Skip to main content
Log in

Comparative Genomic Hybridization As a New Method for Detection of Genomic Imbalance

  • Published:
Russian Journal of Genetics Aims and scope Submit manuscript

Abstract

Comparative Genomic Hybridization (CGH) is a molecular cytogenetic method for detecting chromosomal imbalances by comparing the copy number of DNA sequences in cells of tested tissue and the reference specimen. CGH is based on two-color fluorescence suppressive in situ hybridization of genomic test and reference DNAs, each labeled with a different fluorochrome, to metaphase chromosomes of a healthy individual. First described by Kallioniemi et al. in 1992, the CGH assay has been widely used for identification and characterization of both numerical and unbalanced structural chromosome abnormalities in cells of different tissues at various pathological conditions in humans, especially in tumor diseases. We discuss the specific features and quality control of comparative genomic hybridization, its advantages and limitations in detection of genomic imbalance and the prospects for development of this technology.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Similar content being viewed by others

REFERENCES

  1. Kallioniemi, A., Kallioniemi, O.-P., Sudar, D., et al., Comparative Genomic Hybridization for Molecular Cytogenetic Analysis of Solid Tumors, Science, 1992, vol. 258, pp. 818-821.

    Google Scholar 

  2. du Manoir, S., Speicher, M., Joos, S., et al., Detection of Complete and Partial Chromosome Gains by Comparative Genomic Hybridization, Hum. Genet., 1993, vol. 90, pp. 590-610.

    Google Scholar 

  3. Chang, S.S. and Mark, H.F.L., Emerging Molecular Cytogenetic Technologies, Cytobios, 1997, vol. 90, pp. 7-22.

    Google Scholar 

  4. Kallioniemi, O.-P., Kallioniemi, A., Sudar, D., et al., Comparative Genomic Hybridization: A Rapid New Method for Detecting and Mapping DNA Amplification in Tumors, Cancer Biol., 1993, vol. 4, pp. 41-46.

    Google Scholar 

  5. Kallioniemi, O.-P., Kallioniemi, A., Piper, J., et al., Optimizing Comparative Genomic Hybridization for Analysis of DNA Sequence Copy Number Changes in Solid Tumors, Genes Chromos. Cancer, 1994, vol. 10, pp. 231-243.

    Google Scholar 

  6. Joos, S., Bergerheim, U.S.R., Pan, Y., et al., Mapping of Chromosomal Gains and Losses in Prostate Cancer by Comparative Genomic Hybridization, Genes Chromos.Cancer, 1995, vol. 14, pp. 267-276.

    Google Scholar 

  7. Kuukasjarvi, T., Tanner, M., Pennanen, S., et al., Genetic Changes in Intraductal Breast Cancer Detected by Comparative Genomic Hybridization, Am. J. Pathol., 1997, vol. 150, no. 4, pp. 1465-1471.

    Google Scholar 

  8. Taguchi, T., Cheng, G.Z., Bell, D.W., et al., Combined Chromosome Microdissection and Comparative Genomic Hybridization Detect Multiple Sites of Amplified DNA in a Human Lung Carcinoma Cell Line, Genes Chromos. Cancer, 1997, vol. 20, pp. 208-212.

    Google Scholar 

  9. Testa, J.R., Liu, Z., Feder, M., et al., Advances in the Analysis of Chromosome Alterations in Human Lung Carcinomas, Cancer Genet. Cytogenet., 1997, vol. 95, pp. 20-32.

    Google Scholar 

  10. Zitzelsberger, H., Lehmann, L., Werner, M., and Bauchinger, M., Comparative Genomic Hybridization for the Analysis of Chromosomal Imbalances in Solid Tumors and Hematological Malignancies, Histochem. Cell Biol., 1997, vol. 108, pp. 403-417.

    Google Scholar 

  11. Moore, E., Magee, H., Cjyne, J., et al., Widespread Chromosomal Abnormalities in High-Grade Ductal Carcinoma In Situ of the Breast: Comparative Genomic Hybridization Study of Pure High-Grade DCIS, J. Pathol., 1999, vol. 187, pp. 403-409.

    Google Scholar 

  12. Sigl, E., Behmel, A., Henn, T., et al., Cytogenetic and CGH Studies of Four Neuroendocrine Tumors and Tumor-Derived Cell Lines of a Patient with Multiple Endocrine Neoplasia Type 1, Int. J. Oncol., 1999, vol. 15, pp. 41-51.

    Google Scholar 

  13. Speicher, M.R., du Manoir, S., Schrock, E., et al., Molecular Cytogenetic Analysis of Formalin-Fixed, Paraffin-Embedded Solid Tumors by Comparative Genomic Hybridization after Universal DNA Amplification, Hum. Mol. Genet., 1993, vol. 2, pp. 1907-1914.

    Google Scholar 

  14. Houldsworth, J. and Chaganti, R.S.K., Comparative Genomic Hybridization: An Overview, Am. J. Pathol., 1994, vol. 145, pp. 1253-1260.

    Google Scholar 

  15. Hermsen, M.A.J.A., Meijer, G.A., Baak, J.P.A., et al., Comparative Genomic Hybridization: A New Tool in Cancer Pathology, Hum. Pathol., 1996, vol. 27, pp. 342-349.

    Google Scholar 

  16. Forozan, F., Karhu, R., Kononen, J., et al., Genome Screening by Comparative Genomic Hybridization, Trends Genet., 1997, vol. 13, no. 10, pp. 405-409.

    Google Scholar 

  17. James, L.A., Comparative Genomic Hybridization as a Tool in Tumor Cytogenetics, J. Pathol., 1999, vol. 187, pp. 385-395.

    Google Scholar 

  18. Bryndorf, T., Kirchhoff, M., Rose, H., et al., Comparative Genomic Hybridization in Clinical Cytogenetics, Am. J. Hum. Genet., 1995, vol. 57, pp. 1211-1220.

    Google Scholar 

  19. Erdel, M., Duba, H.-C., Verdorfer, I., et al., Comparative Genomic Hybridization Reveals a Partial De Novo Trisomy 6q23–qter in an Infant with Congenital Malformations: Delineation of the Phenotype, Hum. Genet., 1997, vol. 99, pp. 596-601.

    Google Scholar 

  20. Levy, B., Gershin, I.F., Desnick, R.J., et al., Characterization of a De Novo Unbalanced Chromosome Rearrangement by Comparative Genomic Hybridization and Fluorescence In situ Hybridization, Cytogenet. Cell Genet., 1997, vol. 76, pp. 68-71.

    Google Scholar 

  21. Yu, L.-C., Moore, D.H. II, Magrane, G., et al., Objective Aneuploidy Detection for Fetal and Neonatal Screening Using Comparative Genomic Hybridization (CGH), Cytometry, 1997, vol. 28, pp. 191-197.

    Google Scholar 

  22. Benzacken, B., Lapierre, J.M., Siffroi, J.P., et al., Identification and Characterization of a De Novo Partial Trisomy 10p by Comparative Genomic Hybridization (CGH), Clin. Genet., 1998, vol. 54, pp. 334-340.

    Google Scholar 

  23. Daniely, M., Aviram-Goldring, A., Barkai, G., and Goldman, B., Detection of Chromosomal Aberration in Fetuses Arising from Recurrent Spontaneous Abortion by Comparative Genomic Hybridization, Hum. Reprod., 1998, vol. 13, no. 4, pp. 805-809.

    Google Scholar 

  24. Griffin, D.K., Sanoudou, D., Adamski, E., et al., Chromosome-Specific Comparative Genomic Hybridization for Determining the Origin of Intrachromosomal Duplication, J. Med. Genet., 1998, vol. 35, pp. 37-41.

    Google Scholar 

  25. Nacheva, E.P., Grace, C.D., Bittner, M., et al., Comparative Genomic Hybridization: A Comparison with Molecular and Cytogenetic Analysis, Cancer Genet. Cytogenet., 1998, vol. 100, pp. 93-105.

    Google Scholar 

  26. Breen, C.J., Barton, L., Carey, A., et al., Applications of Comparative Genomic Hybridization in Constitutional Chromosome Studies, J. Med. Genet., 1999, vol. 36, pp. 511-517.

    Google Scholar 

  27. Daniely, M., Barkai, G., Goldman, B., and Aviram-Goldring, A., Detection of Numerical Chromosome Aberrations by Comparative Genomic Hybridization, Prenat. Diagn., 1999, vol. 19, pp. 100-104.

    Google Scholar 

  28. Lestou, V.S., Lomax, B.L., Barrett, I.J., and Kalousek, D.K., Screening of Human Placentas for Chromosomal Mosaicism Using Comparative Genomic Hybridization, Teratology, 1999, vol. 59, pp. 325-330.

    Google Scholar 

  29. Voullaire, L., Wilton, L., Slater, H., and Williamson, R., Detection of Aneuploidy in Single Cell Using Comparative Genomic Hybridization, Prenat. Diagn., 1999, vol. 19, pp. 846-851.

    Google Scholar 

  30. Wells, D., Sherlock, J.K., Handyside, A.H., and Delhanty, J.D.A., Detailed Chromosomal and Molecular Genetic Analyses of Single Cells by Whole Genome Amplification and Comparative Genomic Hybridization, Nucleic Acids Res., 1999, vol. 27, pp. 1214-1218.

    Google Scholar 

  31. Lomax, B., Tang, S., Separovic, E., et al., Comparative Genomic Hybridization in Combination with Flow Cytometry Improves Results of Cytogenetic Analysis of Spontaneous Abortions, Am. J. Hum. Genet., 2000, vol. 66, pp. 1516-1521.

    Google Scholar 

  32. du Manoir, S., Schrock, E., Bentz, M., et al., Quantitative Analysis of Comparative Genomic Hybridization, Cytometry, 1995, vol. 19, pp. 27-41.

    Google Scholar 

  33. Karhu, R., Kahkonen, M., Kuukasjarvi, T., et al., Quality Control of CGH: Impact of Metaphase Chromosomes and the Dynamic Range of Hybridization, Cytometry, 1997, vol. 28, pp. 198-205.

    Google Scholar 

  34. du Manoir, S., Kallioniemi, O.-P., Lichter, P., et al., Hardware and Software Requirements for Quantitative Analysis of Comparative Genomic Hybridization, Cytometry, 1995, vol. 19, pp. 4-9.

    Google Scholar 

  35. Piper, J., Rutovitz, D., Sugar, D., et al., Computer Image Analysis of Comparative Genomic Hybridization, Cytometry, 1995, vol. 19, pp. 10-26.

    Google Scholar 

  36. Kirchhoff, M., Gerdes, T., Rose, H., et al., Detection of Chromosomal Gains and Losses in Comparative Genomic Hybridization Analysis Based on Standard Reference Intervals, Cytometry, 1998, vol. 31, pp. 163-173.

    Google Scholar 

  37. Rooney, D.E. and Czepulkowski, B.N., Human Cytogenetics: A Practical Approach, New York: Oxford Univ. Press, 1992, vol. 1.

    Google Scholar 

  38. Sambrook, J., Fritsch, E.F., and Maniatis, T., Molecular Cloning: A Laboratory Manual, Cold Spring Harbor, New York: Cold Spring Harbor Lab., 1989, 2nd ed.

    Google Scholar 

  39. Ghazvini, S., Char, D.H., Kroll, S., et al., Comparative Genomic Hybridization Analysis of Archival Formalin-Fixed Paraffin-Embedded Uveal Melanomas, Cancer Genet. Cytogenet., 1996, vol. 90, pp. 95-101.

    Google Scholar 

  40. Telenius, H., Carter, N.P., Bebb, C.E., et al., Degenerate Oligonucleotide Primed PCR: General Amplification of Target DNA by a Single Degenerate Primer, Genomics, 1992, vol. 13, pp. 718-725.

    Google Scholar 

  41. Kuukasjarvi, T., Tanner, M., Pennanen, S., et al., Optimizing DOP-PCR for Universal Amplification of Small DNA Samples in Comparative Genomic Hybridization, Genes Chromos. Cancer, 1997, vol. 18, pp. 94-101.

    Google Scholar 

  42. Rosenberg, C., van Gijlswijk, R.P.M., Vos, C.B.J., et al., Comparative Genomic Hybridization with Lissamine-and Fluorescein-Labeled Nucleotides, Cytometry, 1998, vol. 32, pp. 337-341.

    Google Scholar 

  43. de Meulemeester, M., Vink, A., Jakobs, M., et al., The Application of Microwave Denaturation in Comparative Genomic Hybridization, Genet. Analysis, 1996, vol. 13, pp. 129-133.

    Google Scholar 

  44. Ried, T., Liyanage, M., du Manoir, S., et al., Tumor Cytogenetics Revisited: Comparative Genomic Hybridization and Spectral Karyotyping, J. Mol. Med., 1997, vol. 75, pp. 801-814.

    Google Scholar 

  45. Karhu, R., Rummukainen, J., Lorch, T., and Isola, J., Four-Color CGH: A New Method for Quality Control of Comparative Genomic Hybridization, Genes Chromos. Cancer, 1999, vol. 24, pp. 112-118.

    Google Scholar 

  46. Roth, K., Wolf, G., Dietel, M., and Petersen, I., Image Analysis for Comparative Genomic Hybridization Based on a Karyotyping Program for Windows, Anal. Quant. Cytol. Histol., 1997, vol. 19, pp. 461-474.

    Google Scholar 

  47. Moore, D.H.II., Pallavicini, M., Cher, M.L., et al., A t-Statistic for Objective Interpretation of Comparative Genomic Hybridization (CGH) Profiles, Cytometry, 1997, vol. 28, pp. 183-190.

    Google Scholar 

  48. Tirkkonen, M., Kurhu, R., Kallioniemi, O.-P., and Isola, J., Evaluation of Camera Requirements for Comparative Genomic Hybridization, Cytometry, 1996, vol. 25, pp. 394-398.

    Google Scholar 

  49. Thompson, C.T., Gray, M.D., and Gray, J.W., Cytogenetic Profiling Using Fluorescence In Situ Hybridization (FISH) and Comparative Genomic Hybridization (CGH), J. Cell Biochem., 1993, vol. 17, pp. 139-143.

    Google Scholar 

  50. van Dekken, H., Rosenberg, C., Krijtenburg, P.J., and Alers, J.C., Interphase Cytogenetics and Comparative Genomic Hybridization of Human Epithelial Cancers and Precursor Lesions, Histochem. Cell Biol., 1997, vol. 108, pp. 419-430.

    Google Scholar 

  51. Parente, F., Gaudray, P., Carle, G.F., and Turc-Carel, C., Experimental Assessment of the Detection Limit of Genomic Amplification by Comparative Genomic Hybridization (CGH), Cytogenet. Cell Genet., 1997, vol. 78, pp. 65-68.

    Google Scholar 

  52. Bentz, M., Plesch, A., Stilgenbauer, S., et al., Minimal Sizes of Deletions Detected by Comparative Genomic Hybridization, Genes Chromos. Cancer, 1998, vol. 21, pp. 172-175.

    Google Scholar 

  53. Solinas-Toldo, S., Lampel, S., Stilgenbauer, S., et al., Matrix-Based Comparative Genomic Hybridization Biochips to Screen for Genomic Imbalances, Genes Chro-mos. Cancer, 1997, vol. 20, pp. 399-407.

    Google Scholar 

  54. Lampel, S., Nessling, M., Soder, A., et al., Matrix-CGH Allows a Fully Automated Analysis of Genetic Imbalances in B-CLL, Med. Genet., 2000, vol. 12, pp. 95-99.

    Google Scholar 

  55. Pinkel, D., Segraves, R., Sugar, D., et al., High Resolution Analysis of DNA Copy Number Variation Using Comparative Genomic Hybridization to Microarrays, Nat. Genet., 1998, vol. 20, pp. 207-211.

    Google Scholar 

  56. Kraus, J., Weber, R.G., Cremer, M., et al., High-Resolution Comparative Hybridization to Combed DNA Fibers, Hum. Genet., 1997, vol. 99, pp. 374-380.

    Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Rights and permissions

Reprints and permissions

About this article

Cite this article

Ostroverkhova, N.B., Nazarenko, S.A. & Cheremnykh, A.D. Comparative Genomic Hybridization As a New Method for Detection of Genomic Imbalance. Russian Journal of Genetics 38, 95–104 (2002). https://doi.org/10.1023/A:1014342607507

Download citation

  • Issue Date:

  • DOI: https://doi.org/10.1023/A:1014342607507

Keywords

Navigation