Cancer Genomics and Diagnostics

Tobacco smoke alters the trajectory of lung adenocarcinoma evolution via effects on somatic selection and epistasis

This paper quantifies how tobacco smoke alters somatic selection and epistasis in lung adenocarcinoma, showing distinct mutation selection pressures in smokers and non-smokers.

Combining evolution and protein language models for an interpretable cancer driver mutation prediction with D2Deep

D2Deep predicts cancer driver mutations by combining protein language models and evolutionary information, outperforming existing methods and enabling result interpretation.

Benchmarking 13 tools for mutational signature attribution, including a new and improved algorithm

The paper benchmarks 13 mutational signature attribution tools, including a new method called PASA, on synthetic data to evaluate their performance across different cancer types.

SAMURAI: Shallow Analysis of copy nuMber alterations Using a Reproducible And Integrated bioinformatics pipeline

SAMURAI is a bioinformatics pipeline for analyzing copy number alterations from shallow whole-genome sequencing data, validated with simulated and real-world datasets showing high concordance with ground truth.

Driver-associated transcriptional rewiring reveals conditional genetic vulnerabilities in cancer

Dyscovr identifies driver-associated transcriptional changes and prioritizes genes for therapeutic targeting in cancer.

Luminal breast epithelial cells from wildtype and BRCA mutation carriers harbor copy number alterations commonly associated with breast cancer

The paper analyzes copy number alterations in breast epithelial cells from BRCA mutation carriers and wildtype individuals, finding lineage-specific CNAs that mirror cancer genomes.

Computational investigation of missense somatic mutations in cancer and potential links to pH-dependence and proteostasis

The paper investigates missense somatic mutations in cancer, focusing on pH-dependence and proteostasis, and finds no clear separation of mutation subsets by pH-sensing potential.

Unraveling cfDNA Fragmentation Patterns: Linking Chromatin Architecture to Cancer Diagnostic Sensitivity

This study identifies nucleosome breakpoints in cfDNA from cancer patients and shows how chromatin structure affects mutation detection sensitivity.

Pangenome References Improve Biomarker Estimation from Tumor Sequencing Data

This paper shows that using pangenome references improves biomarker estimation in tumor sequencing, reducing bias in TMB calculations for non-European populations.

Pan-cancer study on transition of signaling systems from primary to metastatic tumors

This study identifies signaling pathway changes during cancer metastasis using two models, revealing common and specific factors across 17 cancer types.

Widespread adoption of precision anticancer therapies after implementation of pathologist-directed comprehensive genomic profiling across a large US health system

This study shows that precision therapies have become more common than traditional chemotherapy in advanced cancer patients after implementing comprehensive genomic profiling.

Karyotype Evolution in Response to Chemoradiotherapy and Upon Recurrence of Esophageal Adenocarcinomas.

This study tracks karyotype evolution in esophageal adenocarcinomas during chemoradiotherapy and recurrence, showing that treatment-induced copy number aberrations predict early recurrence and are partially reversed upon recurrence.

Somatic mutation and selection at epidemiological scale

The paper introduces a high-accuracy sequencing method to detect somatic mutations in tissues, revealing extensive selection and driver mutations in oral epithelium and blood samples.

Inferring allele-specific copy number aberrations and tumor phylogeography from spatially resolved transcriptomics

CalicoST infers allele-specific copy number aberrations and tumor phylogeography from spatially resolved transcriptomics data, achieving higher accuracy than existing methods.

Bayesian modeling of mutual exclusivity in cancer mutations

The paper develops a Bayesian framework to model mutual exclusivity in cancer mutations, finding potential mutual exclusivity between EGFR and IDH1 in glioblastoma multiforme.

APOBEC3A, not APOBEC3B, drives deaminase mutagenesis in human gastric epithelium

This study shows APOBEC3A, not APOBEC3B, causes significant mutagenesis in human gastric epithelium through whole-genome sequencing of organoids with inducible APOBEC3A or APOBEC3B.

Improving Accuracy of Somatic Mutation Profiling in Large Epidemiologic Studies: Addressing Cases without Matched Normal Samples

The paper improves somatic mutation detection in tumor samples without matched normal samples by estimating tumor purity and variant allele frequency, reducing false positive and negative rates.

Cosmic signature SBS39 is associated with homologous recombination deficiency

The paper updates the COSMIC database and identifies SBS39 as a new homologous recombination deficiency signature.

Expression-Driven Genetic Dependency Reveals Targets for Precision Medicine

The paper identifies expression-driven genetic dependency targets for precision oncology using a Bayesian approach, revealing new druggable genes and validating their therapeutic potential.

Long-read sequencing of an advanced cancer cohort resolves rearrangements, unravels haplotypes, and reveals methylation landscapes

This paper presents a long-read sequencing dataset of cancer samples, showing its ability to resolve structural variants, haplotypes, and methylation patterns in precision medicine.

Protein Kinases in Phagocytosis: Promising Genetic Biomarkers for Cancer

This study identifies MET and MERTK as frequently mutated protein kinases in cancer, with associations to survival and therapeutic response.

Beyond Tumors: Reduced survival linked to pathogenic PIK3CA and TP53 post-zygotic variants in the uninvolved breast tissue of recurrent cancer patients

The paper identifies pathogenic post-zygotic variants in normal breast tissue of poor-prognosis cancer patients, linking them to reduced survival and disease recurrence.

Somatic mitochondrial DNA mutations are a source of heterogeneity among primary leukemic cells

The paper identifies differences in mtDNA mutation accumulation and selective pressures in pediatric leukemias using bulk and single-cell sequencing, linking these to functional heterogeneity among leukemic cells.

Somatic mutant selection is altered by prior NOTCH1 mutation in aging esophageal epithelium

The paper shows that prior NOTCH1 mutation in aging esophageal epithelium alters the selection of subsequent somatic mutations, increasing NOTCH2 mutants and decreasing TP53 mutants.

A unique interplay of access and selection shapes peritoneal metastasis evolution in colorectal cancer

This study examines the evolutionary dynamics of peritoneal metastases in colorectal cancer, finding they are more heterogeneous than liver metastases but less diverse than locoregional metastases.

Potential Cancer Biomarkers: Mitotic Intra-S DNA Damage Checkpoint Genes

The paper analyzes pan-cancer profiles of 17 mitotic intra-S DNA damage checkpoint genes across 9000+ samples to identify potential diagnostic, prognostic, and therapeutic biomarkers.

Target-enhanced whole-genome sequencing (TE-WGS) shows clinical validity equivalent to commercially available targeted oncology panel

This study compares target-enhanced whole-genome sequencing (TE-WGS) with a commercial targeted panel, showing TE-WGS detects all variants and provides additional clinical insights.

Pan-Cancer Genetic Analysis of Mitochondrial DNA Repair Gene Set

This study analyzes mitochondrial DNA repair genes across cancers, finding TP53 mutations and CNV impacts on survival, and links these genes to cell cycle activation and drug response.

Pervasive Induction of Regulatory Mutation Microclones in Sun-exposed Skin

The paper reports that sun exposure induces pervasive mutations at UV-sensitive RNA-processing gene promoters, with clonal expansion observed in both tumor suppressor gene hotspots and CPD hyperhotspots.

Somatic evolution of cancer genes in sex chromosomes

This study examines somatic evolution of cancer genes on sex chromosomes, finding sex-specific differences in mutation rates and inactivation patterns of tumor suppressor and oncogenes.