Genomic variations and chromosomal abnormalities

Neonatal social communication and single genes predict the variability of post-pubertal social behavior in a mouse model of paternal 15q11-13 duplication

The paper predicts post-pubertal social behavior variability in a mouse model of paternal 15q11-13 duplication using neonatal social communication and gene expression data.

Joint Segmental Duplication Co-option Drives Human-specific Transcriptional Readthrough and Expression Fine-tuning of NPEPPS-TBC1D3

The paper identifies a human-specific genomic structure formed by a joint segmental duplication that drives transcriptional readthrough and expression fine-tuning of NPEPPS-TBC1D3.

NPEPPS segmental duplication drives position effect expression of TBC1D3 in the human brain

The paper identifies a segmental duplication that drives position effect expression of TBC1D3 in the human brain, explaining its high structural heterozygosity.

The landscape of structural variation in coppery titi monkeys (Plecturocebus cupreus)

This study maps structural variation in coppery titi monkeys using whole-genome sequencing, identifying over 13,000 variants, including disease-associated genes and a high de novo mutation rate.

A sensitive and accurate framework for population-scale structural variant discovery and genotyping across sequence types

PSVGT is a framework for population-scale structural variant discovery and genotyping that integrates multiple sequencing data types and outperforms existing tools, especially in complex genomes and low-coverage long-read data.

VACmap: An Accurate Long-Read Aligner for Unraveling Complex Genomic Rearrangements

VACmap improves detection of complex genomic rearrangements like inversions and duplications, which are critical for understanding diseases such as cardiovascular disease and Parkinson's disease.

Developing Del2Phen: a novel phenotype description tool for chromosome deletions

Del2Phen is a software tool that generates phenotype descriptions for chromosome deletions by matching patients to genotypically similar individuals and using gene-phenotype relationships.

CNV-Finder: Streamlining Copy Number Variation Discovery

CNV-Finder uses deep learning to detect copy number variations from array data, improving accuracy and reducing manual workload for downstream analyses.

Zooming into rearranged genome: applying pipeline of cytological, genomic, and transcriptomic methods for structural variant interpretation

The paper demonstrates an integrative approach combining cytological, genomic, and transcriptomic methods to detect and characterize complex structural variants affecting specific genes and report a new neurodevelopmental phenotype.

Suppressive Genetic Interactions Between Haploinsufficient Mitochondrial Genes Encoded in the 22q11.2 Microdeletion Locus Define Brain and Cardiac Phenotypes

The paper identifies haploinsufficient genes MRPL40 and SLC25A1 in the 22q11.2 locus and shows their genetic interactions contribute to cardiac and brain phenotypes in mice.

An Atlas of Extrachromosomal DNA Structures Illuminates Its Evolution and Biogenesis in Cancer

The paper maps ecDNA structures in glioblastoma using long-read sequencing and ecLego3, revealing structural variation, evolutionary dynamics, and transcriptional links to tumor adaptation.

Wakhan: reconstruction of chromosome-scale copy number profiles of tumor genomes with long-read sequencing

Wakhan reconstructs chromosome-scale copy number profiles of tumor genomes using long-read sequencing, showing better consistency with data than existing methods.

Prevalence and spectrum of congenital heart disease in individuals with distal chromosome 22q11.22-23 deletions

This study examines congenital heart disease in individuals with distal 22q11.22-23 deletions, finding lower prevalence compared to proximal deletions and identifying specific cardiac anomalies.

Distinct cellular and transcriptional mechanisms mediate an antioxidant therapeutic response in 22q11-deleted upper layer cortical projection neurons

This study shows NAC treatment improves LgDel 22q11.2 deletion syndrome mouse cortical neurons' growth and connectivity without restoring wild-type gene expression or cell states.

SVCROWS: A User-Defined Tool for Interpreting Significant Structural Variants in Heterogeneous Datasets

SVCROWS improves structural variant interpretation by merging SVs with a size-weighted reciprocal overlap framework, maintaining accuracy and preserving rare genotypes in complex datasets.

StemCNV-check: a pipeline for human pluripotent stem cell (hPSC) genomic integrity control using SNP array data and copy number variant scoring

The paper introduces StemCNV-check, a pipeline for assessing genomic integrity in human pluripotent stem cells using SNP array data and CNV scoring.

High-confidence structural predictions of extrachromosomal DNA with ecDNAInspector

ecDNAInspector identifies high-confidence ecDNA structures from WGS data, linking them to clinical and molecular features in breast cancer.

OMKar automates genome karyotyping using optical maps to identify constitutional abnormalities

OMKar generates virtual karyotypes from optical genome mapping data to identify constitutional abnormalities with high precision and recall.

Benchmark for simple and complex genome inversions

The paper presents a benchmark for detecting simple and complex genome inversions using Strand-seq and long-read assemblies, revealing method strengths and limitations across sequencing platforms.

SaVor - A Reproducible Structural Variant Calling and Benchmarking Platform from Short-Read Data

SaVor is a reproducible SV calling workflow tested on Arabidopsis thaliana genomes, showing trade-offs between precision and recall based on merge strategies.

ExactCN: Predicting Exact Copy Numbers on Whole Exome Sequencing Data

ExactCN improves copy number variation estimation from whole-exome sequencing data using deep learning, achieving better accuracy than existing methods.

CHALLENGER: Detecting Copy Number Variants in Challenging Regions Using Whole Genome Sequencing Data

CHALLENGER improves CNV detection in challenging genomic regions using short-read WGS data, achieving higher F1-scores and capturing CNVs typically requiring long reads.

Evolutionary hotspots of structural variation drive inter-individual differences in the expression of fusion transcripts in the human brain

The paper identifies fusion transcripts in human brain tissues, showing they are enriched in segmental duplication hotspots and contribute to inter-individual expression differences.

Comprehensive detection of structural variations in long and short reads dataset of French cattle

The paper detects structural variants in French cattle using long and short-read data, identifying 25,191 deletions and 30,118 insertions across 14 breeds.

DNA shape and epigenomics distinguish the mechanistic origin of human genomic structural variations

The paper uses genomic and epigenomic data to identify mechanisms underlying the origin of structural variations in the human genome.

Svirlpool: structural variant detection from long read sequencing by local assembly

Svirlpool detects structural variants from ONT data using local consensus assemblies, achieving high Mendelian consistency and outperforming existing methods in certain metrics.

OctopusV and TentacleSV: a one-stop toolkit for multi-sample, cross-platform structural variant comparison and analysis

OctopusV and TentacleSV provide a toolkit for multi-sample, cross-platform structural variant analysis, improving precision and consistency in cancer genomics and rare disease diagnostics.

Comparative analysis of whole genome amplification kits for single-cell genome analysis

This study compares two WGA kits for single-cell genome analysis, finding that PTA/ResolveDNA outperforms MDA/REPLI-g in quality metrics and CNV detection.

Origins of de novo chromosome rearrangements unveiled by coupled imaging and genomics

The paper introduces MAGIC, a platform combining imaging and genomics to study de novo chromosome rearrangements, finding that dicentric chromosomes initiate CA events and TP53 deficiency increases CA rates.

Diploid donor-specific assembly enhances somatic structural variant detection in cancer genomes

This study evaluates diploid donor-specific assemblies for improving somatic structural variant detection in cancer genomes, finding they identify more variants and reduce artifacts compared to standard references.