This overview describes microarray-based tests that combine solution-phase amplification chemistry and microarray hybridization within a single microfluidic chamber. The integrated biochemical approach improves microarray workflow for diagnostic applications by reducing the number of steps and minimizing the potential for sample or amplicon cross-contamination. Examples described herein illustrate a basic, integrated approach for DNA and RNA genomes, and a simple consumable architecture for incorporating wash steps while retaining an entirely closed system. It is anticipated that integrated microarray biochemistry will provide an opportunity to significantly reduce the complexity and cost of microarray consumables, equipment, and workflow, which in turn will enable a broader spectrum of users to exploit the intrinsic multiplexing power of microarrays for infectious disease diagnostics.
References
[1]
Lyon, E.; Wittwer, C.T. LightCycler technology in molecular diagnostics. J. Mol. Diagn. 2009, 11, 93–101, doi:10.2353/jmoldx.2009.080094.
[2]
Liu, Y.T. A technological update of molecular diagnostics for infectious diseases. Infect. Disord. Drug Targets 2008, 8, 183–188.
[3]
Dong, J.; Olano, J.P.; McBride, J.W.; Walker, D.H. Emerging pathogens: Challenges and successes of molecular diagnostics. J. Mol. Diagn. 2008, 10, 185–197, doi:10.2353/jmoldx.2008.070063.
[4]
Yang, S.; Rothman, R.E. PCR-based diagnostics for infectious diseases: Uses, limitations, and future applications in acute-care setting. Lancet Infect Dis. 2004, 4, 337–348, doi:10.1016/S1473-3099(04)01044-8.
[5]
Dumler, J.S.; Valsamakis, A. Molecular diagnostics for existing and emerging infections. Complementary tools for a new era of clinical microbiology. Am. J. Clin. Pathol. 1999, 112, S33–S39.
[6]
Millar, B.C.; Xu, J.; Moore, J.E. Molecular diagnostics of medically important bacterial infections. Curr. Issues Mol. Biol. 2007, 9, 21–39.
[7]
Robertson, B.H.; Nicholson, J.K. New microbiology tools for public health and their implications. Annu. Rev. Public Health 2005, 26, 281–302, doi:10.1146/annurev.publhealth.26.021304.144522.
[8]
O’Connor, L.; Glynn, B. Recent advances in the development of nucleic acid diagnostics. Expert Rev. Med. Devices 2010, 7, 529–539, doi:10.1586/erd.10.22.
[9]
Kaltenboeck, B.; Wang, C. Advances in real-time PCR: Application to clinical laboratory diagnostics. Adv. Clin. Chem. 2005, 40, 219–259, doi:10.1016/S0065-2423(05)40006-2.
[10]
Mackay, I.M. Real-time PCR in the microbiology laboratory. Clin. Microbiol. Infect. 2005, 10, 190–212, doi:10.1111/j.1198-743X.2004.00722.x.
[11]
Procop, G.W. Molecular diagnostics for the detection and characterization of microbial pathogens. Clin. Infect. Dis. 2007, 45, S99–S111, doi:10.1086/519259.
[12]
Easley, C.J.; Karlinsey, J.M.; Bienvenue, J.M.; Legendre, L.A.; Roper, M.G.; Feldman, S.H.; Hughes, M.A.; Hewlett, E.L.; Merkel, T.J.; Ferrance, J.P.; Landers, J.P. A fully integrated microfluidic genetic analysis system with sample-in-answer-out capability. Proc. Natl. Acad. Sci. USA 2006, 103, 19272–19277.
[13]
Mahalanabis, M.; Do, J.; Al Muayad, H.; Zhang, J.Y.; Klapperich, C.M. An integrated disposable device for DNA extraction and helicase dependent amplification. Biomed. Microdevices 2010, 12, 353–359, doi:10.1007/s10544-009-9391-8.
[14]
Chen, D.; Mauk, M.; Qiu, X.; Liu, C.; Kim, J.; Ramprasad, S.; Ongagna, S.; Abrams, W.R.; Malamud, D.; Corstjens, P.L.; Bau, H.H. An integrated, self-contained microfluidic cassette for isolation, amplification, and detection of nucleic acid. Biomed. Microdevices 2010, 12, 705–719, doi:10.1007/s10544-010-9423-4.
[15]
Njoroge, S.K.; Chen, H.W.; Witek, M.A.; Soper, S.A. Integrated microfluidic systems for DNA analysis. Top. Curr. Chem. 2011, 304, 203–260, doi:10.1007/128_2011_153.
[16]
Bissonnette, L.; Bergeron, M.G. Diagnosing infections—Current and anticipated technologies for point-of-care diagnostics and home-based testing. Clin. Microbiol. Infect. 2010, 16, 1044–1053, doi:10.1111/j.1469-0691.2010.03282.x.
[17]
Park, S.; Zhang, Y.; Lin, S.; Wang, T.H.; Yang, S. Advances in microfluidic PCR for point-of-care infectious disease diagnostics. Biotechnol. Adv. 2011, 29, 830–839, doi:10.1016/j.biotechadv.2011.06.017.
Peeling, R.W.; Mabey, D. Point-of-care tests for diagnosing infections in the developing world. Clin. Microbiol. Infect. 2010, 16, 1062–1069, doi:10.1111/j.1469-0691.2010.03279.x.
[20]
Taylor, T.B.; Winn-Deen, E.S.; Picozza, E.; Woudenberg, T.M.; Albin, M. Optimization of the performance of the polymerase chain reaction in silicon-based microstructures. Nucl. Acids Res. 1997, 25, 3164–3168, doi:10.1093/nar/25.15.3164.
[21]
Irwin, P.L.; Nguyen, L.H.; Chen, C.Y. The relationship between purely stochastic sampling error and the number of technical replicates used to estimate concentration at an extreme dilution. Anal. Bioanal. Chem. 2010, 398, 895–903, doi:10.1007/s00216-010-3967-2.
[22]
Walsh, P.S.; Erlich, H.A.; Higuchi, R. Preferential PCR amplification of alleles: Mechanisms and solutions. PCR Methods Appl. 1992, 1, 241–250, doi:10.1101/gr.1.4.241.
[23]
Sykes, P.J.; Neoh, S.H.; Brisco, M.J.; Hughes, E.; Condon, J.; Morley, A.A. Quantitation of targets for PCR by use of limiting dilution. Biotechniques 1992, 13, 444–449.
[24]
Vogelstein, B.; Kinzler, K.W. Digital PCR. Proc. Natl. Acad. Sci. USA 1999, 96, 9236–9241, doi:10.1073/pnas.96.16.9236.
[25]
Zhong, Q.; Bhattacharya, S.; Kotsopoulos, S.; Olson, J.; Taly, V.; Griffiths, A.D.; Link, D.R.; Larson, J.W. Multiplex digital PCR: Breaking the one target per color barrier of quantitative PCR. Lab Chip 2011, 11, 2167–2174, doi:10.1039/c1lc20126c.
[26]
Shen, F.; Davydova, E.K.; Du, W.; Kreutz, J.E.; Piepenburg, O.; SIsmagilov, R.F. Digital isothermal quantification of nucleic acids via simultaneous chemical initiation of recombinase polymerase amplification reactions on SlipChip. Anal. Chem. 2011, 83, 3533–3540.
[27]
Weile, J.; Knabbe, C. Current applications and future trends of molecular diagnostics in clinical bacteriology. Anal. Bioanal. Chem. 2009, 394, 731–742, doi:10.1007/s00216-009-2779-8.
[28]
Shen, Y.; Wu, B.L. Microarray-based genomic DNA profiling technologies in clinical molecular diagnostics. Clin. Chem. 2009, 55, 659–669, doi:10.1373/clinchem.2008.112821.
[29]
Miller, M.B.; Tang, Y.-W. Basic concepts of microarrays and potential applications in clinical microbiology. Clin. Microbiol. Rev. 2009, 22, 611–633, doi:10.1128/CMR.00019-09.
[30]
Wu, L.; Williams, P.M.; Kock, W. Clinical applications of microarray-based diagnostic tests. Biotechniques 2005, 39, S577–S582.
[31]
Clerc, O.; Greub, G. Routine use of point-of-care tests: Usefulness and application in clinical microbiology. Clin. Microbiol. Infect. 2010, 16, 1054–1061, doi:10.1111/j.1469-0691.2010.03281.x.
[32]
Metzgar, D.; Myers, C.A.; Russell, K.L.; Faix, D.; Blair, P.J.; Brown, J.; Vo, S.; Swayne, D.E.; Thomas, C.; Stenger, D.A.; et al. Single assay for simultaneous detection and differential identification of human and avian influenza virus types, subtypes, and emergent variants. PLoS One 2010, 5, e8995.
[33]
Chen, E.C.; Miller, S.A.; DeRisi, J.L.; Chiu, C.Y. Using a pan-viral microarray assay (Virochip) to screen clinical samples for viral pathogens. J. Vis. Exp. 2011, 50, doi:10.3791/2536.
[34]
Mahony, J.; Chong, S.; Merante, F.; Yaghoubian, S.; Sinha, T.; Lisle, C.; Janeczko, R. Development of a respiratory virus panel test for detection of twenty human respiratory viruses by use of multiplex PCR and a fluid microbead-based assay. J. Clin. Microbiol. 2007, 45, 2965–2970, doi:10.1128/JCM.02436-06.
[35]
Kessler, N.; Ferraris, O.; Palmer, K.; Marsh, W.; Steel, A. Use of the DNA flow-thru chip, a three-dimensional biochip, for typing and subtyping of influenza viruses. J. Clin. Microbiol. 2004, 42, 2173–2185, doi:10.1128/JCM.42.5.2173-2185.2004.
Lodes, M.J.; Suciu, D.; Wilmoth, J.L.; Ross, M.; Munro, S.; Dix, K.; Bernards, K.; Stover, A.G.; Quintana, M.; Iihoshi, N.; Lyon, W.J.; Danley, D.L.; McShea, A. Identification of upper respiratory tract pathogens using electrochemical detection on an oligonucleotide array. PLoS ONE 2007, 2, e924.
[38]
Caoili, J.C.; Mayorova, A.; Sikes, D.; Hickman, L.; Plikaytis, B.B.; Shinnick, T.M. Evaluation of the TB-biochip oligonucleotide microarray system for rapid detection of rifampin resistance in Mycobacterium tuberculosis. J. Clin. Microbiol. 2006, 44, 2378–2381, doi:10.1128/JCM.00439-06.
[39]
Liu, R.H.; Yang, J.; Lenigk, R.; Bonanno, J.; Grodzinski, P. Self-contained, fully integrated biochip for sample preparation, polymerase chain reaction amplification, and DNA microarray detection. Anal. Chem. 2004, 76, 1824–1831, doi:10.1021/ac0353029.
[40]
Liu, R.H.; Lodes, M.J.; Nguyen, T.; Siuda, T.; Slota, M.; Fuji, H.S.; McShea, A. Validation of a fully integrated microfluidic array device for influenza A subtype identification and sequencing. Anal. Chem. 2006, 78, 4184–4193.
[41]
Summerer, D.; Hevroni, D.; Jain, A.; Oldenburger, O.; Parker, J.; Caruso, A.; St？hler, C.F.; St？hler, P.F.; Beier, M. A flexible and fully integrated system for amplification, detection and genotyping of genomic DNA targets based on microfluidic oligonucleotide arrays. New Biotechnol. 2010, 27, 149–155.
[42]
Trau, D.; Lee, T.M.H.; Lao, A.I.K.; Lenigk, R.; Hsing, I.-M.; Ip, N.Y.; Carles, M.C.; Sucher, N.J. Genotyping on a complementary metal oxide semiconductor silicon polymerase chain reaction chip with integrated DNA microarray. Anal. Chem. 2002, 74, 3168–3173, doi:10.1021/ac020053u.
[43]
Regan, J.; Létant, S.; Adams, K.; Nguyen, N.; Derlet, R.; Cohen, S.; Vitalis, E.; Tammero, L.; Ortiz, J.; McBride, M.; Birch, J. A sample-in-answer-out instrument for the detection of multiple respiratory pathogens in unprepared nasopharyngeal swab samples. Analyst 2010, 135, 2316–2322, doi:10.1039/c0an00223b.
[44]
Teo, J.; Pietro, P.D.; Biagio, F.S.; Capozzoli, M.; Deng, Y.M.; Barr, I.; Caldwell, N.; Ong, K.L.; Sato, M.; Tan, R.; Lin, R. VereFlu？: An integrated multiplex RT-PCR and microarray assay for rapid detection and identification of human influenza A and B viruses using lab-on-chip technology. Arch. Virol. 2011, 156, 1371–1378, doi:10.1007/s00705-011-0999-7.
[45]
Yeung, S.-W.; Lee, T.M.-H.; Cai, H.; Hsing, I.M. A DNA biochip for on-the-spot multiplexed pathogen identification. Nucl. Acids Res. 2006, 34, doi:10.1093/nar/gkl702.
[46]
Dorris, D.R.; Ramakrishnan, R.; Trakas, D.; Dudzik, F.; Belval, R.; Zhao, C.; Nguyen, A.; Domanus, M.; Mazumder, A. A highly reproducible, linear, and automated sample preparation method for DNA microarrays. Genome Res. 2002, 12, 976–984, doi:10.1101/gr.227402.
[47]
Liu, R.H.; Dill, K.; Fuji, H.S.; McShea, A. Integrated microfluidic biochips for DNA microarray analysis. Expert Rev. Mol. Diagn. 2006, 6, 253–261, doi:10.1586/14737159.6.2.253.
[48]
Raymond, F.; Carbonneau, J.; Boucher, N.; Robitaille, L.; Boisvert, S.; Wu, W.-K.; De Serres, G.; Boivin, G.; Corbeil, J. Comparison of automated microarray detection with real-time PCR assays for detection of respiratory viruses in specimens obtained from children. J. Clin. Microbiol. 2009, 47, 743–750, doi:10.1128/JCM.01297-08.
[49]
Kumar, S.; Wang, L.; Fan, J.; Kraft, A.; Bose, M.E.; Tiwari, S.; Van Dyke, M.; Haigis, R.; Luo, T.; Ghosh, M.; et al. Detection of 11 common viral and bacterial pathogens causing community-acquired pneumonia or sepsis in asymptomatic patients by using a multiplex reverse transcription-PCR assay with manual (enzyme hybridization) or automated (electronic microarray) detection. J. Clin. Microbiol. 2008, 46, 3063–3072, doi:10.1128/JCM.00625-08.
[50]
Foglieni, B.; Brisci, A.; San Biagio, F.; Di Pietro, P.; Petralia, S.; Conoci, S.; Ferrari, M.; Cremonesi, L. Integrated PCR amplification and detection processes on a Lab-on-Chip platform: A new advanced solution for molecular diagnostics. Clin. Chem. Lab. Med. 2010, 48, 329–336.
[51]
Stamm, S.; Brosius, J. Sanchored PCR: PCR with cDNA coupled to a solid phase. Nucl. Acid. Res. 1991, 19, 1350, doi:10.1093/nar/19.6.1350.
[52]
Erdogan, F.; Kirchner, R.; Mann, W.; Ropers, H.-H.; Nuber, U.A. Detection of mitochondrial single nucleotide polymorphisms using a primer elongation reaction on oligonucleotide microarrays. Nucl. Acid. Res. 2001, 29, doi:10.1093/nar/29.7.e36.
[53]
Shapero, M.H.; Leuther, K.K.; Nguyen, A.; Scott, M.; Jones, K.W. SNP genotyping by multiplexed solid-phase amplification and fluorescent minisequencing. Genome Res. 2001, 11, 1926–1934.
[54]
Lockley, A.K.; Jones, C.G.; Bruce, J.S.; Franklin, S.J.; Bardsley, R.G. Colorimetric detection of immobilised PCR products generated on a solid support. Nucl. Acid. Res. 1997, 25, 1313–1314, doi:10.1093/nar/25.6.1313.
[55]
Adessi, C.; Matton, G.; Ayala, G.; Turcatti, G.; Mermod, J.-J.; Mayer, P.; Kawashima, E. Solid phase DNA amplification: characterisation of primer attachment and amplification mechanisms. Nucl. Acid. Res. 2000, 28, e87, doi:10.1093/nar/28.20.e87.
[56]
Adams, C.P.; Kron, S.J. Method for Performing Amplification of Nucleic Acid with Two Primers Bound to a Single Solid Support. U.S. Patent 5,641,658, 24 June 1997.
[57]
Onodera, K.; d’Offay, J.; Melcher, U. Nylon membrane-immobilized PCR for detection of bovine viruses. Biotechniques 2002, 32, 74–80.
[58]
Westin, L.; Xu, X.; Miller, C.; Wang, L.; Edman, C.F.; Nerenberg, M. Anchored multiplex amplification on a microelectronic chip array. Nat. Biotechnol. 2000, 18, 199–204, doi:10.1038/72658.
[59]
Strizhkov, B.N.; Drobyshev, A.L.; Mikhailovich, V.M.; Mirzabekov, A.D. PCR amplification on a microarray of gel-immobilized oligonucleotides: detection of bacterial toxin- and drug-resistant genes and their mutations. Biotechniques 2000, 29, 844–857.
[60]
Turner, M.S.; Penning, S.; Sharp, A.; Hyland, V.J.; Harris, R.; Morris, C.P.; van Daal, A. Solid-phase amplification for detection of C282y and H63D hemochromatosis (HFE) gene mutations. Clin. Chem. 2001, 47, 1384–1389.
[61]
Huber, M.; Losert, D.; Hiller, R.; Harwanegg, C.; Mueller, M.W.; Schmidt, W.M. Detection of single base alterations in genomic DNA by solid phase polymerase chain reaction on oligonucleotide microarrays. Anal. Biochem. 2001, 299, 24–30.
[62]
Tillib, S.V.; Strizhkov, B.N.; Mirzabekov, A.D. Integration of multiple PCR amplifications and DNA mutation analyses by using oligonucleotide microchip. Anal. Biochem. 2001, 292, 155–160.
[63]
Mitterer, G.; Huber, M.; Leidinger, E.; Kirisits, C.; Lubitz, W.; Mueller, M.W.; Schmidt, W.M. Microarray-based identification of bacteria in clinical samples by solid-phase PCR amplification of 23S ribosomal DNA sequences. J. Clin. Microbiol. 2004, 42, 1048–1057, doi:10.1128/JCM.42.3.1048-1057.2004.
[64]
Mitterer, G.; Schmidt, W.M. Microarray-based detection of bacteria by on-chip PCR. Methods Mol. Biol. 2006, 345, 37–51.
[65]
Pemov, A.; Modi, H.; Chandler, D.P.; Bavykin, S. DNA analysis with multiplex microarray-enhanced PCR. Nucl. Acid. Res. 2005, 33, e11, doi:10.1093/nar/gnh184.
[66]
Li, Y.; Guo, S.J.; Shao, N.; Tu, S.; Xu, M.; Ren, Z.R.; Ling, X.; Wang, G.Q.; Lin, Z.X.; Tao, S.C. A universal multiplex PCR strategy for 100-plex amplification using a hydrophobically patterned microarray. Lab Chip 2011, 11, 3609–3618, doi:10.1039/c1lc20526a.
[67]
Sun, Y.; Dhumpa, R.; Bang, D.D.; Handberg, K.; Wolff, A. DNA microarray-based solid-phase RT-PCR for rapid detection and identification of influenza virus type A and subtypes H5 and H7. Diagn. Microbiol. Infect. Dis. 2011, 69, 432–439, doi:10.1016/j.diagmicrobio.2010.11.008.
[68]
von Nickisch-Rosenegk, M.; Marschan, X.; Andresen, D.; Bier, F.F. Reverse transcription-polymerase chain reaction on a microarray: The integrating concept of “active arrays”. Anal. Bioanal. Chem. 2008, 391, 1671–1678, doi:10.1007/s00216-008-2154-1.
[69]
Andresen, D.; Von Nickisch-Rosenegk, M.; Bier, F.F. Helicase-dependent amplification: Use in onchip amplification and potential for point-of-care diagnostics. Expert Rev. Mol. Diagn. 2009, 9, 645–650, doi:10.1586/erm.09.46.
Fredriksson, S.; Banér, J.; Dahl, F.; Chu, A.; Ji, H.; Welch, K.; Davis, R.W. Multiplex amplification of all coding sequences within 10 cancer genes by Gene-Collector. Nucl. Acid. Res. 2007, 35, doi:10.1093/nar/gkm078.
[72]
Borel, N.; Kempf, E.; Hotzel, H.; Schubert, E.; Torgerson, P.; Slickers, P.; Ehricht, R.; Tasara, T.; Pospischil, A.; Sachse, K. Direct identification of chlamydiae from clinical samples using a DNA microarray assay: A validation study. Mol. Cell. Probe 2008, 22, 55–64, doi:10.1016/j.mcp.2007.06.003.
[73]
Khodakov, D.A.; Zakharova, N.V.; Gryadunov, D.A.; Filatov, F.P.; Zasedatelev, A.S.; Mikhailovich, V.M. An oligonucleotide microarray for multiplex real-time PCR identification of HIV-1, HBV, and HCV. Biotechniques 2008, 44, 241–248.
[74]
Pierik, A.; Boamfa, M.; van Zelst, M.; Clout, D.; Stapert, H.; Dijksman, F.; Broer, D.; Wimberger-Friedl, R. Real time quantitative amplification detection on a microarray: Towards high multiplex quantitative PCR. Lab Chip 2012, 12, 1897–1902, doi:10.1039/c2lc20740k.
[75]
Yershov, G.; Barsky, V.; Belgovskiy, A.; Kirillov, E.; Kreindlin, E.; Ivanov, I.; Parinov, S.; Guschin, D.; Drobishev, A.; Dubiley, S.; Mirzabekov, A. DNA analysis and diagnostics on oligonucleotide microchips. Proc. Natl. Acad. Sci. USA 1996, 93, 4913–4918.
[76]
Cooney, C.G.; Sipes, D.; Thakore, N.; Holmberg, R.; Belgrader, P. A plastic, disposable microfluidic flow cell for coupled on-chip PCR and microarray detection of infectious agents. Biomed. Microdevices 2012, 14, 45–53, doi:10.1007/s10544-011-9584-9.
WHO Global Tuberculosis Control 2011; Publication No. WHO/HTM/TB/2011.16, World Health Organization, WHO Press, Geneva, Switzerland, 2011, 248.
[83]
Sanchez, J.A.; Pierce, K.E.; Rice, J.E.; Wangh, L.J. Linear-After-The-Exponential (LATE)–PCR: An advanced method of asymmetric PCR and its uses in quantitative real-time analysis. Proc. Natl. Acad. Sci. USA 2004, 101, 1933–1938.
[84]
Edman, C.F.; Mehta, P.; Press, R.; Spargo, C.A.; Walker, G.T.; Nerenberg, M. Pathogen analysis and genetic predisposition testing using microelectronic arrays and isothermal amplification. Amer. J. Inv. Med. 2000, 48, 93–101.
Hataoka, Y.; Zhang, L.; Mori, Y.; Tomita, N.; Notomi, T.; Baba, Y. Analysis of specific gene by integration of isothermal amplification and electrophoresis on poly(methyl methacrylate) microchips. Anal. Chem. 2004, 76, 3689–3693, doi:10.1021/ac035032u.
[87]
Parida, M.; Horioke, K.; Ishida, H.; Dash, P.K.; Saxena, P.; Jana, A.M.; Islam, M.A.; Inoue, S.; Hosaka, N.; Morita, K. Rapid detection and differentiation of dengue virus serotypes by a real-time reverse transcription-loop-mediated isothermal amplification assay. J. Clin. Microbiol. 2005, 43, 2895–2903, doi:10.1128/JCM.43.6.2895-2903.2005.
[88]
Takakura, S.; Tsuchiya, S.; Fujihara, N.; Kudo, T.; Iinuma, Y.; Mitarai, S.; Ichiyama, S.; Yasukawa, K.; Ishiguro, T. Isothermal RNA sequence amplification method for rapid antituberculosis drug susceptibility testing of Mycobacterium tuberculosis. J. Clin. Microbiol. 2005, 43, 2489–2491.
[89]
Demidov, V.V. Rolling-circle amplification in DNA diagnostics: the power of simplicity. Expert Rev. Mol. Diagn. 2002, 2, 89–95.
