Genomic variations and chromosomal abnormalities

Mining Thousands of Genomes to Classify Somatic and Pathogenic Structural Variants

The paper presents a method to index and search raw alignments from thousands of samples to improve the classification of somatic and pathogenic structural variants.

SVhound: Detection of future Structural Variation hotspots

SVhound predicts regions likely to contain novel structural variations by analyzing population-level SV datasets, showing high correlation with full datasets and applicability across species.

Overexpression of CD47 is associated with brain overgrowth in 16p11.2 deletion syndrome

The paper investigates the role of CD47 overexpression in 16p11.2 deletion syndrome, showing it contributes to brain overgrowth by inhibiting phagocytosis in neural progenitor and oligodendrocyte progenitor cells.

Functional assessment of the "two-hit" model for neurodevelopmental defects in Drosophila and X. laevis

The paper tests a 'two-hit' model for neurodevelopmental defects by examining interactions between 16p12.1 homologs and 'second-hit' genes in Drosophila and Xenopus laevis, finding genetic interactions in 63% of tested pairs.

HandyCNV: Standardized Summary, Annotation, Comparison, and Visualization of CNV, CNVR and ROH

HandyCNV is an R package for summarizing, annotating, comparing, and visualizing CNV and ROH from SNP data, providing a standardized and user-friendly tool for human and livestock research.

Association of Structural Variation with Cardiometabolic Traits in Finns

This study identifies 31 genome-wide significant associations between structural variations and cardiometabolic traits in Finns, including two novel loci with strong phenotypic effects.

CNAHap: a germline haplotyping method using tumor allele-specific copy number alteration

CNAHap phases germline variants using tumor allele-specific copy number alterations, achieving accurate haplotyping and long phasing blocks in Hepatocellular carcinoma.

LEVIATHAN: efficient discovery of large structural variants by leveraging long-range information from Linked-Reads data

LEVIATHAN is a structural variant caller that improves scalability and applicability across organisms using Linked-Reads data.

stLFRsv: a germline SV analysis pipeline using co-barcoded reads

stLFRsv detects structural variations using co-barcoded long reads, achieving 74.2% precision and 22.3% recall for deletions in HG002/NA24385.

Combinatorial patterns of gene expression changes contribute to variable expressivity of the developmental delay-associated 16p12.1 deletion

The paper investigates how gene expression changes from a 16p12.1 deletion and second-hit variants contribute to phenotypic variability in developmental delay.

De novo structural mutation rates and gamete-of-origin biases revealed through genome sequencing of 2,396 families

The paper reports de novo structural mutation rates and gamete-of-origin biases using genome sequencing of 2,396 families, finding higher rates in autism cases and paternal origin dominance.

Analysis of diffusion tensor imaging data from UK Biobank confirms dosage effect of 15q11.2 copy-number variation on white matter and shows association with cognition

The paper analyzes diffusion tensor imaging data from UK Biobank to show that 15q11.2 copy-number variation affects white matter and is associated with cognitive performance.

Robust Benchmark Structural Variant Calls of An Asian Using the State-of-Art Long Fragment Sequencing Technologies

The paper establishes high-confidence structural variant calls in an Asian individual using long-read sequencing technologies and validates them through PCR and Sanger sequencing.

Network effects of the neuropsychiatric 15q13.3 microdeletion on the transcriptome and epigenome in human induced neurons

This study examines the transcriptome and epigenome effects of the 15q13.3 microdeletion in human induced neurons, identifying gene expression and pathway changes linked to neuropsychiatric disorders.

De novo assembly of 64 haplotype-resolved human genomes of diverse ancestry and integrated analysis of structural variation

The paper presents 64 haplotype-resolved human genomes using long-read sequencing and identifies structural variants, SV-eQTLs, and adaptive selection candidates.

Identification of Somatic Structural Variants in Solid Tumors By Optical Genome Mapping

This paper describes a method using optical genome mapping to identify somatic structural variants in solid tumors, showing high reliability and functional relevance.

Analysis of Structural Variation Among Inbred Mouse Strains Identifies Genetic Factors for Autism-Related Traits

The paper analyzes structural variation in inbred mouse strains to identify genetic factors associated with autism-related traits.

frenchFISH: Poisson models for quantifying DNA copy-number from fluorescence in situ hybridisation of tissue sections

FrenchFISH improves DNA copy number quantification from FISH images by using Poisson models, outperforming manual and automated methods in ovarian cancer tissue sections.

Comprehensive phenotyping of 3q29 deletion syndrome: recommendations for clinical care

This study evaluates 32 individuals with 3q29 deletion syndrome to identify common medical and neurodevelopmental features and provides clinical care recommendations.

PopDel identifies medium-size deletions jointly in tens of thousands of genomes

PopDel identifies medium-size deletions in tens of thousands of genomes with high accuracy and scalability.

Whole-genome analysis of de novo and polymorphic retrotransposon insertions in Autism Spectrum Disorder

This study identifies de novo and polymorphic retrotransposon insertions in ASD families, finding increased exonic and intronic insertions in ASD cases compared to controls.

Genome-wide analysis of mobile element insertions in human genomes

The paper reports a comprehensive map of 36,699 non-reference mobile element insertions (MEIs) from 5,675 human genomes and builds a database for public use.

Invivo and systematic analysis of random multigenic deletions associated with human diseases during epithelial morphogenesis using Drosophila

The paper uses Drosophila deficiency lines to analyze multigenic deletions and their implications in human diseases related to epithelial morphogenesis and cytoskeletal processes.

SeeCiTe: a method to assess CNV calls from SNP arrays using trio data

SeeCiTe improves CNV call quality using trio data by classifying calls and visualizing probe-level data, enhancing specificity and sensitivity in biobank-scale studies.

Nebula: Ultra-efficient mapping-free structural variant genotyper

Nebula efficiently genotypes structural variants without requiring alignment, outperforming mapping-based methods in speed while maintaining accuracy.

Contribution of mitochondrial DNA heteroplasmy to the phenotypic variability in maternally transmitted 22q11.2 deletion syndrome

This study investigates how mitochondrial DNA heteroplasmy contributes to phenotypic variability in maternally transmitted 22q11.2 deletion syndrome, finding significant variation in palatal phenotype but not cardiac phenotype.

Application of Optical Genome Mapping For Comprehensive Assessment of Chromosomal Structural Variants for Clinical Evaluation of Myelodysplastic Syndromes

This study evaluates optical genome mapping's ability to detect chromosomal variants in MDS patients, showing high concordance with standard methods and identifying additional clinically relevant aberrations.

Large mosaic copy number variations confer autism risk

The paper investigates the role of mosaic copy number variants (mCNVs) in autism spectrum disorder (ASD) by analyzing genetic data from ASD probands and unaffected siblings, finding a significant association between large mCNVs and ASD risk.

Aquila_stLFR: diploid genome assembly basedstructural variant calling package for stLFRlinked-read

Aquila_stLFR is a tool for diploid genome assembly and structural variant calling using stLFR linked-read data, achieving high sensitivity for deletions and specificity for insertions.

Pan cancer patterns of allelic imbalance from chromosomal aberrations in 33 tumor types

The paper analyzes allelic imbalance across 33 tumor types using haplotype-based methods on TCGA data, finding high prevalence of AI and recurrent chromosomal aberrations.