Genomic variations and chromosomal abnormalities

This paper introduces RIDDLER, a single-cell ATAC-seq CNV detection algorithm that outperforms existing methods in cancer cell line models and 10x multimome data.

The paper identifies chromosomal locations of top upregulated and downregulated genes in cancer cell lines using copy number variation data from DepMap.

The paper investigates DUP-TRP/INV-DUP genomic rearrangements in neurodevelopmental disorders, identifying four SV haplotypes and refining template switching points using multiple sequencing technologies.

The paper estimates population-based risks of psychiatric disorders associated with 34 recurrent CNVs using a large case-cohort sample, finding moderate risks for ADHD, autism, and schizophrenia, but not depression.

CoFrEE estimates DNA copy number from RNA expression data, performing comparably to existing RNAseq methods and applicable to older expression-array datasets.

This paper presents a standardized protocol for visualizing extrachromosomal DNA (ecDNA) using scanning electron microscopy (SEM) in human cancer cell lines.

This study identifies 73 CNV-related disease signals in 331,522 UK Biobank participants, showing CNVs increase disease risk and earlier onset, with polygenic effects and gene dosage impacts.

This study examines structural brain changes and social behavior in Tbx1 heterozygous mice, linking reduced amygdala volume to impaired social incentive learning.

The paper introduces TRGT, a tool for tandem repeat genotyping, and a database of 937,122 TRs across 100 genomes, achieving high concordance and detecting repeat expansions, methylation, and mosaicism.

Experiments across four laboratories found that arbaclofen rescued cognitive deficits in mouse models of 16p11.2 deletion, without sedation or significant off-target behavioral effects.

SurVIndel2 improves CNV detection from NGS by using hidden split reads, outperforming existing methods and generating a comprehensive CNV catalogue.

This study evaluates how FASTQ read order affects structural variation calling in long-read sequencing data using PacBio data from C. elegans isolates.

The paper identifies great-ape-specific structural variants and their potential role in evolutionary phenotypic innovations.

The paper identifies and validates copy number variants in single human neurons using a new method, revealing nonrandom CNV locations and complex karyotypes in a subset of neurons.

The paper develops a method to detect complex structural variants across human genomes and finds they are associated with phenotypic hotspots and evolutionary changes.

MHCnvex is a likelihood-based model for accurately calling copy number variations and loss of heterozygosity in MHC class I and II loci, improving accuracy by integrating adjacent chromosome 6 regions.

The paper presents a comprehensive catalog of structural variants across 138,134 individuals, identifying novel variants and their associations with cardio-metabolic and hematologic traits.

This study compares optical genome mapping (OGM) and chromosomal microarray (CMA) for detecting copy number variants and structural variants, finding high concordance and additional structural insights from OGM.

This study validates optical genome mapping (OGM) as a clinical test for detecting structural variations in hematological malignancies, showing high accuracy and sensitivity compared to standard-of-care methods.

This study demonstrates that optical genome mapping (OGM) achieves high concordance with standard-of-care testing and identifies additional reportable variants in neurodevelopmental disorder cohorts.

The paper identifies and categorizes large-scale genomic differences between the T2T-CHM13 and GRCh38 human genome assemblies, highlighting their implications for disease and evolution.

The paper develops a method to identify prognostic copy-number alterations by integrating segmentation and lasso regularization, showing improved recovery of significant regions and survival prediction in multiple myeloma.

This study analyzes a large cohort of individuals with terminal 6q deletions to identify a common phenotype linked to the DLL1 gene and highlights the variability associated with larger deletions involving QKI.

The paper analyzes the phenotypic spectrum of terminal and subterminal 6p deletions using a social media-derived cohort and literature review, identifying common and subgroup-specific features.

The study uses nanopore sequencing to analyze structural variations in rhesus macaques, finding more SVs on the X chromosome and evidence of positive selection.

Benign-Ex identifies genome regions tolerant to copy number variation by integrating CNV databases, finding 41.1% and 37.6% of the genome benign using DGV and ClinGen respectively.

The paper analyzes inversion polymorphisms in a complete human genome assembly, showing improved detection and orientation accuracy with the T2T reference compared to GRCh38.

DISCRIMINATOR assigns provisional pathogenicity classifications to CNVs in a cohort, identifying common benign and primary CNVs and improving classification consistency.

The paper investigates the association between gene copy number variation and mental health traits in children, finding links to ADHD, OCD, and cognitive biomarkers.

GATK-gCNV detects rare copy number variants from exome sequencing data, achieving high recall in benchmarking and generating a reference catalog of rare coding CNVs in the UK Biobank.