Abstract
Infectious diseases account for between 14 and 17 million deaths worldwide each year. Accurate and rapid diagnosis of bacterial, fungal, viral, and parasitic infections is therefore essential to reduce the morbidity and mortality associated with these diseases. Classical microbiological and serological methods have long served as the gold standard for diagnosis but are increasingly being replaced by molecular diagnostic methods that demonstrate increased sensitivity and specificity and provide an identification of the etiologic agent in a shorter period of time. PCR/LDR coupled with universal array detection provides a highly sensitive and specific platform for the detection and identification of bacterial and viral infections.
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Boissinot M, Bergeron MG (2002) Toward rapid real-time molecular diagnostic to guide smart use of antimicrobials. Curr Opin Microbiol 5:478-482
Muldrew KL (2009) Molecular diagnostics of infectious diseases. Curr Opin Pediatr 21:102-111
Pfaller MA (2001) Molecular approaches to diagnosing and managing infectious diseases: practicality and costs. Emerg Infect Dis 7:312-318
Procop Gary W (2007) Molecular diagnostics for the detection and characterization of microbial pathogens. Clin Infect Dis 45:S99-S111
Barany F (1991) The ligase chain reaction in a PCR world. PCR Methods Appl 1:5-16
Barany F (1991) Genetic disease detection and DNA amplification using cloned thermostable ligase. Proc Natl Acad Sci USA 88:189-193
Day DJ, Speiser PW, White PC, Barany F (1995) Detection of steroid 21-hydroxylase alleles using gene-specific PCR and a multiplexed ligation detection reaction. Genomics 29:152-162
Khanna M, Cao W, Zirvi M, Paty P, Barany F (1999) Ligase detection reaction for identification of low abundance mutations. Clin Biochem 32:287-290
Favis R, Gerry NP, Cheng YW, Barany F (2005) Applications of the universal DNA microarray in molecular medicine. Methods Mol Med 114:25-58
Gerry NP, Witowski NE, Day J, Hammer RP, Barany G, Barany F (1999) Universal DNA microarray method for multiplex detection of low abundance point mutations. J Mol Biol 292:251-262
Dong SM, Traverso G, Johnson C, Geng L, Favis R, Boynton K, Hibi K, Goodman SN, D’Allessio M, Paty P, Hamilton SR, Sidransky D, Barany F, Levin B, Shuber A, Kinzler KW, Vogelstein B, Jen J (2001) Detecting colorectal cancer in stool with the use of multiple genetic targets. J Natl Cancer Inst 93:858-865
Favis R, Barany F (2000) Mutation detection in K-ras, BRCA1, BRCA2, and p53 using PCR/LDR and a universal DNA microarray. Ann N Y Acad Sci 906:39-43
Favis R, Day JP, Gerry NP, Phelan C, Narod S, Barany F (2000) Universal DNA array detection of small insertions and deletions in BRCA1 and BRCA2. Nat Biotechnol 18:561-564
Favis R, Huang J, Gerry NP, Culliford A, Paty P, Soussi T, Barany F (2004) Harmonized microarray/mutation scanning analysis of TP53 mutations in undissected colorectal tumors. Hum Mutat 24:63-75
Fouquet C, Antoine M, Tisserand P, Favis R, Wislez M, Commo F, Rabbe N, Carette MF, Milleron B, Barany F, Cadranel J, Zalcman G, Soussi T (2004) Rapid and sensitive p53 alteration analysis in biopsies from lung cancer patients using a functional assay and a universal oligonucleotide array: a prospective study. Clin Cancer Res 10:3479-3489
Consolandi C, Busti E, Pera C, Delfino L, Ferrara GB, Bordoni R, Castiglioni B, Bernardi LR, Battaglia C, De Bellis G (2003) Detection of HLA polymorphisms by ligase detection reaction and a universal array format: a pilot study for low resolution genotyping. Hum Immunol 64:168-178
Cheng YW, Shawber C, Notterman D, Paty P, Barany F (2006) Multiplexed profiling of candidate genes for CpG island methylation status using a flexible PCR/LDR/Universal Array assay. Genome Res 16:282-289
Pingle MR, Granger K, Feinberg P, Shatsky R, Sterling B, Rundell M, Spitzer E, Larone D, Golightly L, Barany F (2007) Multiplexed identification of blood-borne bacterial pathogens by use of a novel 16S rRNA gene PCR-ligase detection reaction-capillary electrophoresis assay. J Clin Microbiol 45:1927-1935
Busti E, Bordoni R, Castiglioni B, Monciardini P, Sosio M, Donadio S, Consolandi C, Rossi Bernardi L, Battaglia C, De Bellis G (2002) Bacterial discrimination by means of a universal array approach mediated by LDR (ligase detection reaction). BMC Microbiol 2:27
Castiglioni B, Rizzi E, Frosini A, Sivonen K, Rajaniemi P, Rantala A, Mugnai MA, Ventura S, Wilmotte A, Boutte C, Grubisic S, Balthasart P, Consolandi C, Bordoni R, Mezzelani A, Battaglia C, De Bellis G (2004) Development of a universal microarray based on the ligation detection reaction and 16S rrna gene polymorphism to target diversity of cyanobacteria. Appl Environ Microbiol 70:7161-7172
Rondini S, Pingle MR, Das S, Tesh R, Rundell MS, Hom J, Stramer S, Turner K, Rossmann SN, Lanciotti R, Spier EG, Munoz-Jordan J, Larone D, Spitzer E, Barany F, Golightly LM (2008) Development of multiplex PCR-ligase detection reaction assay for detection of West Nile virus. J Clin Microbiol 46:2269-2279
Das S, Pingle MR, Munoz-Jordan J, Rundell MS, Rondini S, Granger K, Chang GJ, Kelly E, Spier EG, Larone D, Spitzer E, Barany F, Golightly LM (2008) Detection and serotyping of dengue virus in serum samples by multiplex reverse transcriptase PCR-ligase detection reaction assay. J Clin Microbiol 46:3276-3284
Hashimoto M, Barany F, Soper SA (2006) Polymerase chain reaction/ligase detection reaction/hybridization assays using flow-through microfluidic devices for the detection of low-abundant DNA point mutations. Biosens Bioelectron 21:1915-1923
Hashimoto M, Hupert ML, Murphy MC, Soper SA, Cheng YW, Barany F (2005) Ligase detection reaction/hybridization assays using three-dimensional microfluidic networks for the detection of low-abundant DNA point mutations. Anal Chem 77:3243-3255
Acknowledgments
Support for this work was provided by the National Cancer Institute (P01-CA65930) and the National Institute of Allergy and Infectious Diseases (UC1-AI062579).
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Pingle, M., Rundell, M., Das, S., Golightly, L.M., Barany, F. (2010). PCR/LDR/Universal Array Platforms for the Diagnosis of Infectious Disease. In: Chittur, S.V. (eds) Microarray Methods for Drug Discovery. Methods in Molecular Biology, vol 632. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-60761-663-4_9
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DOI: https://doi.org/10.1007/978-1-60761-663-4_9
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