Genomic variations and chromosomal abnormalities

GeneToCN: An Alignment-Free Method for Gene Copy Number Estimation Directly from Next-Generation Sequencing Reads

GeneToCN estimates gene copy numbers from NGS reads using gene-specific k-mer frequencies, showing strong correlation with experimental data across multiple genes and sequencing technologies.

MosaiCatcher v2: a single-cell structural variations detection and analysis reference framework based on Strand-seq

MosaiCatcher v2 provides a standardized workflow for single-cell structural variation detection using Strand-seq, enhancing reproducibility and portability in human genetics research.

KmerSV: a visualization and annotation tool for structural variants using Human Pangenome derived k-mers

KmerSV visualizes and annotates structural variants using k-mers and the Human Pangenome reference.

Low-pass whole genome sequencing is a reliable and cost-effective approach for copy number variant analysis in the clinical setting

This study validates low-pass whole genome sequencing as a reliable and cost-effective method for detecting copy number variants in clinical settings.

Comparison of germline and somatic structural variants in cancers reveal systematic differences in variant generating and selection processes

The paper compares germline and somatic structural variants in cancer, identifying differences in their generating processes and selection, and develops a classifier to distinguish them in tumor samples without matched normals.

Robust CNV detection using single-cell ATAC-seq

This paper introduces RIDDLER, a single-cell ATAC-seq CNV detection algorithm that outperforms existing methods in cancer cell line models and 10x multimome data.

Connecting Cancers to Chromosomal Locations Through Copy Number Variations

The paper identifies chromosomal locations of top upregulated and downregulated genes in cancer cell lines using copy number variation data from DepMap.

Break-induced replication underlies formation of inverted triplications and generates unexpected diversity in haplotype structures

The paper investigates DUP-TRP/INV-DUP genomic rearrangements in neurodevelopmental disorders, identifying four SV haplotypes and refining template switching points using multiple sequencing technologies.

Musculoskeletal phenotypes in 3q29 deletion syndrome

This study describes musculoskeletal phenotypes in 3q29 deletion syndrome, finding high prevalence of congenital anomalies and bone fractures.

Population-based Risk of Psychiatric Disorders Associated with Recurrent CNVs

The paper estimates population-based risks of psychiatric disorders associated with 34 recurrent CNVs using a large case-cohort sample, finding moderate risks for ADHD, autism, and schizophrenia, but not depression.

CoFrEE: An Application to Estimate DNA Copy Number from Genome-wide RNA Expression Data

CoFrEE estimates DNA copy number from RNA expression data, performing comparably to existing RNAseq methods and applicable to older expression-array datasets.

A Standardized Protocol for Sample Preparation for Scanning Electron Microscopy (SEM) to Visualize Extrachromosomal DNA (ecDNA)

This paper presents a standardized protocol for visualizing extrachromosomal DNA (ecDNA) using scanning electron microscopy (SEM) in human cancer cell lines.

Copy-number variants as modulators of common disease susceptibility

This study identifies 73 CNV-related disease signals in 331,522 UK Biobank participants, showing CNVs increase disease risk and earlier onset, with polygenic effects and gene dosage impacts.

Subcortical brain alterations in carriers of genomic copy number variants

This study examines subcortical brain alterations in CNV carriers across multiple neuropsychiatric disorders, finding shared and distinct patterns of structural changes.

Schizophrenia-associated somatic copy number variants from 12,834 cases reveal contribution to risk and recurrent, isoform-specific NRXN1 disruptions

This study identifies somatic copy number variants (sCNVs) in schizophrenia cases, revealing their contribution to risk and specific NRXN1 disruptions.

Visual-motor integration deficits in 3q29 deletion syndrome

This study examines visual-motor integration deficits in 3q29 deletion syndrome, finding significant gender differences and associations with ADHD and cognitive ability.

Structural alterations in the amygdala and impaired social incentive learning in a mouse model of a genetic variant associated with neurodevelopmental disorders

This study examines structural brain changes and social behavior in Tbx1 heterozygous mice, linking reduced amygdala volume to impaired social incentive learning.

Precise characterization of somatic complex structural variations from paired long-read sequencing data with nanomonsv

nanomonsv detects somatic structural variations from long-read sequencing data with high precision and recall, revealing complex SV features in cancer.

Combinations of genes at the 16p11.2 and 22q11.2 CNVs contribute to neurobehavioral traits

The paper investigates how combinations of genes in the 16p11.2 and 22q11.2 CNVs contribute to neurobehavioral traits by comparing pairwise and single-gene effects in GWAS data.

Resolving the unsolved: Comprehensive assessment of tandem repeats at scale

The paper introduces TRGT, a tool for tandem repeat genotyping, and a database of 937,122 TRs across 100 genomes, achieving high concordance and detecting repeat expansions, methylation, and mosaicism.

Multi-modal investigation of the schizophrenia-associated 3q29 genomic interval reveals global genetic diversity with unique haplotypes and segments that increase the risk for non-allelic homologous recombination

The paper investigates the 3q29 genomic region, identifying novel haplotypes and breakpoint segments associated with deletion and duplication syndromes, and categorizes cases into distinct classes.

Towards Preclinical Validation of Arbaclofen (R-baclofen) Treatment for 16p11.2 Deletion Syndrome

Experiments across four laboratories found that arbaclofen rescued cognitive deficits in mouse models of 16p11.2 deletion, without sedation or significant off-target behavioral effects.

SurVIndel2: improving local CNVs calling from next-generation sequencing using novel hidden information

SurVIndel2 improves CNV detection from NGS by using hidden split reads, outperforming existing methods and generating a comprehensive CNV catalogue.

Resolution of structural variation in diverse mouse genomes reveals chromatin remodeling due to transposable elements

The paper identifies structural variants in 20 mouse strains using long-read sequencing, revealing transposable elements' role in chromatin remodeling and gene expression in mESCs.

The impact of FASTQ and alignment read order on structural variation calling from long-read sequencing data

This study evaluates how FASTQ read order affects structural variation calling in long-read sequencing data using PacBio data from C. elegans isolates.

Comparative genomic analysis identifies great-ape-specific structural variants and their evolutionary significance

The paper identifies great-ape-specific structural variants and their potential role in evolutionary phenotypic innovations.

Mapping the Complex Genetic Landscape of Human Neurons

The paper identifies and validates copy number variants in single human neurons using a new method, revealing nonrandom CNV locations and complex karyotypes in a subset of neurons.

Rescue of neuropsychiatric phenotypes in a mouse model of 16p11.2 duplication syndrome by genetic correction of an epilepsy network hub

This study identifies PRRT2 as a key hub in an epilepsy network disrupted by 16p11.2 duplication and shows its correction rescues multiple neuropsychiatric and seizure-related phenotypes in mice.

Automatic detection of complex structural genome variation across world populations

The paper develops a method to detect complex structural variants across human genomes and finds they are associated with phenotypic hotspots and evolutionary changes.

MHCnvex: Likelihood-based model for calling the copy number variations and loss of heterozygosity in MHC class I and II locus

MHCnvex is a likelihood-based model for accurately calling copy number variations and loss of heterozygosity in MHC class I and II loci, improving accuracy by integrating adjacent chromosome 6 regions.