Genomic variations and chromosomal abnormalities

Population-level structural variant characterization from pangenome graph

Swave identifies structural variants from pangenome graphs, revealing complex SV patterns and pathogenic variants in human populations.

LYCEUM: Learning to call copy number variants on low coverage ancient genomes

LYCEUM is a machine learning-based CNV caller for ancient DNA that improves detection accuracy in low-coverage samples by pre-training on high-quality data and fine-tuning on limited aDNA samples.

An optimised computational approach for the identification of somatic structural variants in cancer

The paper benchmarks structural variant callers in cancer genomics and recommends a consensus approach combining Delly, GRIDSS, Manta, and SvABA for improved performance.

Regenotyping structural variants through an accurate force-calling method

The paper introduces cuteSV2, a long-read-based method for accurate structural variant regenotyping, outperforming existing methods in benchmarking.

Nanopore Sequencing Unveils Somatic Structural Variations as Biomarkers in Laryngeal squamous cell carcinoma Genomes

This study introduces SomaGauss-SV, a nanopore-based method for detecting somatic structural variations in LSCC, revealing correlations with smoking and gene expression.

Mapping Cerebellar Morphology in 15q11.2 CNV Carriers Using Normative Modeling

The paper uses normative modeling to assess cerebellar morphology differences in 15q11.2 CNV carriers compared to non-carriers, finding modest and individualized effects.

SAVANA: reliable analysis of somatic structural variants and copy number aberrations in clinical samples using long-read sequencing

SAVANA improves detection of somatic structural variants and copy number aberrations in cancer using long-read sequencing with higher sensitivity and specificity than existing tools.

Resolving the full set of human polymorphic inversions and other complex variants from ultra-long read data

The paper identifies 612 human inversion variants using ultra-long read sequencing and develops a bioinformatic tool to genotype them across 54 individuals.

Accurate detection of pathogenic structural variants guided by multi-platform comparison

The paper introduces dicast, a machine-learning method that improves the detection of pathogenic structural variants from short-read sequencing by leveraging genomic context and alignment features.

CNVPipe: An enhanced pipeline for accurate analysis of copy number variation from whole-genome sequencing

CNVPipe improves CNV detection in WGS by integrating CNV tools with machine learning, reducing FDR and increasing sensitivity for both bulk and single-cell data.

ConsensuSV-ONT - a modern method for accurate structural variant calling

ConsensuSV-ONT combines six structural variant callers with a neural network to improve accuracy in Oxford Nanopore long-read structural variant calling.

Neurodevelopmental copy number variants increase risk of internalising and cardiometabolic multimorbidity: findings from UK Biobank

The paper investigates the association between neurodevelopmental copy number variants (ND-CNVs) and increased risk of internalising and cardiometabolic multimorbidity using UK Biobank data.

Formation of chromosomal rearrangements in Saccharomyces cerevisiae diploids through regionally-biased non-allelic homologous recombination

The paper identifies a bias for chromosomal rearrangements at the right arm of Chr7 in yeast, showing that this bias is due to inefficient repair rather than increased breakage.

eLaRodON: identification of large genomic rearrangements in Oxford Nanopore sequencing data

eLaRodON improves large genomic rearrangement detection in Oxford Nanopore data, outperforming existing tools with higher accuracy across multiple datasets.

Extrachromosomal DNA Gives Cancer a New Evolutionary Pathway

The paper shows that ecDNA allows tumors to adapt rapidly by maintaining a spectrum of gene expression levels across cells, rather than relying on clonal expansion.

Chromosomal Aneuploidy in Normal, Non-Neuronal Brain Nuclei of Glioblastoma Patients is Not a Cancer Driver

The paper examines aneuploidy in non-neuronal brain nuclei of GBM patients and finds it is common in normal tissue and not associated with GBM risk.

An antisense oligonucleotide-based strategy to ameliorate cognitive dysfunction in the 22q11.2 Deletion Syndrome

This study shows that reducing EMC10 levels in 22q11.2 deletion syndrome models improves cognitive function and sustains benefits for over two months.

Severus: accurate detection and characterization of somatic structural variation in tumor genomes using long reads

Severus detects and characterizes somatic structural variations in tumor genomes using long reads, outperforming existing methods in accuracy and revealing clinically relevant rearrangements.

K-mer analysis of long-read alignment pileups for structural variant genotyping

This paper introduces a method called kanpig for accurately genotyping structural variants using long-read alignment pileups, achieving higher concordance than existing tools.

Sawfish: Improving long-read structural variant discovery and genotyping with local haplotype modeling

Sawfish improves long-read structural variant calling accuracy by modeling local haplotypes, outperforming existing tools in benchmark tests and joint-genotyping analyses.

Charm is a flexible pipeline to simulate chromosomal rearrangements on Hi-C-like data.

Charm simulates Hi-C-like data with chromosomal rearrangements to benchmark SV detection tools and provides a dataset for future benchmarking.

Cell-cycle dependent DNA repair and replication unifies patterns of chromosome instability

The paper develops a computational cell-cycle model to quantify SV generation and unify genomic patterns from chromosomal instability.

Performance evaluation of structural variation detection using DNBSEQ whole-genome sequencing

The paper evaluates SV detection performance across DNBSEQ and Illumina platforms using 40 tools, finding consistent results in metrics and genomic characteristics.

Synaptic-dependent developmental dysconnectivity in 22q11.2 deletion syndrome

This study investigates developmental dysconnectivity in 22q11.2 deletion syndrome using a cross-species approach, finding age-specific fMRI connectivity changes with synaptic origins.

Genome-wide profiling of highly similar paralogous genes using HiFi sequencing

The paper develops Paraphase, a HiFi-based method to resolve highly similar paralogous genes, revealing genetic diversity and de novo events in segmental duplications.

Pivotal role of biallelic frequency analysis in identifying copy number alterations using genome-wide methods in tumors with a high level of aneuploidy

The paper identifies copy number alterations in highly aneuploid tumors using genome-wide methods and highlights the bias from improper normal ploidy level setting in LPWGS and methylation arrays.

Investigation of a Pathogenic Inversion in UNC13D and Comprehensive Analysis of Chromosomal Inversions Across Diverse Datasets

The paper reports a pathogenic inversion in UNC13D and analyzes chromosomal inversions across multiple datasets to identify their molecular characteristics and implications in genetic diseases.

Resolving somatic SVs via full-length sequence model-based local graph-genome optimization

SVscope improves somatic SV detection using full-length sequence models and local graph-genome optimization, achieving higher accuracy than existing methods.

gcSV: a unified framework for comprehensive structural variant detection

gcSV is a structural variant detection framework that improves accuracy and yield across long, hybrid, and short-read data, identifying over 93,000 novel SVs.

Long-read sequencing of 945 Han individuals identifies novel structural variants associated with phenotypic diversity and disease susceptibility

The paper identifies novel structural variants in Han Chinese genomes using long-read sequencing and links them to phenotypic diversity and disease susceptibility.