Mark Pieterse
A5059181239- Immunotherapy and Immune Responses
- Monoclonal and Polyclonal Antibodies Research
- Cancer Immunotherapy and Biomarkers
- Colorectal Cancer Treatments and Studies
- Genetic factors in colorectal cancer
- CRISPR and Genetic Engineering
- DNA Repair Mechanisms
- SARS-CoV-2 detection and testing
- Cancer Genomics and Diagnostics
- PARP inhibition in cancer therapy
- Hepatocellular Carcinoma Treatment and Prognosis
- BRCA gene mutations in cancer
- Genetics, Bioinformatics, and Biomedical Research
- Molecular Biology Techniques and Applications
- vaccines and immunoinformatics approaches
- Genomics and Chromatin Dynamics
- Lymphoma Diagnosis and Treatment
- Gene expression and cancer classification
- Plant Molecular Biology Research
- RNA and protein synthesis mechanisms
- Colorectal and Anal Carcinomas
- Advanced biosensing and bioanalysis techniques
- SARS-CoV-2 and COVID-19 Research
- RNA modifications and cancer
- Viral-associated cancers and disorders
Oncode Institute
2010-2021
University Medical Center Utrecht
2014-2021
Utrecht University
2020
Hubrecht Institute for Developmental Biology and Stem Cell Research
2017
The Netherlands Cancer Institute
2010-2016
Cancer Genomics Centre
2013-2016
Heterozygous germline mutations in breast cancer 1 (BRCA1) strongly predispose women to cancer. BRCA1 plays an important role DNA double-strand break (DSB) repair via homologous recombination (HR), which is for tumor suppression. Although BRCA1-deficient cells are highly sensitive treatment with DSB-inducing agents through their HR deficiency (HRD), BRCA1-associated tumors display heterogeneous responses platinum drugs and poly(ADP-ribose) polymerase (PARP) inhibitors clinical trials. It...
Abstract Mutations in BRCA1 and BRCA2 account for the majority of hereditary breast ovarian cancers, therefore sequence analysis both genes is routinely conducted patients with early-onset cancer. Besides mutations that clearly abolish protein function or are known to increase cancer risk, a large number variants uncertain significance (VUS) have been identified. Although several functional assays VUSs described, thus far it has not possible conduct high-throughput context full-length...
Abstract Genomic rearrangements that give rise to oncogenic gene fusions can offer actionable targets for cancer therapy. Here we present a systematic analysis of among clinically well-characterized, prospectively collected set 278 primary colon cancers spanning diverse tumor stages and clinical outcomes. Gene somatic genetic variations were identified in fresh frozen specimens by Illumina RNA-sequencing, the STAR fusion detection pipeline, GATK RNA-seq variant calling. We considered be...
In routine diagnostic pathology, cancer biopsies are preserved by formalin-fixed, paraffin-embedding (FFPE) procedures for examination of (intra-) cellular morphology. Such inadvertently induce DNA fragmentation, which compromises sequencing-based analyses chromosomal rearrangements. Yet, rearrangements drive many types hematolymphoid malignancies and solid tumors, their manifestation is instructive diagnosis, prognosis, treatment. Here, we present FFPE-targeted locus capture (FFPE-TLC)...
Abstract PALB2 interacts with BRCA1 and BRCA2 in supercomplexes involved DNA repair via homologous recombination. Heterozygous germline mutations confer a moderate risk of breast cancer, while biallelic are linked to severe form Fanconi anaemia characterized by early childhood solid tumours chromosomal instability. In contrast BRCA1‐ or BRCA2‐associated cancers, heterozygous mutation carriers do not show loss the wild‐type allele, suggesting might be haploinsufficient for tumour suppression....
Identification of immunogenic cancer neoantigens as targets for therapy is challenging. Here, we integrate the whole-genome and long-read transcript sequencing cancers to identify collection neo-open reading frame peptides (NOP) expressed in tumors. We termed this NOPs tumor framome. represent tumor-specific that are different from wild-type proteins may be strongly immunogenic. describe a class hidden derive structural genomic variants involving an upstream protein coding gene driving...
Resistance to treatment is the main problem of targeted for cancer. We followed ten patients during with vemurafenib, by three-dimensional imaging. In all patients, only a subset lesions progressed. Next-generation DNA sequencing was performed on sequential biopsies in four uncover mechanisms resistance. two we identified mutations that explained resistance vemurafenib; one these had secondary BRAF L505H mutation. This first observation mutation vemurafenib-resistant patient-derived melanoma...
<p>Figure S10: A) NOP expression compared to normal genes.</p>
<p>Figure S15: Tetramer gating strategy.</p>
<p>Figure S7: Protein mass spectrometry results for A375 NOPs.</p>
<p>Figure S16: Expansion of FRM-specific CD8T cells after priming with relevant peptide in PBMC from healthy individuals.</p>
<p>Figure S14: A375 immunopeptidomics.</p>
<p>Figure S1: RNA-guided tumor genome reconstruction.</p>
<p>Figure S4: Overview of somatic mutation statistics for tumor samples analyzed by WGS in this study.</p>
<p>Figure S16: Expansion of FRM-specific CD8T cells after priming with relevant peptide in PBMC from healthy individuals.</p>
<p>Figure S8: Comparison of EasyFuse short-read fusion gene caller with long-read and WGS guided NOP identification.</p>
<p>Figure S11: Example of a hidden NOP resulting from complex chromosomal rearrangement in tumor sample LUN022.</p>
<p>Figure S13: In silico determined immunogenic properties of NOPs.</p>
<p>Figure S8: Comparison of EasyFuse short-read fusion gene caller with long-read and WGS guided NOP identification.</p>
<div>Abstract<p>Identification of immunogenic cancer neoantigens as targets for therapy is challenging. Here, we integrate the whole-genome and long-read transcript sequencing cancers to identify collection neo-open reading frame peptides (NOP) expressed in tumors. We termed this NOPs tumor framome. represent tumor-specific that are different from wild-type proteins may be strongly immunogenic. describe a class hidden derive structural genomic variants involving an upstream...