scholarly journals CNView: a visualization and annotation tool for copy number variation from whole-genome sequencing

2016 ◽  
Author(s):  
Ryan L. Collins ◽  
Matthew R. Stone ◽  
Harrison Brand ◽  
Joseph T. Glessner ◽  
Michael E. Talkowski
Keyword(s):  
Copy Number Variation ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Copy Number ◽  
Software Tool ◽  
Whole Genome ◽  
Data Types ◽  
Recent Emergence ◽  
Number Variation ◽  
Population Scale

AbstractSummaryCopy number variation (CNV) is a major component of structural differences between individual genomes. The recent emergence of population-scale whole-genome sequencing (WGS) datasets has enabled genome-wide CNV delineation. However, molecular validation at this scale is impractical, so visualization is an invaluable preliminary screening approach when evaluating CNVs. Standardized tools for visualization of CNVs in large WGS datasets are therefore in wide demand.Methods & ResultsTo address this demand, we developed a software tool, CNView, for normalized visualization, statistical scoring, and annotation of CNVs from population-scale WGS datasets. CNView surmounts challenges of sequencing depth variability between individual libraries by locally adapting to cohort-wide variance in sequencing uniformity at any locus. Importantly, CNView is broadly extensible to any reference genome assembly and most current WGS data types.Availability and ImplementationCNView is written in R, is supported on OS X, MS Windows, and Linux, and is freely distributed under the MIT license. Source code and documentation are available from https://github.com/RCollins13/[email protected]

scholarly journals SCCNV: a software tool for identifying copy number variation from single-cell whole-genome sequencing

2019 ◽  
Author(s):  
Xiao Dong ◽  
Lei Zhang ◽  
Xiaoxiao Hao ◽  
Tao Wang ◽  
Jan Vijg
Keyword(s):  
Copy Number Variation ◽  
Whole Genome Sequencing ◽  
Single Cell ◽  
Genome Sequencing ◽  
Copy Number ◽  
De Novo ◽  
Single Cells ◽  
Software Tool ◽  
Whole Genome ◽  
Number Variation

AbstractBackgroundIdentification of de novo mutations from cell populations requires single-cell whole-genome sequencing (SCWGS). Although many experimental protocols of SCWGS have been developed, few computational tools are available for downstream analysis of different types of somatic mutations, including copy number variation (CNV).ResultsWe developed SCCNV, a software tool for detecting CNVs from whole genome-amplified single cells. SCCNV is a read-depth based approach with adjustment for the whole-genome amplification bias.ConclusionsWe demonstrate its performance by analyzing data collected from most of the single-cell amplification methods, including DOP-PCR, MDA, MALBAC and LIANTI. SCCNV is freely available at https://github.com/biosinodx/SCCNV.

scholarly journals Effective normalization for copy number variation detection from whole genome sequencing

BMC Genomics ◽  
2012 ◽  
Vol 13 (Suppl 6) ◽  
pp. S16 ◽  
Author(s):  
Angel Janevski ◽  
Vinay Varadan ◽  
Sitharthan Kamalakaran ◽  
Nilanjana Banerjee ◽  
Nevenka Dimitrova
Keyword(s):  
Copy Number Variation ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Copy Number ◽  
Whole Genome ◽  
Number Variation ◽  
Copy Number Variation Detection

scholarly journals Identification of Copy Number Variation in Domestic Chicken Using Whole-Genome Sequencing Reveals Evidence of Selection in the Genome

Animals ◽  
2019 ◽  
Vol 9 (10) ◽  
pp. 809
Author(s):  
Donghyeok Seol ◽  
Byung June Ko ◽  
Bongsang Kim ◽  
Han-Ha Chai ◽  
Dajeong Lim ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Copy Number ◽  
Breeding Systems ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
Genetic Characteristics ◽  
Red Jungle Fowl ◽  
Number Variation

Copy number variation (CNV) has great significance both functionally and evolutionally. Various CNV studies are in progress to find the cause of human disease and to understand the population structure of livestock. Recent advances in next-generation sequencing (NGS) technology have made CNV detection more reliable and accurate at whole-genome level. However, there is a lack of CNV studies on chickens using NGS. Therefore, we obtained whole-genome sequencing data of 65 chickens including Red Jungle Fowl, Cornish (broiler), Rhode Island Red (hybrid), and White Leghorn (layer) from the public databases for CNV region (CNVR) detection. Using CNVnator, a read-depth based software, a total of 663 domesticated-specific CNVRs were identified across autosomes. Gene ontology analysis of genes annotated in CNVRs showed that mainly enriched terms involved in organ development, metabolism, and immune regulation. Population analysis revealed that CN and RIR are closer to each other than WL, and many genes (LOC772271, OR52R1, RD3, ADH6, TLR2B, PRSS2, TPK1, POPDC3, etc.) with different copy numbers between breeds found. In conclusion, this study has helped to understand the genetic characteristics of domestic chickens at CNV level, which may provide useful information for the development of breeding systems in chickens.

scholarly journals Similar genomic proportions of copy number variation within gray wolves and modern dog breeds inferred from whole genome sequencing

BMC Genomics ◽  
2017 ◽  
Vol 18 (1) ◽  
Author(s):  
Aitor Serres-Armero ◽  
Inna S. Povolotskaya ◽  
Javier Quilez ◽  
Oscar Ramirez ◽  
Gabriel Santpere ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Copy Number ◽  
Whole Genome ◽  
Gray Wolves ◽  
Number Variation
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