Genomic variations and chromosomal abnormalities

Systematic and comprehensive benchmarking of an exome sequencing based germline copy-number variant detection pipeline to detect clinically relevant CNVs

This study benchmarks an exome sequencing-based CNV detection pipeline, showing improved sensitivity and reduced false discovery rate for clinically relevant variants.

Behavioral changes and growth deficits in a CRISPR engineered mouse model of the schizophrenia-associated 3q29 deletion

This study creates a CRISPR-engineered mouse model of the 3q29 deletion, showing behavioral and growth deficits, and demonstrates that these effects are not solely due to Dlg1 haploinsufficiency.

Evaluation of the performance of copy number variant prediction tools for the detection of deletions from whole genome sequencing data

This study evaluates CNV detection tools for deletions in WGS data, finding Breakdancer and Delly perform best with high sensitivity and moderate FDR.

HumCFS: A database of fragile sites in human chromosomes

HumCFS is a manually curated database of human chromosomal fragile sites with annotated genes, miRNAs, and disease associations.

duphold: scalalable, depth-based annotation and curation of high-confidence structural variant calls.

duphold improves structural variant call confidence by integrating depth-based annotations, enhancing specificity of deletion calls.

Discovery of tandem and interspersed segmental duplications using high throughput sequencing

The paper develops TARDIS, a tool for accurately detecting complex structural variations, including tandem and interspersed segmental duplications, using short-read whole genome sequencing data.

Fine-scale characterization of genomic structural variation in the human genome reveals adaptive and biomedically relevant hotspots

This study identifies 1,148 SV hotspots in the human genome, showing they are enriched for genes involved in critical functions and associated with medically relevant structural variations.

TSD: A computational tool to study the complex structural variants using PacBio targeted sequencing data

TSD is a tool for discovering complex structural variants using PacBio targeted sequencing data, showing better performance than other tools in detecting complex genomic structural variants.

Comprehensive, integrated, and phased whole-genome analysis of the primary ENCODE cell line K562

The paper provides a comprehensive whole-genome analysis of K562, identifying genomic structural features and their impact on functional genomics data.

Haplotype-resolved and integrated genome analysis of the cancer cell line HepG2

This paper provides a haplotype-resolved genome analysis of the HepG2 cell line, identifying genomic features and allele-specific regulation to support functional genomics studies.

An Integrated Framework for Genome Analysis Reveals Numerous Previously Unrecognizable Structural Variants in Leukemia Patients' Samples

The paper identifies numerous previously undetected structural variants in leukemia samples using integrated genome analysis and computational methods, revealing their impact on gene expression and patient survival.

Genetic risk for schizophrenia and developmental delay is associated with shape and microstructure of midline white matter structures

The paper investigates how genetic risk for schizophrenia and developmental delay relates to structural brain abnormalities in midline white matter.

Loss of function mutation of mouse Snap29 on a mixed genetic background phenocopy abnormalities found in CEDNIK and 22q11.2 Deletion Syndrome patients

This study shows that a Snap29 loss-of-function mutation on a mixed genetic background in mice replicates multiple abnormalities seen in CEDNIK and 22q11.2DS patients, including skin, neurological, and fertility issues.

rMETL: sensitive and fast mobile element insertion detection with long read realignment

rMETL detects mobile element insertions using long read realignment, improving sensitivity and reducing false positives in genomic studies.

Modelling double strand break susceptibility to interrogate structural variation in cancer

The paper develops genome-wide models of DNA double strand break (DSB) susceptibility to identify structural variants (SVs) under positive or purifying selection in cancer.

EnsembleCNV: An ensemble machine learning algorithm to identify and genotype copy number variation using SNP array data

EnsembleCNV improves CNV detection and genotyping using SNP arrays, achieving high accuracy and sensitivity for downstream GWAS.

Intronic CNVs cause gene expression variation in human population

The paper identifies intronic copy number variants (CNVs) as a significant source of gene expression variation in human populations, showing their association with gene expression differences and 3D genomic interactions.

An interaction-based model for neuropsychiatric features of copy-number variants

The paper proposes an interaction-based model to explain neuropsychiatric features of copy-number variants by considering gene interactions within CNV regions.

SVIM: Structural Variant Identification using Mapped Long Reads

SVIM detects and characterizes structural variants from long-read sequencing data, outperforming existing tools on simulated and real datasets.

Copy number variation and neurodevelopmental problems in females and males in the general population

This study investigates the association between rare copy number variants (CNVs) and neurodevelopmental problems (NPs) in children, finding sex-specific effects in anxiety/depression.

Mapping and characterization of structural variation in 17,795 deeply sequenced human genomes

The paper maps and characterizes structural variants in 17,795 human genomes, revealing their frequency, impact, and relationship to gene dosage and regulatory elements.

ReALLEN: structural variation discovery in cancer genome by sensitive analysis of single-end reads.

ReALLEN detects genomic rearrangements from single-end reads with high precision and sensitivity, outperforming existing tools in simulated and real datasets.

Microdeletions excluding YWHAE and PAFAH1B1 cause a unique leukoencephalopathy and hypermobility syndrome: Further delineation of the 17p13.3 microdeletion spectrum

The paper investigates 17p13.3 deletions between YWHAE/CRK and PAFAH1B1, identifying white matter lesions and hypermobility, and narrows the critical region to 345 kb with RTN4RL1 as a candidate gene.

Local and global chromatin interactions are altered by large genomic deletions associated with human brain development

The paper investigates how large genomic deletions affect chromatin interactions and states in human brain development using Hi-C and ChIP-Seq analyses.

Complex Structural Variants Resolved by Short-Read and Long-Read Whole Genome Sequencing in Mendelian Disorders

The paper identifies complex structural variants in Mendelian disorders using short-read and long-read sequencing, showing their clinical significance and the utility of long-read technology for resolution.

Effects of pathogenic CNVs on physical traits in participants of the UK Biobank

The paper investigates the effects of pathogenic CNVs on physical traits in UK Biobank adults, finding 214 significant associations with traits like weight and body fat.

CODEX2: full-spectrum copy number variation detection by high-throughput DNA sequencing

CODEX2 improves CNV detection sensitivity and reduces false discoveries in whole-exome and targeted sequencing data.

Clustering-based optimization method of reference set selection for improved CNV callers performance

This paper evaluates reference set selection methods for CNV callers using WES data and finds that clustering-based approaches improve detection performance and efficiency.

CrowdVariant: a crowdsourcing approach to classify copy number variants

The paper introduces CrowdVariant, a crowdsourcing framework to classify copy number variants (CNVs) using NGS data, and identifies 1,781 high-confidence CNVs in a reference sample.

Parental infections disrupt clustered genes encoding related functions required for nervous system development in newborns

This study investigates how parental infections disrupt gene clusters involved in nervous system development, leading to chromosomal anomalies and neurodevelopmental disorders.