Skip to main content
PMC home page
Molecular Pathology : MP logoLink to Molecular Pathology : MP
. 1999 Oct;52(5):243–251. doi: 10.1136/mp.52.5.243

Comparative genomic hybridisation.

M M Weiss 1, M A Hermsen 1, G A Meijer 1, N C van Grieken 1, J P Baak 1, E J Kuipers 1, P J van Diest 1
PMCID: PMC395705  PMID: 10748872

Abstract

Comparative genomic hybridisation (CGH) is a technique that permits the detection of chromosomal copy number changes without the need for cell culturing. It provides a global overview of chromosomal gains and losses throughout the whole genome of a tumour. Tumour DNA is labelled with a green fluorochrome, which is subsequently mixed (1:1) with red labelled normal DNA and hybridised to normal human metaphase preparations. The green and red labelled DNA fragments compete for hybridisation to their locus of origin on the chromosomes. The green to red fluorescence ratio measured along the chromosomal axis represents loss or gain of genetic material in the tumour at that specific locus. In addition to a fluorescence microscope, the technique requires a computer with dedicated image analysis software to perform the analysis. This review aims to provide a detailed discussion of the CGH technique, and to provide a protocol with an emphasis on crucial steps.

Full Text

The Full Text of this article is available as a PDF (244.6 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Bastian B. C., LeBoit P. E., Hamm H., Bröcker E. B., Pinkel D. Chromosomal gains and losses in primary cutaneous melanomas detected by comparative genomic hybridization. Cancer Res. 1998 May 15;58(10):2170–2175. [PubMed] [Google Scholar]
  2. Bentz M., Döhner H., Huck K., Schütz B., Ganser A., Joos S., du Manoir S., Lichter P. Comparative genomic hybridization in the investigation of myeloid leukemias. Genes Chromosomes Cancer. 1995 Mar;12(3):193–200. doi: 10.1002/gcc.2870120306. [DOI] [PubMed] [Google Scholar]
  3. Bentz M., Huck K., du Manoir S., Joos S., Werner C. A., Fischer K., Döhner H., Lichter P. Comparative genomic hybridization in chronic B-cell leukemias shows a high incidence of chromosomal gains and losses. Blood. 1995 Jun 15;85(12):3610–3618. [PubMed] [Google Scholar]
  4. Bentz M., Plesch A., Stilgenbauer S., Döhner H., Lichter P. Minimal sizes of deletions detected by comparative genomic hybridization. Genes Chromosomes Cancer. 1998 Feb;21(2):172–175. [PubMed] [Google Scholar]
  5. Craig J. M., Kraus J., Cremer T. Removal of repetitive sequences from FISH probes using PCR-assisted affinity chromatography. Hum Genet. 1997 Sep;100(3-4):472–476. doi: 10.1007/s004390050536. [DOI] [PubMed] [Google Scholar]
  6. Daniely M., Aviram-Goldring A., Barkai G., Goldman B. Detection of chromosomal aberration in fetuses arising from recurrent spontaneous abortion by comparative genomic hybridization. Hum Reprod. 1998 Apr;13(4):805–809. doi: 10.1093/humrep/13.4.805. [DOI] [PubMed] [Google Scholar]
  7. Forozan F., Karhu R., Kononen J., Kallioniemi A., Kallioniemi O. P. Genome screening by comparative genomic hybridization. Trends Genet. 1997 Oct;13(10):405–409. doi: 10.1016/s0168-9525(97)01244-4. [DOI] [PubMed] [Google Scholar]
  8. Heller R. A., Schena M., Chai A., Shalon D., Bedilion T., Gilmore J., Woolley D. E., Davis R. W. Discovery and analysis of inflammatory disease-related genes using cDNA microarrays. Proc Natl Acad Sci U S A. 1997 Mar 18;94(6):2150–2155. doi: 10.1073/pnas.94.6.2150. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Hermsen M. A., Baak J. P., Meijer G. A., Weiss J. M., Walboomers J. W., Snijders P. J., van Diest P. J. Genetic analysis of 53 lymph node-negative breast carcinomas by CGH and relation to clinical, pathological, morphometric, and DNA cytometric prognostic factors. J Pathol. 1998 Dec;186(4):356–362. doi: 10.1002/(SICI)1096-9896(199812)186:4<356::AID-PATH196>3.0.CO;2-Z. [DOI] [PubMed] [Google Scholar]
  10. Hermsen M. A., Joenje H., Arwert F., Welters M. J., Braakhuis B. J., Bagnay M., Westerveld A., Slater R. Centromeric breakage as a major cause of cytogenetic abnormalities in oral squamous cell carcinoma. Genes Chromosomes Cancer. 1996 Jan;15(1):1–9. doi: 10.1002/(SICI)1098-2264(199601)15:1<1::AID-GCC1>3.0.CO;2-8. [DOI] [PubMed] [Google Scholar]
  11. Hermsen M. A., Meijer G. A., Baak J. P., Joenje H., Walboomers J. J. Comparative genomic hybridization: a new tool in cancer pathology. Hum Pathol. 1996 Apr;27(4):342–349. doi: 10.1016/s0046-8177(96)90106-9. [DOI] [PubMed] [Google Scholar]
  12. Isola J. J., Kallioniemi O. P., Chu L. W., Fuqua S. A., Hilsenbeck S. G., Osborne C. K., Waldman F. M. Genetic aberrations detected by comparative genomic hybridization predict outcome in node-negative breast cancer. Am J Pathol. 1995 Oct;147(4):905–911. [PMC free article] [PubMed] [Google Scholar]
  13. Kallioniemi A., Kallioniemi O. P., Sudar D., Rutovitz D., Gray J. W., Waldman F., Pinkel D. Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors. Science. 1992 Oct 30;258(5083):818–821. doi: 10.1126/science.1359641. [DOI] [PubMed] [Google Scholar]
  14. Kallioniemi O. P., Kallioniemi A., Piper J., Isola J., Waldman F. M., Gray J. W., Pinkel D. Optimizing comparative genomic hybridization for analysis of DNA sequence copy number changes in solid tumors. Genes Chromosomes Cancer. 1994 Aug;10(4):231–243. doi: 10.1002/gcc.2870100403. [DOI] [PubMed] [Google Scholar]
  15. Kallioniemi O. P., Kallioniemi A., Sudar D., Rutovitz D., Gray J. W., Waldman F., Pinkel D. Comparative genomic hybridization: a rapid new method for detecting and mapping DNA amplification in tumors. Semin Cancer Biol. 1993 Feb;4(1):41–46. [PubMed] [Google Scholar]
  16. Karhu R., Kähkönen M., Kuukasjärvi T., Pennanen S., Tirkkonen M., Kallioniemi O. Quality control of CGH: impact of metaphase chromosomes and the dynamic range of hybridization. Cytometry. 1997 Jul 1;28(3):198–205. doi: 10.1002/(sici)1097-0320(19970701)28:3<198::aid-cyto3>3.0.co;2-a. [DOI] [PubMed] [Google Scholar]
  17. Kirchhoff M., Gerdes T., Rose H., Maahr J., Ottesen A. M., Lundsteen C. Detection of chromosomal gains and losses in comparative genomic hybridization analysis based on standard reference intervals. Cytometry. 1998 Mar 1;31(3):163–173. [PubMed] [Google Scholar]
  18. Knuutila S., Armengol G., Björkqvist A. M., el-Rifai W., Larramendy M. L., Monni O., Szymanska J. Comparative genomic hybridization study on pooled DNAs from tumors of one clinical-pathological entity. Cancer Genet Cytogenet. 1998 Jan 1;100(1):25–30. doi: 10.1016/s0165-4608(97)00001-0. [DOI] [PubMed] [Google Scholar]
  19. Knuutila S., Björkqvist A. M., Autio K., Tarkkanen M., Wolf M., Monni O., Szymanska J., Larramendy M. L., Tapper J., Pere H. DNA copy number amplifications in human neoplasms: review of comparative genomic hybridization studies. Am J Pathol. 1998 May;152(5):1107–1123. [PMC free article] [PubMed] [Google Scholar]
  20. Kuukasjärvi T., Tanner M., Pennanen S., Karhu R., Visakorpi T., Isola J. Optimizing DOP-PCR for universal amplification of small DNA samples in comparative genomic hybridization. Genes Chromosomes Cancer. 1997 Feb;18(2):94–101. [PubMed] [Google Scholar]
  21. Lapierre J. M., Cacheux V., Da Silva F., Collot N., Hervy N., Wiss J., Tachdjian G. Comparative genomic hybridization: technical development and cytogenetic aspects for routine use in clinical laboratories. Ann Genet. 1998;41(1):56–62. [PubMed] [Google Scholar]
  22. Larramendy M. L., El-Rifai W., Knuutila S. Comparison of fluorescein isothiocyanate- and Texas red-conjugated nucleotides for direct labeling in comparative genomic hybridization. Cytometry. 1998 Mar 1;31(3):174–179. [PubMed] [Google Scholar]
  23. Liang B. C., Meltzer P. S., Guan X. Y., Trent J. M. Gene amplification elucidated by combined chromosomal microdissection and comparative genomic hybridization. Cancer Genet Cytogenet. 1995 Mar;80(1):55–59. doi: 10.1016/0165-4608(94)00153-3. [DOI] [PubMed] [Google Scholar]
  24. Lucito R., Nakimura M., West J. A., Han Y., Chin K., Jensen K., McCombie R., Gray J. W., Wigler M. Genetic analysis using genomic representations. Proc Natl Acad Sci U S A. 1998 Apr 14;95(8):4487–4492. doi: 10.1073/pnas.95.8.4487. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Lundsteen C., Maahr J., Christensen B., Bryndorf T., Bentz M., Lichter P., Gerdes T. Image analysis in comparative genomic hybridization. Cytometry. 1995 Jan 1;19(1):42–50. doi: 10.1002/cyto.990190106. [DOI] [PubMed] [Google Scholar]
  26. Meijer G. A., Hermsen M. A., Baak J. P., van Diest P. J., Meuwissen S. G., Beliën J. A., Hoovers J. M., Joenje H., Snijders P. J., Walboomers J. M. Progression from colorectal adenoma to carcinoma is associated with non-random chromosomal gains as detected by comparative genomic hybridisation. J Clin Pathol. 1998 Dec;51(12):901–909. doi: 10.1136/jcp.51.12.901. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Monni O., Oinonen R., Elonen E., Franssila K., Teerenhovi L., Joensuu H., Knuutila S. Gain of 3q and deletion of 11q22 are frequent aberrations in mantle cell lymphoma. Genes Chromosomes Cancer. 1998 Apr;21(4):298–307. doi: 10.1002/(sici)1098-2264(199804)21:4<298::aid-gcc3>3.0.co;2-u. [DOI] [PubMed] [Google Scholar]
  28. Moore D. H., 2nd, Pallavicini M., Cher M. L., Gray J. W. A t-statistic for objective interpretation of comparative genomic hybridization (CGH) profiles. Cytometry. 1997 Jul 1;28(3):183–190. doi: 10.1002/(sici)1097-0320(19970701)28:3<183::aid-cyto1>3.0.co;2-f. [DOI] [PubMed] [Google Scholar]
  29. Nupponen N. N., Kakkola L., Koivisto P., Visakorpi T. Genetic alterations in hormone-refractory recurrent prostate carcinomas. Am J Pathol. 1998 Jul;153(1):141–148. doi: 10.1016/S0002-9440(10)65554-X. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Pinkel D., Segraves R., Sudar D., Clark S., Poole I., Kowbel D., Collins C., Kuo W. L., Chen C., Zhai Y. High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat Genet. 1998 Oct;20(2):207–211. doi: 10.1038/2524. [DOI] [PubMed] [Google Scholar]
  31. Piper J., Rutovitz D., Sudar D., Kallioniemi A., Kallioniemi O. P., Waldman F. M., Gray J. W., Pinkel D. Computer image analysis of comparative genomic hybridization. Cytometry. 1995 Jan 1;19(1):10–26. doi: 10.1002/cyto.990190104. [DOI] [PubMed] [Google Scholar]
  32. Ried T., Knutzen R., Steinbeck R., Blegen H., Schröck E., Heselmeyer K., du Manoir S., Auer G. Comparative genomic hybridization reveals a specific pattern of chromosomal gains and losses during the genesis of colorectal tumors. Genes Chromosomes Cancer. 1996 Apr;15(4):234–245. doi: 10.1002/(SICI)1098-2264(199604)15:4<234::AID-GCC5>3.0.CO;2-2. [DOI] [PubMed] [Google Scholar]
  33. Riopel M. A., Spellerberg A., Griffin C. A., Perlman E. J. Genetic analysis of ovarian germ cell tumors by comparative genomic hybridization. Cancer Res. 1998 Jul 15;58(14):3105–3110. [PubMed] [Google Scholar]
  34. Schena M. Genome analysis with gene expression microarrays. Bioessays. 1996 May;18(5):427–431. doi: 10.1002/bies.950180513. [DOI] [PubMed] [Google Scholar]
  35. Schena M., Shalon D., Davis R. W., Brown P. O. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science. 1995 Oct 20;270(5235):467–470. doi: 10.1126/science.270.5235.467. [DOI] [PubMed] [Google Scholar]
  36. Schena M., Shalon D., Heller R., Chai A., Brown P. O., Davis R. W. Parallel human genome analysis: microarray-based expression monitoring of 1000 genes. Proc Natl Acad Sci U S A. 1996 Oct 1;93(20):10614–10619. doi: 10.1073/pnas.93.20.10614. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Shalon D., Smith S. J., Brown P. O. A DNA microarray system for analyzing complex DNA samples using two-color fluorescent probe hybridization. Genome Res. 1996 Jul;6(7):639–645. doi: 10.1101/gr.6.7.639. [DOI] [PubMed] [Google Scholar]
  38. Simon R., Bürger H., Brinkschmidt C., Böcker W., Hertle L., Terpe H. J. Chromosomal aberrations associated with invasion in papillary superficial bladder cancer. J Pathol. 1998 Aug;185(4):345–351. doi: 10.1002/(SICI)1096-9896(199808)185:4<345::AID-PATH109>3.0.CO;2-0. [DOI] [PubMed] [Google Scholar]
  39. Szymanska J., Virolainen M., Tarkkanen M., Wiklund T., Asko-Seljavaara S., Tukiainen E., Elomaa I., Blomqvist C., Knuutila S. Overrepresentation of 1q21-23 and 12q13-21 in lipoma-like liposarcomas but not in benign lipomas: a comparative genomic hybridization study. Cancer Genet Cytogenet. 1997 Nov;99(1):14–18. doi: 10.1016/s0165-4608(96)00436-0. [DOI] [PubMed] [Google Scholar]
  40. Taguchi T., Cheng G. Z., Bell D. W., Balsara B., Liu Z., Siegfried J. M., Testa J. R. Combined chromosome microdissection and comparative genomic hybridization detect multiple sites of amplification DNA in a human lung carcinoma cell line. Genes Chromosomes Cancer. 1997 Oct;20(2):208–212. doi: 10.1002/(sici)1098-2264(199710)20:2<208::aid-gcc13>3.0.co;2-m. [DOI] [PubMed] [Google Scholar]
  41. Tarkkanen M., Böhling T., Gamberi G., Ragazzini P., Benassi M. S., Kivioja A., Kallio P., Elomaa I., Picci P., Knuutila S. Comparative genomic hybridization of low-grade central osteosarcoma. Mod Pathol. 1998 May;11(5):421–426. [PubMed] [Google Scholar]
  42. Telenius H., Carter N. P., Bebb C. E., Nordenskjöld M., Ponder B. A., Tunnacliffe A. Degenerate oligonucleotide-primed PCR: general amplification of target DNA by a single degenerate primer. Genomics. 1992 Jul;13(3):718–725. doi: 10.1016/0888-7543(92)90147-k. [DOI] [PubMed] [Google Scholar]
  43. Tienari J., Reima I., Larramendy M. L., Knuutila S., von Boguslawsky K., Kaartinen M., Virtanen I., Lehtonen E. A cloned human germ cell tumor-derived cell line differentiating in culture. Int J Cancer. 1998 Aug 31;77(5):710–719. doi: 10.1002/(sici)1097-0215(19980831)77:5<710::aid-ijc9>3.0.co;2-y. [DOI] [PubMed] [Google Scholar]
  44. Tirkkonen M., Karhu R., Kallioniemi O., Isola J. Evaluation of camera requirements for comparative genomic hybridization. Cytometry. 1996 Dec 1;25(4):394–398. doi: 10.1002/(SICI)1097-0320(19961201)25:4<394::AID-CYTO12>3.0.CO;2-Q. [DOI] [PubMed] [Google Scholar]
  45. Tirkkonen M., Tanner M., Karhu R., Kallioniemi A., Isola J., Kallioniemi O. P. Molecular cytogenetics of primary breast cancer by CGH. Genes Chromosomes Cancer. 1998 Mar;21(3):177–184. [PubMed] [Google Scholar]
  46. Wang B. B., Yu L. C., Peng W., Falk R. E., Williams J., 3rd Prenatal identification of i(Yp) by molecular cytogenetic analysis. Prenat Diagn. 1995 Dec;15(12):1115–1119. doi: 10.1002/pd.1970151206. [DOI] [PubMed] [Google Scholar]
  47. Weber R. G., Scheer M., Born I. A., Joos S., Cobbers J. M., Hofele C., Reifenberger G., Zöller J. E., Lichter P. Recurrent chromosomal imbalances detected in biopsy material from oral premalignant and malignant lesions by combined tissue microdissection, universal DNA amplification, and comparative genomic hybridization. Am J Pathol. 1998 Jul;153(1):295–303. doi: 10.1016/S0002-9440(10)65571-X. [DOI] [PMC free article] [PubMed] [Google Scholar]
  48. Weber R. G., Sommer C., Albert F. K., Kiessling M., Cremer T. Clinically distinct subgroups of glioblastoma multiforme studied by comparative genomic hybridization. Lab Invest. 1996 Jan;74(1):108–119. [PubMed] [Google Scholar]
  49. Yu L. C., Moore D. H., 2nd, Magrane G., Cronin J., Pinkel D., Lebo R. V., Gray J. W. Objective aneuploidy detection for fetal and neonatal screening using comparative genomic hybridization (CGH). Cytometry. 1997 Jul 1;28(3):191–197. [PubMed] [Google Scholar]
  50. Zitzelsberger H., Kulka U., Lehmann L., Walch A., Smida J., Aubele M., Lörch T., Höfler H., Bauchinger M., Werner M. Genetic heterogeneity in a prostatic carcinoma and associated prostatic intraepithelial neoplasia as demonstrated by combined use of laser-microdissection, degenerate oligonucleotide primed PCR and comparative genomic hybridization. Virchows Arch. 1998 Oct;433(4):297–304. doi: 10.1007/s004280050252. [DOI] [PubMed] [Google Scholar]
  51. de Meulemeester M., Vink A., Jakobs M., Hermsen M., Steenman M., Slater R., Dietrich A., Mannens M. The application of microwave denaturation in comparative genomic hybridization. Genet Anal. 1996 Nov;13(5):129–133. doi: 10.1016/s1050-3862(96)00162-3. [DOI] [PubMed] [Google Scholar]
  52. du Manoir S., Kallioniemi O. P., Lichter P., Piper J., Benedetti P. A., Carothers A. D., Fantes J. A., García-Sagredo J. M., Gerdes T., Giollant M. Hardware and software requirements for quantitative analysis of comparative genomic hybridization. Cytometry. 1995 Jan 1;19(1):4–9. doi: 10.1002/cyto.990190103. [DOI] [PubMed] [Google Scholar]
  53. du Manoir S., Schröck E., Bentz M., Speicher M. R., Joos S., Ried T., Lichter P., Cremer T. Quantitative analysis of comparative genomic hybridization. Cytometry. 1995 Jan 1;19(1):27–41. doi: 10.1002/cyto.990190105. [DOI] [PubMed] [Google Scholar]
  54. du Manoir S., Speicher M. R., Joos S., Schröck E., Popp S., Döhner H., Kovacs G., Robert-Nicoud M., Lichter P., Cremer T. Detection of complete and partial chromosome gains and losses by comparative genomic in situ hybridization. Hum Genet. 1993 Feb;90(6):590–610. doi: 10.1007/BF00202476. [DOI] [PubMed] [Google Scholar]
  55. el-Rifai W., Larramendy M. L., Björkqvist A. M., Hemmer S., Knuutila S. Optimization of comparative genomic hybridization using fluorochrome conjugated to dCTP and dUTP nucleotides. Lab Invest. 1997 Dec;77(6):699–700. [PubMed] [Google Scholar]

Articles from Molecular Pathology are provided here courtesy of BMJ Publishing Group

RESOURCES