Genomic variations and chromosomal abnormalities

MCNV2 (Mendelian CNV Validation): Mendelian Precision for CNV quality assessment

MCNV2 assesses CNV quality using Mendelian Precision, offering tools to compute, explore, and optimize CNV call accuracy in parent-offspring trios.

Combinatorial effects of gene dosage, polygenic background and environment on complex traits

The paper examines how gene dosage, polygenic background, and environment influence complex traits like height and BMI using large-scale data from multiple cohorts.

gSV: a general structural variant detector using the third-generation sequencing data

gSV improves structural variant detection in long-read sequencing data by integrating alignment and assembly approaches, showing better sensitivity for complex variants and uncovering new SVs in breast cancer.

Optical genome mapping identifies clinically relevant somatic structural variation in epilepsy-affected brain tissue

This study uses optical genome mapping to detect somatic structural variants in epilepsy brain tissue, revealing variants missed by short-read sequencing and providing insights into their mechanisms.

Genomic Variability of the HCT116 Cell Line Identified Using Oxford Nanopore Sequencing

This study identifies large genomic rearrangements and copy number variants in HCT116 cell line samples using Oxford Nanopore sequencing and compares common and unique variants across samples.

Population differences of chromosome 22q11.2 duplication structure predispose differentially to microdeletion and inversion.

The paper analyzes chromosome 22q11.2 haplotypes to show how structural variations in specific regions correlate with microdeletion and inversion risks across populations.

Fast and accurate resolution of ecDNA sequence using Cycle-Extractor

Cycle-Extractor accurately reconstructs ecDNA structures from both short- and long-read sequencing data, outperforming existing methods in speed and completeness.

Long-read analysis of tetrameric microsatellites with vmwhere supports GGAA repeat length-dependent chromatin state association in Ewing sarcoma

The paper introduces vmwhere, a tool for analyzing tetrameric microsatellites from long-read sequencing data, and shows its application in linking GGAA repeat structure to chromatin state in Ewing sarcoma.

DNA replication errors drive genome-wide small inverted triplication dynamics

The paper identifies DNA replication errors as a source of small inverted triplication (SIT) structural variants in yeast, showing their formation mechanism and characteristics.

Genetic diversity and regulatory features of human-specific NOTCH2NL duplications

The paper characterizes the genetic diversity and regulatory features of human-specific NOTCH2NL duplications using long-read sequencing and organoid models.

MEIsensor: a deep-learning method for mobile element insertion discovery

MEIsensor detects and classifies mobile element insertions from long-read sequencing data, outperforming existing tools in accuracy and efficiency, especially for complex insertions.

Integrating Long-Read Structural Variant Analysis with single-nucleus RNA-seq to Elucidate Gene Expression Effects in Disease

This study integrates long-read WGS and single-nucleus RNA-seq to identify structural variants affecting gene expression in Parkinson's disease with cell type resolution.

Dynamic optimization of extrachromosomal DNA copy number drives tumour evolution

This study shows ecDNA copy number plasticity drives tumour evolution by generating functional heterogeneity and promoting drug resistance.

Long-Read Genome Sequencing Improves Detection and Functional Interpretation of Structural and Repeat Variants in Autism

This study shows that long-read genome sequencing improves detection of structural and repeat variants in autism and links them to functional consequences.

Single-molecule spatial genomics reveals the multi-scale organization and plasticity of extrachromosomal DNA in glioblastoma

This study uses single-molecule spatial genomics to show how extrachromosomal DNA is organized and regulated in glioblastoma, linking it to tumor heterogeneity and microenvironmental influences.

Evolutionary instability drives structural diversity and disease susceptibility at the 16p12.2 locus

The paper examines the evolutionary instability and structural diversity at the 16p12.2 locus across human and non-human primate haplotypes, identifying mechanisms driving deletion susceptibility and neurodevelopmental disorders.

Convergent and Divergent Cerebellar Alterations in 22q11.2 Copy Number Variants

This study compares cerebellar volume changes in 22q11.2 deletion and duplication carriers, finding divergent structural and behavioral associations.

Structural variants in human congenital heart disease disrupt distal genomic regulatory contacts of developmental genes

The paper develops a machine-learning model to predict how structural variants disrupt 3D chromatin structure in congenital heart disease and validates its predictions using induced pluripotent stem cells.

Integrative modeling of read depth and B-allele frequency improves single-cell copy number calling from targeted DNA sequencing panels

The paper introduces scPloidyR, a hidden Markov model that jointly models read depth and B-allele frequency for improved single-cell copy number calling from targeted DNA sequencing, showing better performance when allelic information is available.

Haplotype-resolved reconstruction and functional interrogation of cancer karyotypes

This paper introduces refLinker, a method for haplotype-resolved analysis of cancer karyotypes, revealing transcriptional consequences of somatic Xi rearrangements.

Chromosome engineering to correct a complex rearrangement on Chromosome 8 reveals the effects of 8p syndrome on gene expression and neural differentiation

This study corrects a complex Chromosome 8 rearrangement in vitro, identifies differentially expressed genes, and shows partial rescue of neural differentiation defects.

Donor-specific assemblies enhance somatic structural variant detection in complex genomic regions

This study benchmarks donor-specific assemblies for improved detection of somatic structural variants in a melanoma cell line, finding they identify more variants, especially in repeat-rich regions.

An Enhancement of Extrachromosomal Circular DNA Enrichment and Amplification to Address the Extreme Low Overlap Between Replicates

This paper improves eccDNA enrichment and amplification methods, achieving >50% overlap in technical replicates compared to <1% previously observed.

Cost-effective hybrid long- and short-read sequencing enables accurate somatic structural variant detection

This paper introduces SomaSV, a hybrid sequencing framework that improves somatic structural variant detection accuracy while reducing costs by combining long- and short-read data.

Stability of germline structural variation under dietary and ethanol challenges

This study investigates whether dietary and ethanol exposures alter germline structural variation in mice, finding no significant changes in SV profiles across different conditions.

PanCNV-Explorer: Deciphering copy number alterations across human cancers

PanCNV-Explorer integrates and normalizes copy number variation data across 33 cancer types to provide a unified resource for analyzing CNV frequency and functional impact.

A systematic assessment of machine learning for structural variant filtering

This study benchmarks machine learning methods for structural variant filtering in long-read sequencing data, finding that simple models match complex ones in accuracy.

A comprehensive tandem repeat catalog of the human genome

The paper creates a comprehensive catalog of tandem repeat loci in the human genome using long-read sequencing data from 272 genomes.

CNValidatron: Accurate And Efficient Validation of PennCNV Calls Using Computer Vision

The paper develops a convolutional neural network to automate CNV validation, achieving high accuracy comparable to human visual inspection.

Systematic assessment of rare and de novo structural variants in 57 patient-parent trios using optical genome mapping

This study uses optical genome mapping to identify de novo and rare inherited structural variants in 57 patient-parent trios, finding 13 de novo SVs and 11 rare inherited SVs, some of which are pathogenic or candidate disease-causing.