Cancer Genomics and Diagnostics

The Interplay between Mutagenesis and Extrachromosomal DNA Shapes Urothelial Cancer Evolution

This study examines how mutagenesis and extrachromosomal DNA contribute to urothelial cancer evolution, revealing clonal APOBEC3 mutations and chemotherapy-induced mutational bursts within ecDNA.

A Series of Composited Tumor DNA Reference Materials Containing Three Genes and Ten Mutation Positions for CNV and SNV Detection

The paper develops tumor DNA reference materials with CNV and SNV properties for EGFR, HER2, MET, PIK3CA, KRAS, BRAF, and NRAS, validated for stability, homogeneity, and commutability.

Single molecule methylation profiles of cell-free DNA in cancer with nanopore sequencing

The paper develops a nanopore sequencing strategy to measure cfDNA methylomes in cancer patients, enabling longitudinal monitoring during treatment.

Integrating gene mutation spectra from tumors and the general population with gene expression topological networks to identify novel cancer driver genes

DGAT-cancer integrates mutation spectra and gene expression networks to identify 571 novel cancer drivers, with EEF1A1 validated as a glioma driver.

Targeted in silico characterization of fusion transcripts in tumor and normal tissues via FusionInspector

FusionInspector identifies and characterizes biologically relevant fusion transcripts from RNA-seq data in tumor and normal tissues using clustering and machine learning.

Systematic Pan-cancer Functional Inference and Validation of Hyper, Hypo and Neomorphic Mutations

The paper functionally characterizes 577,866 non-recurrent mutations across TCGA cohorts by analyzing TF activity, identifying neomorphic and mimicry mutations, and validating them with knock-in assays.

Dynamic ctDNA mutational complexity in melanoma patients receiving immunotherapy

This study tracks ctDNA mutational complexity in melanoma patients on immunotherapy, finding dynamic mutations and clinical correlations.

Defining Multiple Layers of Intratumor Heterogeneity Based on Variations of Perturbations in Multi-omics Profiling

The paper develops multi-omics ITH measures using information entropy across six molecular levels and shows their correlations with clinical outcomes and molecular regulatory relationships.

The origins and functional effects of postzygotic mutations throughout the human lifespan

This study maps postzygotic mutations across tissues and lifespan, showing their functional variation and selection pressures, suggesting multiple dynamic genomes per individual.

Systematic integration of protein affecting mutations, gene fusions, and copy number alterations into a comprehensive somatic mutational profile

OncoMerge integrates protein-affecting mutations, gene fusions, and copy number alterations to create a unified somatic mutation profile, improving downstream cancer analysis.

Somatic small-variant calling methods in Illumina DRAGEN™ Secondary Analysis

The paper introduces DRAGEN's somatic variant calling pipeline, demonstrating its speed and accuracy in whole-genome sequencing tumor-normal analysis compared to existing tools.

Discovering cryptic splice mutations in cancers via a deep neural network framework

This study uses SpliceAI to identify cryptic splice mutations in cancer, finding over 100,000 such mutations across 18,115 tumors and uncovering new candidate driver genes.

Pan-cancer association of DNA repair deficiencies with whole-genome mutational patterns

The paper identifies DNA repair deficiency genes using mutational patterns and develops predictive models for their loss-of-function variants across cancers.

Influence network model uncovers relations between biological processes and mutational signatures

The paper introduces a network-based method to uncover relationships between mutational signatures and biological processes in cancer data.

A large-scale retrospective study in metastatic breast cancer patients using circulating tumor DNA and machine learning to predict treatment outcome and progression-free survival

This study uses ctDNA from metastatic breast cancer patients and a Bayesian model to predict treatment response and progression-free survival, outperforming alternative methods.

Clonal phylogenies inferred from bulk, single cell, and spatial transcriptomic analysis of cancer

The paper evaluates the accuracy of transcript-based inferred tumor phylogenies compared to DNA-based phylogenies in prostate cancer using single-cell, spatial transcriptomic, and bulk data.

SMITH: Spatially Constrained Stochastic Model for Simulation of Intra-Tumour Heterogeneity

SMITH simulates cancer evolution with spatial constraints, showing that confinement mechanisms can reproduce clonal dynamics efficiently.

Systematic analysis of disease-linked rare germline variants reveals new classes of cancer predisposing genes

The paper identifies new cancer predisposing genes by analyzing rare germline variants in Mendelian disease genes across cancer cohorts.

PipeIT2: A tumor-only somatic variant calling workflow for Molecular Diagnostic Ion Torrent sequencing data

PipeIT2 is a somatic variant calling workflow for Ion Torrent sequencing data that identifies mutations without germline control, achieving >95% recall for variants with >10% allele fraction.

Copy number footprints of platinum-based anticancer therapies

The paper identifies a specific copy number footprint in tumors from patients exposed to platinum-based therapies using whole genome sequencing data.

The repertoire of copy number alteration signatures in human cancer

This study identifies 14 CNA signatures from pan-cancer WGS and TCGA SNP array data, revealing novel patterns and prognostic implications for cancer patients.

An intravenous DNA-binding priming agent protects cell-free DNA and improves the sensitivity of liquid biopsies

A DNA-binding agent increases cfDNA levels in blood, improving ctDNA detection and cancer sensitivity in mice.

A nanoparticle priming agent reduces cellular uptake of cell-free DNA and enhances the sensitivity of liquid biopsies

A nanoparticle priming agent increases cfDNA levels in blood, improving ctDNA detection sensitivity in tumor-bearing mice.

Analysis of fragment ends in plasma DNA from patients with cancer

Analyzing the positioning and nucleotide sequence at fragment ends in plasma DNA may enable cancer diagnostics.

mSigHdp: hierarchical Dirichlet process mixture modeling for mutational signature discovery

mSigHdp improves mutational signature discovery using hierarchical Dirichlet process mixture models, outperforming NMF-based methods on synthetic data.

BRDriver: Breast Cancer Driver Gene Predictor

BRDriver predicts high-confidence breast cancer driver genes using multiple computational tools and machine learning, achieving high accuracy and identifying new potential driver genes.

Katdetectr: utilising unsupervised changepoint analysis for robust kataegis detection

Katdetectr detects kataegis loci in genomic data using unsupervised changepoint analysis, showing high accuracy and speed compared to existing tools.

COOBoostR: an extreme gradient boosting-based tool for robust tissue or cell-of-origin prediction of tumors

COOBoostR uses extreme gradient boosting to predict tumor tissue or cell-of-origin using chromatin marks and mutation density data, outperforming random forest methods in speed and accuracy.

C-ToMExO: Learning Cancer Progression Dynamics from Clonal Composition of Tumors

The paper introduces a method to infer cancer progression models from clone-level data, showing improved robustness and scalability using a novel MCMC algorithm.

Finding the best cell lines across pan-cancer to use in pre-clinical research as a proxy for patient tumor samples considering immune cells, multi-omics, and cancer pathways

The paper evaluates cell lines across 22 cancer types to find those most similar to patient tumor samples using multi-omics data, immune cell presence, and cancer pathways, showing they can recapitulate drug responses.