Genomic variations and chromosomal abnormalities

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.

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

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

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

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.

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.

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

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.

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.

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.

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

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

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.

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

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.

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

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.

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.

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.

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

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

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

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.

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 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.

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

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.