Genomic variations and chromosomal abnormalities

Detecting genomic deletions from high-throughput sequence data with unsupervised learning

EigenDel detects genomic deletions using discordant read-pairs and unsupervised learning, outperforming existing methods in accuracy and sensitivity on low coverage data.

The impact of 22q11.2 copy number variants on human traits in the general population.

This study investigates the phenotypic effects of 22q11.2 copy number variants in the general population using UK Biobank data, finding associations with BMI, platelet volume, and other traits.

Structural variation across 138,134 samples in the TOPMed consortium

The paper presents a comprehensive catalog of structural variants across 138,134 individuals, identifying novel variants and their associations with cardio-metabolic and hematologic traits.

Comparative benchmarking of optical genome mapping and chromosomal microarray reveals high technological concordance in CNV identification and structural variant refinement

This study compares optical genome mapping (OGM) and chromosomal microarray (CMA) for detecting copy number variants and structural variants, finding high concordance and additional structural insights from OGM.

Jasmine: Population-scale structural variant comparison and analysis

Jasmine improves SV comparison and analysis by refining SVs, reducing Mendelian discordance, and revealing high-confidence de novo SVs across diverse samples.

Whole genome sequencing of hematologically stained cells catapulted from Cell smears

The paper develops a new laser-based cell isolation technique and optimized whole genome amplification protocol to enable whole genome analysis from stained blood cells.

Detection of mosaic chromosomal alterations in children with severe developmental disorders recruited to the DDD study

The paper identifies mosaic chromosomal alterations in children with developmental disorders using SNP array data from the DDD study, finding that many are tissue-specific and undetectable in blood.

Different structural variant prediction tools yield considerably different results in Caenorhabditis elegans

The paper benchmarks structural variant prediction tools in C. elegans, showing performance varies by variant type and sequencing depth, and highlights the need for real-data reference datasets.

Truvari: Refined Structural Variant Comparison Preserves Allelic Diversity

Truvari improves structural variant comparison by preserving allelic diversity, reducing allele frequency inflation compared to other methods.

Clinical Validation of Optical Genome Mapping for the Detection of Structural Variations in Hematological Malignancies

This study validates optical genome mapping (OGM) as a clinical test for detecting structural variations in hematological malignancies, showing high accuracy and sensitivity compared to standard-of-care methods.

Multisite Study of Optical Genome Mapping of Retrospective and Prospective Constitutional Disorder Cohorts

This study demonstrates that optical genome mapping (OGM) achieves high concordance with standard-of-care testing and identifies additional reportable variants in neurodevelopmental disorder cohorts.

Ultra-fast Prediction of Somatic Structural Variations by Reduced Read Mapping via Pan-Genome k-mer Sets

ETCHING is an ultra-fast somatic structural variation caller that reduces mapping costs and false positives using pan-genome k-mer sets and a Random Forest classifier.

A refined characterization of large-scale genomic differences in the first complete human genome

The paper identifies and categorizes large-scale genomic differences between the T2T-CHM13 and GRCh38 human genome assemblies, highlighting their implications for disease and evolution.

Unsupervized identification of prognostic copy-numberalterations using segmentation and lasso regularization

The paper develops a method to identify prognostic copy-number alterations by integrating segmentation and lasso regularization, showing improved recovery of significant regions and survival prediction in multiple myeloma.

CONGA: Copy number variation genotyping in ancient genomes and low-coverage sequencing data

CONGA genotypes copy number variants in ancient genomes and low-coverage data, showing coherent deletion frequencies and purifying selection across 50 ancient human genomes.

Somatic copy number variant load in neurons of healthy controls and Alzheimer's disease patients

The paper examines somatic copy number variant (CNV) frequencies in neurons from Alzheimer's disease patients and healthy controls using low-coverage single-cell whole-genome sequencing, finding slightly higher CNV frequencies in AD patients but no statistically significant differences.

Transposable element-mediated rearrangements are prevalent in human genomes

The paper identifies transposable element-mediated rearrangements (TEMRs) in human genomes, showing they are enriched in genic regions and can create risk alleles.

The phenotypic spectrum of terminal 6q deletions based on a large cohort derived from social media and literature: a prominent role for DLL1

This study analyzes a large cohort of individuals with terminal 6q deletions to identify a common phenotype linked to the DLL1 gene and highlights the variability associated with larger deletions involving QKI.

The phenotypic spectrum of terminal and subterminal 6p deletions based on a social media-derived cohort and literature review

The paper analyzes the phenotypic spectrum of terminal and subterminal 6p deletions using a social media-derived cohort and literature review, identifying common and subgroup-specific features.

Duet: SNP-Assisted Structural Variant Calling and Phasing Using Oxford Nanopore Sequencing

Duet improves structural variant calling and phasing using low-coverage Oxford Nanopore sequencing data, outperforming existing tools at 8X coverage and maintaining strong performance at higher coverage.

Increased Prevalence of Rare Copy Number Variants in Treatment-Resistant Psychosis

The paper finds that rare copy number variants (CNVs) are more common in treatment-resistant psychosis patients compared to a general schizophrenia cohort, with duplications at 15q11.2-q13.1 and 16p11.2 linked to treatment resistance.

The nanopore sequencing of a Chinese rhesus macaque revealed patterns of methylation, recombination, and selection for structural variations

The study uses nanopore sequencing to analyze structural variations in rhesus macaques, finding more SVs on the X chromosome and evidence of positive selection.

Benign-Ex: Delineating Regions of the Human Genome Benign to Copy Number Variation.

Benign-Ex identifies genome regions tolerant to copy number variation by integrating CNV databases, finding 41.1% and 37.6% of the genome benign using DGV and ClinGen respectively.

Optical Genome Mapping: Clinical Validation and Diagnostic Utility for Enhanced Cytogenomic Analysis of Hematological Neoplasms

This study validates optical genome mapping (OGM) as a clinical tool for detecting structural variations in hematological neoplasms, showing high sensitivity and specificity compared to standard methods.

CNAViz: An interactive webtool for user-guided segmentation of tumor DNA sequencing data

CNAViz improves copy-number segmentation in DNA sequencing data by combining local and global approaches, achieving better accuracy than existing methods in simulated and real data.

Optical mapping compendium of structural variants across global cattle breeds

This study uses optical mapping to identify structural variants in cattle breeds, providing a database for further genetic and evolutionary studies.

Inversion polymorphism in a complete human genome assembly

The paper analyzes inversion polymorphisms in a complete human genome assembly, showing improved detection and orientation accuracy with the T2T reference compared to GRCh38.

svaRetro and svaNUMT: modular packages for annotation of retrotransposed transcripts and nuclear integration of mitochondrial DNA in genome sequencing data

svaRetro and svaNUMT are R packages for annotating retrotransposed transcripts and nuclear mitochondrial DNA integration in genome sequencing data, evaluated using simulations and benchmarking datasets.

Influences of rare copy number variation on human complex traits

This paper develops a computational method to detect rare CNVs in UK Biobank data, identifies 269 CNV-trait associations, and highlights novel gene-trait relationships.

DISCRIMINATOR: Assigning Cohort-Wide Provisional Pathogenicity Classifications to CNVs

DISCRIMINATOR assigns provisional pathogenicity classifications to CNVs in a cohort, identifying common benign and primary CNVs and improving classification consistency.