Genomic variations and chromosomal abnormalities

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

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

The paper investigates the molecular effects of 16p11.2 CNVs on gene expression and DNA methylation using an iPSC-to-iN model and identifies potential contributing genes.

This study assesses genome imaging in 48 leukemia cases, showing it can detect complex structural variants and chromosomal aberrations with high accuracy, potentially replacing traditional cytogenetic methods.

AmpliconReconstructor integrates optical mapping and NGS to resolve focal amplifications in cancer, revealing complex structures and origins of ecDNA and other rearrangements.

The paper presents a method to accurately identify CNVs and mosaicism from few cells with low GC bias using a single-molecule sequencing platform.

This study identifies NCBP2 as a key modifier gene in the 3q29 deletion, showing it enhances developmental defects through disrupted apoptosis and cell cycle mechanisms in Drosophila and Xenopus models.

This study uses single-cell transcriptomics to analyze gene expression changes in trisomy 18 samples, identifying altered cell groups and new critical regions associated with the syndrome.

The paper estimates the rate of de novo CNVs in healthy individuals using UK Biobank data and compares it to previous studies.

The paper examines the effects of pathogenic CNVs on biochemical and haematology markers using UK Biobank data, finding significant associations and unexpected lipid level reductions in CNV carriers.

This paper introduces scTRIP, a method to detect structural variations in single cells, revealing new SV classes and mutational processes in cancer samples.

A three-tool chain calls somatic structural variants, purity, ploidy and copy number from paired tumour/normal whole genomes, then clusters breakpoints into derivative chromosome structures and gene fusions.

This paper reviews and benchmarks methods for detecting copy number aberrations in single-cell DNA sequencing data, highlighting their strengths, limitations, and accuracy.

This study examines the association of a 15q11.2 BP1-BP2 deletion with neuropsychiatric, cognitive, and cardiovascular phenotypes in ~500,000 UK Biobank individuals, finding increased prevalence in disease cases and reduced cognitive function in carriers.

Genome in a Bottle benchmark of 12745 sequence-resolved insertions and deletions of 50 bp or more, integrating 19 calling methods, scores false negatives and false positives alike.

This paper investigates the link between infections and chromosomal anomalies in neurodevelopmental disorders by analyzing microbial DNA and chromosomal deletions.

The paper evaluates copy number burden in specific epilepsy types using a genome-wide study of 18,564 subjects, identifying novel CNV loci and showing deletion burden outside known hotspots in lesional focal epilepsies.

The paper identifies ALDOA and KIF22 as the only 16p11.2 transcripts enriched in human fetal cortical progenitors and hypothesizes their dosage changes may contribute to ASD in CNV patients.

This study benchmarks an exome sequencing-based CNV detection pipeline, showing improved sensitivity and reduced false discovery rate for clinically relevant variants.

The paper identifies numerous previously undetected structural variants in leukemia samples using integrated genome analysis and computational methods, revealing their impact on gene expression and patient survival.

This study shows that a Snap29 loss-of-function mutation on a mixed genetic background in mice replicates multiple abnormalities seen in CEDNIK and 22q11.2DS patients, including skin, neurological, and fertility issues.

The paper maps and characterizes structural variants in 17,795 human genomes, revealing their frequency, impact, and relationship to gene dosage and regulatory elements.

ReALLEN detects genomic rearrangements from single-end reads with high precision and sensitivity, outperforming existing tools in simulated and real datasets.

This paper evaluates reference set selection methods for CNV callers using WES data and finds that clustering-based approaches improve detection performance and efficiency.

This study investigates how parental infections disrupt gene clusters involved in nervous system development, leading to chromosomal anomalies and neurodevelopmental disorders.

The paper uses single-cell transcriptomes to analyze gene dosage imbalance in aneuploidies, revealing both temporal and spatial dimensions of gene expression changes in trisomies.

Parliament2 combines multiple structural variant callers to improve accuracy and speed, offering a Docker-based solution for efficient variant calling.

FirstSV detects structural variations from short DNA fragments with high sensitivity, precision, and efficiency, outperforming existing methods.

The paper analyzes somatic retrotransposition events in 2,954 cancer genomes, identifying L1 insertions as significant contributors to structural variations and oncogenesis.