Chapter 18 : Solid- and Liquid-Phase Array Technologies

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

Preview this chapter:
Zoom in

Solid- and Liquid-Phase Array Technologies, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555816834/9781555814977_Chap18-1.gif /docserver/preview/fulltext/10.1128/9781555816834/9781555814977_Chap18-2.gif


This chapter focuses on DNA-based hybridization array technology. The chapter reviews the methodologies of cDNA, oligonucleotide, electronic, and liquid bead arrays. In each of these methodologies, the probe refers to the DNA sequence bound to the solid surface support in the microarray, whereas the target is the ‘‘unknown’’ sequence of interest. Printed microarrays have the advantages of simplicity and relatively low cost compared to synthesized microarrays, which are discussed in the chapter. While two-dimensional microarrays have had an impact on our understanding of the microbial world and the application of this diagnostic potential to infectious diseases, the most widespread and practical application is the use of liquid bead suspension arrays in diagnostic microbiology, which is therefore emphasized when applicable. The potential use of low- or medium-density arrays for the simultaneous detection of large numbers of microbial genetic targets is one of the most promising areas in applying microarray technology to diagnostic microbiology. Broad-range amplification often focuses on the rRNA genes (16S, 18S, 23S, or intergenic transcribed spacers) due to the inherent dichotomy of conserved and polymorphic sequences. Though the range of organisms included was relatively limited (species of , , , , , , , , , , and ), this study provides proof of principle for the use of suspension arrays for the identification of broad-range amplification products. Though broad-range amplification typically focuses on the rRNA genes, other targets have been employed.

Citation: Miller M. 2011. Solid- and Liquid-Phase Array Technologies, p 275-297. In Persing D, Tenover F, Tang Y, Nolte F, Hayden R, van Belkum A (ed), Molecular Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555816834.ch18

Key Concept Ranking

Severe Acute Respiratory Syndrome
Highlighted Text: Show | Hide
Loading full text...

Full text loading...


Image of FIGURE 1

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 compared by extracting mRNA and converting the RNA sets into differentially labeled cDNA sets for hybridization. The inclusion of multiple fluorescent labels allows color differentiation based on the quantity of target cDNA from each set that hybridizes to the microarray probes. The fluorescence signal is then scanned and analyzed. Adapted and reprinted from reference with permission from Elsevier.

Citation: Miller M. 2011. Solid- and Liquid-Phase Array Technologies, p 275-297. In Persing D, Tenover F, Tang Y, Nolte F, Hayden R, van Belkum A (ed), Molecular Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555816834.ch18
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 2

GeneChip oligonucleotide microarray. (Top) 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. (Middle) 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. (Bottom) Dicing and cartridge assembly. Once the wafer is completely synthesized, it can be diced into 49 to 400 individual microarrays, each then packaged into a plastic cartridge. Adapted and reprinted from reference with permission from Elsevier and Affymetrix.

Citation: Miller M. 2011. Solid- and Liquid-Phase Array Technologies, p 275-297. In Persing D, Tenover F, Tang Y, Nolte F, Hayden R, van Belkum A (ed), Molecular Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555816834.ch18
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 3

Electronic microarray. (A) An electronically activated pad creates a positive current, which enables the movement and concentration of negatively charged DNA probes to the activated locations. Once in the targeted location, the probes are secured by streptavidin-biotin bonds. (B) Once the first probe is bound to its targeted site, its activated pad can be turned off and a different pad can be activated. The repeated application of a positive current to test pad sites allows the probes to be arrayed. (C) Details of the RVA ASR. Once the probes have been bound, extracted and amplified nucleic acids from a patient sample are added and allowed to passively hybridize. After hybridization, secondary probes specific for the targets of interest with a nonspecific detector sequence are added along with fluorescent detector oligonucleotides. A positive hybridization event is measured following washing steps to remove unhybridized nucleic acids. The use of multiple fluorophores allows multiple probes to be used per site. P1, parainfluenza virus 1; P2, parainfluenza virus 2; P3, parainfluenza virus 3; FB, influenza virus B; FA, influenza virus A; IC, internal control; BKGD, background. Images courtesy of Nanogen.

Citation: Miller M. 2011. Solid- and Liquid-Phase Array Technologies, p 275-297. In Persing D, Tenover F, Tang Y, Nolte F, Hayden R, van Belkum A (ed), Molecular Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555816834.ch18
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 4

Liquid bead suspension microarray. (A) Microspheres 5.6 μm in diameter are filled with various 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: 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: 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: 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: Miller M. 2011. Solid- and Liquid-Phase Array Technologies, p 275-297. In Persing D, Tenover F, Tang Y, Nolte F, Hayden R, van Belkum A (ed), Molecular Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555816834.ch18
Permissions and Reprints Request Permissions
Download as Powerpoint


1. Akhras, M. S.,, S. Thiyagarajan,, A. C. Villablanca,, R. W. Davis,, P. Nyren, and, N. Pourmand. 2007. PathogenMip assay: a multiplex pathogen detection assay. PLoS ONE 2:e223.
2. Albrecht, V.,, A. Chevallier,, V. Magnone,, P. Barbry,, F. Vandenbos,, A. Bongain,, J. C. Lefebvre, and, V. Giordanengo. 2006. Easy and fast detection and genotyping of high-risk human papillomavirus by dedicated DNA microarrays. J. Virol. Methods 137:236244.
3. Anthony, R. M.,, T. J. Brown, and, G. L. French. 2000. Rapid diagnosis of bacteremia by universal amplification of 23S ribosomal DNA followed by hybridization to an oligonucleotide array. J. Clin. Microbiol. 38:781788.
4. Aragon, L. M.,, F. Navarro,, V. Heiser,, M. Garrigo,, M. Espanol, and, P. Coll. 2006. Rapid detection of specific gene mutations associated with isoniazid or rifampicin resistance in Mycobacterium tuberculosis clinical isolates using non-fluorescent low-density DNA microarrays. J. Antimicrob. Chemother. 57:825831.
5. Armstrong, B.,, M. Stewart, and, A. Mazumder. 2000. Suspension arrays for high throughput, multiplexed single nucleotide polymorphism genotyping. Cytometry 40:102108.
6. Balajee, S. A.,, L. Sigler, and, M. E. Brandt. 2007. DNA and the classical way: identification of medically important molds in the 21st century. Med. Mycol. 45:475490.
7. Ballmer, K.,, B. M. Korczak,, P. Kuhnert,, P. Slickers,, R. Ehricht, and, H. Hachler. 2007. Fast DNA serotyping of Escherichia coli by use of an oligonucleotide microarray. J. Clin. Microbiol. 45:370379.
8. Barker, K. S.,, and P. D. Rogers. 2005. Application of deoxyribonucleic acid microarray analysis to the study of azole antifungal resistance in Candida albicans. Methods Mol. Med. 118:4556.
9. Barlaan, E. A.,, M. Sugimori,, S. Furukawa, and, K. Takeuchi. 2005. Electronic microarray analysis of 16S rDNA amplicons for bacterial detection. J. Biotechnol. 115:1121.
10. Ben, R. J.,, S. Kung,, F. Y. Chang,, J. J. Lu,, N. H. Feng, and, Y. D. Hsieh. 2008. Rapid diagnosis of bacterial meningitis using a microarray. J. Formos. Med. Assoc. 107:448453.
11. Boriskin, Y. S.,, P. S. Rice,, R. A. Stabler,, J. Hinds,, H. Al-Ghusein,, K. Vass, and, P. D. Butcher. 2004. DNA microarrays for virus detection in cases of central nervous system infection. J. Clin. Microbiol. 42:58115818.
12. Brazas, M. D.,, and R. E. Hancock. 2005. Using microarray gene signatures to elucidate mechanisms of antibiotic action and resistance. Drug Discov. Today 10:12451252.
13. Brown, D. W.,, K. B. Gunning,, D. M. Henry,, Z. L. Awdeh,, J. P. Brinker,, S. Tzipori, and, J. E. Herrmann. 2008. A DNA oligonucleotide microarray for detecting human astrovirus serotypes. J. Virol. Methods 147:8692.
14. Bruant, G.,, C. Maynard,, S. Bekal,, I. Gaucher,, L. Masson,, R. Brousseau, and, J. Harel. 2006. Development and validation of an oligonucleotide microarray for detection of multiple virulence and antimicrobial resistance genes in Escherichia coli. Appl. Environ. Microbiol. 72:37803784.
15. Brunstein, J.,, and E. Thomas. 2006. Direct screening of clinical specimens for multiple respiratory pathogens using the Genaco Respiratory Panels 1 and 2. Diagn. Mol. Pathol. 15:169173.
16. Brunstein, J. D.,, C. L. Cline,, S. McKinney, and, E. Thomas. 2008. Evidence from multiplex molecular assays for complex multipathogen interactions in acute respiratory infections. J. Clin. Microbiol. 46:97102.
17. Bryant, P. A.,, D. Venter,, R. Robins-Browne, and, N. Curtis. 2004. Chips with everything: DNA microarrays in infectious diseases. Lancet Infect. Dis. 4:100111.
18. Burr, A.,, K. Bogart,, J. Conaty, and, J. Andrews. 2006. Automated liquid handling and high-throughput preparation of polymerase chain reaction-amplified DNA for microarray fabrication. Methods Enzymol. 410:99120.
19. Call, D. R. 2005. Challenges and opportunities for pathogen detection using DNA microarrays. Crit. Rev. Microbiol. 31:9199.
20. Call, D. R.,, M. K. Bakko,, M. J. Krug, and, M. C. Roberts. 2003. Identifying antimicrobial resistance genes with DNA microarrays. Antimicrob. Agents Chemother. 47:32903295.
21. Caoili, J. C.,, A. Mayorova,, D. Sikes,, L. Hickman,, B. B. Plikaytis, and, T. M. Shinnick. 2006. Evaluation of the TB-Biochip oligonucleotide microarray system for rapid detection of rifampin resistance in Mycobacterium tuberculosis. J. Clin. Microbiol. 44:23782381.
22. Chen, J.,, M. A. Iannone,, M. S. Li,, J. D. Taylor,, P. Rivers,, A. J. Nelsen,, K. A. Slentz-Kesler,, A. Roses, and, M. P. Weiner. 2000. A microsphere-based assay for multiplexed single nucleotide polymorphism analysis using single base chain extension. Genome Res. 10:549557.
23. Chen, S.,, S. Zhao,, P. F. McDermott,, C. M. Schroeder,, D. G. White, and, J. Meng. 2005. A DNA microarray for identification of virulence and antimicrobial resistance genes in Salmonella serovars and Escherichia coli. Mol. Cell. Probes 19:195201.
24. Chen, T. C.,, G. W. Chen,, C. A. Hsiung,, J. Y. Yang,, S. R. Shih,, Y. K. Lai, and, J. L. Juang. 2006. Combining multiplex reverse transcription-PCR and a diagnostic microarray to detect and differentiate enterovirus 71 and coxsackievirus A16. J. Clin. Microbiol. 44:22122219.
25. Cheung, V. G.,, M. Morley,, F. Aguilar,, A. Massimi,, R. Kucherlapati, and, G. Childs. 1999. Making and reading microarrays. Nat. Genet. 21:1519.
26. Chiu, C. Y.,, A. A. Alizadeh,, S. Rouskin,, J. D. Merker,, E. Yeh,, S. Yagi,, D. Schnurr,, B. K. Patterson,, D. Ganem, and, J. L. DeRisi. 2007. Diagnosis of a critical respiratory illness caused by human metapneumovirus by use of a panvirus microarray. J. Clin. Microbiol. 45:23402343.
27. Chiu, C. Y.,, S. Rouskin,, A. Koshy,, A. Urisman,, K. Fischer,, S. Yagi,, D. Schnurr,, P. B. Eckburg,, L. S. Tompkins,, B. G. Blackburn,, J. D. Merker,, B. K. Patterson,, D. Ganem, and, J. L. DeRisi. 2006. Microarray detection of human parainfluenzavirus 4 infection associated with respiratory failure in an immunocompetent adult. Clin. Infect. Dis. 43:e71e76.
28. Chiu, C. Y.,, A. Urisman,, T. L. Greenhow,, S. Rouskin,, S. Yagi,, D. Schnurr,, C. Wright,, W. L. Drew,, D. Wang,, P. S. Weintrub,, J. L. Derisi, and, D. Ganem. 2008. Utility of DNA microarrays for detection of viruses in acute respiratory tract infections in children. J. Pediatr. 153:7683.
29. Chizhikov, V.,, M. Wagner,, A. Ivshina,, Y. Hoshino,, A. Z. Kapikian, and, K. Chumakov. 2002. Detection and genotyping of human group A rotaviruses by oligonucleotide microarray hybridization. J. Clin. Microbiol. 40:23982407.
30. Chou, C. C.,, C. H. Chen,, T. T. Lee, and, K. Peck. 2004. Optimization of probe length and the number of probes per gene for optimal microarray analysis of gene expression. Nucleic Acids Res. 32:e99.
31. Chou, C. C.,, T. T. Lee,, C. H. Chen,, H. Y. Hsiao,, Y. L. Lin,, M. S. Ho,, P. C. Yang, and, K. Peck. 2006. Design of microarray probes for virus identification and detection of emerging viruses at the genus level. BMC Bioinform. 7:232.
32. Cleven, B. E.,, M. Palka-Santini,, J. Gielen,, S. Meembor,, M. Kronke, and, O. Krut. 2006. Identification and characterization of bacterial pathogens causing bloodstream infections by DNA microarray. J. Clin. Microbiol. 44:23892397.
33. Crameri, A.,, J. Marfurt,, K. Mugittu,, N. Maire,, A. Regos,, J. Y. Coppee,, O. Sismeiro,, R. Burki,, E. Huber,, D. Laubscher,, O. Puijalon,, B. Genton,, I. Felger, and, H. P. Beck. 2007. Rapid microarray-based method for monitoring of all currently known single-nucleotide polymorphisms associated with parasite resistance to antimalaria drugs. J. Clin. Microbiol. 45:36853691.
34. Dalma-Weiszhausz, D. D.,, J. Warrington,, E. Y. Tanimoto, and, C. G. Miyada. 2006. The Affymetrix GeneChip platform: an overview. Methods Enzymol. 410:328.
35. Dankbar, D. M.,, E. D. Dawson,, M. Mehlmann,, C. L. Moore,, J. A. Smagala,, M. W. Shaw,, N. J. Cox,, R. D. Kuchta, and, K. L. Rowlen. 2007. Diagnostic microarray for influenza B viruses. Anal. Chem. 79:20842090.
36. Das, S.,, T. M. Brown,, K. L. Kellar,, B. P. Holloway, and, C. J. Morrison. 2006. DNA probes for the rapid identification of medically important Candida species using a multianalyte profiling system. FEMS Immunol. Med. Microbiol. 46:244250.
37. Davignon, L.,, E. A. Walter,, K. M. Mueller,, C. P. Barrozo,, D. A. Stenger, and, B. Lin. 2005. Use of resequencing oligonucleotide microarrays for identification of Streptococcus pyogenes and associated antibiotic resistance determinants. J. Clin. Microbiol. 43:56905695.
38. Dawson, E. D.,, C. L. Moore,, D. M. Dankbar,, M. Mehlmann,, M. B. Townsend,, J. A. Smagala,, C. B. Smith,, N. J. Cox,, R. D. Kuchta, and, K. L. Rowlen. 2007. Identification of A/H5N1 influenza viruses using a single gene diagnostic microarray. Anal. Chem. 79:378384.
39. Deng, J. Y.,, X. E. Zhang,, H. B. Lu,, Q. Liu,, Z. P. Zhang,, Y. F. Zhou,, W. H. Xie, and, Z. J. Fu. 2004. Multiplex detection of mutations in clinical isolates of rifampin-resistant Mycobacterium tuberculosis by short oligonucleotide ligation assay on DNA chips. J. Clin. Microbiol. 42:48504852.
40. de Souza Luna, L. K.,, V. Heiser,, N. Regamey,, M. Panning,, J. F. Drexler,, S. Mulangu,, L. Poon,, S. Baumgarte,, B. J. Haijema,, L. Kaiser, and, C. Drosten. 2007. Generic detection of coronaviruses and differentiation at the prototype strain level by reverse transcription-PCR and non-fluorescent low-density microarray. J. Clin. Microbiol. 45:10491052.
41. Diaz, M. R.,, and J. W. Fell. 2005. Use of a suspension array for rapid identification of the varieties and genotypes of the Cryptococcus neoformans species complex. J. Clin. Microbiol. 43:36623672.
42. Dorrell, N.,, J. A. Mangan,, K. G. Laing,, J. Hinds,, D. Linton,, H. Al-Ghusein,, B. G. Barrell,, J. Parkhill,, N. G. Stoker,, A. V. Karlyshev,, P. D. Butcher, and, B. W. Wren. 2001. Whole genome comparison of Campylobacter jejuni human isolates using a low-cost microarray reveals extensive genetic diversity. Genome Res. 11:17061715.
43. Dunbar, S. A. 2006. Applications of Luminex xMAP technology for rapid, high-throughput multiplexed nucleic acid detection. Clin. Chim. Acta 363:7182.
44. Ehrenreich, A. 2006. DNA microarray technology for the microbiologist: an overview. Appl. Microbiol. Biotechnol. 73:255273.
45. Fitzgerald, C.,, M. Collins,, S. van Duyne,, M. Mikoleit,, T. Brown, and, P. Fields. 2007. Multiplex, bead-based suspension array for molecular determination of common Salmonella serogroups. J. Clin. Microbiol. 45:33233334.
46. Fitzgerald, J. R.,, D. E. Sturdevant,, S. M. Mackie,, S. R. Gill, and, J. M. Musser. 2001. Evolutionary genomics of Staphylococcus aureus: insights into the origin of methicillin-resistant strains and the toxic shock syndrome epidemic. Proc. Natl. Acad. Sci. USA 98:88218826.
47. Fleischmann, R. D.,, M. D. Adams,, O. White,, R. A. Clayton,, E. F. Kirkness,, A. R. Kerlavage,, C. J. Bult,, J. F. Tomb,, B. A. Dougherty,, J. M. Merrick, et al. 1995. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269:496512.
48. Fodor, S. P.,, J. L. Read,, M. C. Pirrung,, L. Stryer,, A. T. Lu, and, D. Solas. 1991. Light-directed, spatially addressable parallel chemical synthesis. Science 251:767773.
49. Frye, J. G.,, T. Jesse,, F. Long,, G. Rondeau,, S. Porwollik,, M. McClelland,, C. R. Jackson,, M. Englen, and, P. J. Fedorka-Cray. 2006. DNA microarray detection of antimicrobial resistance genes in diverse bacteria. Int. J. Antimicrob. Agents 27:138151.
50. Fukushima, M.,, K. Kakinuma,, H. Hayashi,, H. Nagai,, K. Ito, and, R. Kawaguchi. 2003. Detection and identification of Mycobacterium species isolates by DNA microarray. J. Clin. Microbiol. 41:26052615.
51. Fulton, R. J.,, R. L. McDade,, P. L. Smith,, L. J. Kienker, and, J. R. Kettman, Jr. 1997. Advanced multiplexed analysis with the FlowMetrix system. Clin. Chem. 43:17491756.
52. Garaizar, J.,, A. Rementeria, and, S. Porwollik. 2006. DNA microarray technology: a new tool for the epidemiological typing of bacterial pathogens? FEMS Immunol. Med. Microbiol. 47:178–0189.
53. Gegia, M.,, N. Mdivani,, R. E. Mendes,, H. Li,, M. Akhalaia,, J. Han,, G. Khechinashvili, and, Y. W. Tang. 2008. Prevalence of and molecular basis for tuberculosis drug resistance in the Republic of Georgia: validation of a QIAplex system for detection of drug resistance-related mutations. Antimicrob. Agents Chemother. 52:725729.
54. Gentry, T. J.,, and J. Zhou. 2006. Microarray-based microbial identification and characterization, p. 276-290. In Y. W. Tang and, C. W. Stratton (ed.), Advanced Techniques in Diagnostic Microbiology. Springer Science and Business Media, New York, NY.
55. Gerner-Smidt, P.,, K. Hise,, J. Kincaid,, S. Hunter,, S. Rolando,, E. Hyytia-Trees,, E. M. Ribot, and, B. Swaminathan. 2006. PulseNet USA: a five-year update. Foodborne Pathog. Dis. 3:919.
56. Gheit, T.,, G. Billoud,, M. N. de Koning,, F. Gemignani,, O. Forslund,, B. S. Sylla,, S. Vaccarella,, S. Franceschi,, S. Landi,, W. G. Quint,, F. Canzian, and, M. Tommasino. 2007. Development of a sensitive and specific multiplex PCR method combined with DNA microarray primer extension to detect betapapillomavirus types. J. Clin. Microbiol. 45:25372544.
57. Gryadunov, D.,, V. Mikhailovich,, S. Lapa,, N. Roudinskii,, M. Donnikov,, S. Pan’kov,, O. Markova,, A. Kuz’min,, L. Chernousova,, O. Skotnikova,, A. Moroz,, A. Zasedatelev, and, A. Mirzabekov. 2005. Evaluation of hybridisation on oligonucleotide microarrays for analysis of drug-resistant Mycobacterium tuberculosis. Clin. Microbiol. Infect. 11:531539.
58. Hager, J. 2006. Making and using spotted DNA microarrays in an academic core laboratory. Methods Enzymol. 410:135168.
59. Han, J.,, D. C. Swan,, S. J. Smith,, S. H. Lum,, S. E. Sefers,, E. R. Unger, and, Y. W. Tang. 2006. Simultaneous amplification and identification of 25 human papillomavirus types with Templex technology. J. Clin. Microbiol. 44:41574162.
60. Hayward, R. E.,, J. L. Derisi,, S. Alfadhli,, D. C. Kaslow,, P. O. Brown, and, P. K. Rathod. 2000. Shotgun DNA microarrays and stage-specific gene expression in Plasmodium falciparum malaria. Mol. Microbiol. 35:614.
61. Honma, S.,, V. Chizhikov,, N. Santos,, M. Tatsumi,, C. Timenetsky Mdo,, A. C. Linhares,, J. D. Mascarenhas,, H. Ushijima,, G. E. Armah,, J. R. Gentsch, and, Y. Hoshino. 2007. Development and validation of DNA microarray for genotyping group A rotavirus VP4 (P[4], P[6], P[8], P[9], and P[14]) and VP7 (G1 to G6, G8 to G10, and G12) genes. J. Clin. Microbiol. 45:26412648.
62. Horan, P. K.,, and L. L. Wheeless, Jr. 1977. Quantitative single cell analysis and sorting. Science 198:149157.
63. Hou, X. L.,, H. L. Jiang,, Q. Y. Cao,, L. Y. Zhao,, B. J. Chang, and, Z. Chen. 2008. Using oligonucleotide suspension arrays for laboratory identification of bacteria responsible for bacteremia. J. Zhejiang Univ. Sci. B 9:291298.
64. Hsiao, C. R.,, L. Huang,, J. P. Bouchara,, R. Barton,, H. C. Li, and, T. C. Chang. 2005. Identification of medically important molds by an oligonucleotide array. J. Clin. Microbiol. 43:37603768.
65. Huang, A.,, J. W. Li,, Z. Q. Shen,, X. W. Wang, and, M. Jin. 2006. High-throughput identification of clinical pathogenic fungi by hybridization to an oligonucleotide microarray. J. Clin. Microbiol. 44:32993305.
66. Hughes, T. R.,, M. Mao,, A. R. Jones,, J. Burchard,, M. J. Marton,, K. W. Shannon,, S. M. Lefkowitz,, M. Ziman,, J. M. Schelter,, M. R. Meyer,, S. Kobayashi,, C. Davis,, H. Dai,, Y. D. He,, S. B. Stephaniants,, G. Cavet,, W. L. Walker,, A. West,, E. Coffey,, D. D. Shoemaker,, R. Stoughton,, A. P. Blanchard,, S. H. Friend, and, P. S. Linsley. 2001. Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer. Nat. Biotechnol. 19:342347.
67. Iannone, M. A.,, J. D. Taylor,, J. Chen,, M. S. Li,, P. Rivers,, K. A. Slentz-Kesler, and, M. P. Weiner. 2000. Multiplexed single nucleotide polymorphism genotyping by oligonucleotide ligation and flow cytometry. Cytometry 39:131140.
68. Jaaskelainen, A. J.,, and L. Maunula. 2006. Applicability of microarray technique for the detection of noro- and astroviruses. J. Virol. Methods 136:210216.
69. Jaaskelainen, A. J.,, H. Piiparinen,, M. Lappalainen,, M. Koskiniemi, and, A. Vaheri. 2006. Multiplex-PCR and oligonucleotide microarray for detection of eight different herpesviruses from clinical specimens. J. Clin. Virol. 37:8390.
70. Jaaskelainen, A. J.,, H. Piiparinen,, M. Lappalainen, and, A. Vaheri. 2008. Improved multiplex-PCR and microarray for herpesvirus detection from CSF. J. Clin. Virol. 42:172175.
71. Jiang, H. L.,, H. H. Zhu,, L. F. Zhou,, F. Chen, and, Z. Chen. 2006. Genotyping of human papillomavirus in cervical lesions by L1 consensus PCR and the Luminex xMAP system. J. Med. Microbiol. 55:715720.
72. Jin, D.,, H. Qi,, S. Chen,, T. Zeng,, Q. Liu, and, S. Wang. 2008. Simultaneous detection of six human diarrheal pathogens by using DNA microarray combined with tyramide signal amplification. J. Microbiol. Methods 75:365368.
73. Johnson, S. C.,, D. J. Marshall,, G. Harms,, C. M. Miller,, C. B. Sherrill,, E. L. Beaty,, S. A. Lederer,, E. B. Roesch,, G. Madsen,, G. L. Hoffman,, R. H. Laessig,, G. J. Kopish,, M. W. Baker,, S. A. Benner,, P. M. Farrell, and, J. R. Prudent. 2004. Multiplexed genetic analysis using an expanded genetic alphabet. Clin. Chem. 50:20192027.
74. Jones, T. F.,, E. Scallan, and, F. J. Angulo. 2007. FoodNet: overview of a decade of achievement. Foodborne Pathog. Dis. 4:6066.
75. Kafatos, F. C.,, C. W. Jones, and, A. Efstratiadis. 1979. Determination of nucleic acid sequence homologies and relative concentrations by a dot hybridization procedure. Nucleic Acids Res. 7:15411552.
76. Kakinuma, K.,, M. Fukushima, and, R. Kawaguchi. 2003. Detection and identification of Escherichia coli, Shigella, and Salmonella by microarrays using the gyrB gene. Biotechnol. Bioeng. 83:721728.
77. Kellar, K. L.,, and M. A. Iannone. 2002. Multiplexed microsphere-based flow cytometric assays. Exp. Hematol. 30:12271237.
78. Kistler, A.,, P. C. Avila,, S. Rouskin,, D. Wang,, T. Ward,, S. Yagi,, D. Schnurr,, D. Ganem,, J. L. Derisi, and, H. A. Boushey. 2007. Pan-viral screening of respiratory tract infections in adults with and without asthma reveals unexpected human coronavirus and human rhinovirus diversity. J. Infect. Dis. 196:817825.
79. Klaassen, C. H.,, C. F. Prinsen,, H. A. de Valk,, A. M. Horrevorts,, M. A. Jeunink, and, F. B. Thunnissen. 2004. DNA microarray format for detection and subtyping of human papillomavirus. J. Clin. Microbiol. 42:21522160.
80. Koessler, T.,, P. Francois,, Y. Charbonnier,, A. Huyghe,, M. Bento,, S. Dharan,, G. Renzi,, D. Lew,, S. Harbarth,, D. Pittet, and, J. Schrenzel. 2006. Use of oligoarrays for characterization of community-onset methicillin-resistant Staphylococcus aureus. J. Clin. Microbiol. 44:10401048.
81. Korimbocus, J.,, N. Scaramozzino,, B. Lacroix,, J. M. Crance,, D. Garin, and, G. Vernet. 2005. DNA probe array for the simultaneous identification of herpesviruses, enteroviruses, and flaviviruses. J. Clin. Microbiol. 43:37793787.
82. Kostic, T.,, A. Weilharter,, S. Rubino,, G. Delogu,, S. Uzzau,, K. Rudi,, A. Sessitsch, and, L. Bodrossy. 2007. A microbial diagnostic microarray technique for the sensitive detection and identification of pathogenic bacteria in a background of nonpathogens. Anal. Biochem. 360:244254.
83. Kostrzynska, M.,, and A. Bachand. 2006. Application of DNA microarray technology for detection, identification, and characterization of food-borne pathogens. Can. J. Microbiol. 52:18.
84. Kozal, M. J.,, N. Shah,, N. Shen,, R. Yang,, R. Fucini,, T. C. Merigan,, D. D. Richman,, D. Morris,, E. Hubbell,, M. Chee, and, T. R. Gingeras. 1996. Extensive polymorphisms observed in HIV-1 clade B protease gene using high-density oligonucleotide arrays. Nat. Med. 2:753759.
85. Kreil, D. P.,, R. R. Russell, and, S. Russell. 2006. Microarray oligonucleotide probes. Methods Enzymol. 410:7398.
86. Krunic, N.,, T. D. Yager,, D. Himsworth,, F. Merante,, S. Yaghoubian, and, R. Janeczko. 2007. xTAG RVP assay: analytical and clinical performance. J. Clin. Virol. 40(Suppl. 1):S39S46.
87. Ksiazek, T. G.,, D. Erdman,, C. S. Goldsmith,, S. R. Zaki,, T. Peret,, S. Emery,, S. Tong,, C. Urbani,, J. A. Comer,, W. Lim,, P. E. Rollin,, S. F. Dowell,, A. E. Ling,, C. D. Humphrey,, W. J. Shieh,, J. Guarner,, C. D. Paddock,, P. Rota,, B. Fields,, J. DeRisi,, J. Y. Yang,, N. Cox,, J. M. Hughes,, J. W. LeDuc,, W. J. Bellini, and, L. J. Anderson. 2003. A novel coronavirus associated with severe acute respiratory syndrome. N. Engl. J. Med. 348:19531966.
88. Kumar, S.,, L. Wang,, J. Fan,, A. Kraft,, M. E. Bose,, S. Tiwari,, M. Van Dyke,, R. Haigis,, T. Luo,, M. Ghosh,, H. Tang,, M. Haghnia,, E. L. Mather,, W. G. Weisburg, and, K. J. Henrickson. 2008. 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. 46:30633072.
89. Lee, W. M.,, K. Grindle,, T. Pappas,, D. J. Marshall,, M. J. Moser,, E. L. Beaty,, P. A. Shult,, J. R. Prudent, and, J. E. Gern. 2007. High-throughput, sensitive, and accurate multiplex PCR-microsphere flow cytometry system for large-scale comprehensive detection of respiratory viruses. J. Clin. Microbiol. 45:26262634.
90. Leinberger, D. M.,, U. Schumacher,, I. B. Autenrieth, and, T. T. Bachmann. 2005. Development of a DNA microarray for detection and identification of fungal pathogens involved in invasive mycoses. J. Clin. Microbiol. 43:49434953.
91. Li, H.,, M. A. McCormac,, R. W. Estes,, S. E. Sefers,, R. K. Dare,, J. D. Chappell,, D. D. Erdman,, P. F. Wright, and, Y. W. Tang. 2007. Simultaneous detection and high-throughput identification of a panel of RNA viruses causing respiratory tract infections. J. Clin. Microbiol. 45:21052109.
92. Li, J.,, S. Chen, and, D. H. Evans. 2001. Typing and subtyping influenza virus using DNA microarrays and multiplex reverse transcriptase PCR. J. Clin. Microbiol. 39:696704.
93. Li, Y.,, D. Liu,, B. Cao,, W. Han,, Y. Liu,, F. Liu,, X. Guo,, D. A. Bastin,, L. Feng, and, L. Wang. 2006. Development of a serotype-specific DNA microarray for identification of some Shigella and pathogenic Escherichia coli strains. J. Clin. Microbiol. 44:43764383.
94. Li, Y.,, Y. Wang,, C. Jia,, Y. Ma,, Y. Lan, and, S. Wang. 2008. Detection of human papillomavirus genotypes with liquid bead microarray in cervical lesions of northern Chinese patients. Cancer Genet. Cytogenet. 182:1217.
95. Li, Z. G.,, L. Y. Chen,, J. Huang,, P. Qiao,, J. M. Qiu, and, S. Q. Wang. 2005. Quantification of the relative levels of wild-type and lamivudine-resistant mutant virus in serum of HBV-infected patients using microarray. J. Viral Hepat. 12:168175.
96. Lin, B.,, A. P. Malanoski,, Z. Wang,, K. M. Blaney,, A. G. Ligler,, R. K. Rowley,, E. H. Hanson,, E. von Rosenvinge,, F. S. Ligler,, A. W. Kusterbeck,, D. Metzgar,, C. P. Barrozo,, K. L. Russell,, C. Tibbetts,, J. M. Schnur, and, D. A. Stenger. 2007. Application of broad-spectrum, sequence-based pathogen identification in an urban population. PLoS ONE 2:e419.
97. Lin, B.,, G. J. Vora,, D. Thach,, E. Walter,, D. Metzgar,, C. Tibbetts, and, D. A. Stenger. 2004. Use of oligonucleotide microarrays for rapid detection and serotyping of acute respiratory disease-associated adenoviruses. J. Clin. Microbiol. 42:32323239.
98. Lin, B.,, Z. Wang,, G. J. Vora,, J. A. Thornton,, J. M. Schnur,, D. C. Thach,, K. M. Blaney,, A. G. Ligler,, A. P. Malanoski,, J. Santiago,, E. A. Walter,, B. K. Agan,, D. Metzgar,, D. Seto,, L. T. Daum,, R. Kruzelock,, R. K. Rowley,, E. H. Hanson,, C. Tibbetts, and, D. A. Stenger. 2006. Broad-spectrum respiratory tract pathogen identification using resequencing DNA microarrays. Genome Res. 16:527535.
99. Lin, Z. H.,, X. H. Shen,, Z. Jin,, Y. Kim,, E. Lee,, H. Kim, and, I. Kim. 2005. Human papillomavirus genotyping by oligonucleotide microarray and p16 expression in uterine cervical intraepithelial neoplasm and in invasive carcinoma in Korean women. Pathol. Int. 55:491496.
100. Long, W. H.,, H. S. Xiao,, X. M. Gu,, Q. H. Zhang,, H. J. Yang,, G. P. Zhao, and, J. H. Liu. 2004. A universal microarray for detection of SARS coronavirus. J. Virol. Methods 121:5763.
101. Lopez, M. F.,, and M. G. Pluskal. 2003. Protein micro-and macroarrays: digitizing the proteome. J. Chromatogr. B 787:1927.
102. Lopez-Campos, G.,, M. Coiras,, J. P. Sanchez-Merino,, M. R. Lopez-Huertas,, I. Spiteri,, F. Martin-Sanchez, and, P. Perez-Brena. 2007. Oligonucleotide microarray design for detection and serotyping of human respiratory adenoviruses by using a virtual amplicon retrieval software. J. Virol. Methods 145:127136.
103. Lovmar, L.,, C. Fock,, F. Espinoza,, F. Bucardo,, A. C. Syvanen, and, K. Bondeson. 2003. Microarrays for genotyping human group a rotavirus by multiplex capture and type-specific primer extension. J. Clin. Microbiol. 41:51535158.
104. MacBeath, G. 2002. Protein microarrays and proteomics. Nat. Genet. 32(Suppl.):526532.
105. Mahony, J.,, S. Chong,, F. Merante,, S. Yaghoubian,, T. Sinha,, C. Lisle, and, R. Janeczko. 2007. 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. 45:29652970.
106. Majtan, T.,, L. Majtanova,, J. Timko, and, V. Majtan. 2007. Oligonucleotide microarray for molecular characterization and genotyping of Salmonella spp. strains. J. Antimicrob. Chemother. 60:937946.
107. Malorny, B.,, C. Bunge,, B. Guerra,, S. Prietz, and, R. Helmuth. 2007. Molecular characterisation of Salmonella strains by an oligonucleotide multiprobe microarray. Mol. Cell. Probes 21:5665.
108. Marlowe, E. M.,, J. J. Hogan,, J. F. Hindler,, I. Andruszkiewicz,, P. Gordon, and, D. A. Bruckner. 2003. Application of an rRNA probe matrix for rapid identification of bacteria and fungi from routine blood cultures. J. Clin. Microbiol. 41:51275133.
109. Marshall, D. J.,, E. Reisdorf,, G. Harms,, E. Beaty,, M. J. Moser,, W. M. Lee,, J. E. Gern,, F. S. Nolte,, P. Shult, and, J. R. Prudent. 2007. Evaluation of a multiplexed PCR assay for detection of respiratory viral pathogens in a public health laboratory setting. J. Clin. Microbiol. 45:38753882.
110. McHugh, R. S.,, W. D. Ratnoff,, R. Gilmartin,, K. W. Sell, and, P. Selvaraj. 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.
111. Mehlmann, M.,, A. B. Bonner,, J. V. Williams,, D. M. Dankbar,, C. L. Moore,, R. D. Kuchta,, A. B. Podsiad,, J. D. Tamerius,, E. D. Dawson, and, K. L. Rowlen. 2007. Comparison of the MChip to viral culture, reverse transcription-PCR, and the QuickVue influenza A+B test for rapid diagnosis of influenza. J. Clin. Microbiol. 45:12341237.
112. Merante, F.,, S. Yaghoubian, and, R. Janeczko. 2007. Principles of the xTAG respiratory viral panel assay (RVP Assay). J. Clin. Virol. 40(Suppl. 1):S31S35.
113. Mikhailovich, V.,, D. Gryadunov,, A. Kolchinsky,, A. A. Makarov, and, A. Zasedatelev. 2008. DNA microarrays in the clinic: infectious diseases. Bioessays 30:673682.
114. Monecke, S.,, B. Berger-Bachi,, G. Coombs,, A. Holmes,, I. Kay,, A. Kearns,, H. J. Linde,, F. O’Brien,, P. Slickers, and, R. Ehricht. 2007. Comparative genomics and DNA array-based genotyping of pandemic Staphylococcus aureus strains encoding Panton-Valentine leukocidin. Clin. Microbiol. Infect. 13:236249.
115. Monecke, S.,, and R. Ehricht. 2005. Rapid genotyping of methicillin-resistant Staphylococcus aureus (MRSA) isolates using miniaturised oligonucleotide arrays. Clin. Microbiol. Infect. 11:825833.
116. Monecke, S.,, P. Slickers, and, R. Ehricht. 2008. Assignment of Staphylococcus aureus isolates to clonal complexes based on microarray analysis and pattern recognition. FEMS Immunol. Med. Microbiol. 53:237251.
117. Monecke, S.,, P. Slickers,, H. Hotzel,, G. Richter-Huhn,, M. Pohle,, S. Weber,, W. Witte, and, R. Ehricht. 2006. Microarray-based characterisation of a Panton-Valentine leukocidin-positive community-acquired strain of methicillin-resistant Staphylococcus aureus. Clin. Microbiol. Infect. 12:718728.
118. Morrison, D. A.,, and J. T. Ellis. 2003. The design and analysis of microarray experiments: applications in parasitology. DNA Cell Biol. 22:357394.
119. Nolte, F. S.,, D. J. Marshall,, C. Rasberry,, S. Schievelbein,, G. G. Banks,, G. A. Storch,, M. Q. Arens,, R. S. Buller, and, J. R. Prudent. 2007. MultiCode-PLx System for multiplexed detection of seventeen respiratory viruses. J. Clin. Microbiol. 45:27792786.
120. Odenthal, M.,, S. Koenig,, P. Farbrother,, U. Drebber,, Y. Bury,, H. P. Dienes, and, L. Eichinger. 2007. Detection of opportunistic infections by low-density microarrays: a diagnostic approach for granulomatous lymphadenitis. Diagn. Mol. Pathol. 16:1826.
121. Oh, T. J.,, C. J. Kim,, S. K. Woo,, T. S. Kim,, D. J. Jeong,, M. S. Kim,, S. Lee,, H. S. Cho, and, S. An. 2004. Development and clinical evaluation of a highly sensitive DNA microarray for detection and genotyping of human papillomaviruses. J. Clin. Microbiol. 42:32723280.
122. Pabbaraju, K.,, K. L. Tokaryk,, S. Wong, and, J. D. Fox. 2008. Comparison of the Luminex xTAG respiratory viral panel with in-house nucleic acid amplification tests for diagnosis of respiratory virus infections. J. Clin. Microbiol. 46:30563062.
123. Palacios, G.,, P. L. Quan,, O. J. Jabado,, S. Conlan,, D. L. Hirschberg,, Y. Liu,, J. Zhai,, N. Renwick,, J. Hui,, H. Hegyi,, A. Grolla,, J. E. Strong,, J. S. Towner,, T. W. Geisbert,, P. B. Jahrling,, C. Buchen-Osmond,, H. Ellerbrok,, M. P. Sanchez-Seco,, Y. Lussier,, P. Formenty,, M. S. Nichol,, H. Feldmann,, T. Briese, and, W. I. Lipkin. 2007. Panmicrobial oligonucleotide array for diagnosis of infectious diseases. Emerg. Infect. Dis. 13:7381.
124. Palmer, C.,, E. M. Bik,, D. B. Digiulio,, D. A. Relman, and, P. O. Brown. 2007. Development of the human infant intestinal microbiota. PLoS Biol. 5:e177.
125. Palmer, C.,, E. M. Bik,, M. B. Eisen,, P. B. Eckburg,, T. R. Sana,, P. K. Wolber,, D. A. Relman, and, P. O. Brown. 2006. Rapid quantitative profiling of complex microbial populations. Nucleic Acids Res. 34:e5.
126. Pas, S. D.,, N. Tran,, R. A. de Man,, C. Burghoorn-Maas,, G. Vernet, and, H. G. Niesters. 2008. Comparison of reverse hybridization, microarray, and sequence analysis for genotyping hepatitis B virus. J. Clin. Microbiol. 46:12681273.
127. Perreten, V.,, L. Vorlet-Fawer,, P. Slickers,, R. Ehricht,, P. Kuhnert, and, J. Frey. 2005. Microarray-based detection of 90 antibiotic resistance genes of gram-positive bacteria. J. Clin. Microbiol. 43:22912302.
128. Perrin, A.,, D. Duracher,, M. Perret,, P. Cleuziat, and, B. Mandrand. 2003. A combined oligonucleotide and protein microarray for the codetection of nucleic acids and antibodies associated with human immunodeficiency virus, hepatitis B virus, and hepatitis C virus infections. Anal. Biochem. 322:148155.
129. Porwollik, S.,, R. M. Wong, and, M. McClelland. 2002. Evolutionary genomics of Salmonella: gene acquisitions revealed by microarray analysis. Proc. Natl. Acad. Sci. USA 99:89568961.
130. Quan, P. L.,, G. Palacios,, O. J. Jabado,, S. Conlan,, D. L. Hirschberg,, F. Pozo,, P. J. Jack,, D. Cisterna,, N. Renwick,, J. Hui,, A. Drysdale,, R. Amos-Ritchie,, E. Baumeister,, V. Savy,, K. M. Lager,, J. A. Richt,, D. B. Boyle,, A. Garcia-Sastre,, I. Casas,, P. Perez-Brena,, T. Briese, and, W. I. Lipkin. 2007. Detection of respiratory viruses and subtype identification of influenza A viruses by GreeneChipResp oligonucleotide microarray. J. Clin. Microbiol. 45:23592364.
131. Ramdas, L.,, D. E. Cogdell,, J. Y. Jia,, E. E. Taylor,, V. R. Dunmire,, L. Hu,, S. R. Hamilton, and, W. Zhang. 2004. Improving signal intensities for genes with lowexpression on oligonucleotide microarrays. BMC Genomics 5:35.
132. Raymond, F.,, J. Carbonneau,, N. Boucher,, L. Robitaille,, S. Boivert,, W. K. Wu,, G. De Serres,, G. Boivin, and, J. Corbeil. 2009. Comparison of automated microarray detection with real-time PCR assays for detection of respiratory viruses in specimens obtained from children. J. Clin. Microbiol. 47:743750.
133. Ryabinin, V. A.,, L. A. Shundrin,, E. B. Kostina,, M. Laassri,, V. Chizhikov,, S. N. Shchelkunov,, K. Chumakov, and, A. N. Sinyakov. 2006. Microarray assay for detection and discrimination of Orthopoxvirus species. J. Med. Virol. 78:13251340.
134. Schena, M.,, D. Shalon,, R. W. Davis, and, P. O. Brown. 1995. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270:467470.
135. Scherl, A.,, P. Francois,, Y. Charbonnier,, J. M. Deshusses,, T. Koessler,, A. Huyghe,, M. Bento,, J. Stahl-Zeng,, A. Fischer,, A. Masselot,, A. Vaezzadeh,, F. Galle,, A. Renzoni,, P. Vaudaux,, D. Lew,, C. G. Zimmermann-Ivol,, P. A. Binz,, J. C. Sanchez,, D. F. Hochstrasser, and, J. Schrenzel. 2006. Exploring glycopeptide-resistance in Staphylococcus aureus: a combined proteomics and tran-scriptomics approach for the identification of resistance-related markers. BMC Genomics 7:296.
136. Scillian, J. J.,, T. M. McHugh,, M. P. Busch,, M. Tam,, M. J. Fulwyler,, D. Y. Chien, and, G. N. Vyas. 1989. Early detection of antibodies against rDNA-produced HIV proteins with a flow cytometric assay. Blood 73:20412048.
137. Sengupta, S.,, K. Onodera,, A. Lai, and, U. Melcher. 2003. Molecular detection and identification of influenza viruses by oligonucleotide microarray hybridization. J. Clin. Microbiol. 41:45424550.
138. Shalon, D.,, S. J. Smith, and, P. O. Brown. 1996. A DNA microarray system for analyzing complex DNA samples using two-color fluorescent probe hybridization. Genome Res. 6:639645.
139. Shang, S.,, G. Chen,, Y. Wu,, L. Du, and, Z. Zhao. 2005. Rapid diagnosis of bacterial sepsis with PCR amplification and microarray hybridization in 16S rRNA gene. Pediatr. Res. 58:143148.
140. Shi, G.,, S. Y. Wen,, S. H. Chen, and, S. Q. Wang. 2005. Fabrication and optimization of the multiplex PCR-based oligonucleotide microarray for detection of Neisseria gonorrhoeae, Chlamydia trachomatis and Ureaplasma urealyticum. J. Microbiol. Methods 62:245256.
141. Shimizu, Y.,, K. Dobashi,, Y. Yoshikawa,, S. Yabe,, S. Higuchi,, Y. Koike,, Y. Mita,, M. Utsugi,, K. Endou,, K. Takahashi,, S. Watanabe,, R. Saito, and, M. Mori. 2008. Five-antituberculosis drug-resistance genes detection using array system. J. Clin. Biochem. Nutr. 42:228234.
142. Singh, D. V.,, and H. Mohapatra. 2008. Application of DNA-based methods in typing Vibrio cholerae strains. Future Microbiol. 3:8796.
143. Sosnowski, R. G.,, E. Tu,, W. F. Butler,, J. P. O’Connell, and, M. J. Heller. 1997. Rapid determination of single base mismatch mutations in DNA hybrids by direct electric field control. Proc. Natl. Acad. Sci. USA 94:11191123.
144. Sougakoff, W.,, M. Rodrigue,, C. Truffot-Pernot,, M. Renard,, N. Durin,, M. Szpytma,, R. Vachon,, A. Troesch, and, V. Jarlier. 2004. Use of a high-density DNA probe array for detecting mutations involved in rifampicin resistance in Mycobacterium tuberculosis. Clin. Microbiol. Infect. 10:289294.
145. Southern, E. M. 1975. Detection of specific sequences among DNA fragments separated by gel electrophoresis. J. Mol. Biol. 98:503517.
146. Spiess, B.,, W. Seifarth,, M. Hummel,, O. Frank,, A. Fabarius,, C. Zheng,, H. Morz,, R. Hehlmann, and, D. Buchheidt. 2007. DNA microarray-based detection and identification of fungal pathogens in clinical samples from neutropenic patients. J. Clin. Microbiol. 45:37433753.
147. Spiro, A.,, M. Lowe, and, D. Brown. 2000. A bead-based method for multiplexed identification and quantitation of DNA sequences using flow cytometry. Appl. Environ. Microbiol. 66:42584265.
148. Takahashi, H.,, S. A. Norman,, E. L. Mather, and, B. K. Patterson. 2008. Evaluation of the NanoChip 400 system for detection of influenza A and B, respiratory syncytial, and parainfluenza viruses. J. Clin. Microbiol. 46:17241727.
149. Tang, X.,, S. L. Morris,, J. J. Langone, and, L. E. Bockstahler. 2005. Microarray and allele specific PCR detection of point mutations in Mycobacterium tuberculosis genes associated with drug resistance. J. Microbiol. Methods 63:318330.
150. Tang, Y. W.,, A. Kilic,, Q. Yang,, S. K. McAllister,, H. Li,, R. S. Miller,, M. McCormac,, K. D. Tracy,, C. W. Stratton,, J. Han, and, B. Limbago. 2007. StaphPlex system for rapid and simultaneous identification of antibiotic resistance determinants and Panton-Valentine leukocidin detection of staphylococci from positive blood cultures. J. Clin. Microbiol. 45:18671873.
151. Taylor, J. D.,, D. Briley,, Q. Nguyen,, K. Long,, M. A. Iannone,, M. S. Li,, F. Ye,, A. Afshari,, E. Lai,, M. Wagner,, J. Chen, and, M. P. Weiner. 2001. Flow cytometric platform for high-throughput single nucleotide polymorphism analysis. BioTechniques 30:661666, 668–669.
152. Tomiuk, S.,, and K. Hofmann. 2001. Microarray probe selection strategies. Brief. Bioinform. 2:329340.
153. Townsend, M. B.,, E. D. Dawson,, M. Mehlmann,, J. A. Smagala,, D. M. Dankbar,, C. L. Moore,, C. B. Smith,, N. J. Cox,, R. D. Kuchta, and, K. L. Rowlen. 2006. Experimental evaluation of the FluChip diagnostic microarray for influenza virus surveillance. J. Clin. Microbiol. 44:28632871.
154. Tran, N.,, R. Berne,, R. Chann,, M. Gauthier,, D. Martin,, M. A. Armand,, A. Ollivet,, C. G. Teo,, S. Ijaz,, D. Flichman,, M. Brunetto,, K. P. Bielawski,, C. Pichoud,, F. Zoulim, and, G. Vernet. 2006. European multicenter evaluation of high-density DNA probe arrays for detection of hepatitis B virus resistance mutations and identification of genotypes. J. Clin. Microbiol. 44:27922800.
155. Troesch, A.,, H. Nguyen,, C. G. Miyada,, S. Desvarenne,, T. R. Gingeras,, P. M. Kaplan,, P. Cros, and, C. Mabilat. 1999. Mycobacterium species identification and rifampin resistance testing with high-density DNA probe arrays. J. Clin. Microbiol. 37:4955.
156. Ugozzoli, L. A. 2004. Multiplex assays with fluorescent microbead readout: a powerful tool for mutation detection. Clin. Chem. 50:19631965.
157. Vahey, M.,, M. E. Nau,, S. Barrick,, J. D. Cooley,, R. Sawyer,, A. A. Sleeker,, P. Vickerman,, S. Bloor,, B. Larder,, N. L. Michael, and, S. A. Wegner. 1999. Performance of the Affymetrix GeneChip HIV PRT 440 platform for antiretroviral drug resistance genotyping of human immunodeficiency virus type 1 clades and viral isolates with length polymorphisms. J. Clin. Microbiol. 37:25332537.
158. van Ijperen, C.,, P. Kuhnert,, J. Frey, and, J. P. Clewley. 2002. Virulence typing of Escherichia coli using microarrays. Mol. Cell. Probes 16:371378.
159. van Leeuwen, W. B.,, C. Jay,, S. Snijders,, N. Durin,, B. Lacroix,, H. A. Verbrugh,, M. C. Enright,, A. Troesch, and, A. van Belkum. 2003. Multilocus sequence typing of Staphylococcus aureus with DNA array technology. J. Clin. Microbiol. 41:33233326.
160. Vernet, G.,, C. Jay,, M. Rodrigue, and, A. Troesch. 2004. Species differentiation and antibiotic susceptibility testing with DNA microarrays. J. Appl. Microbiol. 96:5968.
161. Vianna, M. E.,, H. P. Horz,, B. P. Gomes, and, G. Conrads. 2005. Microarrays complement culture methods for identification of bacteria in endodontic infections. Oral Microbiol. Immunol. 20:253258.
162. Volokhov, D.,, V. Chizhikov,, K. Chumakov, and, A. Rasooly. 2003. Microarray-based identification of thermophilic Campylobacter jejuni, C. coli, C. lari, and C. upsaliensis. J. Clin. Microbiol. 41:40714080.
163. Vora, G. J.,, C. E. Meador,, M. M. Bird,, C. A. Bopp,, J. D. Andreadis, and, D. A. Stenger. 2005. Microarray-based detection of genetic heterogeneity, antimicrobial resistance, and the viable but nonculturable state in human pathogenic Vibrio spp. Proc. Natl. Acad. Sci. USA 102:1910919114.
164. Wallace, J.,, B. A. Woda, and, G. Pihan. 2005. Facile, comprehensive, high-throughput genotyping of human genital papillomaviruses using spectrally addressable liquid bead microarrays. J. Mol. Diagn. 7:7280.
165. Wang, D.,, L. Coscoy,, M. Zylberberg,, P. C. Avila,, H. A. Boushey,, D. Ganem, and, J. L. DeRisi. 2002. Microarray-based detection and genotyping of viral pathogens. Proc. Natl. Acad. Sci. USA 99:1568715692.
166. Wang, D.,, A. Urisman,, Y. T. Liu,, M. Springer,, T. G. Ksiazek,, D. D. Erdman,, E. R. Mardis,, M. Hickenbotham,, V. Magrini,, J. Eldred,, J. P. Latreille,, R. K. Wilson,, D. Ganem, and, J. L. DeRisi. 2003. Viral discovery and sequence recovery using DNA microarrays. PLoS Biol. 1:E2.
167. Wang, R. F.,, M. L. Beggs,, B. D. Erickson, and, C. E. Cerniglia. 2004. DNA microarray analysis of predominant human intestinal bacteria in fecal samples. Mol. Cell. Probes 18:223234.
168. Wang, Z.,, P. A. Orlandi, and, D. A. Stenger. 2005. Simultaneous detection of four human pathogenic microsporidian species from clinical samples by oligonucleotide microarray. J. Clin. Microbiol. 43:41214128.
169. Wang, Z.,, G. J. Vora, and, D. A. Stenger. 2004. Detection and genotyping of Entamoeba histolytica, Entamoeba dispar, Giardia lamblia, and Cryptosporidium parvum by oligonucleotide microarray. J. Clin. Microbiol. 42:32623271.
170. Wiesinger-Mayr, H.,, K. Vierlinger,, R. Pichler,, A. Kriegner,, A. M. Hirschl,, E. Presterl,, L. Bodrossy, and, C. Noehammer. 2007. Identification of human pathogens isolated from blood using microarray hybridisation and signal pattern recognition. BMC Microbiol. 7:78.
171. Willse, A.,, T. M. Straub,, S. C. Wunschel,, J. A. Small,, D. R. Call,, D. S. Daly, and, D. P. Chandler. 2004. Quantitative oligonucleotide microarray fingerprinting of Salmonella enterica isolates. Nucleic Acids Res. 32:18481856.
172. Wilson, J. W.,, P. Bean,, T. Robins,, F. Graziano, and, D. H. Persing. 2000. Comparative evaluation of three human immunodeficiency virus genotyping systems: the HIV-GenotypR method, the HIV PRT GeneChip assay, and the HIV-1 RT line probe assay. J. Clin. Microbiol. 38:30223028.
173. Wilson, W. J.,, C. L. Strout,, T. Z. DeSantis,, J. L. Stilwell,, A. V. Carrano, and, G. L. Andersen. 2002. Sequence-specific identification of 18 pathogenic microorganisms using microarray technology. Mol. Cell. Probes 16:119127.
174. Wolber, P. K.,, P. J. Collins,, A. B. Lucas,, A. De Witte, and, K. W. Shannon. 2006. The Agilent in situ-synthesized microarray platform. Methods Enzymol. 410:2857.
175. Wong, C. W.,, C. L. Heng,, L. Wan Yee,, S. W. Soh,, C. B. Kartasasmita,, E. A. Simoes,, M. L. Hibberd,, W. K. Sung, and, L. D. Miller. 2007. Optimization and clinical validation of a pathogen detection microarray. Genome Biol. 8:R93.
176. Wu, Z.,, Y. Tsumura,, G. Blomquist, and, X. R. Wang. 2003. 18S rRNA gene variation among common airborne fungi, and development of specific oligonucleotide probes for the detection of fungal isolates. Appl. Environ. Microbiol. 69:53895397.
177. Ye, F.,, M. S. Li,, J. D. Taylor,, Q. Nguyen,, H. M. Colton,, W. M. Casey,, M. Wagner,, M. P. Weiner, and, J. Chen. 2001. Fluorescent microsphere-based readout technology for multiplexed human single nucleotide polymorphism analysis and bacterial identification. Hum. Mutat. 17:305316.
178. Yu, X.,, M. Susa,, C. Knabbe,, R. D. Schmid, and, T. T. Bachmann. 2004. Development and validation of a diagnostic DNA microarray to detect quinolone-resistant Escherichia coli among clinical isolates. J. Clin. Microbiol. 42:40834091.
179. Yu, X.,, M. Susa,, J. Weile,, C. Knabbe,, R. D. Schmid, and, T. T. Bachmann. 2007. Rapid and sensitive detection of fluoroquinolone-resistant Escherichia coli from urine samples using a genotyping DNA microarray. Int. J. Med. Microbiol. 297:417429.
180. Yue, J.,, W. Shi,, J. Xie,, Y. Li,, E. Zeng,, L. Liang, and, H. Wang. 2004. Detection of rifampin-resistant Mycobacterium tuberculosis strains by using a specialized oligonucleotide microarray. Diagn. Microbiol. Infect. Dis. 48:4754.
181. Zhang, G. Q.,, Y. Y. Guan,, H. H. Sheng,, B. Zheng,, S. Wu,, H. S. Xiao, and, L. H. Tang. 2008. Multiplex PCR and oligonucleotide microarray for detection of single-nucleotide polymorphisms associated with Plasmodium falciparum drug resistance. J. Clin. Microbiol. 46:21672174.
182. Zhang, H.,, Z. Gong,, O. Pui,, Y. Liu, and, X. F. Li. 2006. An electronic DNA microarray technique for detection and differentiation of viable Campylobacter species. Analyst 131:907915.
183. Zheng, Z. B.,, Y. D. Wu,, X. L. Yu, and, S. Q. Shang. 2008. DNA microarray technology for simultaneous detection and species identification of seven human herpesviruses. J. Med. Virol. 80:10421050.
184. Zhu, L. X.,, Z. W. Zhang,, D. Liang,, D. Jiang,, C. Wang,, N. Du,, Q. Zhang,, K. Mitchelson, and, J. Cheng. 2007. Multiplex asymmetric PCR-based oligonucleotide microarray for detection of drug resistance genes containing single mutations in Enterobacteriaceae. Antimicrob. Agents Chemother. 51:37073713.
185. Zhu, L. X.,, Z. W. Zhang,, C. Wang,, H. W. Yang,, D. Jiang,, Q. Zhang,, K. Mitchelson, and, J. Cheng. 2007. Use of a DNA microarray for simultaneous detection of antibiotic resistance genes among staphylococcal clinical isolates. J. Clin. Microbiol. 45:35143521.
186. Zimmermann, K.,, T. Eiter, and, F. Scheiflinger. 2003. Consecutive analysis of bacterial PCR samples on a single electronic microarray. J. Microbiol. Methods 55:471474.
187. Zou, S.,, J. Han,, L. Wen,, Y. Liu,, K. Cronin,, S. H. Lum,, L. Gao,, J. Dong,, Y. Zhang,, Y. Guo, and, Y. Shu. 2007. Human influenza A virus (H5N1) detection by a novel multiplex PCR typing method. J. Clin. Microbiol. 45:18891892.


Generic image for table

Summary of differentiating characteristics of microarray platforms

Citation: Miller M. 2011. Solid- and Liquid-Phase Array Technologies, p 275-297. In Persing D, Tenover F, Tang Y, Nolte F, Hayden R, van Belkum A (ed), Molecular Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555816834.ch18
Generic image for table

Summary of key characteristics of the commercially available microarray products for respiratory viral diagnosis

Citation: Miller M. 2011. Solid- and Liquid-Phase Array Technologies, p 275-297. In Persing D, Tenover F, Tang Y, Nolte F, Hayden R, van Belkum A (ed), Molecular Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555816834.ch18

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