Advertisement

Signal Amplification Technologies

  • Ted E. Schutzbank
Chapter

Abstract

The introduction of target nucleic acid amplification technologies, such as polymerase chain reaction (PCR), nucleic acid sequence-based amplification (NASBA), and strand displacement amplification (SDA), was accompanied by a plethora of technology patents. This made it very difficult for companies without access to these amplification technologies to compete in the area of assay development for ultrasensitive infectious disease detection and quantification. One way around this intellectual property roadblock was the development of highly sensitive assays that depended not on target amplification, but signal amplification. Signal amplification technologies have one major advantage over target amplification in that the issue of contaminating one test run with previously amplified material from a previous run is not an issue. Also, the three signal amplification technologies that are discussed in this chapter are isothermal, meaning that unlike PCR, thermocycling instrumentation is not required. Lastly, assays can be designed to detect and or quantify specific DNA or RNA targets using each of these methods, and, in the case of RNA, without the need to first convert the RNA target to DNA via reverse transcription. Care must still be taken, however, to minimize cross-contamination between samples being tested due to the enhanced analytical sensitivity inherent in assays using signal amplification technologies. An inherent concern with signal amplification methods is that great care must be taken during the design of the assay to ensure that carryover of the different assay components, from one step to the next, is minimized to reduce background noise, which will degrade the analytical sensitivity of the test in question.

Keywords

Capture Probe Hairpin Probe Viral Load Assay bDNA Assay Cystic Fibrosis Transmembrane Receptor 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

References

  1. 1.
    Horn T, Chang C, Urdea MS (1997) Chemical synthesis and characterization of branched oligodeoxyribonucleotides (bDNA) for use as signal amplifiers in nucleic acid quantification assays. Nucleic Acids Res 25:4842–4849PubMedCrossRefGoogle Scholar
  2. 2.
    Collins ML (1997) Irvine, Tyner D, et al. A branched DNA signal amplification assay for quantification of nucleic acid targets below 100 molecules/mL. Nucleic Acids Res 25:2979–2984PubMedCrossRefGoogle Scholar
  3. 3.
    Horn T, Urdea M (1989) Forks and combs and DNA: the synthesis of branched oligodeoxyribonucleotides. Nucleic Acids Res 17:6959–6967PubMedCrossRefGoogle Scholar
  4. 4.
    Beck S, Koster S (1990) Applications of dioxetane chemiluminescent probes to molecular biology. Anal Chem 62:2258–2270PubMedCrossRefGoogle Scholar
  5. 5.
    Colby C, Stollar BD, Simon MI (1971) Interferon induction: DNA-RNA hybrid or double stranded RNA? Nat New Biol 229:172–174PubMedCrossRefGoogle Scholar
  6. 6.
    Rudkin GT, Stoller BD (1977) High resolution detection of DNA-RNA hybrids in situ by indirect immunofluorescence. Nature 265:472–473PubMedCrossRefGoogle Scholar
  7. 7.
    Stollar BD (1970) Double-helical polynucleotides: immunochemical recognition of differing conformations. Science 169:609–611PubMedCrossRefGoogle Scholar
  8. 8.
    Boguslawski S, Smith DE, Michalak MA (1986) Characterization of monoclonal antibody to DNA· RNA and its application to immunodetection of hybrids. J lmmunol Methods 89:123–130CrossRefGoogle Scholar
  9. 9.
    Carpenter WR, Schutzbank TE, Tevere VJ et al (1993) A transcriptionally amplified DNA probe assay with ligatable probes and immunochemical detection. Clin Chem 39:1934–1938PubMedGoogle Scholar
  10. 10.
    Schiffman MH, Kiviat NB, Burk RD et al (1995) Accuracy and interlaboratory reliability of human papillomavirus DNA testing by hybrid capture. J Clin Microbiol 33:545–550PubMedGoogle Scholar
  11. 11.
    Lyamichev V, Mast AL, Hall JG et al (1999) Polymorphism identification and quantitative detection of genomic DNA by invasive cleavage of oligonucleotide probes. Nat Biotechnol 17:292–296PubMedCrossRefGoogle Scholar
  12. 12.
    Lyamichev VI, Kaiser MW, Lyamicheva NE et al (2000) Experimental and theoretical analysis of the invasive signal amplification reaction. Biochemistry 39:9523–9532PubMedCrossRefGoogle Scholar
  13. 13.
    Stryer L (1978) Fluorescence energy transfer as a spectroscopic ruler. Ann Rev Biochem 47:819–846PubMedCrossRefGoogle Scholar
  14. 14.
    Kwiatkowski RW, Lyamichev V (1999) de Arruda, et al. Clinical genetic and pharmacogenetic applications of the Invader Assay. Mol Diagn 4:353–364PubMedCrossRefGoogle Scholar
  15. 15.
    Hall JG, Eis PS, Law SM et al (2000) Sensitive detection of DNA polymorphisms by the serial invasive signal amplification reaction. Proc Natl Acad Sci U S A 97(15):8272–8277PubMedCrossRefGoogle Scholar
  16. 16.
    Harris E, Detmer J, Dungan J et al (1996) Detection of Trypanosoma brucei spp. in human blood by a nonradioactive branched DNA-based technique. J Clin Microbiol 34:2401–2407PubMedGoogle Scholar
  17. 17.
    Chernoff DN, Miner RC, Hoo BS et al (1997) Quantification of cytomegalovirus DNA in peripheral blood leukocytes by a branched-DNA signal amplification assay. J Clin Microbiol 35:2740–2744PubMedGoogle Scholar
  18. 18.
    Kolbert CP, Arruda J, Varga-Delmore P et al (1998) Branched-DNA assay for detection of mecA gene in oxacillin-resistant and oxacillin-sensitive staphylococci. J Clin Microbiol 36:2640–2644PubMedGoogle Scholar
  19. 19.
    Player AN, Shen L-P, Kenny D et al (2001) Single-copy gene detection using branched DNA (bDNA) in situ hybridization. J Histochem Cytochem 49:603–611PubMedCrossRefGoogle Scholar
  20. 20.
    Hendricks DA, Stowe BJ, Hoo BS et al (1995) Quantitation of HBV DNA in human serum using a branched DNA (bDNA) signal amplification assay. Am J Clin Pathol 104:537–546PubMedGoogle Scholar
  21. 21.
    Pachl C, Todd JA, Kern DG et al (1995) Rapid and precise quantification of HIV-1 RNA in plasma using a branched DNA (bDNA) signal amplification assay. J Acquir Immune Defic Syndr Hum Retrovirol 8:446–454PubMedCrossRefGoogle Scholar
  22. 22.
    Alter HJ, Sanchez-Pescador R, Urdea MS et al (1995) Evaluation of branched DNA signal amplification for the detection of hepatitis C virus RNA. J Viral Hepat 2:121–132PubMedCrossRefGoogle Scholar
  23. 23.
    Kern D, Collins M, Fultz T et al (1996) An enhanced-sensitivity branched-DNA assay for quantification of human immunodeficiency virus type 1 RNA in plasma. J Clin Microbiol 34:3196–3202PubMedGoogle Scholar
  24. 24.
    Nolte FS, Boysza J, Thurmond C et al (1998) Clinical comparison of an enhanced-sensitivity branched-DNA assay and reverse transcription–PCR for quantitation of human immunodeficiency virus type 1 RNA in plasma. J Clin Microbiol 36:716–720PubMedGoogle Scholar
  25. 25.
    Keeffe EB, Dieterich DT, Han SH (2004) A treatment algorithm for the management of chronic hepatitis B virus infection in the United States. Clin Gastroenterol Hepatol 2:87–106PubMedCrossRefGoogle Scholar
  26. 26.
    Player AN, Shen LP, Keny D et al (2001) Single-copy gene detection using branched DNA (bDNA) in situ hybridization. J Histochem Cytochem 49:603–612PubMedCrossRefGoogle Scholar
  27. 27.
    Honkavuori KS, Shivaprasad HL, Briese T et al (2011) Novel picornavirus in Turkey poults with hepatitis, California, USA. Emerg Infect Dis 17:480–487PubMedCrossRefGoogle Scholar
  28. 28.
    Lee K, Kunkeaw N, Jeon SH et al (2011) Precursor miR-886, a novel noncoding RNA repressed in cancer, associates with PKR and modulates its activity. RNA 17:1076–1089PubMedCrossRefGoogle Scholar
  29. 29.
    Piotrowska J, Hansen SJ, Park N et al (2010) Stable formation of compositionally unique stress granules in virus-infected cells. J Virol 84:3654–3665PubMedCrossRefGoogle Scholar
  30. 30.
    Ting DT, Lipson D, Suchismeta P et al (2011) Aberrant overexpression of satellite repeats in pancreatic and other epithelial cancers. Science 331:593–596PubMedCrossRefGoogle Scholar
  31. 31.
    Uniacke J, Colon-Ramos D, Zerges W (2011) FISH and immunofluorescence staining in Chlamydomonas. Methods Mol Biol 714:15–29PubMedCrossRefGoogle Scholar
  32. 32.
    Rutherford ST, van Kessel JC, Shao Y et al (2011) AphA and LuxR/HapR reciprocally control quorum sensing in vibrios. Genes Dev 25:397–408PubMedCrossRefGoogle Scholar
  33. 33.
    Woodson SE, Freiberg AN, Holbrook MR (2011) Differential cytokine responses from primary human Kupffer cells following infection with wild-type or vaccine strain yellow fever virus. Virology 412:188–195PubMedCrossRefGoogle Scholar
  34. 34.
    Cha W, Ma Y, Saif YM et al (2010) Development of microsphere-based multiplex branched DNA assay for detection and differentiation of avian influenza virus strains. J Clin Microbiol 48(7):2575–2577PubMedCrossRefGoogle Scholar
  35. 35.
    Momose H, Mizukami T, Ochiai M et al (2010) A new method for the evaluation of vaccine safety based on comprehensive gene expression analysis. J Biomed Biotechnol 2010:361841PubMedCrossRefGoogle Scholar
  36. 36.
    Munger K, Baldwin A, Edwards KM et al (2004) Mechanisms of human papillomavirus-induced oncogenesis. J Virol 78:11451–11460PubMedCrossRefGoogle Scholar
  37. 37.
    Snijders PJ, Steen Bergen RD, Heideman DA et al (2006) HPV-mediated cervical carcinogenesis: concepts and clinical implications. J Pathol 208:152–164PubMedCrossRefGoogle Scholar
  38. 38.
    zur Hausen H (1976) Condylomata acuminate and human genital cancer. Cancer Res 36(2 pt 2):794PubMedGoogle Scholar
  39. 39.
    zur Hausen H (2002) Papillomaviruses and cancer: from basic studies to clinical application. Nat Rev Cancer 2:342–350PubMedCrossRefGoogle Scholar
  40. 40.
    Schiffman MH (1994) Epidemiology of cervical human papillomaviruses. In: zur Hausen H (ed) Human pathogenic papillomaviruses. Springer, HeidelbergGoogle Scholar
  41. 41.
    Munoz N, Bosch FX, de Sanjose S et al (2003) Epidemiologic classification of human papillomavirus types associated with cervical cancer. N Engl J Med 348:518–527PubMedCrossRefGoogle Scholar
  42. 42.
    Wright T, Massad L, Dunton C et al (2007) 2006 Consensus guidelines for the management of women with abnormal cervical cancer screening tests. Am J Obstet Gynecol 197:340–345PubMedCrossRefGoogle Scholar
  43. 43.
    Arney A, Bennett K (2010) Molecular diagnostics of human papillomavirus. Lab Med 41:523–530CrossRefGoogle Scholar
  44. 44.
    Burd E (2003) Human papillomavirus and cervical cancer. Clin Microbiol Rev 16:1–17PubMedCrossRefGoogle Scholar
  45. 45.
    Castle PE, Solomon D, Wheeler CM et al (2008) Human papillomavirus genotype specificity of hybrid capture 2. J Clin Microbiol 46:2595–2604PubMedCrossRefGoogle Scholar
  46. 46.
    Schutzbank T, Jarvis C, Kahman N et al (2007) Detection of high-risk papillomavirus DNA with commercial invader-technology-based analyte-specific reagents following automated extraction of DNA from cervical brushings in ThinPrep Media. J Clin Microbiol 45:4067–4069PubMedCrossRefGoogle Scholar
  47. 47.
    Munson E, Du Chateau BK, Bellerose B (2011) Clinical laboratory evaluation of Invader® chemistry and hybrid capture for detection of high-risk human papillomavirus in liquid-based cytology specimens. Diagn Microbiol Infect Dis 71:230–235PubMedCrossRefGoogle Scholar
  48. 48.
    Schachter J, Hook EW, McCormack WM et al (1999) Ability of the Digene Hybrid Capture II Test to identify Chlamydia trachomatis and Neisseria gonorrhoeae in cervical specimens. J Clin Microbiol 37:3668–3671PubMedGoogle Scholar
  49. 49.
    Darwin LH, Cullen AP, Crowe SR et al (2002) Evaluation of the Hybrid Capture 2 CT/GC DNA tests and the GenProbe PACE 2 tests from the same male urethral swab specimens. Sex Transm Dis 29:576–580PubMedCrossRefGoogle Scholar
  50. 50.
    Quint K, Porras C et al (2007) Evaluation of a novel PCR-based assay for detection and identification of Chlamydia trachomatis serovars in cervical specimens. J Clin Microbiol 45:3986–3991PubMedCrossRefGoogle Scholar
  51. 51.
    Mazzulli T, Drew LW, Yen-Lieberman B et al (1999) Multicenter comparison of the Digene Hybrid Capture CMV DNA Assay (Version 2.0) and the pp 65 antigenemia assay, and cell culture for detection of cytomegalovirus viremia. J Clin Microbiol 37:958–963PubMedGoogle Scholar
  52. 52.
    Walmsey S, O’Rourke K, Mortimer C et al (1998) Predictive value of cytomegalovirus (CMV) antigenemia and Digene Hybrid Capture DNA assays for CMV disease in human immunodeficiency virus-infected patients. Clin Infect Dis 27:573–581CrossRefGoogle Scholar
  53. 53.
    Hanson KE, Reller LB, Kurtzberg J et al (2007) Comparison of the Digene Hybrid Capture System Cytomegalovirus (CMV) DNA (Version 2.0), Roche CMV UL54 analyte-specific-reagent, and QIAGE RealART CMV Light Cycler PCR reagent tests using AcroMetrix OptiQuant CMV DNA quantification panels and specimens from allogeneic-stem-cell transplant recipients. J Clin Microbiol 45:1972–1973PubMedCrossRefGoogle Scholar
  54. 54.
    Yuan HJ, Yuen MF, Wong DKH et al (2004) Clinical evaluation of the Digene Hybrid Capture II Test and the COBAS AMPLICOR Monitor test for determination of hepatitis B virus DNA levels. J Clin Microbiol 42:3513–3517PubMedCrossRefGoogle Scholar
  55. 55.
    Konnick EQ, Erali M, Ashwood ER et al (2005) Evaluation of the COBAS amplicor HBV monitor assay and comparison with the ultrasensitive HBV hybrid capture 2 assay for quantification of hepatitis B virus DNA. J Clin Microbiol 43:596–603PubMedCrossRefGoogle Scholar
  56. 56.
    Ledford M, Friedman KID, Hessner MJ et al (2000) A Multi-site study for detection of the factor V (Leiden) mutation from genomic DNA using a homogeneous Invader microtiter plate fluorescence resonance energy transfer (FRET) assay. J Mol Diagn 2:97–104PubMedCrossRefGoogle Scholar
  57. 57.
    Ando Y, Saka H, Ando M et al (2000) Polymorphisms of UDP-glucoruonosyltransferase gene and irinotecan toxicity: a pharmacogenetic analysis. Cancer Res 60:6921–6926PubMedGoogle Scholar
  58. 58.
    Innocenti R, Undevia SD, Iyer L et al (2004) Genetic variants in the UDP-glucuronosyltransferase 1A1 gene predict the risk of severe neutropenia of irinotecan. J Clin Oncol 22:1382–1388PubMedCrossRefGoogle Scholar
  59. 59.
    Harvey M, Stout S, Starkey CR et al (2009) The clinical performance of Invader® technology and SurePath® when detecting the presence of high-risk HPV cervical infection. J Clin Virol 51:S79–S83CrossRefGoogle Scholar
  60. 60.
    Ginocchio CC, Barth D, Zhang F (2008) Comparison of the third wave invader human papillomavirus (HPV) assay and the Digene HPV Hybrid Capture 2 assay for detection of high-risk HPV DNA. J Clin Microbiol 46:1641–1646PubMedCrossRefGoogle Scholar
  61. 61.
    Johnson LR, Starkey CR, Palmer J et al (2008) A comparison of two methods to determine the presence of high-risk HPV cervical infections. Am J Clin Pathol 130:401–408PubMedCrossRefGoogle Scholar
  62. 62.
    Wong AK, Chan RCK, Nichols S et al (2008) Human papillomavirus (HPV) in atypical squamous cervical cytology: the Invader HPV test as a new screening assay. J Clin Microbiol 46:869–875PubMedCrossRefGoogle Scholar
  63. 63.
    Tang YW, Allawi HT, DeLeon-Carnes M et al (2007) Detection and differentiation of wild-type vaccine mutant varicella-zoster viruses using an Invader Plus® method. J Clin Virol 40(2):129–134PubMedCrossRefGoogle Scholar
  64. 64.
    Cooksey RC, Holloway BP, Oldenburg MC et al (2000) Evaluation of the Invader Assay, a linear signal amplification method, for identification of mutations associated with resistance to rifampin and isoniazid in Mycobacterium tuberculosis. Antimicrob Agents Chemother 44:1296–1301PubMedCrossRefGoogle Scholar
  65. 65.
    Tadokoro K, Yamaguchi T, Kawamura K et al (2010) Rapid quantification of periodontitis-related bacteria using a novel modification of Invader PLUS technologies. Microbiol Res 165:43–49PubMedCrossRefGoogle Scholar
  66. 66.
    Takodoro K, Kobayashi M, Yamaguchi T et al (2006) Classification of hepatitis B virus genotypes by the PCR-Invader method with genotype-specific probes. J Virol Methods 138:30–39CrossRefGoogle Scholar
  67. 67.
    Tadokiro K, Suzuki F, Kobayashi M et al (2011) Rapid detection of drug-resistant mutations in hepatitis B virus by the PCR-Invader assay. J Virol Methods 171:67–73CrossRefGoogle Scholar
  68. 68.
    Xie MJ, Fukui K, Horie M et al (2008) A novel sensitive immunoassay method based on the Invader technique. Anal Biochem 374:278–284PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2013

Authors and Affiliations

  1. 1.Covance Central Laboratory Services Inc.IndianapolisUSA

Personalised recommendations