Cancer Genomics and Diagnostics

Combining mutation detection with fragmentomics features leads to improved tumor-informed ctDNA detection

This paper improves ctDNA detection by combining mutation detection with fragmentomic features, achieving higher AUC scores than mutation burden alone.

Breaking the sparsity barrier in clinical targeted-panel sequencing: Mapping the inherited determinants of mutational signatures

This paper introduces GroupSig, a framework to overcome sparsity in clinical targeted-panel sequencing data, identifying inherited determinants of mutational signatures in cancer.

Polyclonal-Monoclonal Transition in Lung Squamous Cell Carcinoma Evolution

This study identifies a polyclonal-to-monoclonal evolutionary trajectory in lung squamous cell carcinoma using genomic and transcriptomic data, with implications for precision therapeutics.

Bayesian inference of tissue-migration histories in metastatic cancer from cell-lineage tracing data

This paper introduces BEAM, a Bayesian framework for inferring tissue migration histories in metastatic cancer from lineage tracing data, showing improved performance over existing methods.

Genome-Wide Variations of End Motif in Cell-Free DNA Fragments Distinguish Immunotherapy Responders from Non-Responders in Head and Neck Cancer: A Multi-Institute Prospective Study

This study identifies a novel cfDNA fragmentomic metric, rMDS, that distinguishes immunotherapy responders from non-responders in HNSCC with high accuracy.

Whole-Genome Landscape of Breast Cancers from India shows Distinct Clinically Actionable Subtypes

This study presents whole-genome and transcriptome analyses of breast tumors from India, identifying novel mutations, copy number alterations, and subtypes with clinical implications.

Whole-genome pre-amplification as a viable approach for genomic screening of FFPE-derived DNA samples

This study evaluates DLMDA for improving DNA yield from FFPE samples but finds it reduces CNA sensitivity.

Molecular insights into early malignant transition of hepatocellular carcinoma

This study profiles early hepatocellular carcinomas to reveal molecular mechanisms of malignancy transition, identifying TERT alterations, CNA burden, and immune evasion as key factors.

Scaling and Generalization of Discrete Diffusion Models for Tumor Phylogenies

This study uses discrete diffusion models to generate tumor phylogenies, finding that mid-scale models outperform deeper ones and that diverse training improves cross-regime generalization.

Comprehensive detection of genetic and epigenetic alterations in cancer using long reads with TumorLens

TumorLens detects genetic and epigenetic alterations in cancer using long reads, revealing key somatic events and methylation patterns across tumor samples.

Metastatic tumor cells in bone marrow differ from paired neuroblastoma tumor and contain subsets with therapy-resistant characteristics

Elevated YBX1 mRNA expression is associated with a genomi-cally unstable and clinically aggressive cancer state: a pan-cancer analysis

This study identifies elevated YBX1 mRNA expression as a marker of genomically unstable and clinically aggressive cancer across multiple tumor types.

Principles of subclonal gene dosage across human cancer

The paper analyzes subclonal gene dosage effects in cancer using DNTR-seq, finding additive and compensatory transcriptional impacts and identifying transient clonality in ovarian and soft tissue sarcomas.

Mutation-centric Network Construction using Long-Range Interactions

The paper introduces a graph-based framework to construct mutation-centric networks using long-range genomic interactions, demonstrating its ability to cluster cancer subtypes and prioritize non-coding driver mutations.

Oncogenes and tumor suppressor genes are enriched in stop-loss mutations generating protein extensions

The paper identifies stop-loss mutations in cancer genomes, showing enrichment in cancer-related genes and potential immunological consequences.

The landscape of structural variation in pediatric cancer

This study analyzes structural variants in 1,616 pediatric cancer genomes, revealing unique SV hotspots and patterns distinct from adult cancers.

Inverse Game Theory Characterizes Frequency-Dependent Selection Driven by Karyotypic Diversity in Triple Negative Breast Cancer

The paper introduces ECO-K, an inverse game theory framework to infer subpopulation interactions from single-cell sequencing data in TNBC, revealing frequency-dependent selection driven by karyotypic diversity.

PULPO: Pipeline of understanding large-scale patterns of oncogenomic signatures

PULPO is a pipeline that processes Optical Genome Mapping data to extract mutational signatures, improving oncogenomic analysis accessibility.

Saturating hepatic clearance drives elevated cfDNA and fragment shortening in cancer

This study shows that elevated cfDNA and fragment shortening in cancer are due to saturated hepatic clearance, not tumor burden alone.

Genome-wide classification of tumor-derived reads from bulk long-read sequencing

ROCIT classifies tumor or non-tumor origin of reads from bulk long-read sequencing with high accuracy, improving somatic variant calling in tumors.

Confounding factors in assessing the enriched expression of somatic mutant allele in bulk tumor samples

The paper shows that mutant allele enrichment in bulk tumor RNA can be confounded by tumor purity and NMD, and demonstrates RNA-Seq can improve driver indel detection.

Pan-cancer tumour classification and risk stratification from whole-genome somatic variants via dual-task representation learning

MuAt2, a Transformer model, classifies tumour types and subtypes from somatic variants, improving accuracy and calibration across cancer types and cohorts.

Clonal evolutionary analysis reveals patterns of malignant transformation in pancreatic cancer from Intraductal Papillary Mucinous IPMN Neoplasms (IPMN)

This study traces the clonal evolution of pancreatic cancer from IPMN using genomic and transcriptomic data, identifying two distinct evolutionary trajectories and their implications for PDAC progression.

Deciphering selection patterns of somatic copy-number events

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: Prioritizing Bulk DNA Inferred Tumor Phylogenies via Low-pass Single-cell DNA Sequencing Data

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

Competing Subclones and Fitness Diversity Shape Tumor Evolution Across Cancer Types

TEATIME estimates evolutionary parameters and fitness diversity from bulk sequencing data, revealing patterns of intratumor heterogeneity across 33 cancer types.

LRSomatic: a highly scalable and robust pipeline for somatic variant calling in long-read sequencing data

LRSomatic is a pipeline for somatic variant calling in long-read sequencing data, achieving state-of-the-art performance on cancer samples and resolving complex variants.

Distinct mutational landscapes when comparing germline and somatic cancer variants in forty tumor suppressor genes.

The paper compares germline and somatic variants in 40 tumor suppressor genes, finding distinct mutational patterns and locations shaped by different selection pressures.

Identifying Robust Subclonal Structures through Tumor Progression Tree Alignment

This paper introduces omlta, an algorithm for aligning clonal trees to compare tumor progression, and applies it to cancer datasets.

POTTR: Identifying Recurrent Trajectories in Evolutionary and Developmental Processes using Posets

POTTR identifies recurrent mutation trajectories in cancer and development using posets, resolving uncertainty in phylogenies and discovering significant new patterns.