Peter Van Loo

The paper quantifies parental mutation burden symmetry in human cancers using PhaSoMix, finding near-equal mutation accumulation between maternal and paternal genomes.

This study uses single-cell and spatial multi-omics to analyze a malignant peripheral nerve sheath tumor, revealing chromosomal instability drives phenotypic diversity and spatial-temporal evolution.

This study identifies two epigenetically distinct cell states in leiomyosarcoma using single-nucleus multiome sequencing and spatial transcriptomics, linking them to clinical outcomes and therapeutic vulnerabilities.

This paper introduces SPICE, a framework to infer copy-number events and model selection in cancer genomes, revealing 460 loci under selection and expanding the known cancer-related loci.

Arborist improves tumor phylogeny reconstruction by integrating bulk DNA-seq and low-pass scDNA-seq data, outperforming existing methods on simulated and biological datasets.

The paper identifies genomic deletions as the rate-limiting mutational processes in breast and ovarian cancer initiation, requiring 1-3 deletions for tumor development.

This study uses whole-exome sequencing and single-cell DNA sequencing to analyze subclonal evolution in breast cancer during aromatase inhibitor treatment, identifying resistance mechanisms and actionable targets.

The paper benchmarks structural variant callers in cancer genomics and recommends a consensus approach combining Delly, GRIDSS, Manta, and SvABA for improved performance.

This study investigates how oncogenic mutations in gliomas influence the tumor microenvironment through integrative multiomic and spatial transcriptomic analysis of glioma samples.

This study investigates the evolutionary timing of immune escape mutations across 38 cancer types using functional genomics and tumor evolution reconstruction.

This study identifies epigenetic changes and accelerated ageing in multifocal small intestinal neuroendocrine tumours, revealing altered metabolic gene regulation and tumour-specific methylation patterns.

This study shows brush biopsies can accurately reflect the genomic profile of oral premalignant lesions and their progression to OSCC, capturing most SNVs and CNAs comparable to tissue biopsies.

The paper identifies a novel mechanism where focal deletions of an intronic element in FTO lead to IRX3 activation in T-ALL through enhancer hijacking.

The paper analyzes L1 retrotransposition in tumors using long-read sequencing, revealing synchronous L1 insertions drive chromosomal crossovers early in tumorigenesis.

The paper develops CliPP to estimate subclonal mutation load (sML) and shows it predicts survival and immunotherapy response in cancers with low to moderate TMB.

This paper introduces GRITIC, a method to time genomic gains in tumors, finding that copy number gains often accumulate after genome duplication.

The paper investigates the evolution of chromosome 4p loss in basal breast cancer, identifying C4orf19 as a novel gene that suppresses proliferation and is part of a kinase module.

Refphase uses multi-sample reference phasing to infer haplotype-specific copy numbers and reveal intra-tumour heterogeneity in cancer samples.

The paper identifies pan-cancer evolutionary signatures linked to clonal expansion and immune microenvironment changes using TCGA data.

MEDICC2 infers cancer phylogenies from copy-number data, accounting for whole-genome doubling and parallel evolution, and performs well on simulated and real datasets.

The paper presents a genetic model of central chondrosarcoma using genomic and epigenomic data to identify mutations and methylation patterns associated with patient outcomes.

The paper benchmarks 31 subclonal reconstruction algorithms on simulated tumours, finding that algorithm choice significantly impacts performance and no single algorithm excels across all tasks.

The paper analyzes whole-genome data from Nigerian breast cancer patients, identifying ethnic-driven somatic evolution and distinct genomic subtypes associated with African ancestry.

The paper analyzes somatic substitutions in non-unique regions of the human genome across 2,658 cancers, revealing hidden mutations in coding sequences and regulatory elements.

CliPP reconstructs subclonal architecture in cancer DNA sequencing data efficiently and accurately, outperforming existing methods in speed while maintaining high concordance with consensus calls.

This paper introduces CAMDAC, a method to deconvolve tumor-normal DNA methylation profiles while accounting for copy number changes, revealing epigenetic instability and distinct patterns in lung cancer.

The paper quantifies tumor-specific total mRNA expression from bulk data and shows its association with clinical outcomes across 15 cancer types.

This study identifies genomic and methylation patterns associated with benign metastases and malignant transformation in giant cell tumour of bone.

This study develops quantitative metrics and simulated datasets to evaluate subclonal reconstruction methods in tumours.

The paper identifies copy number motifs in breast cancer genomes that predict disease outcome and driver events, outperforming existing clinical and genomic markers.