Genomic variations and chromosomal abnormalities

Drosophila models of pathogenic copy-number variant genes show global and non-neuronal defects during development

The paper systematically analyzes non-neuronal defects in Drosophila models of pathogenic copy-number variant genes, identifying developmental issues in multiple tissues and signaling pathways.

Integration of genetic, transcriptomic, and clinical data provides insight into 16p11.2 and 22q11.2 CNV genes

The paper integrates genetic, transcriptomic, and clinical data to identify CNV gene associations with brain-related and health traits, finding pleiotropy and multigenicity in CNV biology.

SVCurator: A Crowdsourcing app to visualize evidence of structural variants for the human genome

The paper introduces SVCurator, a crowdsourcing app for evaluating structural variants in the human genome, finding high concordance among curators and with existing benchmarks.

Functional annotation of rare structural variation in the human brain

The paper functionally annotates rare structural variants in the human brain by integrating SV calling with RNA-seq data to assess their regulatory effects and prioritize pathogenic deletions.

Population Structure, Stratification and Introgression of Human Structural Variation.

The paper analyzes structural variation in 911 human samples from 54 populations, identifying novel variants and introgressed elements, and highlights the need for diverse high-quality genomes.

Genomic properties of structural variants and short tandem repeats that impact gene expression and complex traits in humans

The paper examines how structural variants and short tandem repeats affect gene expression and complex traits, identifying high-impact variants associated with multiple genes and GWAS traits.

Discovery and Quality Analysis of a Comprehensive Set of Structural Variants and Short Tandem Repeats

The paper discovers and genotypes a comprehensive set of structural variants and short tandem repeats using multiple algorithms and replicates, creating a well-characterized map of these variants.

An open resource of structural variation for medical and population genetics

Short-read genome sequencing of 14,891 diverse genomes yields 433,371 structural variants (SVs) for gnomAD; loss-constrained genes also resist duplication, and clinical SV carrier rates are benchmarked.

Learning What a Good Structural Variant Looks Like.

This paper develops Samplot-ML, a CNN that reduces false positives in structural variant detection by 47% while retaining 97% of true positives using visualization-based training.

SVJedi: Genotyping structural variations with long reads

SVJedi genotypes known structural variants from long read sequencing data with high accuracy, outperforming existing methods for long reads.

Minimum Error Calibration and Normalization for Genomic Copy Number Analysis

This paper introduces Mecan4CNA, a method for normalizing copy number variation data, showing improved accuracy and performance in detecting focal regions in cancer genomes.

A brief report: de novo copy number variants in children with attention deficit hyperactivity disorder

This study identifies de novo copy number variants in children with ADHD, finding a higher mutation rate compared to controls and associations with known neurodevelopmental disorder loci.

Polishing Copy Number Variant Calls on Exome Sequencing Data via Deep Learning

DECoNT improves CNV detection accuracy on WES data by learning from matched WES and WGS data, tripling duplication precision and doubling deletion precision.

Association Tests Using Copy Number Profile Curves (CONCUR) Enhances Power in Rare Copy Number Variant Analysis

CONCUR improves power in rare CNV analysis by comparing copy number profiles without requiring locus definitions.

Multiethnic catalog of structural variants and their translational impact for disease phenotypes across 19,652 genomes

The paper catalogs structural variants across 19,652 genomes and identifies their associations with proteomic measurements and disease phenotypes.

Determining the impact of uncharacterized inversions in the human genome by droplet digital PCR

The paper validates inversions in the human genome using droplet digital PCR, showing their frequency, recurrence, and functional effects across populations.

Genome mapping resolves structural variation within segmental duplications associated with microdeletion/microduplication syndromes

The paper presents a high-throughput optical mapping technique to genotype structural variation in segmental duplications, identifying novel variants and refining breakpoints in microdeletion syndromes across diverse populations.

Leveraging a WGS compression and indexing format with dynamic graph references to call structural variants.

The paper introduces a structural variant calling pipeline called BioGraph, which achieves higher sensitivity for detecting SVs compared to existing pipelines, though with lower precision.

Copy Number Variation at 16p11.2 Imparts Transcriptional Alterations in Neural Development in an hiPSC-derived Model of Corticogenesis

The paper generates 65 hiPSC clones with 16p11.2 CNVs and identifies transcriptional changes in neural development using RNA-Seq.

Characterizing the frequency of non-allelic homologous recombination (NAHR) on the human X chromosome (Xq28) using digital inverted PCR

This study quantifies non-allelic homologous recombination (NAHR) frequency at the Xq28 inversion site using digital PCR, finding a higher rate than previously believed.

Hierarchical Discovery of Large-scale and Focal Copy Number Alterations in Low-coverage Cancer Genomes

CNAtra detects and distinguishes large-scale and focal copy number alterations in low-coverage cancer genomes with high precision and recall.

A comprehensive benchmarking of WGS-based structural variant callers

This study benchmarks WGS-based structural variant callers using a PCR-confirmed gold standard, finding wide performance variation and identifying tools best suited for low and ultra-low pass data.

Neuropsychiatric copy number variants exert shared effects on human brain structure

The paper examines the effects of neuropsychiatric CNVs on brain structure using neuroimaging data and identifies shared anatomical patterns across multiple CNVs.

CNV-PG: a machine-learning framework for accurate copy number variation predicting and genotyping

CNV-PG is a machine-learning framework that improves CNV prediction and genotyping accuracy by reducing false positives and integrating results from multiple callers.

Genome wide analysis of gene dosage in 24,092 individuals shows that 10,000 genes modulate cognitive ability

The paper quantifies the effect of copy number variants on cognitive ability using genomic data from 24,092 individuals, finding that 10,000 genes modulate intelligence.

BAdabouM: a genomic structural variations discovery tool for polymorphism analyses

BAdabouM is a fast and accurate tool for detecting genomic structural variations with high resolution and improved performance over existing methods.

Detection of somatic structural variants from short-read next-generation sequencing data

This paper reviews eight somatic structural variant callers, evaluating their sensitivity and precision across different SV types, sizes, and sequencing conditions.

HiNT: a computational method for detecting copy number variations and translocations from Hi-C data

HiNT detects copy number variations and translocations from Hi-C data with single base-pair resolution, outperforming existing methods on simulated and real data.

Characterization of segmental duplications and large inversions using Linked-Reads

The paper introduces VALOR2, a new software package that uses Linked-Read sequencing to detect large genomic inversions and characterize interspersed segmental duplications.

SVXplorer: Identification of structural variants through overlap of discordant clusters

SVXplorer identifies structural variants by integrating discordant clusters, improving accuracy and reproducibility over existing methods.