Genomic variations and chromosomal abnormalities

SVPopEx: Population-Wide Visualization and Exploration of Structural Variants

SVPopEx is an interactive tool for visualizing and exploring structural variants across populations, excelling in clear representation and cross-genome comparisons.

Determinants of functional burden pleiotropy and gene dosage responses across human traits

The paper develops FunBurd to analyze gene dosage effects on 43 traits in UK-Biobank, finding pleiotropy and non-monotonic responses linked to genetic constraint and brain-specific mechanisms.

Copy number variant association analysis in 94,730 Chinese adults reveals loci influencing anthropometric and cardiometabolic traits

This study identifies 19 CNV associations with anthropometric and cardiometabolic traits in 94,730 Chinese adults, expanding ancestry diversity in CNV research.

AI Analysis of a Copy Number Variant Database Identifies a Genetic Factor for a Murine Model of the Metabolic Syndrome

The paper uses AI to analyze a mouse CNV database and identifies a deletion in Nlrp1b linked to metabolic syndrome in KK mice, with human NLRP1 alleles also associated with metabolic syndrome.

Towards a complete characterization of common human polymorphic inversions and their functional effects

The paper characterizes common human polymorphic inversions and their functional effects, showing they are enriched in functional variants and associated with phenotypic traits.

The Neuropsychiatry of 22q11.2 Deletion Syndrome: An Electronic Health Records Study.

This study uses electronic health records to analyze the neuropsychiatric phenotype of 22q11.2 deletion syndrome at scale, revealing high prevalence of neurodevelopmental and psychiatric disorders.

DNA-FISH Metaphase Spreads to Distinguish Extrachromosomal DNA from Homogeneously Staining Regions in Human Cancer Cell Lines

The paper presents a DNA-FISH protocol to distinguish extrachromosomal DNA from HSRs in cancer cell lines using metaphase spreads and locus-specific probes.

SVkhor: a unified framework for structural variant integration across long-read, short-read, and optical genome mapping data

SVkhor normalizes, merges and integrates long-read, short-read and optical-mapping structural variant calls; on HG002 it retained 98.6% of naive concatenation's true positives with 58.2% fewer false positives.

Population-Scale Landscape of Mobile Element Insertions Across 82 Diverse Indian Populations

The paper catalogs mobile element insertions in 82 Indian populations, revealing population-specific variants not present in European databases and highlighting their potential impact on disease associations.

Human acrocentric chromosome short arm de novo mutation and recombination

The paper investigates mutation and recombination patterns in human acrocentric chromosome short arms using multiple sequencing technologies and a four-generation pedigree.

Sensitive Chromosomal Translocation Quantitation from Amplicon Sequencing Using Primer-Anchored Statistical Translocation Analysis (PASTA)

PASTA quantifies chromosomal translocations from amplicon sequencing with high accuracy and sensitivity, outperforming existing methods in detecting rare rearrangements.

Analysis of 14q12 microdeletions reveals novel regulatory loci for the neurodevelopmental disorder-related gene, FOXG1

The paper identifies a regulatory region in 14q12 that affects FOXG1 expression and contributes to neurodevelopmental disorders through noncoding structural variants.

Recall-by-Genotype of Neurodevelopmental Disorder Copy Number Variants from a Multi-Ancestry, Healthcare-System Biobank

This study recontacts individuals with rare copy number variants associated with neurodevelopmental disorders from a multi-ancestry biobank to assess phenotypes and evaluate recall-by-genotype feasibility in psychiatry.

Machine learning-based prediction of human structural variation and characterization of associated sequence determinants

A sequence-only convolutional neural network and an annotation-based random forest predict human structural variant breakpoints from 400 bp windows (AUROC 0.903, 0.904); their ensemble reaches 0.916.

Determinants of dicentric chromosome breakage in Drosophila

This study maps dicentric chromosome breakage hotspots in Drosophila and identifies structural complexity, replication-transcription conflict, and transposon involvement as key factors.

The 16p11.2 microdeletion enhances gene expression variability between human IPSC derived forebrain interneuron progenitor cells in culture.

This study finds that the 16p11.2 microdeletion increases transcript level variation in human iPSC-derived forebrain interneuron progenitors, affecting gene regulation and potentially contributing to neurodevelopmental and metabolic phenotypes.

Integrated analysis of ribosomal DNA copy number and methylation using nanopore long-read sequencing

RICO quantifies rDNA copy number and methylation using nanopore sequencing, showing accurate results in simulations and human samples, with biological validation in mouse models.

Replication fork directionality reveals how structural variants arise under replication stress

The paper identifies a novel mechanism for large tandem duplications in cancer by analyzing replication fork directionality and develops a classifier to distinguish SV phenotypes based on replication features.

Landscape of copy number variants in Spanish People with Dementia

The paper analyzes copy number variants in a Spanish dementia cohort and identifies potential novel genes associated with ADRD but finds no genome-wide significant associations.

High-fidelity rare structural variant detection with HiFiRE3 reduced representation via restriction enzyme ends

HiFiRe3 improves rare structural variant detection by reducing artifacts through error suppression and correction strategies across long and short-read sequencing platforms.

Structural variation landscape of Middle Eastern and North African individuals from long-read nanopore sequencing reveals medically relevant variants

The paper identifies structural variants in MENA individuals using long-read sequencing, revealing previously unreported variants and population-specific disease-related variants.

A Pan-pangenome illuminates complex structural variation and selection in humans, chimpanzees, and bonobos

This study presents a pan-pangenome of humans, chimpanzees, and bonobos, revealing structural variation, selection patterns, and adaptations related to immunity and malaria resistance.

Evolutionary genomics based on PacBio HiFi long-read sequencing data reveals the importance of structural variants in shaping population-specific differences between Chinese and Indian rhesus macaques (Macaca mulatta)

This study uses PacBio HiFi long-read sequencing to analyze structural variants in Chinese and Indian rhesus macaques, revealing population-specific differences in genes related to neural communication and disease susceptibility.

Preservation and Clonal Behavior of Extrachromosomal DNA in Patient-Derived Xenograft Models of Childhood Cancers

This study compares ecDNA prevalence, conservation, and clonal dynamics in PDX models and primary tumors of childhood cancers, finding high sequence conservation and selective growth advantage of ecDNA-positive clones.

MarkerMatch: A Proximity-Based Probe-Matching Algorithm for Joint Analysis of Copy-Number Variants from Different Genotyping Arrays

MarkerMatch improves CNV detection sensitivity across genotyping arrays by matching probes based on proximity, outperforming consensus probe methods.

Recurrent structural variation and recent turnover at the 17q21.31 locus in humans and great apes

The paper characterizes structural variation at the 17q21.31 locus in humans and great apes, identifying new haplotypes and evolutionary dynamics.

CN-RNN: a Deep Learning Framework for Copy Number Variation Detection with Exome Sequencing Data

CN-RNN is a deep learning framework for detecting copy number variations from exome sequencing data, showing improved performance over existing methods.

Structural variants are enriched in deleterious visible phenotypes in Drosophila

The paper investigates the role of structural variants in Drosophila phenotypes using long-read sequencing, finding that SVs disproportionately contribute to deleterious visible traits.

A family portrait of the genomic factors shaping tandem repeat mutagenesis

This study identifies genomic factors influencing tandem repeat mutagenesis using long-read sequencing in a large family, finding that de novo mutations are more common at longer, uninterrupted, and heterozygous loci.

16p11.2 Copy Number Variation Alters Genome Architecture and Transcriptional Regulation During Neurodevelopment

This study investigates how 16p11.2 copy number variations affect genome architecture and transcription during neurodevelopment, finding both local dosage effects and broader chromatin changes.