Genomic variations and chromosomal abnormalities

Effects of Gene Dosage and Development on Subcortical Nuclei Volumes in Individuals with 22q11.2 Copy Number Variations

This study examines how 22q11.2 copy number variations affect subcortical brain volumes and their development across different age groups.

Structurally divergent and recurrently mutated regions of primate genomes

The paper identifies structurally divergent regions in primate genomes and quantifies the impact of structural variants across multiple species.

SVarp: pangenome-based structural variant discovery

SVarp discovers haplotype-resolved structural variants using a pangenome reference and long reads, achieving high recall in simulated and real data.

Tbx1 haploinsufficiency causes brain metabolic and behavioral anomalies in adult mice which are corrected by vitamin B12 treatment

This study shows that Tbx1 haploinsufficiency in mice causes brain metabolic and behavioral issues, which are partially reversed by vitamin B12 treatment.

Novel syndromic neurodevelopmental disorder caused by de novo deletion of CHASERR, a long noncoding RNA

The paper identifies a novel neurodevelopmental disorder caused by de novo deletion of the lncRNA CHASERR, showing its role in regulating CHD2 expression and causing developmental and epileptic encephalopathy.

Genome-wide maps of highly-similar intrachromosomal repeats that mediate ectopic recombination in three human genome assemblies

The paper characterizes intrachromosomal repeats in three human genome assemblies, finding more repeats in the T2T-CHM13 assembly and identifying gene categories enriched for repeat-associated genomic disorders.

Dissecting 16p11.2 hemi-deletion to study sex-specific striatal phenotypes of neurodevelopmental disorders

This study identifies three genes in the 16p11.2 region that replicate sex-specific striatal phenotypes of 16p11.2 hemi-deletion in mice through CRISPR/Cas9-generated 3g del/+ mice.

Pindel-TD: a tandem duplication detector based on a pattern growth approach

Pindel-TD detects tandem duplications with high precision and recall using a pattern growth approach, outperforming existing methods on simulated and real data.

A unifying model that explains the origins of human inverted copy number variants

The paper proposes a unifying mechanism, ODIRA, to explain the origins of human inverted copy number variants and their role in both inherited syndromes and cancer.

Template switching between the leading and lagging strands at replication forks generates inverted copy number variants through hairpin-capped extrachromosomal DNA

The paper identifies a replication error mechanism called ODIRA that generates inverted copy number variants through template switching at replication forks, using yeast as a model system.

ECOLE: Learning to call copy number variants on whole exome sequencing data

ECOLE is a deep learning model for detecting copy number variants in whole exome sequencing data, achieving improved precision and recall over existing methods.

Comprehensive Structural Variant Detection: From Mosaic to Population-Level

Sniffles2 improves SV detection accuracy and speed, enabling mosaic and population-level SV calling with applications in neurological disorders.

Optical Genome Mapping improves detection and streamlines analysis of structural variants in myeloid neoplasms.

This study evaluates Optical Genome Mapping (OGM) for detecting structural variants in myeloid neoplasms, showing high concordance and identifying additional clinically relevant variants compared to standard of care methods.

Detection and characterisation of copy number variants from exome sequencing in the DDD study

The paper evaluates CNV detection from exome sequencing in the DDD study, finding it has higher sensitivity than low-resolution CMA and comparable sensitivity to exon-resolution CMA.

Small allelic variants are a source of ancestral bias in structural variant breakpoint placement

The paper identifies ancestral bias in structural variant breakpoint placement, showing that small allelic variants contribute to inconsistent breakpoint locations across haplotypes.

labelSeg: segment annotation for tumor copy number alteration profiles

labelSeg annotates tumor copy number alteration segments to improve interpretation of SCNA profiles, showing strong correlation between SCNA and mRNA expression.

KAGE 2: Fast and accurate genotyping of structural variation using pangenomes

KAGE2 improves structural variant genotyping by using pangenomes, offering higher accuracy and speed compared to existing methods.

CytoCellDB: A Resource Database For Classification and Analysis of Extrachromosomal DNA in Cancer

CytoCellDB is a database that expands the number of cancer cell lines with ecDNA annotations, enabling analysis of ecDNA in relation to molecular data and drug responses.

Towards routine long-read sequencing for rare disease: a national pilot study on chromosomal rearrangements

This study evaluates HiFi Revio long-read sequencing for detecting chromosomal rearrangements in rare diseases, showing high accuracy for breakpoint junctions and derivative chromosome structures.

The landscape of genomic structural variation in Indigenous Australians

This study profiles genomic structural variation in Indigenous Australians using whole genome long-read sequencing, revealing abundant and previously unannotated variants and unique STR diversity.

A graph clustering algorithm for detection and genotyping of structural variants from long reads

This paper introduces a graph clustering algorithm for detecting and genotyping structural variants from long-read sequencing data, achieving high accuracy in benchmark tests.

ReConPlot - an R package for the visualization and interpretation of genomic rearrangements

ReConPlot is an R package for visualizing and interpreting complex genome rearrangements by integrating somatic copy number aberrations and structural variants.

Unraveling the Link between CNVs, General Cognition, and Individual Neuroimaging Deviation Scores from a Reference Cohort

This study maps individual brain deviation scores in individuals with pathogenic CNVs using normative modeling and shows correlations between negative deviations and cognitive function.

Random forest classifiers trained on simulated data enable accurate short read-based genotyping of structural variants in the alpha globin region at Chr16p13.3

The paper uses random forest classifiers trained on simulated data to accurately genotype structural variants in the alpha globin region, outperforming existing software in ancestry-specific allele frequency estimation.

GASOLINE: detecting germline and somatic structural variants from long-reads data.

GASOLINE detects germline and somatic structural variants from long-read sequencing data with high accuracy, outperforming existing methods in synthetic and real datasets.

Accurate identification of structural variations from cancer samples

The paper introduces COMSV, a method for identifying structural variations in cancer samples, showing high sensitivity and specificity and detecting hundreds of novel SVs per sample.

16p11.2 Microduplication is Associated with Lobule-Specific Abnormalities in Cerebellar Structure and Function

This study identifies lobule VI-specific structural and functional cerebellar abnormalities in 16p11.2 microduplication mice, linking them to learning impairments and neuropsychiatric disorder symptoms.

A nematode model to evaluate microdeletion phenotype expression

This paper describes a microdeletion allele in C. elegans generated via CRISPR/Cas9, which removes 32 genes and causes complex developmental phenotypes.

Patient brain organoids identify a link between the 16p11.2 copy number variant and the RBFOX1 gene.

The paper uses patient brain organoids to show that 16p11.2 CNVs affect RBFOX1 expression and link it to neurodevelopmental disorders.

Robust identification of extrachromosomal DNA and genetic variants using multiple genetic abnormality sequencing (MGA-Seq)

This study introduces MGA-Seq, a method to detect multiple genomic abnormalities, and finds that focal amplification in tumors is heterogeneous and reveals ecDNA network architecture.