Cancer Genomics and Diagnostics

PMCE: efficient inference of expressive models of cancer evolution with high prognostic power

PMCE infers probabilistic graphical models of cancer evolution from mutational profiles, showing a significant correlation between predicted evolutionary paths and patient survival.

The Mutational Signature Comprehensive Analysis Toolkit (musicatk) for the discovery, prediction, and exploration of mutational signatures

The paper introduces musicatk, a toolkit for analyzing mutational signatures, enabling preprocessing, analysis, visualization, and comparison to COSMIC database.

Clone decomposition based on mutation signatures provides novel insights into mutational processes

SigTracer improves clone decomposition in tumors by modeling mutation signatures, revealing new insights into mutational processes and their genomic targets.

Single-cell DNA and RNA sequencing reveals the dynamics of intra-tumor heterogeneity in a colorectal cancer model

This study uses single-cell DNA and RNA sequencing to analyze intra-tumor heterogeneity dynamics in a mouse colorectal cancer model, finding increased RNA heterogeneity and decreased DNA heterogeneity after transplantation.

CloneSig can jointly infer intra-tumor heterogeneity and mutational signature activity in bulk tumor sequencing data

CloneSig jointly infers intra-tumor heterogeneity and mutational signature activity in bulk tumor sequencing data, outperforming existing methods in scenarios with varying mutational signature distributions across clones.

Oncogene Concatenated Enriched Amplicon Nanopore Sequencing for Rapid, Accurate, and Affordable Somatic Mutation Detection

OCEANS improves nanopore sequencing for detecting low VAF somatic mutations with high accuracy and sensitivity in clinical samples.

Establishing reference samples for detection of somatic mutations and germline variants with NGS technologies

The paper establishes reference samples with high-coverage whole-genome sequencing to create truth sets for somatic mutation and germline variant detection using NGS technologies.

Achieving reproducibility and accuracy in cancer mutation detection with whole-genome and whole-exome sequencing

This study evaluates reproducibility and accuracy of cancer mutation detection using whole-genome and whole-exome sequencing across multiple sequencing centers and bioinformatics pipelines.

A body map of somatic mutagenesis in morphologically normal human tissues

The paper maps somatic mutations and clonal expansions in normal human tissues across nine organs, revealing organ-specific patterns of mutation accumulation and clonal evolution.

Detection of Multiple Types of Cancer Driver Mutations Us-ing Targeted RNA Sequencing in NSCLC

This paper develops an RNA-based panel to detect multiple cancer driver mutations in NSCLC, showing high specificity and sensitivity for SNVs, fusions, and expression, with improved detection limits compared to DNA-seq.

Extreme value theory as a general framework for understanding mutation frequency distribution in cancer genomes

The paper applies extreme value theory to analyze mutation frequency distributions in cancer genomes, finding a Frechet distribution rather than the Gumbel hypothesis.

Multi-organ analysis of low-level somatic mosaicism reveals stage- and tissue-specific mutational features in human development

The paper analyzes low-level somatic mutations across multiple organs and developmental stages, finding stage- and tissue-specific mutational features.

Plasma Contains Ultra-short Single-stranded DNA in Addition to Nucleosomal cfDNA

The paper introduces uscfDNA-seq, a method to sequence single-stranded cell-free DNA in plasma, revealing a novel population of ultrashort cfDNA with a modal size of 50nt.

DeCiFering the elusive cancer cell fraction in tumor heterogeneity and evolution

This paper introduces DeCiFer, a method to more accurately estimate cancer cell fractions and infer tumor evolution by addressing limitations of existing methods in the presence of copy-number aberrations and mutation losses.

Target Enrichment Enhances the Sensitivity of Sanger Sequencing for BRAF V600 Mutation Detection

This paper enhances Sanger sequencing sensitivity for detecting BRAF V600 mutations using target enrichment, achieving 0.04% variant allele frequency detection.

A practical framework RNMF for the potential mechanism of cancer progression with the analysis of genes cumulative contribution abundance

The paper introduces RNMF, a framework for analyzing mutational signatures in cancer, identifying gene associations and survival outcomes in esophageal squamous cell carcinoma.

Temporal stability of human sperm mosaic mutations results in life-long threat of transmission to offspring

The paper analyzes sperm mosaic mutations in healthy males, finding that many are stable over time and pose a lifelong transmission risk to offspring.

RepairSig: Deconvolution of DNA damage and repaircontributions to the mutational landscape of cancer

RepairSig identifies DNA repair deficiency mutational signatures in cancer by modeling interactions between mutagenic processes, replacing multiple signatures with a single representative one in breast cancer.

Evolution and genomic signatures of spontaneous somatic mutation in Drosophila intestinal stem cells

This study analyzes spontaneous somatic mutations in Drosophila intestinal stem cells using whole-genome sequencing to understand early cancer mutation dynamics and genomic signatures.

Highly selective Cooperative Primers for multiplex detection of rare mutations

This paper introduces Highly Selective Cooperative Primers for detecting rare mutations in circulating tumor DNA using real-time PCR, achieving single-copy sensitivity and reliable detection of minor allele fractions as low as 0.01%.

Studying the history of tumor evolution from single-cell sequencing data by exploring the space of binary matrices

This paper reviews methods for inferring tumor evolutionary trees using binary matrix optimization and discusses a deep learning approach for topological inference.

LiquidCNA: tracking subclonal evolution from longitudinal liquid biopsies using somatic copy number alterations

LiquidCNA tracks subclonal evolution from liquid biopsies using somatic copy number alterations, revealing new subpopulations in metastatic lung cancer.

Absolute copy number fitting from shallow whole genome sequencing data

The paper evaluates tools for estimating absolute copy numbers from shallow whole genome sequencing data and introduces an improved tool called Rascal.

A pan-cancer landscape of somatic substitutions in non-unique regions of the human genome

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.

APSiC: Analysis of Perturbation Screens for the Identification of Novel Cancer Genes

APSiC identifies novel cancer genes and non-genetic drivers from perturbation screens, revealing context-dependent oncogenic mechanisms and functional roles in specific cancers.

The spatial landscape of clonal somatic mutations in benign and malignant tissue

The paper uses spatial transcriptomics to analyze copy number variations in benign and malignant tissues, revealing clonal patterns and suggesting early cancer evolution mechanisms.

Tracing the evolution of aneuploid cancers from multiregional sequencing

This paper develops a semi-supervised algorithm to deconvolve clonal variants in tumors, accounting for tumor cell fraction and copy number changes across samples.

Blood-based liquid biopsy for comprehensive cancer genomic profiling using next-generation sequencing: an emerging paradigm for noninvasive cancer detection and management in dogs

This study shows that blood-based liquid biopsy using next-generation sequencing can detect genomic alterations in dogs with cancer, matching tumor tissue findings and identifying alterations from spatially separated tumor sites.

Aperture: Accurate detection of structural variations and viral integrations in circulating tumor DNA using an alignment-free algorithm

Aperture detects structural variations and viral integrations in ctDNA with high sensitivity and specificity using an alignment-free algorithm.

Sensitive detection of tumor mutations from blood and its application to immunotherapy prognosis

This paper introduces cfSNV, a somatic SNV caller for cfDNA that outperforms existing tools in detecting low-frequency mutations and applies it to immunotherapy prognosis in non-small-cell lung cancer.