Genomic variations and chromosomal abnormalities

CNVSIM: an interpretable copy-number reference atlas for cancer subtyping

CNVSIM creates a reference atlas of copy-number variations for cancer subtyping, identifying 112 subtypes across 19 cancer types using the Progenetix dataset.

Mapping chromothripsis across human cancer cell lines reveals genome evolution and therapeutic vulnerabilities

This study maps chromothripsis in 1,646 human cancer cell lines, showing its conservation with tumors, higher prevalence, and therapeutic vulnerabilities to HDAC inhibitors.

Claustrum Morphometry Reveals Spatially Heterogeneous Alterations in 22q11DS

The paper uses surface-based morphometry to analyze claustrum structure in 22q11DS, finding age-related shape changes and reduced deformation in the syndrome.

Perinatal Elimination of Genetically Aberrant Neurons from Human Cerebral Cortex

The paper investigates somatic copy number variants (CNVs) in human neurons across development, finding that perinatal elimination of neurons with aberrant genomes reduces CNV prevalence and targets dosage-sensitive genes.

Copy number variants (CNV) interfere with human Accelerated Regions (HARs) to cause neurodevelopmental disorders: a large-scale cohort study

This study investigates the role of copy number variants (CNVs) disrupting Human Accelerated Regions (HARs) in neurodevelopmental disorders (NDDs) using a large cohort of 821 children, identifying three recurrent HAR loci associated with NDDs.

Streamline CNV - A Handy Nextflow Pipeline for Chromosomal Copy Number Variation Analysis

Streamline CNV is a Nextflow pipeline for CNV analysis that simplifies processing, visualization, and interpretation of copy number data across various sequencing types and species.

Towards standards for analysing structural variants from short-read whole genome sequencing data

The paper benchmarks structural variant analysis tools on short-read WGS data, finding that ensemble pipelines significantly reduce accuracy compared to individual tools.

Biobank-scale genotyping of Robertsonian translocations reveals hidden structural variation on the human acrocentric chromosomes

Short-read genomes can flag Robertsonian translocation carriers by counting rDNA distal junction (DJ) copies (8 rather than 10); UK Biobank screening found 583 candidates, 1 in 841.

Common centromeric variation associates with molecular and complex traits in humans

This study identifies centromeric structural variants linked to molecular traits and complex diseases in humans using long-read sequencing and haplotype-resolved analysis.

p70 ribosomal protein S6 Kinase (p70S6K) as a potential peripheral biomarker for autistic symptoms in 16p11.2 deletion and duplication syndromes

The paper identifies reduced p70S6K levels in PBMCs of individuals with 16p11.2 deletion and duplication syndromes, correlating with autistic symptom severity.

A gene-centric analysis of copy number variation reveals tumour suppressor modulation of cancer risk and novel associations with common diseases

This study uses a gene-centric analysis of copy number variation to identify associations between gene deletions and cancer risk, as well as novel links to common diseases.

Distinct mechanisms of CNV formation at the human 15q13.3 locus

The paper identifies distinct mechanisms of CNV formation at the human 15q13.3 locus, showing that non-allelic homologous recombination is the primary mechanism, influenced by inversion polymorphisms and population-specific susceptibility.

The landscape of structural variants in male infertility identified by optical genome mapping

This study identifies structural variants in male infertility using optical genome mapping, finding rare variants in 25% of patients that may contribute to infertility.

Optical genome mapping identifies source-associated structural variant differences across early-passage human iPSCs

This study uses optical genome mapping to compare structural variant profiles of iPSCs derived from different somatic cell sources, finding differences in SV burden and types between PBMC- and fibroblast-derived clones.

Cerebellar mitochondrial dysfunction coincides with structural and behavioral abnormalities in 3q29Del mice

This study shows that 3q29Del mice exhibit reduced cerebellar volume, motor and vocal impairments, and mitochondrial dysfunction, mirroring human 3q29Del phenotypes.

Gene flux shapes diversity and evolution of the ancient 17q21.31 inversion polymorphism

The paper measures recombination rates between inversion haplotypes at 17q21.31, finds gene flux occurs despite suppression, and shows its impact on fertility and genetic diversity.

Structural variation in repeat elements is widespread in normal human tissues and in tumorigenesis

The paper identifies widespread mosaic structural variants in normal human tissues and tumors, with repeat-mediated variants impacting functional elements and enabling noninvasive tumor monitoring through cell-free DNA.

Wavelet Based Whole Genome Doubling Aware Single Cell Copy Number Calling

Songbird is a single cell whole genome sequencing copy number caller that detects whole genome duplication and outperforms existing tools in breakpoints identification and true copy number detection.

SVPG: A pangenome-based structural variant detection approach and rapid augmentation of pangenome graphs with new samples

SVPG improves structural variant detection using pangenome references and accelerates pangenome graph construction from long-read data.

Pleiotropic and Distributed Neuropsychiatric Effects of Neurodevelopmental Copy Number Variants in the All of Us Biobank

The paper investigates neuropsychiatric effects of neurodevelopmental copy number variants (ND-CNVs) in the All of Us biobank, finding distributed, pleiotropic risk across multiple domains.

Genetic mechanisms of mitotic error in 840,853 blood genomes

This study identifies genetic factors influencing mosaic aneuploidies in blood genomes using whole-genome sequencing data from 840,853 individuals.

Widespread structural variations at human chromosome ends

This study presents complete subtelomeric sequences from diverse populations, revealing extensive haplotype diversity and gene copy-number variation associated with chromosome arms.

gVCF2CNV: a scalable pipeline for CNV detection from whole-genome sequencing data

gVCF2CNV converts gVCF files into CNV-compatible signals for large-scale WGS cohorts, achieving high precision in detecting deletions and duplications.

QuickSeg: A fast, versatile and accurate algorithm for genomic copy number segmentation using dynamic programming

QuickSeg improves copy number segmentation accuracy and efficiency using dynamic programming and median-based error function in cancer whole-genome sequencing data.

Improving long-read somatic structural variant calling with pangenome and de novo personal genome assembly

This paper introduces a method for improving long-read somatic structural variant calling by integrating pangenome and de novo personal genome assembly, reducing false positives while maintaining sensitivity.

Integrative optical genome mapping and long-read sequencing resolve constitutional complex rearrangements at nucleotide resolution

The paper uses optical genome mapping and long-read sequencing to resolve complex rearrangements at nucleotide resolution, revealing additional complexity and enabling accurate genotype-phenotype correlations.

Cross-species discovery of large structural variants reveals distinct evolutionary dynamics in primates

This study introduces LGvar, a tool for cross-species detection of large structural variants, revealing distinct evolutionary dynamics in primates.

A high-resolution human pangenome structural variant resource for improved disease association

The paper constructs a high-resolution human pangenome structural variant resource, identifies disease-associated SVs, and demonstrates its utility in filtering variants from probands and associating SVs with traits in a large cohort.

Detecting CYP2C19 deletions from genotyping array signals using neural networks

This paper develops a neural network model, nnCNV, to detect CYP2C19 deletions from genotyping array signals, achieving higher accuracy than existing methods.

Contrasting selective pressures shape human pepsinogen A gene copy-number variation across Eurasia

The paper examines copy-number variation in the human pepsinogen A gene across Eurasia, linking it to dietary adaptation and selective pressures.