1887

Chapter 9 : Multiplex Technologies

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Ebook: Choose a downloadable PDF or ePub file. Chapter is a downloadable PDF file. File must be downloaded within 48 hours of purchase

Buy this Chapter
Digital (?) $30.00

Preview this chapter:
Zoom in
Zoomout

Multiplex Technologies, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555819071/9781555819088.ch9-1.gif /docserver/preview/fulltext/10.1128/9781555819071/9781555819088.ch9-2.gif

Abstract:

It is well appreciated that the adoption of molecular methods by clinical laboratories has revolutionized the identification of microbial isolates, detection of pathogens directly from clinical specimens, and methods for monitoring response to antiviral therapy. As discussed in chapter 1 of this volume, hybridization and amplification technologies continue to mature and enable new diagnostic applications, particularly as the ability to multiplex has become a reality. Multiplexing allows for the simultaneous detection of more than one target, whether it is a pathogen and internal control, multiple pathogens, pathogen and resistance determinants, or pathogen and host sequences. Multiplex detection performed on a single specimen allows laboratories to expand the breadth of their testing menu while improving efficiency and decreasing reagent and personnel costs. This chapter will review the multiplex technologies with potential diagnostic applications, including multiplexed hybridization and amplification and microarrays. Although the ultimate multiplexing technology could be considered next-generation sequencing, this technology and its applications are discussed in chapters 5 and 6 and section II.

Citation: Alby K, Miller M. 2016. Multiplex Technologies, p 102-114. In Persing D, Tenover F, Hayden R, Ieven M, Miller M, Nolte F, Tang Y, van Belkum A (ed), Molecular Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555819071.ch9
Highlighted Text: Show | Hide
Loading full text...

Full text loading...

Figures

Image of FIGURE 1
FIGURE 1

Signal amplification and hybridization. This diagram depicts the detection of specific DNA using gold nanoparticles followed by signal amplification. The targeted DNA is hybridized to a specific oligonucleotide on an array. A mediator oligonucleotide is bound to a gold nanoparticle and then hybridizes at the specific array site. Following silver-based signal amplification, light scattering is detected at each of the array locations. Image provided by courtesy of Nanosphere.

Citation: Alby K, Miller M. 2016. Multiplex Technologies, p 102-114. In Persing D, Tenover F, Hayden R, Ieven M, Miller M, Nolte F, Tang Y, van Belkum A (ed), Molecular Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555819071.ch9
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 2
FIGURE 2

PCR electrospray ionization with mass spectrometry. Genetic regions of interest are first identified (step 1). Broad primers near the region of interest are utilized to amplify that region (step 2). The products of these reactions are measured using mass spectrometry (step 3). The sample is introduced via an ionization needle into a capillary, where the solvent is stripped away. Ions are then introduced into a chamber, where they are detected via an electron multiplier. The size of the ions is directly related to the base composition of the PCR product (step 4), which is utilized to determine the identity of the target.

Citation: Alby K, Miller M. 2016. Multiplex Technologies, p 102-114. In Persing D, Tenover F, Hayden R, Ieven M, Miller M, Nolte F, Tang Y, van Belkum A (ed), Molecular Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555819071.ch9
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 3
FIGURE 3

General workflow of printed microarrays. Probe preparation begins with the production of either denatured cDNA, genomic PCR products, or oligonucleotides that are subsequently spotted in an array format on a glass slide. In this example, two samples (one control and one experimental) are being compared by extracting mRNA and converting the RNA sets into differentially labeled cDNA sets for hybridization. The inclusion of multiple fluorescent labels allows for color differentiation based upon the quantity of target cDNA from each set that hybridizes to the microarray probes. The fluorescence signal is then scanned and analyzed. Reprinted from reference with permission from Elsevier.

Citation: Alby K, Miller M. 2016. Multiplex Technologies, p 102-114. In Persing D, Tenover F, Hayden R, Ieven M, Miller M, Nolte F, Tang Y, van Belkum A (ed), Molecular Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555819071.ch9
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 4
FIGURE 4

GeneChip oligonucleotide microarray. Photolithography: UV light is passed through a lithographic mask that acts as a filter to either transmit or block the light from the chemically protected quartz wafer. Multiple lithographic masks are applied sequentially to determine the sequence synthesis on the microarray surface. Chemical synthesis cycle: As the mask-filtered UV light removes the protecting groups (squares), a single nucleotide washed over the microarray surface is able to couple to the deprotected oligonucleotide chains. Sequential rounds of nucleotide addition combined with changes in the masks form a quartz wafer with 25-mers of predetermined sequence. Adapted and reprinted from reference with permission from Elsevier and Affymetrix.

Citation: Alby K, Miller M. 2016. Multiplex Technologies, p 102-114. In Persing D, Tenover F, Hayden R, Ieven M, Miller M, Nolte F, Tang Y, van Belkum A (ed), Molecular Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555819071.ch9
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 5
FIGURE 5

Suspension bead microarray. (A) Microspheres 5.6 μm in diameter are filled with varying concentrations of an infrared dye and a red dye to create 100 spectrally distinct beads. (B) Microspheres can then be used in a variety of assays depending on the ligand bound to the bead surface. (Upper inset) Suspension bead direct hybridization. The target is amplified using a biotinylated primer and subsequently denatured and hybridized to microspheres tagged with target-specific sequence probes. A positive hybridization reaction at the microsphere surface is detected using streptavidin--phycoerythrin. (Lower inset) Solution-based chemistries for microsphere capture. ASPE (allele-specific primer extension): 1, denaturation of target DNA in the presence of specific capture sequence-tagged primers; 2, annealing of target DNA and primers; 3, primer extension and incorporation of biotinylated dNTP; 4, capture sequence-tagged ASPE products. OLA (oligonucleotide ligation assay): 1, denaturation of target DNA in the presence of capture sequence–tagged allele-specific probes; 2, annealing of target DNA and probes in a reaction containing a DNA ligase and biotinylated reporter probe; 3, oligonucleotide ligation; 4, capture sequence–tagged OLA products. SBCE (single base chain extension): 1, denaturation of target DNA in the presence of a capture sequence–tagged primer (in separate reactions for each allele); 2, annealing of target DNA and primers; 3, single base primer extension with incorporation of biotinylated ddNTP; 4, capture sequence-tagged SBCE products that can be multiplexed for detection. (C) After hybridization with the target of interest, the microsphere suspension is analyzed using a flow cytometer. A red laser (635 nm) excites the impregnated dyes of the microspheres to determine the spectral identity of the bead and therefore the probe being analyzed. A green (532 nm) laser excites the reporter fluorochrome to quantify the probe-target reaction on the microsphere surface. Insets reprinted from reference with permission from Elsevier. Other images courtesy of Luminex.

Citation: Alby K, Miller M. 2016. Multiplex Technologies, p 102-114. In Persing D, Tenover F, Hayden R, Ieven M, Miller M, Nolte F, Tang Y, van Belkum A (ed), Molecular Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555819071.ch9
Permissions and Reprints Request Permissions
Download as Powerpoint

References

/content/book/10.1128/9781555819071.ch09
1. Li J, Hanna BA,. 2004. DNA probes for culture confirmation and direct detection of bacterial infections: a review of technology, p 1926. In Persing DH, Tenover FC, Versalovic J, Tang Y-W, Unger ER, Relman DA, White TJ (ed), Molecular Microbiology: Diagnostic Principles and Practice. ASM Press, Washington, DC.
2. Moter A, Göbel UB. 2000. Fluorescence in situ hybridization (FISH) for direct visualization of microorganisms. J Microbiol Methods 41:85112[CrossRef].[PubMed]
3. Perry-O'Keefe H, Rigby S, Oliveira K, Sørensen D, Stender H, Coull J, Hyldig-Nielsen JJ. 2001. Identification of indicator microorganisms using a standardized PNA FISH method. J Microbiol Methods 47:281292[CrossRef].[PubMed]
4. Calderaro A, Martinelli M, Motta F, Larini S, Arcangeletti MC, Medici MC, Chezzi C, De Conto F. 2014. Comparison of peptide nucleic acid fluorescence in situ hybridization assays with culture-based matrix-assisted laser desorption/ionization-time of flight mass spectrometry for the identification of bacteria and yeasts from blood cultures and cerebrospinal fluid cultures. Clin Microbiol Infect 20:O468O475[CrossRef].[PubMed]
5. Raich T, Powell S. 2015. Identification of bacterial and fungal pathogens from positive blood culture bottles: a microarray-based approach. Methods Mol Biol 1237:7390[CrossRef].[PubMed]
6. Ririe KM, Rasmussen RP, Wittwer CT. 1997. Product differentiation by analysis of DNA melting curves during the polymerase chain reaction. Anal Biochem 245:154160[CrossRef].[PubMed]
7. Ho CS, Lam CW, Chan MH, Cheung RC, Law LK, Lit LC, Ng KF, Suen MW, Tai HL. 2003. Electrospray ionisation mass spectrometry: principles and clinical applications. Clin Biochem Rev 24:312.[PubMed]
8. Wolk DM, Kaleta EJ, Wysocki VH. 2012. PCR-electrospray ionization mass spectrometry: the potential to change infectious disease diagnostics in clinical and public health laboratories. J Mol Diagn 14:295304[CrossRef].[PubMed]
9. Syrmis MW, Moser RJ, Whiley DM, Vaska V, Coombs GW, Nissen MD, Sloots TP, Nimmo GR. 2011. Comparison of a multiplexed MassARRAY system with real-time allele-specific PCR technology for genotyping of methicillin-resistant Staphylococcus aureus. Clin Microbiol Infect 17:18041810[CrossRef].[PubMed]
10. Dunbar SA, Zhang H, Tang YW. 2013. Advanced techniques for detection and identification of microbial agents of gastroenteritis. Clin Lab Med 33:527552[CrossRef].[PubMed]
11. Gray J, Coupland LJ. 2014. The increasing application of multiplex nucleic acid detection tests to the diagnosis of syndromic infections. Epidemiol Infect 142:111.[PubMed]
12. Reddington K, Tuite N, Barry T, O'Grady J, Zumla A. 2013. Advances in multiparametric molecular diagnostics technologies for respiratory tract infections. Curr Opin Pulm Med 19:298304[CrossRef].[PubMed]
13. Marras SA. 2006. Selection of fluorophore and quencher pairs for fluorescent nucleic acid hybridization probes. Methods Mol Biol 335:316.[PubMed]
14. Dark P, Blackwood B, Gates S, McAuley D, Perkins GD, McMullan R, Wilson C, Graham D, Timms K, Warhurst G. 2015. Accuracy of LightCycler(®) SeptiFast for the detection and identification of pathogens in the blood of patients with suspected sepsis: a systematic review and meta-analysis. Intensive Care Med 41:2133[CrossRef].[PubMed]
15. Garcia EP, Dowding LA, Stanton LW, Slepnev VI. 2005. Scalable transcriptional analysis routine—multiplexed quantitative real-time polymerase chain reaction platform for gene expression analysis and molecular diagnostics. J Mol Diagn 7:444454[CrossRef].[PubMed]
16. Hlousek L, Voronov S, Diankov V, Leblang AB, Wells PJ, Ford DM, Nolling J, Hart KW, Espinoza PA, Bristol MR, Tsongalis GJ, Yen-Lieberman B, Slepnev VI, Kong LI, Lee MC. 2012. Automated high multiplex qPCR platform for simultaneous detection and quantification of multiple nucleic acid targets. Biotechniques 52:316324.[PubMed]
17. Lopez MF, Pluskal MG. 2003. Protein micro- and macroarrays: digitizing the proteome. J Chromatogr B Analyt Technol Biomed Life Sci 787:1927[CrossRef].[PubMed]
18. MacBeath G. 2002. Protein microarrays and proteomics. Nat Genet 32(Suppl):526532[CrossRef].[PubMed]
19. Cheung VG, Morley M, Aguilar F, Massimi A, Kucherlapati R, Childs G. 1999. Making and reading microarrays. Nat Genet 21(Suppl):1519[CrossRef].[PubMed]
20. Hayward RE, Derisi JL, Alfadhli S, Kaslow DC, Brown PO, Rathod PK. 2000. Shotgun DNA microarrays and stage-specific gene expression in Plasmodium falciparum malaria. Mol Microbiol 35:614[CrossRef].[PubMed]
21. Schena M, Shalon D, Davis RW, Brown PO. 1995. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270:467470[CrossRef].[PubMed]
22. Tomiuk S, Hofmann K. 2001. Microarray probe selection strategies. Brief Bioinform 2:329340[CrossRef].[PubMed]
23. Hager J. 2006. Making and using spotted DNA microarrays in an academic core laboratory. Methods Enzymol 410:135168[CrossRef].[PubMed]
24. Kreil DP, Russell RR, Russell S. 2006. Microarray oligonucleotide probes. Methods Enzymol 410:7398[CrossRef].[PubMed]
25. Burr A, Bogart K, Conaty J, Andrews J. 2006. Automated liquid handling and high-throughput preparation of polymerase chain reaction-amplified DNA for microarray fabrication. Methods Enzymol 410:99120[CrossRef].[PubMed]
26. Ehrenreich A. 2006. DNA microarray technology for the microbiologist: an overview. Appl Microbiol Biotechnol 73:255273[CrossRef].[PubMed]
27. Chou CC, Chen CH, Lee TT, Peck K. 2004. Optimization of probe length and the number of probes per gene for optimal microarray analysis of gene expression. Nucleic Acids Res 32:e99[CrossRef].[PubMed]
28. Dalma-Weiszhausz DD, Warrington J, Tanimoto EY, Miyada CG. 2006. The affymetrix GeneChip platform: an overview. Methods Enzymol 410:328[CrossRef].[PubMed]
29. Fodor SP, Read JL, Pirrung MC, Stryer L, Lu AT, Solas D. 1991. Light-directed, spatially addressable parallel chemical synthesis. Science 251:767773[CrossRef].[PubMed]
30. Ramdas L, Cogdell DE, Jia JY, Taylor EE, Dunmire VR, Hu L, Hamilton SR, Zhang W. 2004. Improving signal intensities for genes with low-expression on oligonucleotide microarrays. BMC Genomics 5:35[CrossRef].[PubMed]
31. Hughes TR, Mao M, Jones AR, Burchard J, Marton MJ, Shannon KW, Lefkowitz SM, Ziman M, Schelter JM, Meyer MR, Kobayashi S, Davis C, Dai H, He YD, Stephaniants SB, Cavet G, Walker WL, West A, Coffey E, Shoemaker DD, Stoughton R, Blanchard AP, Friend SH, Linsley PS. 2001. Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer. Nat Biotechnol 19:342347[CrossRef].[PubMed]
32. Wolber PK, Collins PJ, Lucas AB, De Witte A, Shannon KW. 2006. The Agilent in situ-synthesized microarray platform. Methods Enzymol 410:2857[CrossRef].[PubMed]
33. Horan PK, Wheeless LL Jr. 1977. Quantitative single cell analysis and sorting. Science 198:149157[CrossRef].[PubMed]
34. McHugh RS, Ratnoff WD, Gilmartin R, Sell KW, Selvaraj P. 1998. Detection of a soluble form of B7-1 (CD80) in synovial fluid from patients with arthritis using monoclonal antibodies against distinct epitopes of human B7-1. Clin Immunol Immunopathol 87:5059[CrossRef].[PubMed]
35. Scillian JJ, McHugh TM, Busch MP, Tam M, Fulwyler MJ, Chien DY, Vyas GN. 1989. Early detection of antibodies against rDNA-produced HIV proteins with a flow cytometric assay. Blood 73:20412048.[PubMed]
36. Dunbar SA. 2006. Applications of Luminex xMAP technology for rapid, high-throughput multiplexed nucleic acid detection. Clin Chim Acta 363:7182[CrossRef].[PubMed]
37. Armstrong B, Stewart M, Mazumder A. 2000. Suspension arrays for high throughput, multiplexed single nucleotide polymorphism genotyping. Cytometry 40:102108[CrossRef].[PubMed]
38. Spiro A, Lowe M, Brown D. 2000. A bead-based method for multiplexed identification and quantitation of DNA sequences using flow cytometry. Appl Environ Microbiol 66:42584265[CrossRef].[PubMed]
39. Chen J, Iannone MA, Li MS, Taylor JD, Rivers P, Nelsen AJ, Slentz-Kesler KA, Roses A, Weiner MP. 2000. A microsphere-based assay for multiplexed single nucleotide polymorphism analysis using single base chain extension. Genome Res 10:549557[CrossRef].[PubMed]
40. Iannone MA, Taylor JD, Chen J, Li MS, Rivers P, Slentz-Kesler KA, Weiner MP. 2000. Multiplexed single nucleotide polymorphism genotyping by oligonucleotide ligation and flow cytometry. Cytometry 39:131140[CrossRef].[PubMed]
41. Taylor JD, Briley D, Nguyen Q, Long K, Iannone MA, Li MS, Ye F, Afshari A, Lai E, Wagner M, Chen J, Weiner MP. 2001. Flow cytometric platform for high-throughput single nucleotide polymorphism analysis. Biotechniques 30:661666, 668–669.[PubMed]
42. Ye F, Li MS, Taylor JD, Nguyen Q, Colton HM, Casey WM, Wagner M, Weiner MP, Chen J. 2001. Fluorescent microsphere-based readout technology for multiplexed human single nucleotide polymorphism analysis and bacterial identification. Hum Mutat 17:305316[CrossRef].[PubMed]
43. Fulton RJ, McDade RL, Smith PL, Kienker LJ, Kettman JR Jr. 1997. Advanced multiplexed analysis with the FlowMetrix system. Clin Chem 43:17491756.[PubMed]
44. Mikhailovich V, Gryadunov D, Kolchinsky A, Makarov AA, Zasedatelev A. 2008. DNA microarrays in the clinic: infectious diseases. BioEssays 30:673682[CrossRef].[PubMed]
45. McLoughlin KS. 2011. Microarrays for pathogen detection and analysis. Brief Funct Genomics 10:342353[CrossRef].[PubMed]
46. Leveque N, Van Haecke A, Renois F, Boutolleau D, Talmud D, Andreoletti L. 2011. Rapid virological diagnosis of central nervous system infections by use of a multiplex reverse transcription-PCR DNA microarray. J Clin Microbiol 49:38743879[CrossRef].[PubMed]
47. Huguenin A, Moutte L, Renois F, Leveque N, Talmud D, Abely M, Nguyen Y, Carrat F, Andreoletti L. 2012. Broad respiratory virus detection in infants hospitalized for bronchiolitis by use of a multiplex RT-PCR DNA microarray system. J Med Virol 84:979985[CrossRef].[PubMed]
48. Renois F, Talmud D, Huguenin A, Moutte L, Strady C, Cousson J, Lévêque N, Andréoletti L. 2010. Rapid detection of respiratory tract viral infections and coinfections in patients with influenza-like illnesses by use of reverse transcription-PCR DNA microarray systems. J Clin Microbiol 48:38363842[CrossRef].[PubMed]
49. Lévêque N, Renois F, Andréoletti L. 2013. The microarray technology: facts and controversies. Clin Microbiol Infect 19:1014[CrossRef].[PubMed]
50. Chiu CY, Alizadeh AA, Rouskin S, Merker JD, Yeh E, Yagi S, Schnurr D, Patterson BK, Ganem D, DeRisi JL. 2007. Diagnosis of a critical respiratory illness caused by human metapneumovirus by use of a pan-virus microarray. J Clin Microbiol 45:23402343[CrossRef].[PubMed]
51. Chiu CY, Rouskin S, Koshy A, Urisman A, Fischer K, Yagi S, Schnurr D, Eckburg PB, Tompkins LS, Blackburn BG, Merker JD, Patterson BK, Ganem D, DeRisi JL. 2006. Microarray detection of human parainfluenzavirus 4 infection associated with respiratory failure in an immunocompetent adult. Clin Infect Dis 43:e71e76[CrossRef].[PubMed]
52. Rota PA, Oberste MS, Monroe SS, Nix WA, Campagnoli R, Icenogle JP, Peñaranda S, Bankamp B, Maher K, Chen MH, Tong S, Tamin A, Lowe L, Frace M, DeRisi JL, Chen Q, Wang D, Erdman DD, Peret TC, Burns C, Ksiazek TG, Rollin PE, Sanchez A, Liffick S, Holloway B, Limor J, McCaustland K, Olsen-Rasmussen M, Fouchier R, Günther S, Osterhaus AD, Drosten C, Pallansch MA, Anderson LJ, Bellini WJ. 2003. Characterization of a novel coronavirus associated with severe acute respiratory syndrome. Science 300:13941399[CrossRef].[PubMed]
53. Palacios G, Quan PL, Jabado OJ, Conlan S, Hirschberg DL, Liu Y, Zhai J, Renwick N, Hui J, Hegyi H, Grolla A, Strong JE, Towner JS, Geisbert TW, Jahrling PB, Büchen-Osmond C, Ellerbrok H, Sanchez-Seco MP, Lussier Y, Formenty P, Nichol MS, Feldmann H, Briese T, Lipkin WI. 2007. Panmicrobial oligonucleotide array for diagnosis of infectious diseases. Emerg Infect Dis 13:7381[CrossRef].[PubMed]
54. Quan PL, Palacios G, Jabado OJ, Conlan S, Hirschberg DL, Pozo F, Jack PJ, Cisterna D, Renwick N, Hui J, Drysdale A, Amos-Ritchie R, Baumeister E, Savy V, Lager KM, Richt JA, Boyle DB, García-Sastre A, Casas I, Perez-Breña P, Briese T, Lipkin WI. 2007. Detection of respiratory viruses and subtype identification of influenza A viruses by GreeneChipResp oligonucleotide microarray. J Clin Microbiol 45:23592364[CrossRef].[PubMed]
55. Bryant PA, Venter D, Robins-Browne R, Curtis N. 2004. Chips with everything: DNA microarrays in infectious diseases. Lancet Infect Dis 4:100111[CrossRef].[PubMed]

Tables

Generic image for table
TABLE 1

Common fluorophores used in multiplex detection

Citation: Alby K, Miller M. 2016. Multiplex Technologies, p 102-114. In Persing D, Tenover F, Hayden R, Ieven M, Miller M, Nolte F, Tang Y, van Belkum A (ed), Molecular Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555819071.ch9
Generic image for table
TABLE 2

Common quenchers used in multiplex detection

Citation: Alby K, Miller M. 2016. Multiplex Technologies, p 102-114. In Persing D, Tenover F, Hayden R, Ieven M, Miller M, Nolte F, Tang Y, van Belkum A (ed), Molecular Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555819071.ch9

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error