Cancer Genomics and Diagnostics

Discovery of Latent Drivers from Double Mutations in Pan-Cancer Data Reveal their Clinical Impact

The paper identifies latent driver double mutations in pan-cancer data and links them to clinical outcomes and drug response.

Scalable subclonal reconstruction of cancer cells in DNA sequencing data using a penalized likelihood model

CliPP reconstructs subclonal architecture in cancer DNA sequencing data efficiently and accurately, outperforming existing methods in speed while maintaining high concordance with consensus calls.

Comprehensive identification of somatic nucleotide variants in human brain tissue

This study identifies somatic SNVs in non-cancerous human brain tissues and establishes best practices for detecting low-frequency variants.

Ultra-low Input Circulating Tumor DNA Detection by MED-Amp in Early-Stage Pancreatic Cancer

This study evaluates the diagnostic sensitivity of the MED-Amp assay for detecting rare KRAS mutations in ctDNA from localized pancreatic cancer patients, showing improved detection at low DNA input and correlation with survival outcomes.

Profiles of expressed mutations in single cells reveal subclonal expansion patterns and therapeutic impact of intratumor heterogeneity

Trisicell infers subclonal expansion patterns and therapeutic impact of intratumor heterogeneity from scRNAseq data, revealing correlations between mutational composition and tumor aggressiveness.

Genomic signatures of past and present chromosomal instability in the evolution of Barretts esophagus to esophageal adenocarcinoma

This study identifies genomic signatures of chromosomal instability in Barrett's esophagus progressing to esophageal adenocarcinoma, showing sloping copy-number variation as a precursor to complexity.

Elements and Evolutionary Determinants of Genomic Divergence Between Paired Primary and Metastatic Tumors

This paper uses computational modeling to show that metastatic-primary genomic divergence depends on tumor growth dynamics and variant detectability, revealing non-monotonic relationships in some scenarios.

Tracing evolution history of 100 whole genome sequences of diffuse stem brain tumor

The paper analyzes 100 whole genome sequences of DIPG tumors to uncover evolutionary patterns, revealing early WGD acquisition, TP53 loss, complex SVs, and a unique late-stage mutation signature.

Drug-driven reclassification of multiple tumour subtypes reveals intrinsic molecular concordance of therapy across histologically disparate cancers

This study reclassifies tumors based on drug response and genomic alterations, revealing molecular concordance in therapy across histologically different cancers.

Clinical-grade whole genome sequencing of colorectal cancer and 3-prime transcriptome analysis demonstrate targetable alterations in the majority of patients.

The paper uses clinical-grade whole genome sequencing and 3' transcriptome analysis to identify targetable genomic alterations in colorectal cancer patients.

Single-cell copy number lineage tracing enabling gene discovery

The paper introduces MEDALT and LSA to reconstruct copy number lineage trees from single-cell data and identify fitness-associated genes, showing improved accuracy over phylogenetics methods in cancer datasets.

Uniform Genomic Data Analysis in the NCI Genomic Data Commons

The paper describes the pipelines and workflows used to process and harmonize genomic data in the NCI Genomic Data Commons, including data types like somatic mutations and gene expression.

bMSI-CAST: a systematic method for next generation sequencing-based microsatellite instability detection in plasma cell-free DNA

bMSI-CAST improves cfDNA MSI detection by enhancing locus selection, duplicate removal, and calling algorithm, achieving high accuracy in gastrointestinal cancer samples.

Comprehensive Assessment of Somatic Copy Number Variation Calling Using Next-Generation Sequencing Data

This study evaluates somatic CNV callers using NGS data from 91 samples with varying factors, finding that caller choice and tumor purity significantly impact call quality.

Sub-nucleosomal organization in urine cell-free DNA

This study characterizes urine cfDNA fragmentation patterns and shows they reflect sub-nucleosomal organization, with potential for cancer diagnostics.

Computational validation of clonal and subclonal copy number alterations from bulk tumour sequencing

This paper introduces CNAqc, a toolset for validating clonal and subclonal copy number alterations in bulk tumor sequencing by addressing tumor purity, ploidy, and heterogeneity using simulations and single-cell data.

Distinguishing excess mutations and increased cell death based on variant allele frequencies

The paper develops a method to estimate cell turnover and mutation rates from bulk sequencing data, finding both are elevated in a hepatocellular carcinoma sample.

eTumorMetastasis, a network-based algorithm predicts clinical outcomes using whole-exome sequencing data of cancer patients

eTumorMetastasis uses whole-exome sequencing data to predict tumor recurrence by analyzing network-based gene signatures from founding clones.

Adaptor Template Oligo-Mediated Sequencing (ATOM-Seq): A versatile and ultra-sensitive UMI-based NGS library preparation technology, for use with cfDNA and cfRNA.

ATOM-Seq is a new NGS library preparation method that improves sensitivity and reduces errors in detecting low-frequency mutations in cfDNA and cfRNA.

Somatic mutations reveal widespread mosaicism and mutagenesis in human placentas

This study uses whole genome sequencing of placental biopsies to show that human placentas exhibit clonal expansions, copy number changes, and developmental bottlenecks similar to childhood cancer.

MAESTRO affords 'breadth and depth' for mutation testing

MAESTRO enables efficient and accurate tracking of thousands of low-frequency mutations with reduced sequencing, improving mutation testing in cancer and liquid biopsies.

Reconstructing tumor evolutionary histories and clone trees in polynomial-time with SubMARine

This paper introduces SubMARine, a polynomial-time algorithm for reconstructing tumor clone trees that efficiently captures uncertainty and scales to large datasets.

Accucopy: Accurate and Fast Inference of Allele-specific Copy Number Alterations from Low-coverage Low-purity Tumor Sequencing Data

Accucopy infers total and allele-specific copy numbers from low-coverage low-purity tumor data, showing higher accuracy than existing methods.

ChIP-seq of plasma cell-free nucleosomes identifies cell-of-origin gene expression programs

The paper introduces cfChIP-seq to analyze cell-free nucleosomes and shows it can detect disease-related transcriptional changes and patient-specific features in cancer.

A Modular Master Regulator Landscape Determines the Impact of Genetic Alterations on the Transcriptional Identity of Cancer Cells

The paper identifies 407 Master-Regulator proteins that canalize cancer genomics into transcriptional subtypes and links genetic alterations to tumor biology through modular regulatory architectures.

The histologic phenotype of lung cancers may be driven by transcriptomic features rather than genomic characteristics

This study shows that transcriptomic features, not genomic characteristics, drive the histologic phenotype of lung cancers.

Aneuploidy Spectrum Analysis as a Primer for Copy Number Profiling of Cancer Cells

AStra is a framework for aneuploidy profiling of cancer data that assesses suitability for copy number analysis, showing high accuracy in identifying aneuploidy spectra and ploidy levels.

Single-cell and single-variant resolution analysis of clonal evolution in human liver cancer

The paper analyzes clonal evolution in liver cancer at single-cell and single-variant resolution, revealing genetic and phenotypic heterogeneity and their evolutionary relationships.

Sensitive detection of DNA contamination in tumor samples via microhaplotypes

The paper introduces a method to detect DNA contamination in tumor samples using microhaplotypes, achieving sensitivity for 1% contamination without a normal sample.

PyClone-VI: Scalable inference of clonal population structures using whole genome data

PyClone-VI infers cancer clonal structures from whole genome data efficiently and accurately, validated on PCAWG and TRACERx datasets.