Genomic variations and chromosomal abnormalities

Rare Genomic Copy Number Variants Implicate New Candidate Genes for Bicuspid Aortic Valve

The paper identifies rare genomic copy number variants (CNVs) in early-onset bicuspid aortic valve (EBAV) cases, implicating new candidate genes like GATA4 and DSCAM in BAV pathogenesis.

Challenges in Detecting Somatic Recombination of Repeat Elements: Insights from Short and Long Read Datasets

This study identifies technical challenges in detecting somatic recombination of repeat elements using short and long read datasets and highlights PCR-induced artifacts.

Chromosome breakage-replication/fusion enables rapid DNA amplification

The paper identifies breakage-replication/fusion as a mechanism causing DNA duplications and insertions, unifying explanations for complex rearrangements and enabling rapid DNA amplification.

Copy number variants differ in frequency across genetic ancestry groups

The paper examines CNV frequency differences across genetic ancestry groups and finds lower prevalence of deleterious CNVs in non-European ancestry groups.

Chimera-suppressing error-corrected sequencing enables quantitative detection of rare somatic structural-variant breakpoints in human cells

This paper introduces SMM-SV-seq, a method to detect rare somatic structural-variant breakpoints in bulk DNA with high precision and recall, validated using human and Drosophila DNA mixtures and clinical treatments.

A population-scale map of human tandem repeat composition and mutation dynamics from long-read assemblies

The paper constructs TRCompDB, a database of 4.4 million tandem repeat loci across 832 human genomes, revealing mutation rates and dynamics influenced by recombination and duplication context.

Long-range somatic structural variation calling from matched tumor-normal co-assembly graphs

This paper introduces colorSV, a method for calling long-range somatic structural variants using co-assembly graphs, achieving high precision and sensitivity in translocation detection.

VISTA: An integrated framework for structural variant discovery

VISTA improves structural variant detection by integrating multiple callers with a novel filtering algorithm, achieving high accuracy across various SV types and genomic contexts.

Misexpression of inactive genes in whole blood is associated with nearby rare structural variants

The paper identifies misexpression of inactive genes in whole blood and links it to nearby rare structural variants using RNA and genome sequencing data.

NanoRanger enables rapid single base-pair resolution of genomic disorders

NanoRanger identifies disease-causing breakpoints in genomic disorders with single base-pair resolution, enabling accurate diagnosis and carrier status determination.

Optically Mapped Black Genomes: Distinct Structures and 22q11.2 Deletion Syndrome Mechanisms

The paper analyzes optical mapping data from Black and white genomes to reveal structural differences in 22q11.2 low copy repeats (LCR22s) and their potential role in the lower prevalence of 22q11.2DS in Black individuals.

Rare germline disorders implicate long non-coding RNAs disrupted by chromosomal structural rearrangements

The paper identifies chromosomal structural rearrangements disrupting long non-coding RNAs (lncRNAs) in individuals with rare germline disorders, highlighting potential pathogenic roles of lncRNA disruptions.

GGTyper: genotyping complex structural variants using short-read sequencing data

GGTyper genotypes complex structural variants from short-read sequencing data, achieving high accuracy across simulated and real genomes.

Irritability in young people with copy number variants associated with neurodevelopmental disorders (ND-CNVs)

This study examines irritability in young people with neurodevelopmental copy number variants (ND-CNVs) and finds it is more common than in controls, independent of psychiatric diagnoses or IQ.

Ribosomal DNA copy number is associated with body mass in humans and other mammals

The paper identifies an association between ribosomal DNA copy number and body mass in humans and rats, showing it relates to growth rate and BMI but not obesity.

Cell type-specific consequences of mosaic structural variants in hematopoietic stem and progenitor cells

This study identifies cell type-specific molecular consequences of mosaic structural variants in hematopoietic stem and progenitor cells across aging.

Cell-type-specific effects of autism-associated chromosome 15q11.2-13.1 duplications in human brain

This study examines how dup15q affects gene expression and chromatin accessibility in specific brain cell types, finding cell-type-specific effects and distinct regulatory mechanisms in ASD and dup15q.

High-effect gene-coding variants impact cognition, mental well-being, and neighborhood safety substrates in brain morphology

The paper investigates the impact of rare high-effect genetic variants on brain morphology and related behavioral traits in adolescents using the ABCD cohort.

The copy number variant architecture of psychopathology and cognitive development in the ABCD study

This study identifies copy number variants (CNVs) associated with child psychopathology and cognitive function using data from the ABCD study.

AmpliconSuite: an end-to-end workflow for analyzing focal amplifications in cancer genomes

AmpliconSuite identifies focal amplifications in cancer genomes, showing ecDNA has higher copy numbers and stronger oncogene enrichment compared to other amplification types.

Mind the gap: the relevance of the genome reference to resolve rare and pathogenic inversions

The paper investigates how different genome references affect inversion detection, showing that T2T-CHM13 and long-read sequencing improve resolution of challenging inversions.

Contribution of de novo retroelements to birth defects and childhood cancers

The paper identifies de novo retroelements in birth defects and childhood cancers using whole-genome sequencing data and an improved computational tool.

Cas9-directed long-read sequencing to resolve optical genome mapping findings in leukemia diagnostics.

This study uses Cas9-directed long-read sequencing to validate and refine optical genome mapping findings in leukemia diagnostics, improving breakpoint resolution and clinical relevance assessment.

Deciphering the role of germline complex de novo structural variations in rare disorders

This study identifies de novo structural variants in a large cohort of rare disease patients, highlighting their prevalence and potential pathogenicity.

msCNVS: medium throughput single cell copy number variation sequencing with barcoded library construction free of preamplification toward clinical implementation

msCNVS enables efficient CNV profiling of rare clinical samples through barcoded single-cell library construction without preamplification.

OSCAA: A Two-Dimensional Gaussian Mixture Model for Copy Number Variation Association Analysis

OSCAA improves CNV-disease association analysis by integrating CNV detection and association testing in a single step, enhancing accuracy and power.

Discovery of A Polymorphic Gene Fusion via Bottom-Up Chimeric RNA Prediction

The paper identifies 57 polymorphic chimeric RNAs, including SUZ12P1-CRLF3, and links one to Neurofibromatosis Type I through population-specific structural variants.

The benefit of a complete reference genome for cancer structural variant analysis

This paper shows that using a complete reference genome improves the accuracy and reduces false positives in detecting structural variants in cancer genomes.

Multiple paralogues and recombination mechanisms drive the high incidence of 22q11.2 Deletion Syndrome

The paper investigates the mechanisms behind the high incidence of 22q11.2 deletion syndrome by analyzing recombination events and paralogous structures in LCR22 regions.

Structural characterization of a polymorphic repeat at the CACNA1C schizophrenia locus

The paper characterizes a VNTR in CACNA1C associated with schizophrenia, showing linkage to risk variants and reduced gene expression.