VCS: Tool for Visualizing Copy Number Variation and Single Nucleotide Polymorphism

  • Kim, HyoYoung (Department of Agricultural Biotechnology, Seoul National University) ;
  • Sung, Samsun (CHO&KIM Genomics, Seoul National University Research Park) ;
  • Cho, Seoae (CHO&KIM Genomics, Seoul National University Research Park) ;
  • Kim, Tae-Hun (Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Rural Development Administration) ;
  • Seo, Kangseok (Animal Genetic Evaluation Division, National Livestock Research Institute, RDA) ;
  • Kim, Heebal (Department of Agricultural Biotechnology, Seoul National University)
  • Received : 2014.02.25
  • Accepted : 2014.06.21
  • Published : 2014.12.01


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.


Copy Number Variation;Cytomap;Homozygosity;Single Nucleotide Polymorphism;Visualization


Supported by : Rural Development Administration


  1. Bengtsson, H., K. Simpson, J. Bullard, and K. Hansen. 2008. aroma. affymetrix: A generic framework in R for analyzing small to very large Affymetrix data sets in bounded memory. Department of Statistics, University Of California, Berkeley, CA, USA.
  2. Diskin, S., C. Hou, J. Glessner, E. Attiyeh, M. Laudenslager, K. Bosse, K. Cole, Y. Mosse, A. Wood, and J. Lynch et al. 2009. Copy number variation at 1q21. 1 associated with neuroblastoma. Nature 459:987-991.
  3. Feuk, L., A. R. Carson, and S. W. Scherer. 2006. Structural variation in the human genome. Nat. Rev. Genet. 7:85-97.
  4. Glessner, J. T., K. Wang, G. Cai, O. Korvatska, C. E. Kim, S. Wood, H. Zhang, A. Estes, C. Brune, and J. P. Bradfield et al. 2009. Autism genome-wide copy number variation reveals ubiquitin and neuronal genes. Nature 459:569-573.
  5. Kim, H.-Y., M.-J. Byun, and H. Kim. 2011. A replication study of genome-wide CNV association for hepatic biomarkers identifies nine genes associated with liver function. BMB Rep. 44:578-583.
  6. O'Donovan, M., G. Kirov, and M. Owen. 2008. Phenotypic variations on the theme of CNVs. Nat. Genet. 40:1392-1393.
  7. Kim, H. Y., J. Yu, and H. Kim. 2010. Analysis of copy number variation in 8,842 Korean individuals reveals 39 genes associated with hepatic biomarkers AST and ALT. BMB Rep. 43:547-553.
  8. Kim, H.-Y., J.-H. Park, H. Kim, and B.-C. Kang. 2013. Semantic networks for genome-wide CNV associated with AST and ALT in Korean cohorts. Mol. Cell. Toxicol. 9:103-111.
  9. Lockstone, H. E. 2011. Exon array data analysis using Affymetrix power tools and R statistical software. Brief. Bioinform. 12:634-644.
  10. Scharpf, R. B., R. A. Irizarry, M. E. Ritchie, B. Carvalho, and I. Ruczinski. 2011. Using the R package crlmm for genotyping and copy number estimation. J. Stat. Softw. 40:1-32.
  11. Shlien, A. and D. Malkin. 2009. Copy number variations and cancer. Genome Med. 1:62.
  12. Wang, K., M. Li, D. Hadley, R. Liu, J. Glessner, S. F. A. Grant, H. Hakonarson, and M. Bucan. 2007. PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data. Genome Res. 17:1665-1674.
  13. Xu, B., A. Woodroffe, L. Rodriguez-Murillo, J. L. Roos, E. J. van Rensburg, G. R. Abecasis, J. A. Gogos, and M. Karayiorgou. 2009. Elucidating the genetic architecture of familial schizophrenia using rare copy number variant and linkage scans. Proc. Natl. Acad. Sci. USA 106:16746-16751.