Cancer Genomics and Diagnostics

VARION: A Network Propagation Framework for Individual Patient Somatic Mutation Interpretation in Cancer Molecular Subtyping

VARION improves cancer molecular subtyping by integrating mutation data with network propagation, achieving high accuracy across multiple cancer types without retraining.

CRISPR-enhanced assessment of variants of unknown significance nominates oncology therapeutic targets and drug repositioning opportunities

CRISPR-VUS identifies rare variants linked to gene dependency in cancer cell lines, prioritizing potential drivers and therapeutic targets through functional validation.

Transcriptome profiling of cell-free RNAs in prostate cancer patients on active surveillance

This study profiles cell-free RNAs in prostate cancer patients on active surveillance to identify differences between stable disease and progression to radical prostatectomy.

CNSigs: An R Package for the Identification of Copy Number Mutational Signatures

CNSigs identifies copy number mutational signatures across cancers, revealing associations with survival and treatment response.

Single genome analysis of normal cells identifies the early steps of kidney cancer.

The paper identifies a mutational signature in normal kidney cells linked to kidney cancer initiation through hypoxia-driven genetic changes.

Chromosomal mutational signatures of DNA damaging agents at single cell resolution

This paper develops a framework to analyze chromosomal mutational patterns at single-cell resolution, revealing drug-induced mutational signatures in human tissues.

Parent-of-origin phasing of somatic mutations shows equal mutation burden between parental genomes in human cancers

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

A Compendium of 49 Experimental SBS Signatures for Decoding Human Cancer Mutational Processes

The paper curates 49 experimental single-base substitution signatures from cancer genomes to link mutational processes to DNA damage mechanisms.

Integrated map of somatic mosaicism across human tissues in 25 individuals

The paper presents an integrated analysis of somatic mosaicism across 25 individuals, revealing tissue-specific mutational processes and epigenetic states.

Non-invasive forecasting of skin cancer evolution through longitudinal hair sampling

This study tracks somatic mutation evolution in hair follicles to forecast early skin cancer development non-invasively.

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.

A comprehensive atlas of somatic mutation rates and mutational signatures in normal human cells

The paper reports mutation rates and mutational signatures across 53 normal human cell types, revealing variation in mutation accumulation and identifying known and unknown mutational processes.

Gene expression inference from cell-free DNA using uncertainty-aware deep learning

This paper develops a deep learning framework to infer gene expression from cell-free DNA, improving reliability and enabling functional genomics in precision oncology.

Transcriptional Response to Tumor Mutational Burden Is Consistent Across Cancer Types

The paper analyzes ~9,100 tumors across 32 cancer types to determine if the transcriptional response to tumor mutational burden (TMB) is consistent across tissues, finding it to be largely consistent within each cancer type.

Scalable spatial DNA sequencing from archival tissue maps copy number subclones

This paper introduces ARMS DNAseq, a scalable spatial genomic assay that maps copy number subclones in archival tissue, revealing tumor evolution and subclone associations with morphology and transcriptomic features.

APOBEC3B mRNA Expression in Breast Cancer Correlates with Genomic Mutational Signatures

This study examines the relationship between APOBEC3B mRNA expression and mutational signatures in breast cancer, finding that high APOBEC3B expression correlates with specific genetic and metabolic changes affecting drug response.

Chromosomal instability shapes spatial and temporal phenotypic diversity in a malignant peripheral nerve sheath tumour

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.

Benchmarking fragmentation-derived artificial cfDNA reference standards

This study benchmarks artificial cfDNA generated by fragmentation methods against native cfDNA, finding enzymatic methods better replicate native characteristics.

Mutagenic bypass of uracil-derived abasic sites underlies the SBS17 mutational signature

This study identifies the mechanism of SBS17 mutational signature as misincorporation of dUTP during DNA replication and mutagenic bypass of abasic sites, applicable to both spontaneous and chemotherapy-induced mutations in gastrointestinal cancers.

Circulating Microbial DNA as a Potential Cancer Biomarker: Technical Challenges and Controlled Evaluation

This paper evaluates circulating microbial DNA as a cancer biomarker, finding that observed patterns are largely artifacts of sequencing and analysis methods rather than biological signals.

Ultra-deep duplex sequencing reveals unique features of somatic evolution in the normal tissues of a family with Li-Fraumeni syndrome

Duplex sequencing of a Li-Fraumeni family links germline TP53 p.R181H to higher neutral-region mutagenesis and weaker blood TP53 selection, plus recurrent p.R248Q/W hits across proband tissues.

Minimally invasive monitoring of clonal evolution through integrated single cell and ctDNA analysis

cfClone, a Bayesian model, deconvolves cfDNA whole-genome sequencing using scWGS-derived haplotype-specific clone copy-number profiles to estimate tumour fraction, clonal prevalence, and flag missed clones.

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.

pyfraglib: An integrated cfDNA fragmentomics platform

pyfraglib provides a platform for cfDNA fragmentomics analysis, including fragment extraction, feature modeling, cohort comparison, and simulation, and identifies a high-risk subgroup in CNSL patients.

Common germline polymorphisms and somatic cancer mutations exhibit non-random positional overlap across the human genome

The paper identifies non-random positional overlap between common germline polymorphisms and somatic cancer mutations, suggesting intrinsically vulnerable genomic loci.

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.

LACHESIS: real-time inference of evolutionary trajectories of malignant transformation from whole-genome sequencing data

LACHESIS infers evolutionary trajectories of malignant transformation from whole-genome sequencing data and provides risk stratification for childhood and adult cancers.

Pan-cancer benchmarking reveals complementary copy number signatures with distinct multi-omic predictability

This study benchmarks three copy number signature compendia across cancers, showing their distinct predictability from multi-omic data and highlighting framework-dependent performance.

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.

CNVeil resolves haplotype-specific copy number and uncovers subclonal architecture hidden from total copy number profiling in single-cell cancergenomes

CNVeil infers haplotype-specific copy number and subclonal architecture from single-cell cancer genomes, outperforming existing methods in accuracy and resolution.