and COPD. Currently, proteomics analysis pipelines rely on canonical sequences from (curated) public databases such as Ensembl and Uniprot. Simply including all possible ‘translate-able’ sequences leads to a large search space and low statistical power to identify protein variants. The goal of my PhD project is to provide a proteogenomics pipeline, which uses genomics and/or transcriptomics data to make a protein database containing all protein variants present in a clinical/biological proteomics sample that is both small and accurate without including large amounts of hypothetical proteins for which there is no support in the genomics or transcriptomics data. In case you have similar interests - let’s collaborate!

Pleguezuelos-Manzano, C. et al. (2020)

Mutational signature in colorectal cancer caused by genotoxic pks + E. coli. Nature

PMID: 32106218

Publications

In our publications section you will find an archive of publications on which our X-omics consortium members have worked, relevant technological publications and interesting x-omics publications. In the highlight section we will highlight the latest publications.

The publications of the X-omics consortium will be listed here!

  • 2020

    Van der Made, Cl. (2020). Presence of Genetic Variants Among Young Men With COVID-19. JAMA.

    PMID: 32706371

    Beumer, J. et al. (2020). High-Resolution mRNA and Secretome Atlas of Human Enteroendocrine Cells. Cell.

    PMID: 32407674

    Pleguezuelos-Manzano, C. et al. (2020). Mutational signature in colorectal cancer caused by genotoxic pks + E. coli. Nature.

    PMID: 32106218

    Dekker, LJM. et al. (2020). Metabolic changes related to the IDH1 mutation in gliomas preserve TCA-cycle activity: An investigation at the protein level. FASEB J. 34, 3646 – 3657.

    PMID: 31960518

    Lamers, MM. et al. (2020). SARS-CoV-2 productively infects human gut enterocytes. Science.

    PMID: 32358202
    Zajec, M. et al. (2020). Integrating Serum Protein Electrophoresis with Mass Spectrometry, A New Workflow for M-Protein Detection and Quantification. J Proteome Res.

    PMID: 31895568
  • 2019

    Körner, A. et al. (2019). Inhibition of ∆24-dehydrocholesterol reductase activates pro-resolving lipid mediator biosynthesis and inflammation resolution. Proc Natl Acad Sci U S A. 116, 20623 – 20634. 

    PMID: 31548397
    Lageveen-Kammeijer, GSM. et al. (2019). Highly sensitive CE-ESI-MS analysis of N-glycans from complex biological samples. Nat Commun. 10, 2137.

    PMID: 31086181
    Palmblad, M. et al. (2019). Automated workflow composition in mass spectrometry-based proteomics. Bioinformatics. 35, 656 – 664.

    PMID: 30060113
    van der Kant, R. et al. (2019). Cholesterol Metabolism Is a Druggable Axis that Independently Regulates Tau and Amyloid-β in iPSC-Derived Alzheimer’s Disease Neurons. Cell Stem Cell. 24, 363-275.

    PMID: 30686764
    Weintraub, ST. et al. (2019). Special Issue on Software Tools and Resources: Acknowledging the Toolmakers of Science. J Proteome Res. 18, 575.

    PMID: 30704244
    Lacobucci, C. et al. (2019). First Community-Wide, Comparative Cross-Linking Mass Spectrometry Study. Anal Chem. 91, 6953-6961.

    PMID: 31045356
    Masson, GR. et al. (2019). Recommendations for performing, interpreting and reporting hydrogen deuterium exchange mass spectrometry (HDX-MS) experiments. Nat Methods. 16, 595-602.

    PMID: 31249422
    Ressa, A. et al. (2019). PaDuA: A Python Library for High-Throughput (Phospho)proteomics Data Analysis. J Proteome Res. 18, 576-584.

    PMID: 30525654
    Greisch, JF. et al. (2019). Expanding the mass range for UVPD-based native top-down mass spectrometry. Chem Sci. 10, 7163-7171.

    PMID: 31588283
    van der Laarse, SAM. et al. (2019). Targeting proline in (phospho)proteomics. FEBS J.

    PMID: 31863553
    van der Laan, T. et al. (2019). Fast LC-ESI-MS/MS analysis and influence of sampling conditions for gut metabolites in plasma and serum. Sci Rep. 9, 12370.

    PMID: 31451722
  • older

    Van Damme, T. et al. (2017). Mutations in ATP6V1E1 or ATP6V1A …. Am. J. Hum. Genet. 100, 216–227.
    van Gool, A. J. et al. (2017). Bridging the translational innovation gap …. Nat. Rev. Drug Discov.  
    Snijder, J. et al. (2017). Structures of the cyanobacterial circadian oscillator …. Science 355, 1181–1184.

    Blokzijl, F. et al. (2016). Tissue-specific mutation accumulation in human …. Nature 538, 260–264.
    Jansen, E. J. R. et al. (2016). ATP6AP1 deficiency causes an immunodeficiency …. Nat. Commun. 7, 11600.
    Liepe, J. et al. (2016). A large fraction of HLA class I ligands are …. Science 354, 354–358.
    Tarailo-Graovac, M. et al. (2016). Exome Sequencing and the … .N. Engl. J. Med. 374, 2246–2255.
    van Karnebeek, C. D. M. et al. (2016). NANS-mediated synthesis of sialic acid …. Nat. Genet. 48, 777–784.

    Huch, M. et al. (2015). Long-term culture of genome-stable bipotent stem cells…. Cell 160, 299–312.
    Liu, F., Rijkers, et. al. (2015). Proteome-wide profiling of protein a…. Nat. Methods 12, 1179–84.

    Dane, A. D. et al. (2014). Integrating metabolomics profiling …. Anal. Chem. 86, 4110–4.
    Hussein, S. M. I. et al. (2014). Genome-wide characterization of…. Nature 516, 198–206.
    Tegtmeyer, L. C. et al. (2014). Multiple Phenotypes in … N. Engl. J. Med. 370, 533–542.
    van Heesch, S. et al. (2014). Genomic and functional overlap between somatic and …. Cell Rep. 9, 2001–10.

    Altelaar, A. F. M., et. al. (2013). Next-generation proteomics: …. Nat. Rev. Genet. 14, 35–48.
    Gonzalez-Covarrubias, V. et al. (2013). Lipidomics of familial longevity. Aging Cell 12, 426–34.
    Kettleborough, R. N. W. et al. (2013). A systematic genome-wide analysis of…. Nature 496, 494–7.
    Low, T. Y. et al. (2013). Quantitative and qualitative proteome characteristics. Cell Rep. 5, 1469–78.
    Peironcely, J. E. et al. (2013). Automated pipeline for de novo …. Anal. Chem. 85, 3576–83.
    Raterink, R.-J et. al. (2013). T. Three-phase electroextraction: …. Anal. Chem. 85, 7762–8.

    van der Kloet, F. M. et al. (2012). Discovery of early-stage biomarkers …Metabolomics 8, 109–119.

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