Skip to main content
SpringerLink
Log in
Book cover

Predictive Biomarkers in Oncology pp 75–85Cite as

Introduction to Microarray Technology

  • Chapter
  • First Online:

Abstract

Microarrays make it possible to measure the expression levels of a large number of genes simultaneously within a sample. Microarrays have been broadly employed to screen, profile, and quantify genome-wide gene expression levels and play an important role in the discovery and validation of predictive biomarkers. Gene expression array, comparative genomic hybridization (CGH) array, and single nucleotide polymorphism (SNP) arrays are the key methods in detecting changes in gene expression, copy number variation, and sequence polymorphisms in cancer diagnostics and biomarker research.

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

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   149.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book
USD   199.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

References

  1. DeRisi J, Penland L, Brown PO, Bittner ML, Meltzer PS, Ray M, Chen Y, Su YA, Trent JM. Use of a cDNA microarray to analyse gene expression patterns in human cancer. Nat Genet. 1996;14:457–60.

    Article  CAS  PubMed  Google Scholar 

  2. Alizadeh AA, Eisen MB, Davis RE, Ma C, Lossos IS, Rosenwald A, Boldrick JC, Sabet H, Tran T, Yu X, Powell JI, Yang L, Marti GE, Moore T, Hudson J Jr, Lu L, Lewis DB, Tibshirani R, Sherlock G, Chan WC, Greiner TC, Weisenburger DD, Armitage JO, Warnke R, Levy R, Wilson W, Grever MR, Byrd JC, Botstein D, Brown PO, Staudt LM. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature. 2000;403:503–11.

    Article  CAS  PubMed  Google Scholar 

  3. Yam C, Mani SA, Moulder SL. Targeting the molecular subtypes of triple negative breast cancer: understanding the diversity to progress the field. Oncologist. 2017;22:1086–93.

    Article  PubMed  PubMed Central  Google Scholar 

  4. van de Rijn M, Gilks CB. Applications of microarrays to histopathology. Histopathology. 2004;44:97–108.

    Article  PubMed  Google Scholar 

  5. Bumgarner R. Overview of DNA microarrays: types, applications, and their future. Curr Protoc Mol Biol. 2013. Chapter 22:Unit 22 21.

    Google Scholar 

  6. 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;258:818–21.

    Article  CAS  PubMed  Google Scholar 

  7. Palanisamy N, Imanishi Y, Rao PH, Tahara H, Chaganti RS, Arnold A. Novel chromosomal abnormalities identified by comparative genomic hybridization in parathyroid adenomas. J Clin Endocrinol Metab. 1998;83:1766–70.

    CAS  PubMed  Google Scholar 

  8. Pinkel D, Albertson DG. Array comparative genomic hybridization and its applications in cancer. Nat Genet. 2005;37(Suppl):S11–7.

    Article  CAS  PubMed  Google Scholar 

  9. Jonsson G, Staaf J, Vallon-Christersson J, Ringner M, Holm K, Hegardt C, Gunnarsson H, Fagerholm R, Strand C, Agnarsson BA, Kilpivaara O, Luts L, Heikkila P, Aittomaki K, Blomqvist C, Loman N, Malmstrom P, Olsson H, Johannsson OT, Arason A, Nevanlinna H, Barkardottir RB, Borg A. Genomic subtypes of breast cancer identified by array-comparative genomic hybridization display distinct molecular and clinical characteristics. Breast Cancer Res. 2010;12:R42.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Lenz G, Wright GW, Emre NC, Kohlhammer H, Dave SS, Davis RE, Carty S, Lam LT, Shaffer AL, Xiao W, Powell J, Rosenwald A, Ott G, Muller-Hermelink HK, Gascoyne RD, Connors JM, Campo E, Jaffe ES, Delabie J, Smeland EB, Rimsza LM, Fisher RI, Weisenburger DD, Chan WC, Staudt LM. Molecular subtypes of diffuse large B-cell lymphoma arise by distinct genetic pathways. Proc Natl Acad Sci U S A. 2008;105:13520–5.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. O’Hagan RC, Brennan CW, Strahs A, Zhang X, Kannan K, Donovan M, Cauwels C, Sharpless NE, Wong WH, Chin L. Array comparative genome hybridization for tumor classification and gene discovery in mouse models of malignant melanoma. Cancer Res. 2003;63:5352–6.

    PubMed  Google Scholar 

  12. Chinnaiyan AM, Palanisamy N. Chromosomal aberrations in solid tumors. Prog Mol Biol Transl Sci. 2010;95:55–94.

    Article  CAS  PubMed  Google Scholar 

  13. Heselmeyer-Haddad K, Sommerfeld K, White NM, Chaudhri N, Morrison LE, Palanisamy N, Wang ZY, Auer G, Steinberg W, Ried T. Genomic amplification of the human telomerase gene (TERC) in pap smears predicts the development of cervical cancer. Am J Pathol. 2005;166:1229–38.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Przybytkowski E, Ferrario C, Basik M. The use of ultra-dense array CGH analysis for the discovery of micro-copy number alterations and gene fusions in the cancer genome. BMC Med Genet. 2011;4:16.

    CAS  Google Scholar 

  15. Tao J, Deng NT, Ramnarayanan K, Huang B, Oh HK, Leong SH, Lim SS, Tan IB, Ooi CH, Wu J, Lee M, Zhang S, Rha SY, Chung HC, Smoot DT, Ashktorab H, Kon OL, Cacheux V, Yap C, Palanisamy N, Tan P. CD44-SLC1A2 gene fusions in gastric cancer. Sci Transl Med. 2011;3:77ra30.

    Article  CAS  PubMed  Google Scholar 

  16. Williamson SR, Eble JN, Palanisamy N. Sclerosing TFEB-rearrangement renal cell carcinoma: a recurring histologic pattern. Hum Pathol. 2017;62:175–9.

    Article  CAS  PubMed  Google Scholar 

  17. Coe BP, Ylstra B, Carvalho B, Meijer GA, Macaulay C, Lam WL. Resolving the resolution of array CGH. Genomics. 2007;89:647–53.

    Article  CAS  PubMed  Google Scholar 

  18. Garnis C, Coe BP, Lam SL, MacAulay C, Lam WL. High-resolution array CGH increases heterogeneity tolerance in the analysis of clinical samples. Genomics. 2005;85:790–3.

    Article  CAS  PubMed  Google Scholar 

  19. Tucker T, Montpetit A, Chai D, Chan S, Chenier S, Coe BP, Delaney A, Eydoux P, Lam WL, Langlois S, Lemyre E, Marra M, Qian H, Rouleau GA, Vincent D, Michaud JL, Friedman JM. Comparison of genome-wide array genomic hybridization platforms for the detection of copy number variants in idiopathic mental retardation. BMC Med Genet. 2011;4:25.

    Google Scholar 

  20. Coe BP, Lockwood WW, Chari R, Lam WL. Comparative genomic hybridization on BAC arrays. Methods Mol Biol. 2009;556:7–19.

    Article  CAS  PubMed  Google Scholar 

  21. Tanner AK, Chin EL, Duffner PK, Hegde M. Array CGH improves detection of mutations in the GALC gene associated with Krabbe disease. Orphanet J Rare Dis. 2012;7:38.

    Article  PubMed  PubMed Central  Google Scholar 

  22. Garber ME, Troyanskaya OG, Schluens K, Petersen S, Thaesler Z, Pacyna-Gengelbach M, van de Rijn M, Rosen GD, Perou CM, Whyte RI, Altman RB, Brown PO, Botstein D, Petersen I. Diversity of gene expression in adenocarcinoma of the lung. Proc Natl Acad Sci U S A. 2001;98:13784–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Perou CM, Sorlie T, Eisen MB, van de Rijn M, Jeffrey SS, Rees CA, Pollack JR, Ross DT, Johnsen H, Akslen LA, Fluge O, Pergamenschikov A, Williams C, Zhu SX, Lonning PE, Borresen-Dale AL, Brown PO, Botstein D. Molecular portraits of human breast tumours. Nature. 2000;406:747–52.

    Article  CAS  PubMed  Google Scholar 

  24. Pollack JR, Sorlie T, Perou CM, Rees CA, Jeffrey SS, Lonning PE, Tibshirani R, Botstein D, Borresen-Dale AL, Brown PO. Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors. Proc Natl Acad Sci U S A. 2002;99:12963–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Sorlie T, Perou CM, Tibshirani R, Aas T, Geisler S, Johnsen H, Hastie T, Eisen MB, van de Rijn M, Jeffrey SS, Thorsen T, Quist H, Matese JC, Brown PO, Botstein D, Lonning PE, Borresen-Dale AL. Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proc Natl Acad Sci U S A. 2001;98:10869–74.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Engle LJ, Simpson CL, Landers JE. Using high-throughput SNP technologies to study cancer. Oncogene. 2006;25:1594–601.

    Article  CAS  PubMed  Google Scholar 

  27. Zapata W, Aguilar-Jimenez W, Pineda-Trujillo N, Rojas W, Estrada H, Rugeles MT. Influence of CCR5 and CCR2 genetic variants in the resistance/susceptibility to HIV in serodiscordant couples from Colombia. AIDS Res Hum Retrovir. 2013;29:1594–603.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Berndt SI, Wang Z, Yeager M, Alavanja MC, Albanes D, Amundadottir L, Andriole G, Beane Freeman L, Campa D, Cancel-Tassin G, Canzian F, Cornu JN, Cussenot O, Diver WR, Gapstur SM, Gronberg H, Haiman CA, Henderson B, Hutchinson A, Hunter DJ, Key TJ, Kolb S, Koutros S, Kraft P, Le Marchand L, Lindstrom S, Machiela MJ, Ostrander EA, Riboli E, Schumacher F, Siddiq A, Stanford JL, Stevens VL, Travis RC, Tsilidis KK, Virtamo J, Weinstein S, Wilkund F, Xu J, Lilly Zheng S, Yu K, Wheeler W, Zhang H, African Ancestry GC, Prostate Cancer J, Sampson A, Black K, Jacobs RN, Hoover MT, Chanock SJ. Two susceptibility loci identified for prostate cancer aggressiveness. Nat Commun. 2015;6:6889.

    Article  CAS  PubMed  Google Scholar 

  29. Bao BY, Pao JB, Huang CN, Pu YS, Chang TY, Lan YH, Lu TL, Lee HZ, Juang SH, Chen LM, Hsieh CJ, Huang SP. Polymorphisms inside microRNAs and microRNA target sites predict clinical outcomes in prostate cancer patients receiving androgen-deprivation therapy. Clin Cancer Res. 2011;17:928–36.

    Article  CAS  PubMed  Google Scholar 

  30. Preskill C, Weidhaas JB. SNPs in microRNA binding sites as prognostic and predictive cancer biomarkers. Crit Rev Oncog. 2013;18:327–40.

    Article  PubMed  PubMed Central  Google Scholar 

  31. Monzon FA, Hagenkord JM, Lyons-Weiler MA, Balani JP, Parwani AV, Sciulli CM, Li J, Chandran UR, Bastacky SI, Dhir R. Whole genome SNP arrays as a potential diagnostic tool for the detection of characteristic chromosomal aberrations in renal epithelial tumors. Mod Pathol. 2008;21:599–608.

    Article  CAS  PubMed  Google Scholar 

  32. Hagenkord JM, Parwani AV, Lyons-Weiler MA, Alvarez K, Amato R, Gatalica Z, Gonzalez-Berjon JM, Peterson L, Dhir R, Monzon FA. Virtual karyotyping with SNP microarrays reduces uncertainty in the diagnosis of renal epithelial tumors. Diagn Pathol. 2008;3:44.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. MacKinnon RN, Selan C, Zordan A, et al. CGH and SNP array using DNA extracted from fixed cytogenetic preparations and long-term refrigerated bone marrow specimens. Mol Cytogenet. 2012;5:10.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Urology, Henry Ford Health System, Detroit, MI, USA

    Nallasivam Palanisamy

Authors
  1. Nallasivam Palanisamy
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Nallasivam Palanisamy .

Editor information

Editors and Affiliations

  1. Department of Pathology and Lab Medicine, Indiana University School of Medicine, Indianapolis, IN, USA

    Sunil Badve

  2. Targos Inc., Issaquah, WA, USA

    George Louis Kumar

Rights and permissions

Reprints and permissions

Copyright information

© 2019 Springer Nature Switzerland AG

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Palanisamy, N. (2019). Introduction to Microarray Technology. In: Badve, S., Kumar, G. (eds) Predictive Biomarkers in Oncology. Springer, Cham. https://doi.org/10.1007/978-3-319-95228-4_6

Download citation

  • DOI: https://doi.org/10.1007/978-3-319-95228-4_6

  • Published:

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-95227-7

  • Online ISBN: 978-3-319-95228-4

  • eBook Packages: MedicineMedicine (R0)

Publish with us

Policies and ethics

Search

Navigation