Genomic variations and chromosomal abnormalities

Multiplex generation and single cell analysis of structural variants in a mammalian genome

This paper introduces Genome-Shuffle-seq, a method for generating and mapping structural variants in mammalian genomes, and demonstrates its application in mouse embryonic stem cells.

A Murine Database of Structural Variants Enables the Genetic Architecture of a Spontaneous Murine Lymphoma to be Characterized

The paper creates a database of structural variants in 40 inbred mouse strains and identifies an SV linked to lymphoma susceptibility in SJL mice.

Structural polymorphism and diversity of human segmental duplications

The paper analyzes segmental duplications in human genomes using long-read sequencing, identifying structurally polymorphic events and novel genes associated with copy number variation.

Long-Read Structural and Epigenetic Profiling of a Kidney Tumor-Matched Sample with Nanopore Sequencing and Optical Genome Mapping

The paper compares optical genome mapping and nanopore sequencing for structural and epigenetic analysis of a kidney tumor, highlighting their strengths in variant detection and epigenetic profiling.

Genomic deletion and duplication effects on cognitive ability lie at the opposing ends of the cortical sensorimotor-association hierarchy

The paper develops a method to analyze genomic deletions and duplications across the cerebral cortex and finds opposing effects on cognitive ability depending on gene expression patterns in different cortical regions.

Rare germline structural variants increase risk for pediatric solid tumors

This study identifies rare germline structural variants as risk factors for pediatric solid tumors, particularly neuroblastoma, by analyzing genome sequencing data from affected children and controls.

Genetic and functional characterization of inherited complex chromosomal rearrangements in a family with multisystem anomalies

The paper characterizes an inherited complex chromosomal rearrangement in a family with multisystem anomalies using multiple genomic and functional analyses.

Blackbird: structural variant detection using synthetic and low-coverage long-reads

Blackbird improves structural variant detection using synthetic and low-coverage long-reads, achieving comparable performance to high-coverage tools with less data.

Benchmarking of Germline Copy Number Variant Callers from Whole Genome Sequencing Data for Clinical Applications

This study benchmarks CNV callers for WGS clinical applications, finding DRAGEN v4.2 offers the best balance of sensitivity and precision for detecting deletions and some duplications.

Large complex structural rearrangements in human genomes harbor cryptic structures

The paper develops a new method to detect complex structural variants in large genomic regions, revealing previously undetectable structures and improving breakpoint accuracy.

HapCNV: A Comprehensive Framework for CNV Detection in Low-input DNA Sequencing Data

HapCNV improves CNV detection in low-input haploid sequencing data by using a pseudo-reference to reduce bias and enhance accuracy, especially for short CNVs.

CNVizard: a lightweight streamlit application for an interactive analysis of copy number variants

CNVizard is a lightweight Streamlit app for interactive CNV analysis, visualization, and annotation, compatible with CNVkit and AnnotSV.

Haplotype-Resolved Long-Read Sequencing in Hundreds of Diverse Brains Identifies Structural Variant Impacts on Expression and Allele-Specific Methylation

The paper uses long-read sequencing to identify structural variants and their impacts on gene expression and methylation in diverse human brain samples.

Effects of gene dosage on cognitive ability: A function-based association study across brain and non-brain processes

The paper identifies a CNV duplication associated with higher cognitive ability and shows gene-dosage effects differ between deletions and duplications across biological processes.

Full characterization of unresolved structural variation through long-read sequencing and optical genome mapping

This study uses long-read sequencing and optical genome mapping to fully characterize unresolved structural variants, achieving single-basepair resolution and improving diagnostic yield.

CNV-Profile Regression: A New Approach for Copy Number Variant Association Analysis in Whole Genome Sequencing Data

This paper introduces a new framework for CNV association analysis in whole genome sequencing data, identifying additional CNVs linked to Alzheimer's Disease.

FocalSV: target region-based structural variant assembly and refinement using single-molecule long read sequencing data

FocalSV improves structural variant detection by combining assembly-based precision with targeted analysis efficiency using long-read sequencing data.

Rare Copy Number Variant analysis in case-control studies using SNP Array Data: a scalable and automated data analysis pipeline

This paper presents a scalable and automated pipeline for analyzing rare copy number variants in case-control studies using SNP array data, enabling efficient CNV detection, quality control, and impact assessment.

Resolution of ring chromosomes, Robertsonian translocations, and complex structural variants from long-read sequencing and telomere-to-telomere assembly

This paper resolves ring chromosomes, Robertsonian translocations, and complex structural variants using long-read sequencing and telomere-to-telomere assembly, revealing breakpoint structures and methylation changes.

Successful classification of clinical pediatric leukemia genetic subtypes via structural variant detection using HiFi long-read sequencing

This study shows that HiFi long-read sequencing can detect clinically relevant structural variants in pediatric leukemia, improving subtype classification.

Independent expansion, selection and hypervariability of the TBC1D3 gene family in humans

The paper investigates the expansion, selection, and hypervariability of the TBC1D3 gene family in humans using long-read sequencing data, revealing multiple duplications, copy number variation, and expression patterns.

VizCNV: An integrated platform for concurrent phased BAF and CNV analysis with trio genome sequencing data

VizCNV is a tool for analyzing CNVs and phased BAF from trio genome sequencing data, identifying de novo and inherited CNVs in immunodeficiency cases.

sv-channels: filtering genomic deletions using one-dimensional convolutional neural networks

sv-channels improves SV detection precision using deep learning, outperforming GRIDSS while maintaining Manta's recall.

Optical Genome Mapping of the human reference iPSC line KOLF2.1J reveals new smaller structural variants in neurodevelopmental genes

The paper uses optical genome mapping to identify new smaller structural variants in the KOLF2.1J iPSC line, affecting genes relevant to neurodevelopment.

Single-cell somatic copy number variants in brain using different amplification methods and reference genomes

The paper compares single-cell whole genome amplification methods and reference genomes for detecting somatic copy number variants in human brain tissue.

STIX: Long-reads based Accurate Structural Variation Annotation at Population Scale

STIX annotates structural variants using long-read data, achieving high accuracy and identifying common SVs in population-scale datasets.

Disentangling mechanisms behind the pleiotropic effects of proximal 16p11.2 BP4-5 CNVs

The paper identifies pleiotropic effects of 16p11.2 BP4-5 CNVs on 46 phenotypes, showing BMI-dependent and indirect associations through mediation and Mendelian randomization.

Evaluating the Joint Effects of Recurrent Copy Number Variants and Polygenic Scores on the Risk of Psychiatric Disorders in the iPSYCH2015 Case-Cohort Sample

This study examines how rare copy number variants and polygenic scores jointly affect psychiatric disorder risk in a large population sample, finding no significant interaction between the two factors.

Transcriptomic signatures of nine high-risk neuropsychiatric copy number variants in human brain cells

The paper analyzes transcriptomic differences in human brain cells with nine high-risk neuropsychiatric CNVs compared to non-carriers, finding widespread gene expression disruptions and shared functional pathways.

Impact and characterization of serial structural variations across humans and great apes

The paper introduces NAHRwhals, a method to detect serial structural variations in long-read genomes, identifies 37 sSV loci in humans, and shows their relevance to disease.