Genomic variations and chromosomal abnormalities

Systematic Description of 3q29 Duplication Syndrome Reveals New Syndromic Phenotypes: Results from the 3q29 Registry

This study systematically describes 3q29 duplication syndrome using a registry cohort, identifying common early-life issues and social disability features similar to the reciprocal deletion syndrome.

NanoVar: Accurate Characterization of Patients’ Genomic Structural Variants Using Low-Depth Nanopore Sequencing

NanoVar accurately detects structural variants using low-depth Nanopore sequencing, achieving high F1 score in simulated data and uncovering normal alleles in patient samples.

SECNVs: A Simulator of Copy Number Variants and Whole-Exome Sequences from Reference Genomes

SECNVs simulates copy number variants and whole-exome sequences from reference genomes to improve comparison of detection methods.

Genome-wide molecular effects of the neuropsychiatric 16p11 CNVs in an iPSC-to-iN neuronal model

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.

Next generation cytogenetics: comprehensive assessment of 48 leukemia genomes by genome imaging

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.

ATR16 Syndrome: Mechanisms Linking Monosomy to Phenotype

This study investigates ATR-16 syndrome, finding that deletion size correlates with severity but no critical region defines the phenotype, and genetic background significantly affects outcomes.

Comprehensive Analysis of Human Subtelomeres by Whole Genome Mapping

The paper uses optical mapping to analyze subtelomere structure and variation across 154 human genomes, identifying novel haplotypes and population-specific trends.

AmpliconReconstructor: Integrated analysis of NGS and optical mapping resolves the complex structures of focal amplifications in cancer

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

Accurate CNV identification from only a few cells with low GC bias in a single-molecule sequencing platform

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

Localization of balanced chromosome translocation breakpoints by long-read sequencing on the Oxford Nanopore platform

This study uses Oxford Nanopore long-read sequencing to precisely localize breakpoints in balanced translocations and inversions, achieving single-base resolution for some cases.

CaSpER: Identification, visualization and integrative analysis of CNV events in multiscale resolution using single-cell or bulk RNA sequencing data

CaSpER identifies and analyzes CNV events in single-cell and bulk RNA sequencing data, revealing novel sub-clones and therapeutic targets in GBM.

CNVmap: a method and software to detect and map copy number variants from segregation data

CNVmap detects and maps copy number variants using segregation data from genetic mapping panels, identifying up to 33 CNV types in maize and wheat populations.

LinkedSV for detection of mosaic structural variants from linked-read exome and genome sequencing data

LinkedSV detects mosaic structural variants from linked-read sequencing data, outperforming existing tools and identifying SVs missed by conventional sequencing methods.

De novo diploid genome assembly for genome-wide structural variant detection

This study demonstrates that de novo assembly of 10x linked-read data can effectively detect structural variants in personal genomes with high accuracy and cost-effectiveness.

NCBP2 modulates neurodevelopmental defects of the 3q29 deletion in Drosophila and X. laevis models

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.

Single-cell transcriptomics reveals diverse and complex gene expression alterations in human trisomy 18

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.

DeepSV: Accurate calling of genomic deletions from high throughput sequencing data using deep convolutional neural network

DeepSV uses a deep convolutional neural network to accurately call long deletions from sequencing data, outperforming existing methods on the 1000 Genomes Project data.

Paragraph: A graph-based structural variant genotyper for short-read sequence data

Paragraph is a graph-based structural variant genotyper for short-read data that outperforms existing methods in accuracy across diverse samples.

Prioritization of genes driving congenital phenotypes of patients with de novo genomic structural variants

This study prioritizes driver genes in patients with de novo genomic structural variants using integrative analysis of WGS data, phenotype information, and chromatin organization datasets.

The rate of de novo CNVs in healthy controls

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

Effects of pathogenic CNVs on biochemical markers: a study on the UK Biobank

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.

Single cell tri-channel-processing reveals structural variation landscapes and complex rearrangement processes

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

RBV: Read balance validator, a tool for prioritising copy number variations in germline conditions

RBV prioritises and validates copy number variations using read balance from genome or exome sequencing data.

Psychotic symptoms in 16p11.2 copy number variant carriers

The paper examines psychotic symptoms in 16p11.2 CNV carriers and finds that duplication and ASD diagnosis predict psychotic symptoms independently.

Transcriptomic networks implicate neuronal energetic abnormalities in three mouse models harboring autism and schizophrenia-associated mutations

The paper identifies shared gene expression modules in mouse models of autism and schizophrenia that link to neuronal energetic dysfunction.

Hecaton: reliably detecting copy number variation in plant genomes using short read sequencing data

Hecaton detects copy number variation in plant genomes using short read sequencing data, outperforming existing methods and accurately identifying dispersed duplications.

MoMI-G: Modular Multi-scale Integrated Genome Graph Browser

MoMI-G is a web-based genome browser for visualizing structural variants and other genomic annotations, enabling intuitive exploration of large and nested variants.

Structural variants exhibit allelic heterogeneity and shape variation in complex traits

The paper identifies numerous structural variants in Drosophila genomes and shows they contribute to complex trait variation through allelic heterogeneity.

The human-specific BOLA2 duplication modifies iron homeostasis and anemia predisposition in chromosome 16p11.2 autism patients

The paper investigates how BOLA2 duplication in chromosome 16p11.2 affects iron homeostasis and anemia risk in autism patients, finding associations with anemia and iron deficiency.

Contribution of Retrotransposition to Developmental Disorders

The paper identifies retrotransposition events in developmental disorders using exome sequencing data from the DDD study and shows their evolutionary constraints.