Genomic variations and chromosomal abnormalities

Characterization of prevalence and health consequences of uniparental disomy in four million individuals from the general population

The paper characterizes the prevalence and health consequences of uniparental disomy in four million individuals, identifying 675 cases and linking UPD of chromosome 22 to autism.

Characterization of single gene copy number variants in schizophrenia

The paper investigates the role of single-gene copy number variants in schizophrenia risk using exome-sequencing data from a Swedish cohort, identifying significant deletions in voltage-gated calcium channels.

CNAPE: A Machine Learning Method for Copy Number Alteration Prediction from Gene Expression

CNAPE predicts copy number alterations from gene expression data using a machine learning model trained on The Cancer Genome Atlas data, achieving over 90% accuracy for arm-level CNAs.

GRIDSS, PURPLE, LINX: Unscrambling the tumor genome via integrated analysis of structural variation and copy number

A three-tool chain calls somatic structural variants, purity, ploidy and copy number from paired tumour/normal whole genomes, then clusters breakpoints into derivative chromosome structures and gene fusions.

Functional and evolutionary impact of polymorphic inversions in the human genome

The paper studies 45 common human polymorphic inversions, showing their functional and evolutionary impact, including gene disruption and association with phenotypic traits.

Population-wide copy number variation calling using variant call format files from 6,898 individuals

This paper calls copy number variants from whole-genome sequencing data of 6,898 individuals using a regression tree-based method, identifying 1,320 CNVs and their potential clinical impact.

The 22q11 low copy repeats are characterized by unprecedented size and structure variability

The paper characterizes the structural variability of 22q11 low copy repeats (LCRs) using optical and Bionano mapping, revealing high haplotype diversity and population-specific differences.

Evaluation of computational genotyping of Structural Variations for clinical diagnoses.

This study evaluates five SV genotyping software methods using simulated and real data to assess their sensitivity, reliability, and compatibility with VCF formats.

Oligogenic effects of 16p11.2 copy number variation on craniofacial development

The paper investigates the oligogenic effects of 16p11.2 copy number variation on craniofacial development across species, showing that individual genes and their combinations influence facial structure.

Methods for Copy Number Aberration Detection from Single-cell DNA Sequencing Data

This paper reviews and benchmarks methods for detecting copy number aberrations in single-cell DNA sequencing data, highlighting their strengths, limitations, and accuracy.

A Simple Deep Learning Approach for Detecting Duplications and Deletions in Next-Generation Sequencing Data

This paper introduces a deep learning method for detecting copy number variants in short-read sequencing data, showing improved performance over traditional methods in low coverage data.

Large-scale examination of neuropsychiatric, cognitive and cardiovascular phenotypic associations with 15q11.2 BP1-BP2 deletion in ~500,000 UK Biobank individuals

This study examines the association of a 15q11.2 BP1-BP2 deletion with neuropsychiatric, cognitive, and cardiovascular phenotypes in ~500,000 UK Biobank individuals, finding increased prevalence in disease cases and reduced cognitive function in carriers.

Cyfip1 haploinsufficiency is associated with white matter changes, myelin thinning, reduction of mature oligodendrocytes and behavioural inflexibility

This study uses a rat model to show that Cyfip1 haploinsufficiency causes white matter changes, myelin thinning, reduced mature oligodendrocytes, and behavioural inflexibility.

Phenome-wide burden of copy number variation in UK Biobank

The paper assesses the phenome-wide effects of copy number variations in 472,228 UK Biobank participants, identifying known and novel associations with medical traits.

A robust benchmark for germline structural variant detection

Genome in a Bottle benchmark of 12745 sequence-resolved insertions and deletions of 50 bp or more, integrating 19 calling methods, scores false negatives and false positives alike.

Neuropsychiatric phenotypes and a distinct constellation of ASD features in 3q29 deletion syndrome: results from the 3q29 registry

This study examines neuropsychiatric phenotypes in individuals with 3q29 deletion syndrome, finding higher ASD prevalence, especially in females, and distinct ASD features compared to idiopathic ASD.

Structural variants identified by Oxford Nanopore PromethION sequencing of the human genome

The paper benchmarks structural variant calling tools using Oxford Nanopore PromethION sequencing of the human genome, finding Minimap2 and Sniffles to be the most accurate and efficient.

A machine-learning approach for accurate detection of copy-number variants from exome sequencing

CN-Learn improves CNV detection from exome sequencing by integrating multiple callers and machine learning, achieving higher precision and recall than individual methods or Venn diagram approaches.

CytoGPS: A Web-Enabled Karyotype Analysis Tool for Cytogenetics

CytoGPS converts ISCN karyotype data into a machine-readable format and binary LGF model for downstream computational analysis.

A Genome Model Linking Birth Defects to Infections

This paper investigates the link between infections and chromosomal anomalies in neurodevelopmental disorders by analyzing microbial DNA and chromosomal deletions.

svtools: population-scale analysis of structural variation

svtools enables population-scale structural variation analysis by providing a fast, scalable toolkit and cloud pipeline for high-quality SV mapping across thousands of human genomes.

Aneuvis: Web-based exploration of numerical chromosomal variation in single cells

Aneuvis is a web tool that quantifies numerical chromosomal variation in single cells and compares it between treatment groups.

Integrating detection of copy neutral chromosomal losses in a clinical setting in leukemia and lymphoma by means of allelic imbalance and read depth ratio comparison

The paper develops a method to detect copy neutral chromosomal losses in leukemia and lymphoma using allelic imbalance and read depth ratio comparison from whole exome sequencing data.

Evaluation of copy number burden in specific epilepsy types from a genome-wide study of 18,564 subjects

The paper evaluates copy number burden in specific epilepsy types using a genome-wide study of 18,564 subjects, identifying novel CNV loci and showing deletion burden outside known hotspots in lesional focal epilepsies.

Resolving the insertion sites of polymorphic duplications reveals a HERC2 haplotype under selection

The paper identifies insertion sites of polymorphic duplications and finds a HERC2 haplotype under selection in European populations.

Hi-C detects novel structural variants in HL-60 and HL-60/S4 cell lines

The paper uses Hi-C and RNA-seq to identify and compare structural variants in HL-60 and HL-60/S4 cell lines, finding novel SVs and differences in their stability.

Copy number variant syndromes are frequent in schizophrenia: progressing towards a CNV-schizophrenia model

This study finds frequent copy number variant (CNV) syndromes in schizophrenia patients and proposes a CNV-schizophrenia model linking specific phenotypes to CNVs.

Expression of genes in the 16p11.2 locus during human fetal cortical neurogenesis.

The paper identifies ALDOA and KIF22 as the only 16p11.2 transcripts enriched in human fetal cortical progenitors and hypothesizes their dosage changes may contribute to ASD in CNV patients.

Genotype-phenotype relationships in children with Copy Number Variants associated with high neuropsychiatric risk: Findings from the case-control IMAGINE-ID cohort in the United Kingdom

This study examines genotype-phenotype relationships in children with copy number variants (CNVs) associated with high neuropsychiatric risk, finding similar adverse effects across different CNVs with some qualitative differences.

Multi-platform discovery of haplotype-resolved structural variation in human genomes

This study identifies a large number of structural variants in human genomes using multiple sequencing technologies and presents them as a gold standard for future studies.