Genomic variations and chromosomal abnormalities

SVIM-asm: Structural variant detection from haploid and diploid genome assemblies

SVIM-asm detects and genotypes six classes of structural variants from haploid and diploid genome assemblies, outperforming existing tools in sensitivity and F1 scores for insertions and deletions.

SCCNV: a software tool for identifying copy number variation from single-cell whole-genome sequencing

SCCNV identifies copy number variations from single-cell whole-genome sequencing data by adjusting for amplification bias.

Profiling of NUMTs in Gingivobuccal Oral Cancer

The paper analyzes whole genome sequences from OSCC-GB patients to detect NUMTs but finds no somatic NUMTs confirmed by PCR and no germline NUMTs specific to OSCC-GB.

Detection and characterization of copy number variants based on whole-genome sequencing by DNBSEQ platforms

This study evaluates CNV detection performance of DNBSEQ and Illumina platforms using WGS data from NA12878, showing DNBSEQ detects more CNVs with similar sensitivity and precision.

Towards a better understanding of the low recall of insertion variants with short-read based variant callers

The paper investigates why short-read variant callers fail to detect many insertions by analyzing callsets from long-read technologies and simulating the impact of insertion features on recall.

Human-specific expansion of 22q11.2 low copy repeats

The paper investigates the inter- and intra-species variability of LCR22s in non-human primates and finds that LCR22 expansions are unique to humans.

Complete and haplotype-specific sequence assembly of segmental duplication-mediated genome rearrangements using CRISPR-targeted ultra-long read sequencing (CTLR-Seq)

The paper introduces CTLR-Seq, a method to resolve complex genomic regions with high accuracy, and applies it to study CNVs associated with schizophrenia and autism.

Detecting rare copy number variants (CNVs) from Illumina genotyping arrays with the CamCNV pipeline: segmentation of z-scores improves detection and reliability.

CamCNV improves detection of rare CNVs from Illumina arrays by using z-score segmentation, achieving 85% sensitivity for deletions and 65% for duplications with reliable false discovery rate control.

Brain-enriched coding and long non-coding RNA genes are overrepresented in recurrent autism spectrum disorder CNVs

The paper identifies 47 high-confidence ASD-associated CNV regions and shows brain-enriched coding and lncRNA genes are overrepresented in these regions.

Mosaic trisomy of chromosome 1q in human brain tissue associates with unilateral polymicrogyria, very early-onset focal epilepsy, and severe developmental delay

The paper identifies a chromosomal duplication of chromosome 1q in a subset of polymicrogyria patients, associated with specific clinical features and distinct DNA methylation patterns.

Electrophysiological network alterations in adults with copy number variants associated with high neurodevelopmental risk

This study investigates electrophysiological network changes in adults with neurodevelopmental risk copy number variants using MEG, finding decreased connectivity and network segregation differences.

Metabolic effects of the schizophrenia-associated 3q29 deletion are sex-specific and uncoupled from behavioral phenotypes

This study shows that the 3q29 deletion causes sex-specific metabolic changes in mice, which are not linked to behavioral issues, and that a high-fat diet can improve weight in females without worsening behavior.

Effects-sizes of deletions and duplications on autism risk across the genome

The paper estimates the effect sizes of deletions and duplications on autism risk and IQ using statistical models applied to CNV data from multiple cohorts.

Bayesian copy number detection and association in large-scale studies

This paper develops a Bayesian method to detect copy number variants and assess their association with disease in large-scale studies, finding deletions near MYC and TUSC3 linked to pancreatic cancer.

The genetic sequences prone to copy number variation and single nucleotide polymorphism are linked to the repair of the poisoned DNA topoisomerase II

The paper identifies DNA sequences associated with TOP2 poisoning that are linked to genetic variations contributing to multiple diseases.

Comprehensive analysis of structural variants in breast cancer genomes using single molecule sequencing

This study uses long-read sequencing to identify structural variants in breast cancer genomes, showing high accuracy and sensitivity compared to short-read methods.

Language impairment with a microduplication in 1q42.3q43

The paper reports on a girl with a 1q42.3q43 duplication, describing her severe speech and language impairments and identifying potential candidate genes.

Integrating Genomic Correlation Structure Improves Copy Number Variations Detection

This paper introduces LDcnv, a novel algorithm that improves copy number variation detection by integrating genomic correlation structure, showing higher accuracy and precision than existing methods.

Insights into dispersed duplications and complex structural mutations from whole genome sequencing 706 families

The paper identifies dispersed duplications and de novo structural mutations using whole-genome sequencing data from 706 families by analyzing IBD relationships and copy number variations.

Long-read-based Human Genomic Structural Variation Detection with cuteSV

cuteSV improves structural variation detection in long-read sequencing by combining signature-based methods with clustering and refinement, achieving better performance on real datasets.

A method for complete characterization of complex germline rearrangements from long DNA reads

This paper introduces a method to fully characterize complex germline rearrangements using long DNA reads, demonstrating its ability to reconstruct intricate chromosomal translocations.

sideRETRO: a pipeline for identifying somatic and dimorphic insertions of processed pseudogenes or retrocopies

sideRETRO identifies and genotypes somatic and dimorphic retroCNVs from whole-genome or whole-exome sequencing data with high accuracy.

The enrichment of breakpoints in late-replicating chromatin provides novel insights into chromoanagenesis mechanisms

The paper analyzes chromoanagenesis breakpoints in constitutional and cancer cases, finding enrichment in late-replicating chromatin and suggesting similar mechanisms for both.

Next generation cytogenetics: genome-imaging enables comprehensive structural variant detection for 100 constitutional chromosomal aberrations in 85 samples

This study evaluates high-resolution optical mapping for detecting chromosomal aberrations in 85 samples, achieving 100% concordance with standard tests for non-centromeric breakpoints.

Template switching mechanism drives the tandem amplification of chromosome 20q11.21 in human pluripotent stem cells

GRIDSS2: comprehensive characterisation of somatic structural variation using single breakend variants and structural variant phasing

GRIDSS2 identifies somatic structural variants by analyzing single breakends and phasing, achieving a 3.1% false negative rate in metastatic cancers and uncovering a novel duplication signature.

Copy numbers of 45S and 5S ribosomal DNA arrays lack meaningful correlation in humans

The paper investigates the correlation between 45S and 5S rDNA copy numbers in humans and finds no meaningful correlation, challenging previous claims of concerted variation.

Expectations and blind spots for structural variation detection from short-read alignment and long-read assembly

The paper compares structural variant detection using short-read and long-read sequencing in three trios, showing lrWGS finds more SVs but srWGS has high concordance in non-repetitive regions.

Structural variation of the malaria-associated human glycophorin A-B-E region

The paper analyzes structural variation in the glycophorin gene cluster across 6466 genomes, identifies 15 known and 9 new variants, and links structural variants to recombination hotspots.

A new experimental system to study meiotic recurrent non-allelic homologous recombination in budding yeast

This paper develops a yeast experimental system to study meiotic NAHR and CNV formation, finding that larger LCRs increase CNV frequency and interhomolog NAHR is overrepresented.