Joke J.F.A. van Vugt

Characterising the motif composition and allele length distribution of ZFHX3 GGC repeat expansions in amyotrophic lateral sclerosis

This study examines ZFHX3 GGC repeat expansions in ALS and finds no association with disease risk, but identifies diverse repeat motif compositions.

Sex-specific DNA methylation differences in Amyotrophic lateral sclerosis

The paper identifies sex-associated DNA methylation differences in ALS using a large-scale epigenome-wide association study and links them to survival outcomes.

A phenome-wide association study of methylated GC-rich repeats identifies a GCC repeat expansion in AFF3 as a significant cause of intellectual disability

The paper identifies a GCC repeat expansion in AFF3 as a significant cause of intellectual disability through a phenome-wide association study using DNA methylation profiling and UK Biobank data.

REViewer: Haplotype-resolved visualization of read alignments in and around tandem repeats

REViewer visualizes sequencing data around long repeat expansions by reconstructing haplotypes and aligning reads, improving the assessment of repeat genotype calls and detecting interruptions.

ExpansionHunter Denovo: A computational method for locating known and novel repeat expansions in short-read sequencing data

ExpansionHunter Denovo detects known and novel repeat expansions in short-read sequencing data without requiring predefined repeat catalogs.

Chromosomal resolution reveals symbiotic virus colonization of parasitic wasp genomes

The paper shows symbiotic bracovirus genes have spread to all chromosomes of parasitoid wasps and are stably maintained, with synchronized expression and no immune response.

ExpansionHunter: A sequence-graph based tool to analyze variation in short tandem repeat regions

ExpansionHunter is a tool for accurately genotyping short tandem repeats, particularly in complex regions with adjacent variants or imperfect repeats.

Project MinE: study design and pilot analyses of a large-scale whole-genome sequencing study in amyotrophic lateral sclerosis

Project MinE analyzes whole-genome sequencing data from ALS patients and controls to study genetic variation and its implications for disease susceptibility.

Detection of long repeat expansions from PCR-free whole-genome sequence data

The paper introduces ExpansionHunter, a tool for detecting long repeat expansions from PCR-free WGS data, achieving high sensitivity and specificity in identifying pathogenic expansions.