Cancer Genomics and Diagnostics

Identifying, Prioritizing, and Visualizing Functional Promoter SNVs with the Recurrence-agnostic REMIND-Cancer Pipeline and pSNV Hunter

The paper introduces REMIND-Cancer Pipeline and pSNV Hunter to identify and prioritize functional promoter SNVs, including lowly recurrent and singleton mutations, using multi-omics data from the PCAWG dataset.

Copy number-independent allelic imbalance in mRNA is selected in cancer and has prognostic relevance

The paper identifies copy number-independent allelic imbalance in mRNA as a selected feature in cancer with prognostic significance.

On the discovered Cancer Driving Nucleotides (CDNs)-Distributions across genes, cancer types and patients

This study identifies Cancer Driving Nucleotides (CDNs) across cancer types and patients, finding that most remain unidentified and highlights the need for larger sample sizes to improve detection.

Human and bats genome robustness under COSMIC mutational signatures

The paper develops a mutation simulator to assess genome robustness under COSMIC mutational signatures, finding higher resilience in human and bat genomes to APOBEC-related mutations.

Subtype-specific Patterns of Evolution and Clinically Relevant Genomic Instability in Wilms Tumour

This study analyzes the evolutionary patterns and genomic instability in Wilms tumors, identifying subtype-specific evolutionary sequences and proposing CNA diversity as a prognostic biomarker.

Multi-omic lineage tracing predicts the transcriptional, epigenetic and genetic determinants of cancer evolution

The paper uses single-cell multi-omic lineage tracing to identify transcriptional, epigenetic, and genetic factors that predict cancer evolution and drug tolerance.

MetDecode: methylation-based deconvolution of cell-free DNA for non-invasive multi-cancer typing

MetDecode uses methylation patterns to estimate tumor proportion and identify tissue origin in cell-free DNA samples from cancer patients.

Clinical application of whole-genome sequencing for precision oncology of solid tumors

This study evaluates the clinical utility of whole-genome sequencing in solid tumors, showing 72% of reports provided clinically relevant insights and 69% aided therapeutic decision-making.

CaMutQC: An R Package for Integrative Quality Control of Cancer Somatic Mutations

CaMutQC is an R package that performs quality control and filtering of cancer somatic mutations, improving accuracy and comparability across studies.

LBFextract: unveiling transcription factor dynamics from liquid biopsy data

LBFextract extracts transcription factor dynamics from liquid biopsy data to improve reproducibility and subtype classification in prostate cancer.

Somatic mutation phasing and haplotype extension using linked-reads in multiple myeloma

This study uses linked-read sequencing to phase somatic mutations in multiple myeloma, extending haplotype blocks and revealing phasing patterns in key mutated genes.

Analysis of Factors Determining Success in FFPE Based NGS Panel Testing For Lung & Ovarian Cancer

This study identifies pre-analytic factors affecting NGS success in FFPE samples for lung and ovarian cancer, highlighting DNA quality, sample type, and fixation time as key predictors.

Preclinical Pediatric Molecular Analysis for Therapy Choice (MATCH)

This paper establishes a diverse collection of preclinical models for pediatric solid tumors and demonstrates their utility in precision medicine trials and drug testing.

Copy number losses of oncogenes and gains of tumor suppressor genes generate common driver events of human cancer

The paper identifies common driver events in human cancer by analyzing copy number alterations and their interactions with mutations in oncogenes and tumor suppressor genes.

Subclonal mutation load predicts survival and response to immunotherapy in cancers with low to moderate tumor mutation burden

The paper develops CliPP to estimate subclonal mutation load (sML) and shows it predicts survival and immunotherapy response in cancers with low to moderate TMB.

StarSignDNA: Signature tracing for accurate representation of mutational processes

StarSignDNA is an algorithm for mutational signature analysis in cancer sequencing data, improving accuracy and biological validity by addressing overfitting and underfitting.

The history of chromosomal instability in genome doubled tumors

This paper introduces GRITIC, a method to time genomic gains in tumors, finding that copy number gains often accumulate after genome duplication.

Detecting branching rate heterogeneity with tree balance statistics in lineage tracing trees

This study evaluates tree balance statistics for detecting growth rate heterogeneity in lineage tracing trees of cancer populations, finding J1 performs well while Sackin index is less effective.

Disentangling sources of clock-like mutations in germline and soma

The paper develops a mathematical model to disentangle the sources of clock-like mutations in germline and soma, finding distinct origins for SBS signatures 1 and 5.

The promoter mutation paucity as part of the dark matter of the cancer genome

The paper identifies previously overlooked activating promoter mutations in cancer using a computational workflow applied to the PCAWG dataset, validating several candidates through luciferase assays.

Machine Learning Assisted Web Application for Identifying Beneficial Drug Candidates for Genetic Alterations in Cancer Patients

The paper develops a web application that uses machine learning to match genetic alterations with drug candidates for cancer patients, identifying optimal clusters of drugs based on interaction scores.

Machine learning guided signal enrichment for ultrasensitive plasma tumor burden monitoring

This paper introduces MRD-EDGE, a machine learning platform for ultrasensitive ctDNA detection in plasma WGS, showing improved sensitivity and broader applicability for MRD monitoring.

The theory of massively repeated evolution and full identifications of Cancer Driving Nucleotides (CDNs)

This study develops a theory to identify Cancer Driving Nucleotides (CDNs) by analyzing mutation recurrence across large cancer datasets, finding that mutations recurring at least three times are likely CDNs.

In Search of the Perfect Model: How Cancer Cell Lines Relate to Native Cancers

This study compares cancer cell lines to native cancers using CNV profiles and ML to identify cell lines that best represent specific cancer types.

Functional Exploration of Copy Number Alterations in a Drosophila Model of Triple Negative Breast Cancer

The paper identifies 48 functional driver genes from copy number alterations in a Drosophila TNBC model and shows their role in increased therapeutic resistance.

Negative Selection Allows DNA Mismatch Repair-Deficient Mouse Fibroblasts In Vitro to Tolerate High Levels of Somatic Mutations

This study shows that DNA mismatch repair-deficient mouse fibroblasts can tolerate high mutation burdens in vitro without significant growth effects, revealing mutation-driven population changes and negative selection.

Sensitive detection of copy number alterations in samples with low circulating tumor DNA fraction.

The paper introduces Jumble, an algorithm that improves the sensitivity of detecting copy number alterations in low ctDNA samples, achieving detection limits of 1-2% for amplifications and 4-8% for deletions.

Co-occurring Mutations in Different Genes Can Fuel Oncogenic Signaling and Serve as Metastatic Tumor Markers

The paper identifies co-occurring mutation pairs in cancer genomes that are associated with metastasis and provides a tool for predicting metastatic potential.

MUSE-XAE: MUtational Signature Extraction with eXplainable AutoEncoder enhances tumour type classification

MUSE-XAE extracts mutational signatures from cancer genomes using an explainable Auto-Encoder, achieving accurate extraction and improving tumour-type classification.

Technical and biological variations in the purification of extrachromosomal circular DNA (eccDNA) and the finding of more eccDNA in the plasma of lung adenocarcinoma patients compared with healthy donors

The paper develops a method to profile extrachromosomal circular DNA (eccDNA) in plasma and finds higher eccDNA levels in lung adenocarcinoma patients compared to healthy donors.