Wigard P. Kloosterman

This paper introduces NanoRCS, a method using nanopore sequencing and consensus calling to accurately estimate tumor fractions from cfDNA by analyzing SNVs, CNAs, and fragmentomics.

sv-channels improves SV detection precision using deep learning, outperforming GRIDSS while maintaining Manta's recall.

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.

SHARC rapidly identifies somatic genomic structural variations from nanopore sequencing for blood-based cancer monitoring, detecting ten SVs per sample and enabling treatment response tracking in metastatic prostate cancer.

This paper introduces FUDGE, a method for detecting fusion genes using CRISPR/Cas9 enrichment and long-read sequencing, achieving high sensitivity and specificity across various cancer types.

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.

This study identifies novel HPE genes and oligogenic inheritance patterns in holoprosencephaly by integrating clinical data with exome sequencing and gene prioritization.

The paper introduces a new 3C method, MC-4C, to study multi-way DNA conformations and reveals cooperative and competitive chromatin interactions, including enhancer hubs and loop collisions.

The paper analyzes 239 Dutch mate-pairs with whole-genome sequences to test if MHC genetic variation influences mate selection, finding no evidence of MHC-dependent mate choice.

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