scholarly journals HandyCNV: Standardized Summary, Annotation, Comparison, and Visualization of CNV, CNVR and ROH

2021 ◽  
Author(s):  
Jinghang Zhou ◽  
Liyuan Liu ◽  
Thomas J Lopdell ◽  
Dorian Garrick ◽  
Yuangang Shi
Keyword(s):  
Copy Number Variants ◽  
R Package ◽  
Single Nucleotide Polymorphism Genotyping ◽  
Runs Of Homozygosity ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Livestock Species ◽  
One Stop ◽  
Analysis System ◽  
User Friendly

Here we present an R package for summarizing, annotating, converting, comparing and visualizing CNV (copy number variants) and ROH (runs of homozygosity) detected from SNP (single nucleotide polymorphism) genotyping data. This one-stop post-analysis system is standardized, comprehensive, reproducible, timesaving and user friendly for research in humans and most diploid livestock species.

scholarly journals HandyCNV: Standardized Summary, Annotation, Comparison, and Visualization of Copy Number Variant, Copy Number Variation Region, and Runs of Homozygosity

2021 ◽  
Vol 12 ◽  
Author(s):  
Jinghang Zhou ◽  
Liyuan Liu ◽  
Thomas J. Lopdell ◽  
Dorian J. Garrick ◽  
Yuangang Shi
Keyword(s):  
Copy Number ◽  
Copy Number Variants ◽  
Copy Number Variant ◽  
R Package ◽  
Copy Number Variation Region ◽  
Runs Of Homozygosity ◽  
Number Variation ◽  
Genomic Studies ◽  
Computing Platforms ◽  
Analysis System

Detection of CNVs (copy number variants) and ROH (runs of homozygosity) from SNP (single nucleotide polymorphism) genotyping data is often required in genomic studies. The post-analysis of CNV and ROH generally involves many steps, potentially across multiple computing platforms, which requires the researchers to be familiar with many different tools. In order to get around this problem and improve research efficiency, we present an R package that integrates the summarization, annotation, map conversion, comparison and visualization functions involved in studies of CNV and ROH. This one-stop post-analysis system is standardized, comprehensive, reproducible, timesaving, and user-friendly for researchers in humans and most diploid livestock species.

scholarly journals Precision of High-Throughput Single-Nucleotide Polymorphism Genotyping with Fingernail DNA: Comparison with Blood DNA

2008 ◽  
Vol 54 (10) ◽  
pp. 1746-1748 ◽  
Author(s):  
Mitsuko Nakashima ◽  
Masayoshi Tsuda ◽  
Akira Kinoshita ◽  
Tatsuya Kishino ◽  
Shinji Kondo ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
High Throughput ◽  
Single Nucleotide Polymorphism Genotyping ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide

Detection of β-Thalassemia Mutations Using TaqMan Single Nucleotide Polymorphism Genotyping Assays

2016 ◽  
Vol 20 (3) ◽  
pp. 154-157 ◽  
Author(s):  
Wissam A. Alwazani ◽  
Rawabi Zahid ◽  
Aisha Elaimi ◽  
Osamah Bajouh ◽  
Salwa Hindawi ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Single Nucleotide Polymorphism Genotyping ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide

Utilizing Genomic DNA Purified From Clotted Blood Samples for Single Nucleotide Polymorphism Genotyping

2002 ◽  
Vol 126 (3) ◽  
pp. 266-270
Author(s):  
Karissa K. Adkins ◽  
Daniel A. Strom ◽  
Thomas E. Jacobson ◽  
Cara R. Seemann ◽  
Darin P. O'Brien ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Methylenetetrahydrofolate Reductase ◽  
Factor V ◽  
Single Nucleotide Polymorphism Genotyping ◽  
Nucleotide Polymorphism ◽  
High Quality ◽  
Genetic Tests ◽  
Single Nucleotide ◽  
Blood Samples ◽  
Clinical Laboratories

Abstract Context.—Linking single nucleotide polymorphisms to disease etiology is expected to result in a substantial increase in the number of genetic tests available and performed at clinical laboratories. Whole blood serves as the most common DNA source for these tests. Because the number of blood samples rises with the number of genetic tests performed, alternative DNA sources will become important. One such alternative source is clotted blood, a by-product of serum extraction. Efficiently using an already procured blood sample would limit the overall number of samples processed by clinical laboratories. Objective.—To determine if DNA purified from clotted blood can be effectively used for single nucleotide polymorphism genotyping. Design.—DNA was purified from the clotted blood of 15 donors. Single nucleotide polymorphism genotyping for the methylenetetrahydrofolate reductase and factor V Leiden mutations was performed with each DNA sample by 2 independent methods. Results.—High-quality DNA was obtained from each of the 15 individual clotted blood samples as demonstrated by UV spectrophotometric analysis, gel electrophoresis, and polymerase chain reaction amplification. The DNA was used successfully to obtain genotype data from both the methylenetetrahydrofolate reductase and factor V single nucleotide polymorphism assays for all samples tested. Conclusions.—Clotted blood is a clinically abundant sample type that can be used as a source of high-quality DNA for single nucleotide polymorphism genotyping.

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