Joep de Ligt

Whole-genome sequencing reveals tumor T-cell infiltration associated with immunotherapy outcomes

The paper develops a DNA-based T-cell infiltration score from whole-genome sequencing to predict immunotherapy response and survival.

The pan-cancer whole-genome landscape of Adolescent and Young Adult solid cancers

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.

Systematic identification of genomic non-response biomarkers to cancer therapies

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.

A near-complete human pancreatic cancer genome

This paper presents near-complete, haplotype-resolved assemblies of a pancreatic cancer genome and normal tissue, identifying extensive somatic variants and epigenetic changes in previously excluded regions.

Whole genome sequencing-based analysis of genetic predisposition to adult glioblastoma

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

Creating a biomedical knowledge base by addressing GPT inaccurate responses and benchmarking context

GNQA, a retrieval-augmented GPT question-answering system over 3000 GeneNetwork, aging and diabetes papers, cites source paragraphs; RAGAS rated answer relevance above human thumbs-up ratings (89% vs 76%).

Building pangenome graphs

This paper introduces PGGB, a pipeline for building pangenome graphs that includes all variation without bias, enabling variation detection, conservation measurement, recombination event detection, and phylogenetic inference.

Deficiency of nucleotide excision repair explains mutational signature observed in cancer

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.

Integrated Clinical and Omics Approach to Rare Diseases: Novel Genes and Oligogenic Inheritance in Holoprosencephaly

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

Mapping And Phasing Of Structural Variation In Patient Genomes Using Nanopore Sequencing

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