Edwin P. J. G. Cuppen

This study compares whole-genome sequences of adolescent and young adult solid cancers to older adult cancers, finding shared genetic drivers but age-related differences in mutational processes and germline variants.

The paper develops a statistical framework to identify genomic non-response biomarkers in cancer therapies using whole-genome and transcriptome sequencing data from 2,596 patients.

This study identifies pathogenic germline variants in 11% of adult glioblastoma patients, with mismatch repair deficiency as the main predisposition mechanism.

This study evaluates genetic counselling strategies for genome sequencing-based tumour diagnostics, finding that post-test strategies reduce unnecessary referrals while maintaining PGV detection rates.

The paper characterizes genetic immune escape (GIE) across primary and metastatic tumors, finding high prevalence and type-specific differences in immune evasion mechanisms.

This study investigates the mutational consequences of global DNA hypomethylation by analyzing single-cell genetic variation in DNMT1-depleted cells, finding increased chromosomal instability without significant mutational burden or structural changes.

This study shows that EXO1 is essential for survival of BRCA1-deficient cells and identifies it as a potential therapeutic target.

The paper develops a random forest classifier using genome-wide mutation features to classify cancer of unknown primary (CUP) with high accuracy.

This study compares whole-genome sequences of primary and metastatic tumors across 7,152 samples, revealing cancer-type-specific genomic changes and treatment-induced evolutionary bottlenecks.

The paper compiles a comprehensive reference dataset of true somatic structural variations by analyzing melanoma and normal cell lines with multiple sequencing technologies and experimental validation.

This study identifies genomic subgroups in ovarian cancer associated with distinct treatment responses and survival outcomes using whole genome sequencing data.

The paper introduces an updated R/Bioconductor package for analyzing mutational patterns, demonstrating its ability to detect mutational signatures and their biological implications using simulated and real data.

This study validates whole genome sequencing as a reliable single assay for detecting various cancer mutations with high sensitivity and precision.

VIRUSBreakend identifies viral DNA integration with high sensitivity and low false discovery rate using single breakend variant calling in cancer genomes.

This study compares the costs of various diagnostic techniques, including whole genome sequencing, for treating specific cancers in the Netherlands.

GRIDSS2 identifies somatic structural variants by analyzing single breakends and phasing, achieving a 3.1% false negative rate in metastatic cancers and uncovering a novel duplication signature.

This study quantifies and characterizes mutation accumulation in human induced pluripotent stem cells and adult stem cells during in vitro culture, revealing distinct mutational signatures and higher mutation rates compared to in vivo.

Sperm DNA damage leads to genomic defects in embryos through chromosome fragmentation and segregation errors.

This study prioritizes driver genes in patients with de novo genomic structural variants using integrative analysis of WGS data, phenotype information, and chromatin organization datasets.

A three-tool chain calls somatic structural variants, purity, ploidy and copy number from paired tumour/normal whole genomes, then clusters breakpoints into derivative chromosome structures and gene fusions.

The paper predicts cancer cell-of-origin from DNA sequences by matching mutational landscapes to chromatin modification patterns in normal tissues.

The paper quantifies somatic mutation accumulation in fetal liver and intestinal stem cells, finding higher mutation rates and distinct mutation spectra in fetal liver compared to fetal intestine and adult tissues.

The paper shows that NER deficiency increases Signature 8 mutations in specific tissues and suggests this could be a biomarker for NER-deficiency in cancer.

MutationalPatterns analyzes mutational processes genome-wide to quantify mutational signatures and their relation to genomic features.

This study uses nanopore sequencing to detect and phase structural variants in patient genomes, identifying novel variants missed by short-read sequencing.