Genomics & Informatics

Korea Genome Organization (한국유전체학회)
권호 표지
DOI QR코드

DOI QR Code

CGHscape: A Software Framework for the Detection and Visualization of Copy Number Alterations

  • Published : 2008.09.30
Download PDF
⟨ Previous Next ⟩

Abstract

The robust identification and comprehensive profiling of copy number alterations (CNAs) is highly challenging. The amount of data obtained from high-throughput technologies such as array-based comparative genomic hybridization is often too large and it is required to develop a comprehensive and versatile tool for the detection and visualization of CNAs in a genome-wide scale. With this respective, we introduce a software framework, CGHscape that was originally developed to explore the CNAs for the study of copy number variation (CNV) or tumor biology. As a standalone program, CGHscape can be easily installed and run in Microsoft Windows platform. With a user-friendly interface, CGHscape provides a method for data smoothing to cope with the intrinsic noise of array data and CNA detection based on SW-ARRAY algorithm. The analysis results can be demonstrated as log2 plots for individual chromosomes or genomic distribution of identified CNAs. With extended applicability, CGHscape can be used for the initial screening and visualization of CNAs facilitating the cataloguing and characterizing chromosomal alterations of a cohort of samples.

Keywords

References

  1. Freeman, J.L., Perry, G.H., Feuk, L., Redon, R., McCarroll, S.A., Altshuler, D.M., Aburatani, H., Jones, K.W., Tyler-Smith, C., Hurles, M.E., Carter, N.P., Scherer, S.W., and Lee, C. (2006). Copy number variation: new insights in genome diversity. Genome Res. 16, 949-961 https://doi.org/10.1101/gr.3677206
  2. Komura, D., Shen, F., Ishikawa, S., Fitch, K.R., Chen, W., Zhang, J., Liu, G., Ihara, S., Nakamura, H., Hurles, M.E., Lee, C., Scherer, S.W., Jones, K.W., Shapero, M.H., Huang, J., and Aburatani, H. (2006). Genome-wide detection of human copy number variations using high-density DNA oligonucleotide arrays. Genome Res. 16, 1575-1584 https://doi.org/10.1101/gr.5629106
  3. Jong, K., Marchiori, E., Meijer, G., Vaart, A.V., and Ylstra, B. (2004). Breakpoint identification and smoothing of array comparative genomic hybridization data. Bioinformatics 20, 3636-3637 https://doi.org/10.1093/bioinformatics/bth355
  4. Lai, W.R., Johnson, M.D., Kucherlapati, R., and Park, P.J. (2005). Comparative analysis of algorithms for identifying amplifications and deletions in array CGH data. Bioinformatics 21, 3763-3770 https://doi.org/10.1093/bioinformatics/bti611
  5. Lingjaerde, O.C., Baumbusch, L.O., Liestol, K., Glad, I.K., and Borresen-Dale, A.L. (2005). CGH-Explorer: a program for analysis of array-CGH data. Bioinformatics 21, 821-822 https://doi.org/10.1093/bioinformatics/bti113
  6. Margolin, A.A., Greshock, J., Naylor, T.L., Mosse, Y., Maris, J.M., Bignell, G., Saeed, A.I., Quackenbush, J., and Weber, B.L. (2005). CGHAnalyzer: a stand-alone software package for cancer genome analysis using array-based DNA copy number data. Bioinformatics 21, 3308-3311 https://doi.org/10.1093/bioinformatics/bti500
  7. Myers, C.L., Dunham, M.J., Kung, S.Y., and Troyanskaya, O.G. (2004). Accurate detection of aneuploidies in array CGH and gene expression microarray data. Bioinformatics 20, 3533-3543 https://doi.org/10.1093/bioinformatics/bth440
  8. Pinkel, D., and Albertson, D.G. (2005). Array comparative genomic hybridization and its applications in cancer. Nature Genetics 37, Suppl, S11-S17 https://doi.org/10.1038/ng1569
  9. Price, T.S., Regan, R., Mott, R., Hedman, A., Honey, B., Daniels, R.J., Smith, L., Greenfield, A., Tiganescu, A., Buckle, V., Ventress, N., Ayyub, H., Salhan, A., Pedraza-Diaz, S., Broxholme, J., Ragoussis, J., Higgs, D.R., Flint, J., and Knight, S.J. (2005). SW-ARRAY: a dynamic programming solution for the identification of copy-number changes in genomic DNA using array comparative genome hybridization data. Nucleic Acids Res. 33, 3455-3464 https://doi.org/10.1093/nar/gki643
  10. Yim, S.H., and Chung, Y.J. (2004). Current status and future clinical applications of Array based Comparative Genomic Hybridization. Genomics & Informatics 2, 113-120
  11. Ylstra, B., van den Ijssel, P., Carvalho, B., Brakenhoff, R.H., and Meijer, G.A. (2006). BAC to the future! or oligonucleotides: a perspective for micro array comparative genomic hybridization (array CGH). Nucleic Acids Res. 34, 445-450 https://doi.org/10.1093/nar/gkj456

Cited by

  1. Integrated analysis of copy number alteration and RNA expression profiles of cancer using a high-resolution whole-genome oligonucleotide array vol.41, pp.7, 2009, https://doi.org/10.3858/emm.2009.41.7.051
  2. Association Analysis of SERPINB5 Polymorphisms with HBV Clearance and HCC Occurrence in a Korean Population vol.8, pp.1, 2010, https://doi.org/10.5808/GI.2010.8.1.001
  3. Replication of the Association between Copy Number Variation on 8p23.1 and Autism by Using ASD-specific BAC Array vol.8, pp.1, 2010, https://doi.org/10.5808/GI.2010.8.1.019