Geert A. Martens
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View article: AI-derived CT biomarker score for robust COVID-19 mortality prediction across multiple waves and regions using machine learning
AI-derived CT biomarker score for robust COVID-19 mortality prediction across multiple waves and regions using machine learning Open
View article: Development of a General Purpose Targeted LC-MS Method for Accurate Quantification of the SARS-CoV-2 Spike Protein Expression
Development of a General Purpose Targeted LC-MS Method for Accurate Quantification of the SARS-CoV-2 Spike Protein Expression Open
The COVID-19 pandemic has catalyzed interest in immuno-multiple reaction monitoring (immuno-MRM) methods, with the detection of peptides unique to the nucleocapsid protein in nasopharyngeal swabs. While current applications predominantly f…
View article: A nationwide comprehensive genomic profiling and molecular tumor board platform for patients with advanced cancer
A nationwide comprehensive genomic profiling and molecular tumor board platform for patients with advanced cancer Open
The Belgian Approach for Local Laboratory Extensive Tumor Testing (BALLETT) study assessed the feasibility of using comprehensive genomic profiling (CGP) in clinical decision-making for patients with advanced cancers. This multi-center stu…
View article: Unlocking precision oncology by establishing a nationwide comprehensive genomic profiling and molecular tumor board platform for patients with advanced cancer: the BALLETT study
Unlocking precision oncology by establishing a nationwide comprehensive genomic profiling and molecular tumor board platform for patients with advanced cancer: the BALLETT study Open
The increasing complexity of advanced-stage cancer management, coupled with the growing availability of targeted therapies, necessitates innovative approaches to treatment decision-making. The Belgian Approach for Local Laboratory Extensiv…
View article: Emergence of the B.1.214.2 SARS-CoV-2 lineage with an Omicron-like spike insertion and a unique upper airway immune signature
Emergence of the B.1.214.2 SARS-CoV-2 lineage with an Omicron-like spike insertion and a unique upper airway immune signature Open
View article: Patient-centric thresholding of Cobas® EGFR mutation Test v2 for surveillance of EGFR-mutated metastatic non-small cell lung cancer
Patient-centric thresholding of Cobas® EGFR mutation Test v2 for surveillance of EGFR-mutated metastatic non-small cell lung cancer Open
Cobas EGFR mutation Test v2 was FDA-approved as qualitative liquid biopsy for actionable EGFR variants in non-small cell lung cancer (NSCLC). It generates semiquantitative index (SQI) values that correlate with mutant allele levels, but de…
View article: Acoustic ejection mass spectrometry empowers ultra-fast protein biomarker quantification
Acoustic ejection mass spectrometry empowers ultra-fast protein biomarker quantification Open
The global scientific response to COVID 19 highlighted the urgent need for increased throughput and capacity in bioanalytical laboratories, especially for the precise quantification of proteins that pertain to health and disease. Acoustic …
View article: Emergence of the B.1.214.2 SARS-CoV-2 lineage with an Omicron-like spike insertion and a unique upper airway immune signature
Emergence of the B.1.214.2 SARS-CoV-2 lineage with an Omicron-like spike insertion and a unique upper airway immune signature Open
We investigate the emergence, mutation profile, and dissemination of SARS-CoV-2 lineage B.1.214.2, first identified in Belgium in January 2021. This variant, featuring a 3-amino acid insertion in the spike protein similar to the Omicron va…
View article: Patient-centric thresholding of Cobas® EGFR mutation Test v2 for surveillance of EGFR- mutated metastatic Non-Small Cell Lung Cancer
Patient-centric thresholding of Cobas® EGFR mutation Test v2 for surveillance of EGFR- mutated metastatic Non-Small Cell Lung Cancer Open
Cobas EGFR mutation Test v2 was FDA-approved as qualitative liquid biopsy for actionable EGFR variants in non-small cell lung cancer (NSCLC). It generates semiquantitative index (SQI) values that correlate with mutant allele levels, but de…
View article: Nationwide quality assurance of high-throughput diagnostic molecular testing during the SARS-CoV-2 pandemic: role of the Belgian National Reference Centre
Nationwide quality assurance of high-throughput diagnostic molecular testing during the SARS-CoV-2 pandemic: role of the Belgian National Reference Centre Open
View article: Rational thresholding of circulating tumor DNA concentration for improved surveillance of metastatic breast cancer
Rational thresholding of circulating tumor DNA concentration for improved surveillance of metastatic breast cancer Open
View article: Immunovirological and environmental screening reveals actionable risk factors for fatal COVID-19 during post-vaccination nursing home outbreaks
Immunovirological and environmental screening reveals actionable risk factors for fatal COVID-19 during post-vaccination nursing home outbreaks Open
View article: 28P Rational thresholding of circulating tumor DNA copy number for early detection of disease progression in advanced metastatic breast cancer
28P Rational thresholding of circulating tumor DNA copy number for early detection of disease progression in advanced metastatic breast cancer Open
Circulating tumor DNA (ctDNA) is promising as tumor-specific marker for progression surveillance in metastatic cancer. Our aim was to investigate the diagnostic power of ctDNA level for disease progression in metastatic breast cancer and t…
View article: Hereditary Tyrosinemia Type 1 Mice under Continuous Nitisinone Treatment Display Remnants of an Uncorrected Liver Disease Phenotype
Hereditary Tyrosinemia Type 1 Mice under Continuous Nitisinone Treatment Display Remnants of an Uncorrected Liver Disease Phenotype Open
Hereditary tyrosinemia type 1 (HT1) is a genetic disorder of the tyrosine degradation pathway (TIMD) with unmet therapeutic needs. HT1 patients are unable to fully break down the amino acid tyrosine due to a deficient fumarylacetoacetate h…
View article: DeltaMSI: artificial intelligence-based modeling of microsatellite instability scoring on next-generation sequencing data
DeltaMSI: artificial intelligence-based modeling of microsatellite instability scoring on next-generation sequencing data Open
Background DNA mismatch repair deficiency (dMMR) testing is crucial for detection of microsatellite unstable (MSI) tumors. MSI is detected by aberrant indel length distributions of microsatellite markers, either by visual inspection of PCR…
View article: Improved Detection of Disease Progression in Metastatic Breast Cancer by Absolute Molecular Counting of Circulating Tumor DNA: A 100 Copies Question
Improved Detection of Disease Progression in Metastatic Breast Cancer by Absolute Molecular Counting of Circulating Tumor DNA: A 100 Copies Question Open
View article: Additional file 1 of DeltaMSI: artificial intelligence-based modeling of microsatellite instability scoring on next-generation sequencing data
Additional file 1 of DeltaMSI: artificial intelligence-based modeling of microsatellite instability scoring on next-generation sequencing data Open
Additional file 1. Implementation pseudocode DeltaMSI.
View article: Short-term nitisinone discontinuation of hereditary tyrosinemia type 1 mice causes metabolic alterations in glutathione metabolism/biosynthesis and multiple amino acid degradation pathways
Short-term nitisinone discontinuation of hereditary tyrosinemia type 1 mice causes metabolic alterations in glutathione metabolism/biosynthesis and multiple amino acid degradation pathways Open
View article: Predictive model for BNT162b2 vaccine response in cancer patients based on blood cytokines and growth factors
Predictive model for BNT162b2 vaccine response in cancer patients based on blood cytokines and growth factors Open
Background Patients with cancer, especially hematological cancer, are at increased risk for breakthrough COVID-19 infection. So far, a predictive biomarker that can assess compromised vaccine-induced anti-SARS-CoV-2 immunity in cancer pati…
View article: Cov<sup>2</sup>MS: An Automated and Quantitative Matrix-Independent Assay for Mass Spectrometric Measurement of SARS-CoV-2 Nucleocapsid Protein
Cov<sup>2</sup>MS: An Automated and Quantitative Matrix-Independent Assay for Mass Spectrometric Measurement of SARS-CoV-2 Nucleocapsid Protein Open
The pandemic readiness toolbox needs to be extended, targeting different biomolecules, using orthogonal experimental set-ups. Here, we build on our Cov-MS effort using LC-MS, adding SISCAPA technology to enrich proteotypic peptides of the …
View article: Two Years of Genomic Surveillance in Belgium during the SARS-CoV-2 Pandemic to Attain Country-Wide Coverage and Monitor the Introduction and Spread of Emerging Variants
Two Years of Genomic Surveillance in Belgium during the SARS-CoV-2 Pandemic to Attain Country-Wide Coverage and Monitor the Introduction and Spread of Emerging Variants Open
An adequate SARS-CoV-2 genomic surveillance strategy has proven to be essential for countries to obtain a thorough understanding of the variants and lineages being imported and successfully established within their borders. During 2020, ge…
View article: Predictive model for BNT162b2 vaccine response in cancer patients based on cytokines and growth factors
Predictive model for BNT162b2 vaccine response in cancer patients based on cytokines and growth factors Open
A bstract Background Patients with cancer, especially haematological cancer, are at increased risk for breakthrough COVID-19 infection. However, so far, a predictive biomarker that can assess compromised vaccine-induced anti-SARS-CoV-2 imm…
View article: From Delta to Omicron SARS-CoV-2 variant: Switch to saliva sampling for higher detection rate
From Delta to Omicron SARS-CoV-2 variant: Switch to saliva sampling for higher detection rate Open
View article: DeltaMSI: Artificial Intelligence-based modeling of microsatellite instability scoring by next- generation sequencing
DeltaMSI: Artificial Intelligence-based modeling of microsatellite instability scoring by next- generation sequencing Open
Background : DNA mismatch repair deficiency (dMMR) testing is crucial for detection of microsatellite unstable (MSI) tumors eligible for immunotherapy. MSI is detected by aberrant indel length distributions of microsatellite marker loci, e…
View article: From Delta to Omicron SARS-CoV-2 variant: switch to saliva sampling for higher detection rate
From Delta to Omicron SARS-CoV-2 variant: switch to saliva sampling for higher detection rate Open
Background Real-time polymerase chain reaction (RT-PCR) testing on a nasopharyngeal swab is the current standard for SARS-CoV-2 virus detection. Since collection of this sample type is experienced uncomfortable by patients, saliva- and oro…
View article: Three doses of BNT162b2 vaccine confer neutralising antibody capacity against the SARS-CoV-2 Omicron variant
Three doses of BNT162b2 vaccine confer neutralising antibody capacity against the SARS-CoV-2 Omicron variant Open
View article: Cov<sup>2</sup>MS: an automated matrix-independent assay for mass spectrometric detection and measurement of SARS-CoV-2 nucleocapsid protein in infectious patients
Cov<sup>2</sup>MS: an automated matrix-independent assay for mass spectrometric detection and measurement of SARS-CoV-2 nucleocapsid protein in infectious patients Open
INTRODUCTION The pandemic readiness toolbox needs to be extended, providing diagnostic tools that target different biomolecules, using orthogonal experimental setups and fit-for-purpose specification of detection. Here we build on a previo…
View article: Three doses of the BNT162b2 vaccine confer neutralising antibody capacity against the SARS-CoV-2 B.1.1.529 (Omicron) variant of concern
Three doses of the BNT162b2 vaccine confer neutralising antibody capacity against the SARS-CoV-2 B.1.1.529 (Omicron) variant of concern Open
We report the levels of neutralising antibodies against Wuhan, Delta and Omicron variants in healthy individuals pre-infected or not with SARS-CoV-2 and immunized with three doses of the BNT162b2 vaccine. Our observations support the rapid…
View article: Cycle Threshold Probability Score for Immediate and Sensitive Detection of B.1.351 SARS-CoV-2 Lineage
Cycle Threshold Probability Score for Immediate and Sensitive Detection of B.1.351 SARS-CoV-2 Lineage Open
Background Detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern associated with immune escape is important to safeguard vaccination efficacy. We describe the potential of delayed N gene amplificatio…
View article: Reduced humoral immune response after BNT162b2 coronavirus disease 2019 messenger RNA vaccination in cancer patients under antineoplastic treatment
Reduced humoral immune response after BNT162b2 coronavirus disease 2019 messenger RNA vaccination in cancer patients under antineoplastic treatment Open
The BNT162b2 vaccine is well-tolerated in cancer patients under active treatment. However, the antibody response of immunized cancer patients was delayed and diminished, mainly in patients receiving chemotherapy or rituximab, resulting in …