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At GenomeScan, we take pride in providing cutting-edge Next Generation Sequencing (NGS) services and high-quality data to researchers worldwide, and we couldn’t be more excited to see the incredible research work that has resulted from our collaboration. So, we want to celebrate these with an exciting opportunity to showcase research achievements of our scientific community.

Below articles are featured on our website as part of our publications campaign. If you would like to learn more and submit your own article, please visit this page.

Selected Publications

hendrik veelken profile Publications in Collaboration with GenomeScan

Comprehensive diagnostics of acute myeloid leukemia by whole transcriptome RNA sequencing

Hendrik Veelken is Professor of Internal Medicine, specifically Haematology, and chair of the Department of Haematology in LUMC. In addition, he holds the function of coordinator of the LUMC Theme for Innovation “Cancer”.

In their study, Veelken and his colleagues sought to establish whole transcriptome RNA sequencing as a single, comprehensive, and flexible platform for acute myeloid leukemia (AML) diagnostics. In collaboration with GenomeScan, they performed whole transcriptome RNA sequencing on 100 AML cases. As a result, they accurately and simultaneously detected fusion genes, small genetic variants, and tandem insertions with diagnostic relevance for AML.

Marlijn van der Poel profile Publications in Collaboration with GenomeScan

Transcriptional profiling of human microglia reveals grey–white matter heterogeneity and multiple sclerosis-associated changes

Marlijn van der Poel was a PhD candidate in the Netherlands Institute for Neuroscience at the time of the publication, and currently holds a teaching position in University of Amsterdam.

In their study, van der Poel and her colleagues investigated the transcriptional profile of human microglia, isolated from normal-appearing grey matter (GM) and white matter (WM) of multiple sclerosis (MS) and non-neurological control donors, to find possible early changes related to MS pathology. As a result, they identified a region-specific transcriptional profile for human microglia in GM and WM tissue, especially important to consider in the search for novel therapeutic interventions. They also identified microglial changes in normal-appearing MS tissue associated with known MS pathology, pointing toward an important role for microglial metabolic changes in MS pathology.

Robin Mesnage profile Publications in Collaboration with GenomeScan

Impacts of dietary exposure to pesticides on faecal microbiome metabolism in adult twins

Robin Mesnage was a Research Associate in King’s College London at the time of the publication, and currently holds the position Lead Data Scientist in Buchinger Wilhelmi clinics in Germany.

In their study, Mesnage and his colleagues performed the first pesticide biomonitoring survey of the British population, and subsequently used the results to perform the first pesticide association study on gut microbiome composition and function from the TwinsUK registry. They selected 65 twin monozygotic twin pairs for their study and used shotgun metagenomics in collaboration with GenomeScan to analyze faecal microbiota. Their results provided the first evidence of an association between pesticide excretion and changes in gut microbiome metabolism at environmental levels of exposure in the UK population.

quinten ducarmon profile Publications in Collaboration with GenomeScan

Gut colonisation by extended-spectrum β-lactamase-producing Escherichia coli and its association with the gut microbiome and metabolome in Dutch adults: a matched case-control study

Quinten Ducarmon is a Postdoctoral Fellow, in LUMC at the time of the publication, and currently in EMBL Heidelberg.

Ducarmon and his colleagues performed the first study to investigate microbiome-mediated colonisation resistance against extended-spectrum β-lactamase (ESBL)-producing E coli using a combination of metagenomics, metabolomics, and machine-learning approaches. In collaboration with GenomeScan, they applied shotgun metagenomic sequencing to 51 ESBL-positive samples and 51 matched ESBL-negative samples. Their negative findings suggest that microbiome-mediated colonisation resistance might not be as relevant against ESBL-producing E coli as it is for other Gram-positive enteric pathogens.

Alka Rao profile Publications in Collaboration with GenomeScan

Membrane Adaptations and Cellular Responses of Sulfolobus acidocaldarius to the Allylamine Terbinafine

Alka Rao is a PhD candidate in University of Groningen in the field of biotechnology and applied microbiology.

In their study, Rao and her co-authors Niels A. W. de Kok and Arnold J. M. Driessen investigated the effect of terbinafine (an antifungal) on the lipidome and transcriptome of the aerobic crenarchaeon Sulfolobus Acidocaldarius. They were specifically interested in two membrane lipid types: bilayer-forming dialkyl glycerol diethers (DGDs) and monolayer-forming glycerol dialkyl glycerol tetraethers (GDGTs). Their transcriptomic data generated in collaboration with GenomeScan indicated that terbinafine has a multitude of effects, including significant differential expression of genes in the respiratory complex, motility, cell envelope, fatty acid metabolism, and GDGT cyclization.

Eric Snijder profile Publications in Collaboration with GenomeScan

SARS-coronavirus-2 replication in Vero E6 cells: replication kinetics, rapid adaptation and cytopathology

Eric Snijder is professor of Molecular Virology and head of the Section Research of the Department of Medical Microbiology of Leiden University Medical Center (LUMC). He is also a board member of the LUMC Research Theme Infection and involved in a variety research projects on coronaviruses and antiviral drug development.

In their study, the LUMC team characterized the newly emerging SARS-CoV-2 and conducted a comparative analysis of the replication features of SARS-CoV-2 and SARS-CoV in Vero E6 cells, one of the most commonly used cell lines for studying these two viruses. By using NGS, they discovered the rapid evolution of the SARS-CoV-2 Spike protein when using Vero E6 cells. This later resulted in the discovery that the virus can use an alternative entry pathway in this cell line, which differs from the entry route used in human lung cells. This Vero E6 cell culture adaptation had important implications for the interpretation of drug screening data and many other SARS-CoV-2 studies performed in Vero E6 cells.

The authors also kindly added in the acknowledgements section: “We thank various GenomeScan staff members for the pleasant and swift collaboration that facilitated the NGS and data analysis of the first SARS-CoV-2 samples.”

cheng chih hsiao profile Publications in Collaboration with GenomeScan

Osteopontin associates with brain TRM-cell transcriptome and compartmentalization in donors with and without multiple sclerosis

Cheng-Chih Hsiao was a Senior Postdoctoral Fellow in the Netherlands Institute for Neuroscience at the time of the publication and currently holds Research Associate position in The Netherlands Brain Bank.

In their study, Hsiao and his colleagues compared gene expression profiles of tissue-resident memory T (TRM) cells from a total of 22 human brains post-mortem, either with multiple sclerosis (MS)-associated lesions or with normal-appearing white matter. Brain TRM cells showed a characteristic expression profile with presence of MS4A1 (CD20) and SPP1 (osteopontin, OPN) that was conserved in cells isolated from MS lesions. Notable, lesion-associated TRM cells produced less cytokines upon ex vivo, indicative of T-cell activity inhibition.

Karel Scheepstra profile Publications in Collaboration with GenomeScan

Microglia Transcriptional Profiling in Major Depressive Disorder Shows Inhibition of Cortical Gray Matter Microglia

Karel Scheepstra is a psychiatrist and researcher at the Amsterdam UMC and Netherlands Institute for Neuroscience, whose work focuses on the neurobiology and treatment of mood disorders.

In their study, Scheepstra and his colleagues compared gene expression profiles of microglia isolated at brain autopsy from 13 donors with major depressive disorder (MDD) and 10 age-matched control donors. Their analysis on microglia isolated from occipital gray matter revealed 92 differentially expressed genes and indicated an immune-suppressed microglial phenotype in MDD. Microglia isolated from corpus callosum white matter did not show a significant difference between the groups.

More articles coming soon…

Above articles are featured on our website as part of our publications campaign. If you would like to learn more and submit your own article, please visit this page.

For an overview of all featured scientific articles with GenomeScan’s contribution since 2012, please visit our publications page.

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