E. Cuppen

The Minimal Dataset for Cancer of the 1+Million Genomes Initiative

The paper develops a standardized data model for cancer genomics to enable interoperable data sharing across countries.

Genomic and transcriptomic landscape of advanced renal cell cancer to individualize treatment strategy

This study uses genomic and transcriptomic data from advanced renal cell cancer patients to identify actionable mutations and immune signatures to guide personalized treatment strategies.

Recurrent exon-deleting activating mutations in AHR act as drivers of urinary tract cancer

This study identifies AHR{Delta}e8-9 as a novel driver mutation in urinary tract cancer, leading to ligand-independent pathway activation and tumorigenic properties in bladder organoids.

Unscrambling cancer genomes via integrated analysis of structural variation and copy number

This paper introduces LINX, a tool for analyzing structural variation and copy number alterations in cancer genomes, revealing novel insights into oncogenic fusions and inactivation events.

Learning mutational signatures and their multidimensional genomic properties with TensorSignatures

This paper introduces TensorSignatures, an algorithm that jointly learns mutational signatures across mutation types and genomic context, revealing new insights into mutational processes in cancer.

SARS-CoV-2 Productively Infects Human Gut Enterocytes

The paper shows SARS-CoV-2 infects human gut enterocytes in small intestinal organoids, leading to viral replication and a strong immune response.

Pan-cancer landscape of homologous recombination deficiency

This study develops a pan-cancer Classifier of Homologous Recombination Deficiency (CHORD) and identifies HRD frequency and genetic causes across multiple cancer types.

The genomic landscape of metastatic castration-resistant prostate cancers reveals multiple distinct genotypes with potential clinical impact

This study uses whole-genome sequencing to identify four distinct genotypes in metastatic castration-resistant prostate cancers, with potential clinical implications for patient stratification.

Pan-cancer whole genome analyses of metastatic solid tumors

This study analyzes whole genome sequences of metastatic solid tumors to identify genetic variants that may influence treatment outcomes.

Mutational impact of chronic alcohol use on stem cells in cirrhotic liver

This study investigates the mutational impact of chronic alcohol use on liver stem cells in cirrhotic livers and finds no alcohol-specific mutational signatures but identifies enriched oncogenic mutations in cancer genes.

5-Fluorouracil treatment induces characteristic T>G mutations in human cancer

This study shows that 5-FU treatment causes characteristic T>G mutations in cancer, similar to endogenous mutational signatures, and may increase secondary malignancy risk.

A deep learning system can accurately classify primary and metastatic cancers based on patterns of passenger mutations

This paper develops a deep learning classifier using whole genome sequencing data to distinguish cancer types and identify metastatic origins.

Long-term expanding human airway organoids for disease modelling.

This study establishes long-term-expanding human airway organoids from broncho-alveolar biopsies or lavage material, enabling disease modeling of cystic fibrosis, lung cancer, and RSV infection.

A system-wide approach to monitor responses to synergistic BRAF and EGFR inhibition in colorectal cancer cells

The paper investigates molecular responses to BRAF and EGFR inhibition in colorectal cancer cells, revealing metabolic shifts and MAPK pathway reactivation.