Genomic variations and chromosomal abnormalities

Sensitive Chromosomal Translocation Quantitation from Amplicon Sequencing Using Primer-Anchored Statistical Translocation Analysis (PASTA)

PASTA quantifies chromosomal translocations from amplicon sequencing with high accuracy and sensitivity, outperforming existing methods in detecting rare rearrangements.

Machine learning-based prediction of human structural variation and characterization of associated sequence determinants

A sequence-only convolutional neural network and an annotation-based random forest predict human structural variant breakpoints from 400 bp windows (AUROC 0.903, 0.904); their ensemble reaches 0.916.

Determinants of dicentric chromosome breakage in Drosophila

This study maps dicentric chromosome breakage hotspots in Drosophila and identifies structural complexity, replication-transcription conflict, and transposon involvement as key factors.

RICO enables integrated analysis of ribosomal DNA copy number and methylation from nanopore long-read sequencing

RICO quantifies rDNA copy number and methylation using nanopore sequencing, showing accurate results in simulations and human/mouse samples, and revealing correlations between rDNA CN and methylation.

Replication fork directionality reveals how structural variants arise under replication stress

The paper identifies a novel mechanism for large tandem duplications in cancer by analyzing replication fork directionality and develops a classifier to distinguish SV phenotypes based on replication features.

High-fidelity rare structural variant detection with HiFiRE3 reduced representation via restriction enzyme ends

HiFiRe3 improves rare structural variant detection by reducing artifacts through error suppression and correction strategies across long and short-read sequencing platforms.

Structural variation landscape of Middle Eastern and North African individuals from long-read nanopore sequencing reveals medically relevant variants

The paper identifies structural variants in MENA individuals using long-read sequencing, revealing previously unreported variants and population-specific disease-related variants.

A Pan-pangenome illuminates complex structural variation and selection in humans, chimpanzees, and bonobos

This study presents a pan-pangenome of humans, chimpanzees, and bonobos, revealing structural variation, selection patterns, and adaptations related to immunity and malaria resistance.

Evolutionary genomics based on PacBio HiFi long-read sequencing data reveals the importance of structural variants in shaping population-specific differences between Chinese and Indian rhesus macaques (Macaca mulatta)

This study uses PacBio HiFi long-read sequencing to analyze structural variants in Chinese and Indian rhesus macaques, revealing population-specific differences in genes related to neural communication and disease susceptibility.

CN-RNN: a Deep Learning Framework for Copy Number Variation Detection with Exome Sequencing Data

CN-RNN is a deep learning framework for detecting copy number variations from exome sequencing data, showing improved performance over existing methods.

A family portrait of the genomic factors shaping tandem repeat mutagenesis

This study identifies genomic factors influencing tandem repeat mutagenesis using long-read sequencing in a large family, finding that de novo mutations are more common at longer, uninterrupted, and heterozygous loci.

16p11.2 Copy Number Variation Alters Genome Architecture and Transcriptional Regulation During Neurodevelopment

This study investigates how 16p11.2 copy number variations affect genome architecture and transcription during neurodevelopment, finding both local dosage effects and broader chromatin changes.

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.

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.

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.

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.

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.

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.

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.

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.

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.