Skip to main content
Book cover

Genotoxicity Assessment pp 209–234Cite as

Comparative Genomic Hybridization (CGH) in Genotoxicology

  • 740 Accesses

Part of the Methods in Molecular Biology book series (MIMB,volume 2031)

Abstract

In the past two decades, comparative genomic hybridization (CGH) and array CGH have become indispensable tools in clinical diagnostics and toxicological risk assessment. Initially developed for the genome-wide screening of chromosomal imbalances, that is, copy-number variations in tumor cells, both CGH and array CGH have been employed in genotoxicology and most recently in toxicogenomics. The latter allows a multi-end point analysis of how particular genes react to toxic agents, revealing changes in signaling pathways and other underlying molecular mechanisms. This chapter provides background on the use of CGH and array CGH in the context of genotoxicology, and also a protocol for conventional CGH, so that the basic principles of this methodology can be better understood. Conventional and array CGH investigate DNA expression patterns, copy-number variations across the whole genome, and loss of heterozygosity after genotoxic damage. Array CGH is still cost-intensive but produces exponentially more data, requiring suitable analytical algorithms and sophisticated bioinformatic analysis. As toxicogenomics is an emerging sub-discipline of toxicology research, effectively evaluating toxicogenomic microarray data can be hugely advantageous for human risk assessment, even though international regulatory guidelines on toxicogenomics have yet to be fully agreed and implemented.

Key words

  • Comparative genomic hybridization
  • CGH
  • Array CGH
  • Microarray
  • Genomic imbalances
  • Genotoxicology
  • Toxicogenomics

This is a preview of subscription content, access via your institution.

Protocol
USD   49.95
Price excludes VAT (USA)
  • DOI: 10.1007/978-1-4939-9646-9_11
  • Chapter length: 26 pages
  • Instant PDF download
  • Readable on all devices
  • Own it forever
  • Exclusive offer for individuals only
  • Tax calculation will be finalised during checkout
eBook
USD   109.00
Price excludes VAT (USA)
  • ISBN: 978-1-4939-9646-9
  • Instant PDF download
  • Readable on all devices
  • Own it forever
  • Exclusive offer for individuals only
  • Tax calculation will be finalised during checkout
Softcover Book
USD   149.99
Price excludes VAT (USA)
Hardcover Book
USD   219.99
Price excludes VAT (USA)
Learn about institutional subscriptions
Fig. 1
Fig. 2

Springer Nature is developing a new tool to find and evaluate Protocols. Learn more

References

  1. Pinkel D, Straume T, Gray JW (1986) Cytogenetic analysis using quantitative, high-sensitivity, fluorescence hybridization. Proc Natl Acad Sci U S A 83(9):2934–2938

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  2. Ratan ZA, Zaman SB, Mehta V et al (2017) Application of fluorescence in situ hybridization (FISH) technique for the detection of genetic aberration in medical science. Cureus 9(6):e1325

    PubMed  PubMed Central  Google Scholar 

  3. Heng HH, Squire J, Tsui LC (1992) High-resolution mapping of mammalian genes by in situ hybridization to free chromatin. Proc Natl Acad Sci U S A 89(20):9509–9513

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  4. Speicher MR, Gwyn Ballard S, Ward DC (1996) Karyotyping human chromosomes by combinatorial multi-fluor FISH. Nat Genet 12(4):368–375

    CAS  PubMed  CrossRef  Google Scholar 

  5. Schrock E, du Manoir S, Veldman T et al (1996) Multicolor spectral karyotyping of human chromosomes. Science 273(5274):494–497

    CAS  PubMed  CrossRef  Google Scholar 

  6. Tanke HJ, Wiegant J, van Gijlswijk RP et al (1999) New strategy for multi-colour fluorescence in situ hybridisation: COBRA: COmbined Binary RAtio labelling. Eur J Hum Genet 7(1):2–11

    CAS  PubMed  CrossRef  Google Scholar 

  7. Bolzer A, Kreth G, Solovei I et al (2005) Three-dimensional maps of all chromosomes in human male fibroblast nuclei and prometaphase rosettes. PLoS Biol 3(5):e157

    PubMed  PubMed Central  CrossRef  CAS  Google Scholar 

  8. Cremer T, Cremer C (2001) Chromosome territories, nuclear architecture and gene regulation in mammalian cells. Nat Rev Genet 2(4):292–301

    CAS  PubMed  CrossRef  Google Scholar 

  9. Deng W, Shi X, Tjian R et al (2015) CASFISH: CRISPR/Cas9-mediated in situ labeling of genomic loci in fixed cells. Proc Natl Acad Sci U S A 112(38):11870–11875

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  10. Chen B, Gilbert LA, Cimini BA et al (2013) Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system. Cell 155(7):1479–1491

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  11. Speicher MR, Carter NP (2005) The new cytogenetics: blurring the boundaries with molecular biology. Nat Rev Genet 6(10):782–792

    CAS  PubMed  CrossRef  Google Scholar 

  12. Kallioniemi A, Kallioniemi OP, Sudar D et al (1992) Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors. Science 258(5083):818–821

    CAS  PubMed  CrossRef  Google Scholar 

  13. du Manoir S, Speicher MR, Joos S et al (1993) Detection of complete and partial chromosome gains and losses by comparative genomic in situ hybridization. Hum Genet 90(6):590–610

    PubMed  CrossRef  Google Scholar 

  14. Riegel M (2014) Human molecular cytogenetics: from cells to nucleotides. Genet Mol Biol 37(1 Suppl):194–209

    PubMed  CrossRef  Google Scholar 

  15. Kallioniemi OP, Kallioniemi A, Sudar D et al (1993) Comparative genomic hybridization: a rapid new method for detecting and mapping DNA amplification in tumors. Semin Cancer Biol 4(1):41–46

    CAS  PubMed  Google Scholar 

  16. Zitzelsberger H, Lehmann L, Werner M et al (1997) Comparative genomic hybridisation for the analysis of chromosomal imbalances in solid tumours and haematological malignancies. Histochem Cell Biol 108(4-5):403–417

    CAS  PubMed  CrossRef  Google Scholar 

  17. Piper J, Rutovitz D, Sudar D et al (1995) Computer image analysis of comparative genomic hybridization. Cytometry 19(1):10–26

    CAS  PubMed  CrossRef  Google Scholar 

  18. Corso C, Parry EM (1999) The application of comparative genomic hybridization and fluorescence in situ hybridization to the characterization of genotoxicity screening tester strains AHH-1 and MCL-5. Mutagenesis 14(4):417–426

    CAS  PubMed  CrossRef  Google Scholar 

  19. Carlson KM, Gruber A, Liliemark E et al (1999) Characterization of drug-resistant cell lines by comparative genomic hybridization. Cancer Genet Cytogenet 111(1):32–36

    CAS  PubMed  CrossRef  Google Scholar 

  20. Corso C, Parry JM (2004) Comparative genomic hybridization analysis of N-methyl-N′-nitrosoguanidine-induced rat gastrointestinal tumors discloses a cytogenetic fingerprint. Environ Mol Mutagen 43(1):20–27

    CAS  PubMed  CrossRef  Google Scholar 

  21. Payne J, Jones C, Lakhani S et al (2000) Improving the reproducibility of the MCF-7 cell proliferation assay for the detection of xenoestrogens. Sci Total Environ 248(1):51–62

    CAS  PubMed  CrossRef  Google Scholar 

  22. Kim YM, Yang S, Xu W et al (2008) Continuous in vitro exposure to low-dose genistein induces genomic instability in breast epithelial cells. Cancer Genet Cytogenet 186(2):78–84

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  23. Wong N, Lai P, Pang E et al (2000) Genomic aberrations in human hepatocellular carcinomas of differing etiologies. Clin Cancer Res 6(10):4000–4009

    CAS  PubMed  Google Scholar 

  24. Clarke PA, te Poele R, Wooster R et al (2001) Gene expression microarray analysis in cancer biology, pharmacology, and drug development: progress and potential. Biochem Pharmacol 62(10):1311–1336

    CAS  PubMed  CrossRef  Google Scholar 

  25. Solinas-Toldo S, Lampel S, Stilgenbauer S et al (1997) Matrix-based comparative genomic hybridization: biochips to screen for genomic imbalances. Genes Chromosomes Cancer 20(4):399–407

    CAS  PubMed  CrossRef  Google Scholar 

  26. Ylstra B, van den Ijssel P, Carvalho B et al (2006) BAC to the future! or oligonucleotides: a perspective for micro array comparative genomic hybridization (array CGH). Nucleic Acids Res 34(2):445–450

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  27. Brennan C, Zhang Y, Leo C et al (2004) High-resolution global profiling of genomic alterations with long oligonucleotide microarray. Cancer Res 64(14):4744–4748

    CAS  PubMed  CrossRef  Google Scholar 

  28. Chan VSW, Theilade MD (2005) The use of toxicogenomic data in risk assessment: A regulatory perspective. Clin Toxicol 43(2):121–126

    CAS  CrossRef  Google Scholar 

  29. Davies JJ, Wilson IM, Lam WL (2005) Array CGH technologies and their applications to cancer genomes. Chromosom Res 13(3):237–248

    CAS  CrossRef  Google Scholar 

  30. Amin RP, Hamadeh HK, Bushel PR et al (2002) Genomic interrogation of mechanism(s) underlying cellular responses to toxicants. Toxicology 181-182:555–563

    CAS  PubMed  CrossRef  Google Scholar 

  31. Gerhold D, Lu MQ, Xu J et al (2001) Monitoring expression of genes involved in drug metabolism and toxicology using DNA microarrays. Physiol Genomics 5(4):161–170

    CAS  PubMed  CrossRef  Google Scholar 

  32. Aradhya S, Lewis R, Bonaga T et al (2012) Exon-level array CGH in a large clinical cohort demonstrates increased sensitivity of diagnostic testing for Mendelian disorders. Genet Med 14(6):594–603

    CAS  PubMed  CrossRef  Google Scholar 

  33. Wang J, Zhan H, Li FY et al (2012) Targeted array CGH as a valuable molecular diagnostic approach: experience in the diagnosis of mitochondrial and metabolic disorders. Mol Genet Metab 106(2):221–230

    CAS  PubMed  CrossRef  Google Scholar 

  34. Hu DG, Webb G, Hussey N (2004) Aneuploidy detection in single cells using DNA array-based comparative genomic hybridization. Mol Hum Reprod 10(4):283–289

    CAS  PubMed  CrossRef  Google Scholar 

  35. Cheng J, Vanneste E, Konings P et al (2011) Single-cell copy number variation detection. Genome Biol 12(8):R80

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  36. Fiegler H, Geigl JB, Langer S et al (2007) High resolution array-CGH analysis of single cells. Nucleic Acids Res 35(3):e15

    PubMed  CrossRef  CAS  Google Scholar 

  37. Crotwell PL, Hoyme HE (2012) Advances in whole-genome genetic testing: from chromosomes to microarrays. Curr Probl Pediatr Adolesc Health Care 42(3):47–73

    PubMed  CrossRef  Google Scholar 

  38. Auer H, Newsom DL, Nowak NJ et al (2007) Gene-resolution analysis of DNA copy number variation using oligonucleotide expression microarrays. BMC Genomics 8:111

    PubMed  PubMed Central  CrossRef  CAS  Google Scholar 

  39. Zhao XJ, Li C, Paez JG et al (2004) An integrated view of copy number and allelic alterations in the cancer genome using single nucleotide polymorphism arrays. Cancer Res 64(9):3060–3071

    CAS  PubMed  CrossRef  Google Scholar 

  40. Le Scouarnec S, Gribble SM (2012) Characterising chromosome rearrangements: recent technical advances in molecular cytogenetics. Heredity (Edinb) 108(1):75–85

    CrossRef  CAS  Google Scholar 

  41. Schillert A, Ziegler A (2012) Genotype calling for the Affymetrix platform. Methods Mol Biol 850:513–523

    PubMed  CrossRef  Google Scholar 

  42. Hester SD, Reid L, Nowak N et al (2009) Comparison of comparative genomic hybridization technologies across microarray platforms. J Biomol Tech 20(2):135–151

    PubMed  PubMed Central  Google Scholar 

  43. Herzog CR, Desai D, Amin S (2006) Array CGH analysis reveals chromosomal aberrations in mouse lung adenocarcinomas induced by the human lung carcinogen 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone. Biochem Biophys Res Commun 341(3):856–863

    CAS  PubMed  CrossRef  Google Scholar 

  44. Medlin JF (1999) Timely toxicology. Environ Health Perspect 107(5):A256–A258

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  45. Heinloth AN, Shackelford RE, Innes CL et al (2003) Identification of distinct and common gene expression changes after oxidative stress and gamma and ultraviolet radiation. Mol Carcinog 37(2):65–82

    CAS  PubMed  CrossRef  Google Scholar 

  46. Heinloth AN, Shackelford RE, Innes CL et al (2003) ATM-dependent and -independent gene expression changes in response to oxidative stress, gamma irradiation, and UV irradiation. Radiat Res 160(3):273–290

    CAS  PubMed  CrossRef  Google Scholar 

  47. Brown N, Finnon R, Manning G et al (2015) Influence of radiation quality on mouse chromosome 2 deletions in radiation-induced acute myeloid leukaemia. Mutat Res Genet Toxicol Environ Mutagen 793:48–54

    CAS  PubMed  CrossRef  Google Scholar 

  48. Castagnola P, Malacarne D, Scaruffi P et al (2011) Chromosomal aberrations and aneuploidy in oral potentially malignant lesions: distinctive features for tongue. BMC Cancer 11:445

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  49. Fujimoto J, Kadara H, Men T et al (2010) Comparative functional genomics analysis of NNK tobacco-carcinogen induced lung adenocarcinoma development in Gprc5a-knockout mice. PLoS One 5(7):e11847

    PubMed  PubMed Central  CrossRef  CAS  Google Scholar 

  50. Auerbach SS, Shah RR, Mav D et al (2010) Predicting the hepatocarcinogenic potential of alkenylbenzene flavoring agents using toxicogenomics and machine learning. Toxicol Appl Pharmacol 243(3):300–314

    CAS  PubMed  CrossRef  Google Scholar 

  51. Iwahashi H, Kitagawa E, Suzuki Y et al (2007) Evaluation of toxicity of the mycotoxin citrinin using yeast ORF DNA microarray and Oligo DNA microarray. BMC Genomics 8:95

    PubMed  PubMed Central  CrossRef  CAS  Google Scholar 

  52. Huang Y, Fernandez SV, Goodwin S et al (2007) Epithelial to mesenchymal transition in human breast epithelial cells transformed by 17beta-estradiol. Cancer Res 67(23):11147–11157

    CAS  PubMed  CrossRef  Google Scholar 

  53. Hong HJ, Koom WS, Koh WG (2017) Cell microarray technologies for high-throughput cell-based biosensors. Sensors (Basel) 17(6):E1293

    CrossRef  CAS  Google Scholar 

  54. Grant GR, Manduchi E, Stoeckert CJ Jr (2007) Analysis and management of microarray gene expression data [chapter 19, unit 6]. Curr Protoc Mol Biol 77(1):1–30

    Google Scholar 

  55. Vermeesch JR, Melotte C, Froyen G et al (2005) Molecular karyotyping: array CGH quality criteria for constitutional genetic diagnosis. J Histochem Cytochem 53(3):413–422

    CAS  PubMed  CrossRef  Google Scholar 

  56. Guha S, Li Y, Neuberg D (2008) Bayesian Hidden Markov Modeling of Array CGH Data. J Am Stat Assoc 103(482):485–497

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  57. Zhang L, Zhang L (2013) Use of autocorrelation scanning in DNA copy number analysis. Bioinformatics 29(21):2678–2682

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  58. Shaw-Smith C, Redon R, Rickman L et al (2004) Microarray based comparative genomic hybridisation (array-CGH) detects submicroscopic chromosomal deletions and duplications in patients with learning disability/mental retardation and dysmorphic features. J Med Genet 41(4):241–248

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  59. Brazma A, Hingamp P, Quackenbush J et al (2001) Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet 29(4):365–371

    CAS  PubMed  CrossRef  Google Scholar 

  60. Brazma A (2009) Minimum information about a microarray experiment (MIAME)—successes, failures, challenges. ScientificWorldJournal 9:420–423

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  61. Liu Y, Li A, Feng H et al (2015) TAFFYS: An Integrated Tool for Comprehensive Analysis of Genomic Aberrations in Tumor Samples. PLoS One 10(6):e0129835

    PubMed  PubMed Central  CrossRef  CAS  Google Scholar 

  62. Quigley D (2015) Equalizer reduces SNP bias in Affymetrix microarrays. BMC Bioinformatics 16:238

    PubMed  PubMed Central  CrossRef  Google Scholar 

  63. Mayrhofer M, Viklund B, Isaksson A (2016) Rawcopy: Improved copy number analysis with Affymetrix arrays. Sci Rep 6:36158

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  64. Morgan AP (2015) argyle: an R package for analysis of illumina genotyping arrays. G3 (Bethesda) 6(2):281–286

    CrossRef  CAS  Google Scholar 

  65. Tice RR, Austin CP, Kavlock RJ et al (2013) Improving the human hazard characterization of chemicals: a Tox21 update. Environ Health Perspect 121(7):756–765

    PubMed  PubMed Central  CrossRef  CAS  Google Scholar 

  66. Aardema MJ, MacGregor JT (2002) Toxicology and genetic toxicology in the new era of “toxicogenomics”: impact of “-omics” technologies. Mutat Res 499(1):13–25

    CAS  PubMed  CrossRef  Google Scholar 

  67. Ruden DM, Gurdziel K, Aschner M (2017) Frontiers in toxicogenomics in the twenty-first century-the grand challenge: to understand how the genome and epigenome interact with the toxic environment at the single-cell, whole-organism, and multi-generational level. Front Genet 8:173

    PubMed  PubMed Central  CrossRef  CAS  Google Scholar 

  68. Mahadevan B, Snyder RD, Waters MD et al (2011) Genetic toxicology in the 21st century: reflections and future directions. Environ Mol Mutagen 52(5):339–354

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  69. OECD (2009) Series on testing and assessment no. 100 - Report of the second survey on available omics tools (ENV/JM/MONO(2008)35). Available at http://www.oecd.org/officialdocuments/displaydocument/?cote=env/jm/mono(2008)35&doclanguage=en. Accessed 22 June 2018

  70. Karahalil B (2016) Overview of systems biology and omics technologies. Curr Med Chem 23(37):4221–4230

    CAS  PubMed  CrossRef  Google Scholar 

  71. Vrana KE, Freeman WM, Aschner M (2003) Use of microarray technologies in toxicology research. Neurotoxicology 24(3):321–332

    CAS  PubMed  CrossRef  Google Scholar 

  72. Song Y, Asselman J, De Schamphelaere KAC et al (2018) Deciphering the combined effects of environmental stressors on gene transcription: a conceptual approach. Environ Sci Technol 52(9):5479–5489

    CAS  PubMed  CrossRef  Google Scholar 

  73. Jeong J, Choi J (2017) Use of adverse outcome pathways in chemical toxicity testing: potential advantages and limitations. Environ Health Toxicol 33(1):e2018002

    PubMed  PubMed Central  CrossRef  Google Scholar 

  74. Mattingly CJ, Rosenstein MC, Davis AP et al (2006) The comparative toxicogenomics database: a cross-species resource for building chemical-gene interaction networks. Toxicol Sci 92(2):587–595

    CAS  PubMed  CrossRef  Google Scholar 

  75. Davis AP, Grondin CJ, Johnson RJ et al (2017) The Comparative Toxicogenomics Database: update 2017. Nucleic Acids Res 45(D1):D972–D978

    CAS  PubMed  CrossRef  Google Scholar 

  76. Davis AP, Wiegers TC, Wiegers J et al (2018) Chemical-induced phenotypes at CTD help inform the predisease state and construct adverse outcome pathways. Toxicol Sci 165(1):145–156

    CAS  PubMed  CrossRef  PubMed Central  Google Scholar 

  77. Grondin CJ, Davis AP, Wiegers TC et al (2018) Accessing an expanded exposure science module at the Comparative Toxicogenomics Database. Environ Health Perspect 126(1):014501

    PubMed  PubMed Central  CrossRef  Google Scholar 

  78. Young RR (2002) Genetic toxicology: web resources. Toxicology 173(1-2):103–121

    CAS  PubMed  CrossRef  Google Scholar 

  79. Lea IA, Gong H, Paleja A et al (2017) CEBS: a comprehensive annotated database of toxicological data. Nucleic Acids Res 45(D1):D964–D971

    CAS  PubMed  CrossRef  Google Scholar 

  80. Nuwaysir EF, Bittner M, Trent J et al (1999) Microarrays and toxicology: the advent of toxicogenomics. Mol Carcinog 24(3):153–159

    CAS  PubMed  CrossRef  Google Scholar 

  81. Andersen ME, Krewski D (2009) Toxicity testing in the 21st century: bringing the vision to life. Toxicol Sci 107(2):324–330

    CAS  PubMed  CrossRef  Google Scholar 

  82. Testing CoT, Assessment of Environmental Agents NRC (2007) Toxicity testing in the 21st century: a vision and a strategy. The National Academies Press, Washington, D.C.

    Google Scholar 

  83. Andersen ME, Al-Zoughool M, Croteau M et al (2010) The future of toxicity testing. J Toxicol Environ Health B Crit Rev 13(2-4):163–196

    CAS  PubMed  CrossRef  Google Scholar 

  84. Andersen ME, Krewski D (2010) The vision of toxicity testing in the 21st century: moving from discussion to action. Toxicol Sci 117(1):17–24

    CAS  PubMed  CrossRef  Google Scholar 

  85. Jacobs A (2009) An FDA perspective on the nonclinical use of the X-Omics technologies and the safety of new drugs. Toxicol Lett 186(1):32–35

    CAS  PubMed  CrossRef  Google Scholar 

  86. Hendrickx DM, Boyles RR, Kleinjans JC et al (2014) Workshop report: identifying opportunities for global integration of toxicogenomics databases, 26-27 June 2013, Research Triangle Park, NC, USA. Arch Toxicol 88(12):2323–2332

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  87. Bhattacharya S, Zhang Q, Carmichael PL et al (2011) Toxicity testing in the 21 century: defining new risk assessment approaches based on perturbation of intracellular toxicity pathways. PLoS One 6(6):e20887

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  88. Krewski D, Westphal M, Al-Zoughool M et al (2011) New directions in toxicity testing. Annu Rev Public Health 32:161–178

    PubMed  CrossRef  Google Scholar 

  89. Moffat I, Chepelev N, Labib S et al (2015) Comparison of toxicogenomics and traditional approaches to inform mode of action and points of departure in human health risk assessment of benzo[a]pyrene in drinking water. Crit Rev Toxicol 45(1):1–43

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  90. Chepelev NL, Moffat ID, Labib S et al (2015) Integrating toxicogenomics into human health risk assessment: lessons learned from the benzo[a]pyrene case study. Crit Rev Toxicol 45(1):44–52

    CAS  PubMed  CrossRef  Google Scholar 

  91. Jean-Quartier C, Jeanquartier F, Jurisica I et al (2018) In silico cancer research towards 3R. BMC Cancer 18(1):408

    PubMed  PubMed Central  CrossRef  CAS  Google Scholar 

  92. Vachon J, Page-Lariviere F, Sirard MA et al (2018) Availability, quality, and relevance of toxicogenomics data for human health risk assessment: a scoping review of the literature on trihalomethanes. Toxicol Sci 163(2):364–373

    CAS  PubMed  CrossRef  Google Scholar 

  93. Farmahin R, Williams A, Kuo B et al (2017) Recommended approaches in the application of toxicogenomics to derive points of departure for chemical risk assessment. Arch Toxicol 91(5):2045–2065

    CAS  PubMed  CrossRef  Google Scholar 

  94. Telenius H, Carter NP, Bebb CE et al (1992) Degenerate oligonucleotide-primed PCR: general amplification of target DNA by a single degenerate primer. Genomics 13(3):718–725

    CAS  PubMed  CrossRef  Google Scholar 

  95. Zhang L, Cui X, Schmitt K et al (1992) Whole genome amplification from a single cell: implications for genetic analysis. Proc Natl Acad Sci U S A 89(13):5847–5851

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  96. Huber R, Kulka U, Lorch T et al (2001) Technical report: application of the Metafer2 fluorescence scanning system for the analysis of radiation-induced chromosome aberrations measured by FISH-chromosome painting. Mutat Res 492(1-2):51–57

    CAS  PubMed  CrossRef  Google Scholar 

  97. Bangs CD, Donlon TA (2005) Metaphase chromosome preparation from cultured peripheral blood cells. Curr Protoc Hum Genet Chapter 4:Unit 4.1

    PubMed  Google Scholar 

  98. du Manoir S, Kallioniemi OP, Lichter P et al (1995) Hardware and software requirements for quantitative analysis of comparative genomic hybridization. Cytometry 19(1):4–9

    PubMed  CrossRef  Google Scholar 

  99. du Manoir S, Schrock E, Bentz M et al (1995) Quantitative analysis of comparative genomic hybridization. Cytometry 19(1):27–41

    PubMed  CrossRef  Google Scholar 

  100. Lundsteen C, Maahr J, Christensen B et al (1995) Image analysis in comparative genomic hybridization. Cytometry 19(1):42–50

    CAS  PubMed  CrossRef  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Biomedical Science, School of Health Sciences, York St John University, York, UK

    Adi Baumgartner & Jim D. Taylor

  2. MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK

    Veronika Hartleb

Authors
  1. Adi Baumgartner
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Veronika Hartleb
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Jim D. Taylor
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Adi Baumgartner .

Editor information

Editors and Affiliations

  1. CSIR—Indian Institute of Toxicology Research, Lucknow, Uttar Pradesh, India

    Alok Dhawan

  2. New Delhi, Delhi, India

    Mahima Bajpayee

Rights and permissions

Reprints and Permissions

Copyright information

© 2019 Springer Science+Business Media, LLC, part of Springer Nature

About this protocol

Verify currency and authenticity via CrossMark

Cite this protocol

Baumgartner, A., Hartleb, V., Taylor, J.D. (2019). Comparative Genomic Hybridization (CGH) in Genotoxicology. In: Dhawan, A., Bajpayee, M. (eds) Genotoxicity Assessment. Methods in Molecular Biology, vol 2031. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9646-9_11

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-9646-9_11

  • Published:

  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-4939-9645-2

  • Online ISBN: 978-1-4939-9646-9

  • eBook Packages: Springer Protocols