Genomic variations and chromosomal abnormalities

The paper evaluates CNV detection from exome sequencing in the DDD study, finding it has higher sensitivity than low-resolution CMA and comparable sensitivity to exon-resolution CMA.

The paper identifies ancestral bias in structural variant breakpoint placement, showing that small allelic variants contribute to inconsistent breakpoint locations across haplotypes.

labelSeg annotates tumor copy number alteration segments to improve interpretation of SCNA profiles, showing strong correlation between SCNA and mRNA expression.

This study profiles genomic structural variation in Indigenous Australians using whole genome long-read sequencing, revealing abundant and previously unannotated variants and unique STR diversity.

This paper introduces a graph clustering algorithm for detecting and genotyping structural variants from long-read sequencing data, achieving high accuracy in benchmark tests.

ReConPlot is an R package for visualizing and interpreting complex genome rearrangements by integrating somatic copy number aberrations and structural variants.

GASOLINE detects germline and somatic structural variants from long-read sequencing data with high accuracy, outperforming existing methods in synthetic and real datasets.

The paper introduces COMSV, a method for identifying structural variations in cancer samples, showing high sensitivity and specificity and detecting hundreds of novel SVs per sample.

Decoil reconstructs complex extrachromosomal DNA structures from long-read sequencing data, improving resolution of ecDNA topology and heterogeneity in cancer.

This paper describes a microdeletion allele in C. elegans generated via CRISPR/Cas9, which removes 32 genes and causes complex developmental phenotypes.

The paper uses patient brain organoids to show that 16p11.2 CNVs affect RBFOX1 expression and link it to neurodevelopmental disorders.

This study introduces MGA-Seq, a method to detect multiple genomic abnormalities, and finds that focal amplification in tumors is heterogeneous and reveals ecDNA network architecture.

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

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

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

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

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

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

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

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.

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.

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.

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.

EigenDel detects genomic deletions using discordant read-pairs and unsupervised learning, outperforming existing methods in accuracy and sensitivity on low coverage data.

This study investigates the phenotypic effects of 22q11.2 copy number variants in the general population using UK Biobank data, finding associations with BMI, platelet volume, and other traits.

Jasmine improves SV comparison and analysis by refining SVs, reducing Mendelian discordance, and revealing high-confidence de novo SVs across diverse samples.

The paper develops a new laser-based cell isolation technique and optimized whole genome amplification protocol to enable whole genome analysis from stained blood cells.

The paper identifies mosaic chromosomal alterations in children with developmental disorders using SNP array data from the DDD study, finding that many are tissue-specific and undetectable in blood.

The paper benchmarks structural variant prediction tools in C. elegans, showing performance varies by variant type and sequencing depth, and highlights the need for real-data reference datasets.