Cancer Genomics and Diagnostics

A context dependent hierarchy of APOBEC3A and APOBEC3B mutators in lung adenocarcinoma

This study identifies heterogeneous roles of APOBEC3A and APOBEC3B in lung adenocarcinoma mutagenesis using CRISPR-Cas9 and whole-genome sequencing of single-cell clones.

Embryonic origin of cancer in newborn twins

The paper uses whole genome sequencing to study cancer spread between monozygotic twins, revealing asymmetrical embryonic lineage contributions to the placenta and twins.

Goliath clades and in vivo tracking of clonal dynamics show three phases of UV-induced skin carcinogenesis

This study identifies three phases of UV-induced skin carcinogenesis using a mouse model, showing the emergence of large clades, clonal selection, and lesion formation.

Punctuated mutagenesis promotes multi-stepevolutionary adaptation in human cancers

This study shows that punctuated mutagenesis in cancer enhances adaptation by facilitating crossing of fitness valleys through clustered mutations.

Identification of an ERCC2 mutation associated mutational signature of nucleotide excision repair deficiency in targeted panel sequencing data

The paper identifies an ERCC2 mutation-associated mutational signature in targeted panel sequencing data linked to nucleotide excision repair deficiency in bladder cancer and shows its clinical relevance.

Identification and Validation of a Previously Missed Mutational Signature in Colorectal Cancer

The paper identifies and validates a previously missed mutational signature in microsatellite-stable colorectal cancer, showing it is distinct from known signatures and not caused by canonical DNA repair defects.

Simulation-based Bayesian deep learning enables uncertainty-aware tumor fraction estimation in cell-free DNA

This paper introduces purNPE, a Bayesian deep learning framework for estimating tumor fraction in cell-free DNA without labeled cancer samples, achieving comparable performance to existing methods.

Motif-Centered Analyses Reveal Universal and Tissue-Specific Mutagenic Mechanisms Operating in the Human Body

The paper analyzes somatic mutation profiles in normal human tissues to identify mutagenic mechanisms and their association with age, disease, and environmental exposures.

Genetic background sets the trajectory of cancer evolution

This study shows that genetic background and environmental factors determine the trajectory of cancer evolution in mice, with distinct mutational paths despite similar final tumor states.

RNAseq analysis reveals the recurrent loss of heterozygosity in lung cancer and associated transcription patterns

This study uses RNA-seq to infer chromosomal aberrations in lung cancer and identifies shared and deletion-specific transcriptional patterns and biomarkers.

Synth4bench: Synthetic Data Generation for Benchmarking Tumor-Only Somatic Variant Calling Algorithms

The paper develops synth4bench, a synthetic data pipeline to benchmark tumor-only somatic variant callers, revealing inconsistencies in tool performance and highlighting the need for sequencing optimization and caller selection.

The Language of Cancer: Decoding Cancer Signatures with Language Models and cfRNA Sequencing

GeneLLM uses language models to detect cancer from cfRNA sequences, identifying novel biomarkers from unannotated regions with improved accuracy.

Human cancer genomes harbor the mutational signature of tobacco-specific nitrosamines NNN and NNK

The paper identifies mutational signatures in cancer genomes caused by tobacco-specific nitrosamines NNN and NNK, showing their unique contribution to specific cancer types.

FFixR: A Machine Learning Framework for Accurate Somatic Mutation Calling from FFPE RNA-Seq Data in Cancer

FFixR filters artefactual mutations in FFPE RNA-seq data, improving accuracy for somatic variant calling in cancer.

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.

Dynamic Monitoring of Antibody Drug Conjugates Targeting TROP2 or HER2 in Breast Cancer using Circulating Tumor Cells

In metastatic breast cancer on TROP2- or HER2-targeting antibody-drug conjugates, early CTC disappearance or steep decline tracked response, while CTC epitope levels neither predicted benefit nor vanished at resistance.

Circulating DNA reveals nucleosome occupancy patterns that are associated with nucleosome-DNA affinity and are affected in cancer

This study uses circulating DNA to reveal nucleosome occupancy patterns linked to DNA affinity and shows their utility in cancer detection with high specificity and sensitivity.

Impact of preanalytical factors on liquid biopsy in the canine cancer model

This study evaluates how preanalytical factors affect liquid biopsy in canine cancer models, finding that tumor content and metrics vary by blood draw location and cancer type.

Robust discovery of mutational signatures using power posteriors

This paper introduces a Bayesian NMF approach with power posteriors and sparsity-inducing priors to improve mutational signature discovery, showing better accuracy than existing methods.

Deficiency in POLE exonuclease causes synthetic lethality in highly aneuploid cancer cells

The paper identifies synthetic lethality between POLE exonuclease deficiency and high aneuploidy in cancer cells, suggesting POLE inhibition as a therapeutic strategy for aneuploid tumors.

The cumulative impact of passenger mutations on cancer development

This study shows that passenger mutations can significantly impact cancer development by accumulating in tumor suppressor genes, leading to reduced expression and poorer prognosis.

LCR-modules: a collection of workflows for cancer genome analysis

LCR-modules provides a flexible, automated suite of workflows for cancer genome analysis, supporting diverse sequencing types and enabling reproducible, scalable analysis of over 10,800 samples.

Using Cancer Profiles to Identify Synthetic Lethal Therapeutic Targets and Predictive Biomarkers in Cancer Gene Dependency Data

DepMine identifies synthetic lethal relationships and predictive biomarkers in cancer gene dependency data by integrating genetic profiles and dependency data.

Whole genome sequencing of pre-treatment and post-treatment locally advanced rectal cancer using long and short read technologies

The paper compares short-read and long-read WGS in rectal cancer to assess concordance of somatic alterations and detect epigenomic changes.

Pervasive Chromosomal Instability Drives the Karyotypic Evolution of Hypodiploid Tumours

This study analyzes hypodiploid tumors across 34 cancer types, finding widespread chromosomal instability and distinct evolutionary patterns, with implications for prognosis and risk stratification.

Patterns and drivers of 43,617 mosaic chromosomal alterations in blood

The paper identifies 43,617 mosaic chromosomal alterations in blood from 484,081 UK Biobank participants, revealing genomic hotspots and associations with age-related clonal expansions and genetic pathways.

tugMedi: simulator of cancer-cell evolution for personalized medicine based on the genomic data of patients

tugMedi simulates cancer-cell evolution using patient genomic data to predict drug responses and tumor dynamics.

Age distinguishes selection from causation in cancer genomes

The paper distinguishes between mutations that drive cancer and those that arise from normal tissue evolution by analyzing patient age across cancer and normal genomes.

Linking somatic mutations in cancer to the electronic properties of DNA

The paper links somatic mutations in cancer to DNA electronic properties by showing anticorrelations between mutation frequencies and vertical ionization potential (vIP) values of nucleobase motifs.

Adapting Clinical Chemistry Plasma as a Source for Liquid Biopsies

The paper evaluates using residual plasma from heparin separators for cfDNA testing, showing high concordance with EDTA and Streck samples for methylation, fragmentation, and viral detection.