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PCR/LDR/Universal Array Platforms for the Diagnosis of Infectious Disease

  • Maneesh Pingle
  • Mark Rundell
  • Sanchita Das
  • Linnie M. Golightly
  • Francis Barany
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 632)

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.

Key words

Ligase detection reaction Microarray Multiplexed detection Bacterial identification Viral identification 

Notes

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).

References

  1. 1.
    Boissinot M, Bergeron MG (2002) Toward rapid real-time molecular diagnostic to guide smart use of antimicrobials. Curr Opin Microbiol 5:478-482PubMedCrossRefGoogle Scholar
  2. 2.
    Muldrew KL (2009) Molecular diagnos­tics of infectious diseases. Curr Opin Pediatr 21:102-111PubMedCrossRefGoogle Scholar
  3. 3.
    Pfaller MA (2001) Molecular approaches to diagnosing and managing infectious diseases: practicality and costs. Emerg Infect Dis 7:312-318PubMedCrossRefGoogle Scholar
  4. 4.
    Procop Gary W (2007) Molecular diagnostics for the detection and characterization of microbial pathogens. Clin Infect Dis 45:S99-S111PubMedCrossRefGoogle Scholar
  5. 5.
    Barany F (1991) The ligase chain reaction in a PCR world. PCR Methods Appl 1:5-16PubMedCrossRefGoogle Scholar
  6. 6.
    Barany F (1991) Genetic disease detection and DNA amplification using cloned thermostable ligase. Proc Natl Acad Sci USA 88:189-193PubMedCrossRefGoogle Scholar
  7. 7.
    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 29:152-162PubMedCrossRefGoogle Scholar
  8. 8.
    Khanna M, Cao W, Zirvi M, Paty P, Barany F (1999) Ligase detection reaction for identification of low abundance mutations. Clin Biochem 32:287-290PubMedCrossRefGoogle Scholar
  9. 9.
    Favis R, Gerry NP, Cheng YW, Barany F (2005) Applications of the universal DNA microarray in molecular medicine. Methods Mol Med 114:25-58PubMedGoogle Scholar
  10. 10.
    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 292:251-262PubMedCrossRefGoogle Scholar
  11. 11.
    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 93:858-865PubMedCrossRefGoogle Scholar
  12. 12.
    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 906:39-43PubMedCrossRefGoogle Scholar
  13. 13.
    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 18:561-564PubMedCrossRefGoogle Scholar
  14. 14.
    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 24:63-75PubMedCrossRefGoogle Scholar
  15. 15.
    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 10:3479-3489PubMedCrossRefGoogle Scholar
  16. 16.
    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 64:168-178PubMedCrossRefGoogle Scholar
  17. 17.
    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 16:282-289PubMedCrossRefGoogle Scholar
  18. 18.
    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 45:1927-1935PubMedCrossRefGoogle Scholar
  19. 19.
    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 2:27PubMedCrossRefGoogle Scholar
  20. 20.
    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 70:7161-7172PubMedCrossRefGoogle Scholar
  21. 21.
    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 46:2269-2279PubMedCrossRefGoogle Scholar
  22. 22.
    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 46:3276-3284PubMedCrossRefGoogle Scholar
  23. 23.
    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 21:1915-1923PubMedCrossRefGoogle Scholar
  24. 24.
    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 77:3243-3255PubMedCrossRefGoogle Scholar

Copyright information

© Humana Press, a part of Springer Science+Business Media, LLC 2010

Authors and Affiliations

  • Maneesh Pingle
    • 1
  • Mark Rundell
    • 1
  • Sanchita Das
    • 1
  • Linnie M. Golightly
    • 1
  • Francis Barany
    • 1
  1. 1.Department of MicrobiologyWeill Medical College, Cornell UniversityNew YorkUSA

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