Genomic variations and chromosomal abnormalities

Medical consequences of pathogenic CNVs in adults: Analysis of the UK Biobank

This study examines the medical consequences of pathogenic CNVs in adults using UK Biobank data, finding significant associations between CNVs and various health outcomes.

Time and space dimensions of gene dosage imbalance of aneuploidies revealed by single cell transcriptomes.

The paper uses single-cell transcriptomes to analyze gene dosage imbalance in aneuploidies, revealing both temporal and spatial dimensions of gene expression changes in trisomies.

Parliament2: Fast Structural Variant Calling Using Optimized Combinations of Callers

Parliament2 combines multiple structural variant callers to improve accuracy and speed, offering a Docker-based solution for efficient variant calling.

FirstSV: Fast and Accurate Approach of Structural Variations Detection for Short DNA fragments

FirstSV detects structural variations from short DNA fragments with high sensitivity, precision, and efficiency, outperforming existing methods.

Pan-cancer analysis of whole genomes reveals driver rearrangements promoted by LINE-1 retrotransposition in human tumours

The paper analyzes somatic retrotransposition events in 2,954 cancer genomes, identifying L1 insertions as significant contributors to structural variations and oncogenesis.

SimulateCNVs: a novel software application for simulating CNVs in WES and WGS data

SimulateCNVs is a software tool that simulates copy number variations in whole exome and whole genome sequencing data, producing rearranged genomes, short reads, and BAM files.

Ximmer: A System for Improving Accuracy and Consistency of CNV Calling from Exome Data

Ximmer improves CNV calling accuracy and consistency from exome data through systematic quality control, parameter adjustment, and confidence calibration.

Rare variants in the genetic background modulate the expressivity of neurodevelopmental disorders

The paper shows that rare secondary mutations in functionally intolerant genes affect the expressivity of neurodevelopmental disorders in individuals with primary mutations.

An Integrative Framework For Detecting Structural Variations In Cancer Genomes

This paper presents an integrative framework to detect structural variants in cancer genomes using multiple methods and finds that non-coding structural variation significantly impacts genome function in cancer cells.

CNVkit-RNA: Copy number inference from RNA-Sequencing data

CNVkit-RNA infers copy number from RNA-sequencing data by correcting technical biases and prioritizing stable, highly expressed genes, showing high concordance with aCGH in melanoma samples.

Low-cost and clinically applicable copy number profiling using repeat DNA

The paper introduces conliga, a method for inferring high-resolution SCNA profiles from a low-cost and simple assay, addressing the need for affordable SCNA analysis in clinical settings.

Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line

The paper uses long-read sequencing to analyze structural variations in the SK-BR-3 breast cancer cell line, revealing complex rearrangements and novel gene fusions.

Detection of de novo copy number deletions from targeted sequencing of trios

The paper develops MDTS, a method for detecting de novo copy number deletions in parent-offspring trios from targeted sequencing, achieving higher precision and scalability than existing tools.

Whole-genome sequencing analysis of copy number variation (CNV) using low-coverage and paired-end strategies is efficient and outperforms array-based CNV analysis

The paper compares low-coverage whole-genome sequencing strategies to array-based methods for detecting copy number variations, finding WGS more efficient and accurate.

The role of rare copy number variants in depression

The paper investigates the role of rare copy number variants (CNVs) in depression, finding that neurodevelopmental CNVs are associated with increased depression risk.

Large-scale structural variation detection in subterranean clover subtypes using optical mapping validated at nucleotide level

This study validates large-scale structural variations detected by optical mapping in subterranean clover using Illumina short reads, showing BOM detects total SV sizes but lacks precision in location and quantity.

GtTR: Bayesian estimation of absolute tandem repeat copy number using sequence capture and high throughput sequencing

GtTR is a Bayesian method for estimating absolute tandem repeat copy numbers using targeted sequencing and reference data, achieving high accuracy in population-scale genotyping.

npInv: accurate detection and genotyping of inversions mediated by non-allelic homologous recombination using long read sub-alignment

npInv detects and genotypes NAHR inversions using long read sub-alignment, identifying 30 inversions in NA12878 with 94% accuracy, including 15 novel ones.

Mosaic Chromosomal Aneuploidy Detection By Sequencing (MAD-seq)

MAD-seq detects low-level mosaic chromosomal aneuploidy using a new sequencing assay and analysis method, revealing previously unrecognized aneuploidy in public datasets.

SVEngine: an efficient and versatile simulator of genome structural variations with features of cancer clonal evolution

SVEngine simulates genome structural variations with cancer clonal evolution features, producing sequence data with variants and ground truth BED files.

Pervasive epistasis modulates neurodevelopmental defects of the autism-associated 16p11.2 deletion

The paper identifies genetic interactions within the 16p11.2 deletion that modulate neurodevelopmental phenotypes in Drosophila and links these interactions to human brain networks.

Deep SNP: An End-to-end Deep Neural Network with Attention-based Localization for Break-point Detection in SNP Array Genomic data

Deep SNP uses a deep neural network with attention-based localization to detect genomic breakpoints in SNP array data, outperforming existing methods.

Human copy number variants are enriched in regions of low mappability

The paper identifies recurrent copy number variants in low-mappability regions using PopSV, finding they are 5 times more common in germline than somatic CNVs.

SVCollector: Optimized sample selection for validating and long-read resequencing of structural variants

SVCollector selects optimal samples for validating and long-read resequencing of structural variants to maximize discovery and validation accuracy.

Validation of an ultra-fast CNV calling tool for Next Generation Sequencing data using MLPA-verified copy number alterations

The paper validates Genalice CNV, an ultra-fast tool for detecting CNVs in NGS data, showing high sensitivity, specificity, and speed.

SV-plaudit: A cloud-based framework for manually curating thousands of structural variants

SV-plaudit enables rapid manual curation of thousands of structural variants through a cloud-based framework with image visualization and collaborative reporting.

NextSV: a meta-caller for structural variants from low-coverage long-read sequencing data

NextSV is a meta-caller for structural variants from low-coverage long-read sequencing data, providing sensitive and stringent call sets with balanced performance.

Whole genome optical mapping reveals multiple fusion events chained by large novel sequences in cancer

The paper uses whole genome optical mapping to reveal complex chained fusion events and novel sequences in cancer genomes that are not detected by short-read sequencing.

Nanopore Sequencing Reveals High-Resolution Structural Variation in the Cancer Genome

This study uses nanopore sequencing to identify structural variants in breast cancer with high specificity and sensitivity, revealing repetitive DNA as a major source of variation.

Accurate detection of complex structural variations using single molecule sequencing

The paper introduces open-source tools for detecting structural variations using long-read sequencing, achieving high sensitivity and precision in complex regions and identifying novel variants in human genomes.