Genomic variations and chromosomal abnormalities

Segmental duplications and their variation in a complete human genome

The paper presents a comprehensive analysis of segmental duplications in a complete human genome, revealing their distribution, variation, and evolutionary significance.

SENSV: Detecting Structural Variations with Precise Breakpoints using Low-Depth WGS Data from a Single Oxford Nanopore MinION Flowcell

SENSV detects structural variations with high sensitivity and precise breakpoints using low-depth Oxford Nanopore WGS data from a single MinION flowcell, outperforming existing tools in pathogenic SV detection.

SavvyCNV: genome-wide CNV calling from off-target reads

SavvyCNV calls genome-wide CNVs using off-target reads from exome and targeted sequencing, outperforming existing tools and detecting clinically relevant CNVs previously missed.

A distinct cognitive profile in individuals with 3q29 deletion syndrome

This study evaluates cognitive profiles in individuals with 3q29 deletion syndrome, finding verbal ability strengths and associations with intellectual disability and adaptive behavior.

The impact of genomic structural variation on the transcriptome, chromatin, and proteome in the human brain

The paper identifies structural variants in the human brain and their associations with molecular traits and neurodegenerative diseases.

RF4Del: A Random Forest approach for accurate deletion detection

RF4Del is a random forest method for accurate deletion detection that outperforms existing tools and is robust to sequencing coverage and deletion size variations.

The individual and global impact of copy number variants on complex human traits

This study identifies 131 CNV signals associated with 47 complex traits in the UK Biobank, revealing new gene functions and linking CNVs to decreased longevity and health outcomes.

CoverageMaster: comprehensive CNV detection and visualization from NGS short reads for genetic medicine applications

CoverageMaster detects and visualizes CNVs in exome and genome data using wavelet compression and HMM, potentially replacing probe-based methods.

Improved structural variant discovery in hard-to-call regions using sample-specific string detection from accurate long reads

SVDSS improves structural variant discovery in hard-to-call regions using long-read sequencing by combining multiple methodologies, outperforming existing methods in repetitive genomic regions.

GCAT|Panel, a comprehensive structural variant haplotype map of the Iberian population from high-coverage whole-genome sequencing

The paper generates a comprehensive haplotype map of the Iberian population using high-coverage whole-genome sequencing, focusing on structural variants and their imputation capabilities.

Dysgu: efficient structural variant calling using short or long reads

Dysgu calls structural variants and indels from paired-end or long reads, outperforming existing tools in speed and accuracy.

JAX-CNV: A whole genome sequencing-based algorithm for copy number detection at clinical grade level

JAX-CNV is a whole genome sequencing-based algorithm for copy number variant detection, achieving 100% recall and 4% false discovery rate in clinical validation.

OptiDiff: structural variation detection from single optical mapping reads

OptiDiff detects and classifies homozygous and heterozygous structural variations from optical mapping data with better performance than existing methods at low coverage.

Hi-C detects genomic structural variants in peripheral blood of pediatric leukemia patients

The paper demonstrates that Hi-C can detect structural variants, including translocations, in peripheral blood samples of pediatric B-ALL patients, offering a non-invasive alternative to bone marrow biopsies.

Low frequency somatic copy number alterations in normal human lymphocytes revealed by large scale single-cell whole genome profiling

The paper uses single-cell whole genome sequencing to identify low frequency somatic copy number alterations in normal human lymphocytes, finding 7.5% of cells have large-size copy number alterations.

Chimeric chromosome landscapes of human somatic cell cultures show dependence on stress and regulation of genomic repeats by CGGBP1.

The paper investigates chromosomal chimeras in human cell cultures, showing their occurrence at genomic repeats and regulation by stress and CGGBP1 depletion.

Multi-site Technical Performance and Concordance of Optical Genome Mapping: Constitutional Postnatal Study for SV, CNV, and Repeat Array Analysis

This study evaluates the performance and reproducibility of optical genome mapping (OGM) across multiple sites for detecting structural variations and copy number variations in constitutional disorders, showing high concordance with standard of care methods.

Haplotype-resolved inversion landscape reveals hotspots of mutational recurrence associated with genomic disorders

The paper identifies recurrent inversions in human genomes and links them to genomic disorders through mutational recurrence and structural diversity.

Dynamic interplay between structural variations and 3D chromosome organization in pancreatic cancer

The paper investigates structural variations and 3D chromatin organization in pancreatic cancer using SMRT and Hi-C sequencing, revealing their interplay and impact on gene expression and genome stability.

A comparison of tools for copy-number variation detection in germline whole exome and whole genome sequencing data

The paper benchmarks CNV detection tools on WGS and WES data using clinical standards and reference samples, finding that combining multiple tools improves recall but precision remains a challenge.

HolistiC: Leveraging Hi-C and Whole Genome Shotgun Sequencing for Double Minute Chromosome Discovery

HolistIC integrates Hi-C and WGS data to accurately predict double minutes in cancer genomes, resolving ambiguities from overlapping amplicon coordinates.

A benchmark of structural variation detection by long reads through a realistic simulated model.

The paper benchmarks structural variation detection using long reads through a simulated model, finding that combining multiple callers improves recall and precision.

Structural variants are a major source of gene expression differences in humans and often affect multiple nearby genes

The paper identifies structural variants as a major source of gene expression differences, showing they affect multiple genes and have broader expression effects than SNVs or indels.

MCKAT, a multi-dimensional copy numbervariant kernel association test

The paper introduces MCKAT, a multi-dimensional CNV kernel association test, which detects significant associations between CNVs and disease traits more effectively than a uni-dimensional method.

PerSVade: Personalized Structural Variation detection in your species of interest

PerSVade improves structural variant detection by optimizing parameters for each species, enhancing accuracy across diverse eukaryotes.

SCYN: Single cell CNV profiling method using dynamic programming

SCYN is a single-cell CNV segmentation method using dynamic programming, showing high accuracy and speed on scDNA datasets.

Haplotype-aware single-cell multiomics uncovers functional effects of somatic structural variation

This paper introduces scNOVA, a method to analyze somatic structural variants in single-cell multiomics data, revealing their functional impacts on gene regulation and cancer pathways.

Structural variants in Chinese population and their impact on phenotypes, diseases and population adaptation

The paper performs long-read sequencing in 405 Chinese individuals to discover and characterize structural variants, finding novel SVs and their associations with phenotypes and diseases.

Tbx1, a 22q11.2-encoded gene, is a link between alterations in fimbria myelination and cognitive speed in mice

This study shows that Tbx1 deletion in mice affects myelination and cognitive speed, linking 22q11.2 CNV alterations to cognitive deficits.

SVJAM: Joint Analysis of Structural Variants Using Linked Read Sequencing Data

SVJAM improves structural variant calling in linked-read data by jointly analyzing multiple samples, recovering missed variants and correcting incorrect types compared to LongRanger.