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Mol Pathol. Oct 1999; 52(5): 243–251.
PMCID: PMC395705

Comparative genomic hybridisation.

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.

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Selected References

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  • Kallioniemi A, Kallioniemi OP, Sudar D, Rutovitz D, Gray JW, Waldman F, Pinkel D. Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors. Science. 1992 Oct 30;258(5083):818–821. [PubMed]
  • du Manoir S, Speicher MR, 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. [PubMed]
  • Kallioniemi OP, Kallioniemi A, Piper J, Isola J, Waldman FM, Gray JW, 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. [PubMed]
  • 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. [PubMed]
  • 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. [PubMed]
  • Hermsen MA, Baak JP, Meijer GA, Weiss JM, Walboomers JW, Snijders PJ, van Diest PJ. 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. [PubMed]
  • Meijer GA, Hermsen MA, Baak JP, van Diest PJ, Meuwissen SG, Beliën JA, Hoovers JM, Joenje H, Snijders PJ, Walboomers JM. 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. [PMC free article] [PubMed]
  • Riopel MA, Spellerberg A, Griffin CA, Perlman EJ. Genetic analysis of ovarian germ cell tumors by comparative genomic hybridization. Cancer Res. 1998 Jul 15;58(14):3105–3110. [PubMed]
  • Tarkkanen M, Böhling T, Gamberi G, Ragazzini P, Benassi MS, 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]
  • 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. [PubMed]
  • Weber RG, Scheer M, Born IA, Joos S, Cobbers JM, Hofele C, Reifenberger G, Zöller JE, 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. [PMC free article] [PubMed]
  • Tirkkonen M, Tanner M, Karhu R, Kallioniemi A, Isola J, Kallioniemi OP. Molecular cytogenetics of primary breast cancer by CGH. Genes Chromosomes Cancer. 1998 Mar;21(3):177–184. [PubMed]
  • Nupponen NN, Kakkola L, Koivisto P, Visakorpi T. Genetic alterations in hormone-refractory recurrent prostate carcinomas. Am J Pathol. 1998 Jul;153(1):141–148. [PMC free article] [PubMed]
  • Taguchi T, Cheng GZ, Bell DW, Balsara B, Liu Z, Siegfried JM, Testa JR. 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. [PubMed]
  • Weber RG, Sommer C, Albert FK, Kiessling M, Cremer T. Clinically distinct subgroups of glioblastoma multiforme studied by comparative genomic hybridization. Lab Invest. 1996 Jan;74(1):108–119. [PubMed]
  • Bastian BC, LeBoit PE, Hamm H, Bröcker EB, 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]
  • 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. [PubMed]
  • Simon R, Bürger H, Brinkschmidt C, Böcker W, Hertle L, Terpe HJ. Chromosomal aberrations associated with invasion in papillary superficial bladder cancer. J Pathol. 1998 Aug;185(4):345–351. [PubMed]
  • Tienari J, Reima I, Larramendy ML, 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. [PubMed]
  • Isola JJ, Kallioniemi OP, Chu LW, Fuqua SA, Hilsenbeck SG, Osborne CK, Waldman FM. 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]
  • 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. [PubMed]
  • Yu LC, Moore DH, 2nd, Magrane G, Cronin J, Pinkel D, Lebo RV, Gray JW. Objective aneuploidy detection for fetal and neonatal screening using comparative genomic hybridization (CGH). Cytometry. 1997 Jul 1;28(3):191–197. [PubMed]
  • Wang BB, Yu LC, Peng W, Falk RE, Williams J., 3rd Prenatal identification of i(Yp) by molecular cytogenetic analysis. Prenat Diagn. 1995 Dec;15(12):1115–1119. [PubMed]
  • Knuutila S, Björkqvist AM, Autio K, Tarkkanen M, Wolf M, Monni O, Szymanska J, Larramendy ML, Tapper J, Pere H, et al. 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]
  • Forozan F, Karhu R, Kononen J, Kallioniemi A, Kallioniemi OP. Genome screening by comparative genomic hybridization. Trends Genet. 1997 Oct;13(10):405–409. [PubMed]
  • Hermsen MA, Meijer GA, Baak JP, Joenje H, Walboomers JJ. Comparative genomic hybridization: a new tool in cancer pathology. Hum Pathol. 1996 Apr;27(4):342–349. [PubMed]
  • Lapierre JM, 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]
  • Larramendy ML, 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]
  • Kirchhoff M, Gerdes T, Rose H, Maahr J, Ottesen AM, 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]
  • 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]
  • el-Rifai W, Larramendy ML, Björkqvist AM, 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]
  • Knuutila S, Armengol G, Björkqvist AM, el-Rifai W, Larramendy ML, 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. [PubMed]
  • 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]
  • 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. [PubMed]
  • Moore DH, 2nd, Pallavicini M, Cher ML, Gray JW. A t-statistic for objective interpretation of comparative genomic hybridization (CGH) profiles. Cytometry. 1997 Jul 1;28(3):183–190. [PubMed]
  • 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. [PubMed]
  • Tirkkonen M, Karhu R, Kallioniemi O, Isola J. Evaluation of camera requirements for comparative genomic hybridization. Cytometry. 1996 Dec 1;25(4):394–398. [PubMed]
  • 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. [PubMed]
  • du Manoir S, Kallioniemi OP, Lichter P, Piper J, Benedetti PA, Carothers AD, Fantes JA, García-Sagredo JM, Gerdes T, Giollant M, et al. Hardware and software requirements for quantitative analysis of comparative genomic hybridization. Cytometry. 1995 Jan 1;19(1):4–9. [PubMed]
  • du Manoir S, Schröck E, Bentz M, Speicher MR, Joos S, Ried T, Lichter P, Cremer T. Quantitative analysis of comparative genomic hybridization. Cytometry. 1995 Jan 1;19(1):27–41. [PubMed]
  • Piper J, Rutovitz D, Sudar D, Kallioniemi A, Kallioniemi OP, Waldman FM, Gray JW, Pinkel D. Computer image analysis of comparative genomic hybridization. Cytometry. 1995 Jan 1;19(1):10–26. [PubMed]
  • Liang BC, Meltzer PS, Guan XY, Trent JM. Gene amplification elucidated by combined chromosomal microdissection and comparative genomic hybridization. Cancer Genet Cytogenet. 1995 Mar;80(1):55–59. [PubMed]
  • Kallioniemi OP, Kallioniemi A, Sudar D, Rutovitz D, Gray JW, 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]
  • Bentz M, Huck K, du Manoir S, Joos S, Werner CA, 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]
  • Hermsen MA, Joenje H, Arwert F, Welters MJ, Braakhuis BJ, 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. [PubMed]
  • 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. [PubMed]
  • Telenius H, Carter NP, Bebb CE, Nordenskjöld M, Ponder BA, Tunnacliffe A. Degenerate oligonucleotide-primed PCR: general amplification of target DNA by a single degenerate primer. Genomics. 1992 Jul;13(3):718–725. [PubMed]
  • Lucito R, Nakimura M, West JA, Han Y, Chin K, Jensen K, McCombie R, Gray JW, Wigler M. Genetic analysis using genomic representations. Proc Natl Acad Sci U S A. 1998 Apr 14;95(8):4487–4492. [PMC free article] [PubMed]
  • Craig JM, 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. [PubMed]
  • Schena M, Shalon D, Davis RW, Brown PO. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science. 1995 Oct 20;270(5235):467–470. [PubMed]
  • Schena M, Shalon D, Heller R, Chai A, Brown PO, Davis RW. 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. [PMC free article] [PubMed]
  • Schena M. Genome analysis with gene expression microarrays. Bioessays. 1996 May;18(5):427–431. [PubMed]
  • Heller RA, Schena M, Chai A, Shalon D, Bedilion T, Gilmore J, Woolley DE, Davis RW. 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. [PMC free article] [PubMed]
  • Pinkel D, Segraves R, Sudar D, Clark S, Poole I, Kowbel D, Collins C, Kuo WL, Chen C, Zhai Y, et al. High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat Genet. 1998 Oct;20(2):207–211. [PubMed]
  • Shalon D, Smith SJ, Brown PO. A DNA microarray system for analyzing complex DNA samples using two-color fluorescent probe hybridization. Genome Res. 1996 Jul;6(7):639–645. [PubMed]

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