Awesome papers and projects about CNV and SV using NGS data 📚

Relevant studies with Structual Variants and Copy Number Variants in NGS (Genome, Exome and Amplicon Sequencing) pipelines.

Background CNV and SV

• 2008 Integrated detection and population-genetic analysis of SNPs and copy number variation
• 2010 Origins and functional impact of copy number variation in the human genome
• 2011 Genome structural variation discovery and genotyping
• 2011 Modeling read counts for CNV detection in exome sequencing data
• 2012 Read count approach for DNA copy number variants detection
• 2013 Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features and perspectives
• 2014 An Evaluation of Copy Number Variation Detection Tools from Whole-Exome Sequencing Data
• 2014 Refining analyses of copy number variation identifies specific genes associated with developmental delay
• 2015 Allele-specific copy-number discovery from whole-genome and whole-exome sequencing
• 2015 Copy number variant analysis from exome data in 349 patients with epileptic encephalopathy
• 2015 Evaluation of somatic copy number estimation tools for whole-exome sequencing data
• 2016 Frequency and Complexity of De Novo Structural Mutation in Autism
• 2016 Evaluation of somatic copy number estimation tools for whole-exome sequencing data
• 2016 Detection of Clinically Relevant Copy Number Variants with Whole-Exome Sequencing
• 2016 Sacral agenesis: a pilot whole exome sequencing and copy number study
• 2016 Assessing the reproducibility of exome copy number variations predictions
• 2016 Statistical models for DNA copy number variation detection using read-depth data from next generation sequencing experiments
• 2016 Patterns of genic intolerance of rare copy number variation in 59,898 human exomes
• 2016 Challenges in detecting genomic copy number aberrations using next-generation sequencing data and the eXome Hidden Markov Model: a clinical exome-first diagnostic approach
• 2016 Statistical models for DNA copy number variation detection using read-depth data from next generation sequencing experiments
• 2017 Profiling copy number variation and disease associations from 50,726 DiscovEHR Study exomes
• 2017 Validation of copy number variation analysis for next-generation sequencing diagnostics
• 2017 Evaluation of three read-depth based CNV detection tools using whole-exome sequencing data
• 2017 Clinical relevance of small copy-number variants in chromosomal microarray clinical testing
• 2017 Germline copy number variations are associated with breast cancer risk and prognosis
• 2017 Evaluation of copy-number variants as modifiers of breast and ovarian cancer risk for BRCA1 pathogenic variant carriers

Long read

• 2017 Mapping and phasing of structural variation in patient genomes using nanopore sequencing - github
• 2018 NextSV: a meta-caller for structural variants from low-coverage long-read sequencing data

WGS

• FindSV: FindSV is a structural variation pipeline written in nextflow and python. FindSV performs variant calling using TIDDIT and CNVnator, and Manta.
• SvABA: Structural variation and indel analysis by assembly.
• 2007 PennCNV: An integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data
• 2012 DELLY: structural variant discovery by integrated paired-end and split-read analysis - github: Delly2 was the best sv caller in the DREAM challenge
• 2014 LUMPY: a probabilistic framework for structural variant discovery - github
• 2015 Wham: Identifying Structural Variants of Biological Consequence - github - mergeSVcallers
• 2015 MetaSV: an accurate and integrative structural-variant caller for next generation sequencing - github
• 2016 Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications - github
• 2017 SV2: Accurate Structural Variation Genotyping and De Novo Mutation Detection - github
• 2017 GRIDSS: sensitive and specific genomic rearrangement detection using positional de Bruijn graph assembly - github
• 2017 Detection of complex structural variation from paired-end sequencing data
• 2017 CLImAT-HET: detecting subclonal copy number alterations and loss of heterozygosity in heterogeneous tumor samples from whole-genome sequencing data
• 2018 Detection of complex structural variation from paired-end sequencing data
• 2018 GIGGLE: a search engine for large-scale integrated genome analysis
• 2018 FusorSV: an algorithm for optimally combining data from multiple structural variation detection methods
• 2018 SvABA: genome-wide detection of structural variants and indels by local assembly
• 2018 Global characterization of copy number variants in epilepsy patients from whole genome sequencing
• 2018 Human copy number variants are enriched in regions of low mappability

WES

• 2015 CODEX: a normalization and copy number variation detection method for whole exome sequencing
• 2016 Enhanced copy number variants detection from whole-exome sequencing data using EXCAVATOR2
• 2016 CLAMMS: a scalable algorithm for calling common and rare copy number variants from exome sequencing data - github

KaryoScan: abnormal karyotype detection from whole-exome sequence - github

• 2016 Challenges in detecting genomic copy number aberrations using next-generation sequencing data and the eXome Hidden Markov Model: a clinical exome-first diagnostic approach
• 2016 CloneCNA: detecting subclonal somatic copy number alterations in heterogeneous tumor samples from whole-exome sequencing data
• 2017 ExCNVSS: A Noise-Robust Method for Copy Number Variation Detection in Whole Exome Sequencing Data
• 2017 Anaconda: AN automated pipeline for somatic COpy Number variation Detectio and Annotation from tumor exome sequencing data
• 2017 WISExome: a within-sample comparison approach to detect copy number variations in whole exome sequencing data
• 2017 An evaluation of copy number variation detection tools for cancer using whole exome sequencing data
• 2017 WISExome: a within-sample comparison approach to detect copy number variations in whole exome sequencing data
• 2018 A Comprehensive Workflow for Read Depth-Based Identification of Copy-Number Variation from Whole-Genome Sequence Data - github

AS

• 2012 A robust model for read count data in exome sequencing experiments and implications for copy number variant calling
• 2013 CNV-TV: A robust method to discover copy number variation from short sequencing reads
• 2015 VisCap: inference and visualization of germ-line copy-number variants from targeted clinical sequencing data
• 2016 CoNVaDING: Single Exon Variation Detection in Targeted NGS Data
• 2016 Accurate clinical detection of exon copy number variants in a targeted NGS panel using DECoN
• 2016 PureCN: copy number calling and SNV classification using targeted short read sequencing - github
• 2017 SeqCNV: a novel method for identification of copy number variations in targeted next-generation sequencing data
• 2017 panelcn.MOPS: Copy-number detection in targeted NGS panel data for clinical diagnostics
• 2017 An enhanced method for targeted next generation sequencing copy number variant detection using ExomeDepth
• 2017 CODEX2: full-spectrum copy number variation detection by high-throughput DNA sequencing
• 2017 Clinical Validation of Copy Number Variant Detection from Targeted Next-Generation Sequencing Panels
• 2017 ‘COV’COP’ allows to detect CNVs responsible for inherited diseases among amplicons sequencing data - git
• 2018 Ioncopy: an R Shiny app to call copy number alterations in targeted NGS data
• 2018 Validation of an ultra-fast CNV calling tool for Next Generation Sequencing data using MLPA-verified copy number alterations

Annotation

• StructuralVariantAnnotation: contains useful helper functions for dealing with structural variants in VCF format.
• 2015 SpeedSeq: ultra-fast personal genome analysis and interpretation - SVTyper - github
• 2016 SVScore: an impact prediction tool for structural variation - github
• 2016 Prioritisation of Structural Variant Calls in Cancer Genomes - github
• 2016 cnvScan: a CNV screening and annotation tool to improve the clinical utility of computational CNV prediction from exome sequencing data
• 2017 Annotation Education Series: CNV Annotations

Visualization

• CNVplot: Plot CNV data with a genome viewer in R.
• cnvgram: Draw CNV diagrams.
• Stupid Simple Structural Variant View: A two-step process that can help visualize the coverage near a variant across multiple BAMs.
• CNView: Visualization, quantitation, and annotation of CNVs from population-scale whole-genome sequencing data.
• 2015 svviz: a read viewer for validating structural variants - github
• 2016 Ribbon: Visualizing complex genome alignments and structural variation - github
• samplot:

Others

• SVsim: a tool that generates synthetic Structural Variant calls as benchmarks to test/evaluate SV calling pipelines.
• Structural Variant Catalog: A repository for human genetic structural variants (SVs) discovered by Delly in the 1000 Genomes cohort of samples.
• SVDB: SVDB is a toolkit for constructing and querying structural variant databases. The databases are constructed using the output vcf files from structural variant callers such as TIDDIT, Manta, Fermikit or Delly. The thousand genomes structural variant calls may also be used as a database
• 2017 Bamgineer: Introduction of simulated allele-specific copy number variants into exome and targeted sequence data sets - github
• 2017 CNVbase: Batch identification of novel and rare copy number variations based on multi-ethnic population data - CNVbase
• 2018 SVEngine: an efficient and versatile simulator of genome structural variations with features of cancer clonal evolution
• 2018 RBV: Read balance validator, a tool for prioritising copy number variations in germline conditions - github