VCS: Tool for Visualizing Copy Number Variation and Single Nucleotide Polymorphism
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초록
Copy number variation (CNV) or single nucleotide phlyorphism (SNP) is useful genetic resource to aid in understanding complex phenotypes or deseases susceptibility. Although thousands of CNVs and SNPs are currently avaliable in the public databases, they are somewhat difficult to use for analyses without visualization tools. We developed a web-based tool called the VCS (visualization of CNV or SNP) to visualize the CNV or SNP detected. The VCS tool can assist to easily interpret a biological meaning from the numerical value of CNV and SNP. The VCS provides six visualization tools: i) the enrichment of genome contents in CNV; ii) the physical distribution of CNV or SNP on chromosomes; iii) the distribution of log2 ratio of CNVs with criteria of interested; iv) the number of CNV or SNP per binning unit; v) the distribution of homozygosity of SNP genotype; and vi) cytomap of genes within CNV or SNP region.
Abstract
Copy number variation (CNV) or single nucleotide phlyorphism (SNP) is useful genetic resource to aid in understanding complex phenotypes or deseases susceptibility. Although thousands of CNVs and SNPs are currently avaliable in the public databases, they are somewhat difficult to use for analyses without visualization tools. We developed a web-based tool called the VCS (visualization of CNV or SNP) to visualize the CNV or SNP detected. The VCS tool can assist to easily interpret a biological meaning from the numerical value of CNV and SNP. The VCS provides six visualization tools: i) the enrichment of genome contents in CNV; ii) the physical distribution of CNV or SNP on chromosomes; iii) the distribution of log2 ratio of CNVs with criteria of interested; iv) the number of CNV or SNP per binning unit; v) the distribution of homozygosity of SNP genotype; and vi) cytomap of genes within CNV or SNP region.
참고문헌 (13)
- Bengtsson, H., "aroma. affymetrix: A generic framework in R for analyzing small to very large Affymetrix data sets in bounded memory" (2008), University Of California
- Diskin, S., "Copy number variation at 1q21. 1 associated with neuroblastoma", Nature, 459, pp.987~991 (2009)
- Feuk, L., "Structural variation in the human genome", Nat. Rev. Genet, 7, pp.85~97 (2006)
- Glessner, J. T., "Autism genome-wide copy number variation reveals ubiquitin and neuronal genes", Nature, 459, pp.569~573 (2009)
- Hyo-Young Kim, "A replication study of genome-wide CNV association for hepatic biomarkers identifies nine genes associated with liver function", BMB Reports, 44(9), pp.578~583 (2011), 생화학분자생물학회
- Hyo Young Kim, "Analysis of copy number variation in 8,842 Korean individuals reveals 39 genes associated with hepatic biomarkers AST and ALT", BMB Reports, 43(8), pp.547~553 (2010), 생화학분자생물학회
- Kim, H.-Y, "Semantic networks for genome-wide CNV associated with AST and ALT in Korean cohorts", Mol. Cell. Toxicol, 9, pp.103~111 (2013)
- Lockstone, H. E., "Exon array data analysis using Affymetrix power tools and R statistical software", Brief. Bioinform, 12, pp.634~644 (2011)
- O'Donovan, M., "Phenotypic variations on the theme of CNVs", Nat. Genet, 40, pp.1392~1393 (2008)
- Scharpf, R. B., "Using the R package crlmm for genotyping and copy number estimation", J. Stat. Softw, 40, pp.1~32 (2011)
- Shlien, A., "Copy number variations and cancer", Genome Med, 1, pp.62~ (2009)
- Wang, K, "PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data", Genome Res, 17, pp.1665~1674 (2007)
- Xu, B., "Elucidating the genetic architecture of familial schizophrenia using rare copy number variant and linkage scans", Proc. Natl. Acad. Sci. USA, 106, pp.16746~16751 (2009)