Thomas van Overeem Hansen

Low-cost rare variant detection for population scale genetic screening

This paper introduces DoBSeq, a low-cost framework for detecting rare variants in population-scale genetic screening, achieving 95% variant detection and recovering all clinically relevant pathogenic variants in ACMG genes.

DoBSeqWF: A framework for sensitive detection of individual genetic variation in pooled sequencing data

DoBSeqWF is a pipeline for analyzing pooled sequencing data to detect rare genetic variants, improving sensitivity with machine learning filters.

Analysis of BRCA1, BRCA2 and PALB2 related Fanconi anemia identifies scope to expand disease phenotypic features and predict breast cancer risk in heterozygotes

Mismatch repair gene specifications to the ACMG/AMP classification criteria: Consensus recommendations from the InSiGHT ClinGen Hereditary Colorectal Cancer / Polyposis Variant Curation Expert Panel

The paper specifies MMR gene-specific criteria to the ACMG/AMP classification system, reclassifying some variants and providing a framework for improved pathogenicity assessment.

Systematic large-scale application of ClinGen InSiGHT APC-specific ACMG/AMP variant classification criteria substantially alleviates the burden of variants of uncertain significance in ClinVar and LOVD databases

Large-scale genome-wide association study of 398,238 women unveils seven novel loci associated with high-grade serous epithelial ovarian cancer risk

This study identifies seven novel genetic loci associated with high-grade serous ovarian cancer risk using a large-scale GWAS and develops polygenic scores for improved risk prediction.

Predicting the impact of rare variants on RNA splicing in CAGI6

The paper evaluates splicing prediction methods on 56 clinically validated variants, finding some methods match or exceed SpliceAI's performance but highlighting ongoing challenges in accuracy.

Population-based whole-genome sequencing with constrained gene analysis identifies predisposing germline variants in children with central nervous system tumors

This study identifies 10% of pediatric CNS tumors as being caused by rare germline variants in known cancer predisposition genes through whole-genome sequencing and evolutionary constraint analysis.