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Laboratory efforts to eliminate contamination problems in the real-time RT-PCR detection of noroviruses36840

Public Access

Published

Peer reviewed scientific article

DOI : http://dx.doi.org/10.1016/j.mimet.2009.01.018 [1]

Authors

Stals,A. [2]; Werbrouck,H. [3]; Baert,L. [4]; N Botteldoorn [5]; Herman,L. [6]; Uyttendaele,M. [7]; E. Van Coillie [8]

Keywords

  1. a [9]
  2. Absence [10]
  3. an [11]
  4. article [12]
  5. AS [13]
  6. Belgium [14]
  7. Case [15]
  8. cause [16]
  9. Control [17]
  10. Correlation [18]
  11. data [19]
  12. detection [20]
  13. Dna [21]
  14. effect [22]
  15. effects [23]
  16. electronic [24]
  17. EVALUATION [25]
  18. Flemish [26]
  19. food [27]
  20. Frequency [28]
  21. function [29]
  22. general [30]
  23. genetics [31]
  24. genomic [32]
  25. im [33]
  26. Institute [34]
  27. IS [35]
  28. journal [36]
  29. Laboratories [37]
  30. methods [38]
  31. Migration [39]
  32. Norovirus [40]
  33. ON [41]
  34. PCR [42]
  35. performance [43]
  36. Plasmids [44]
  37. prevent [45]
  38. problems [46]
  39. real time PCR [47]
  40. Real-time PCR [48]
  41. Reference Standards [49]
  42. Research [50]
  43. Research Support [51]
  44. result [52]
  45. results [53]
  46. Reverse Transcriptase Polymerase Chain Reaction [54]
  47. risk [55]
  48. Risk factor [56]
  49. Risk-factor [57]
  50. SB - IM [58]
  51. SENSITIVITY [59]
  52. Size [60]
  53. STANDARD [61]
  54. standards [62]
  55. study [63]
  56. Technique [64]
  57. technology [65]
  58. Type [66]
  59. use [67]
  60. WATER [68]

Abstract:

In the current study, laboratory efforts to prevent the presence of positive NTCs (no template controls) during the optimization of a quantitative real-time reverse transcriptase PCR assay for detection of Noroviruses (NoVs) are described. Two DNA types (single-stranded (ss)DNA fragments and plasmid DNA) were used to generate a real-time PCR standard and a high frequency of positive NTCs was noticed in the case of ssDNA fragments. To investigate our suspicion of well-to-well migration of DNA during real-time PCR runs as possible cause of the positive NTCs, an “evaporation-experiment” was se…
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Abstract

In the current study, laboratory efforts to prevent the presence of positive NTCs (no template controls) during the optimization of a quantitative real-time reverse transcriptase PCR assay for detection of Noroviruses (NoVs) are described. Two DNA types (single-stranded (ss)DNA fragments and plasmid DNA) were used to generate a real-time PCR standard and a high frequency of positive NTCs was noticed in the case of ssDNA fragments. To investigate our suspicion of well-to-well migration of DNA during real-time PCR runs as possible cause of the positive NTCs, an "evaporation-experiment" was set up in which the evaporation of water and the possible co-evaporation of DNA were measured as a function of the DNA type (ssDNA-fragments, plasmid DNA and genomic DNA), the reaction plate seal type (adhesive film or 8-cap strips) and the use of 7 microl of mineral oil as cover layer. Results of this experiment indicated that evaporation of water occurred during real-time PCR runs regardless of the DNA type, the seal type and whether or not 7 microl of mineral oil was used as cover layer. Data from this experiment also suggested co-evaporation of DNA, with an apparent negative correlation between the size of the DNA type and the extent of this co-evaporation. The use of 7 microl of mineral oil as cover layer seemed to prevent to some extent co-evaporation of DNA. The use of plasmids as standard combined with 7 microl of mineral oil as cover layer in the real-time PCR setup resulted in a complete absence of positive NTCs while only minor effects were noticed on the performance of the real-time PCR. In general, our results showed that the high sensitivity of an optimized real-time PCR assay should be considered as--besides a great advantage--a potential risk factor for obtaining false-positive results when using this technique

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Source URL:https://www.sciensano.be/en/biblio/laboratory-efforts-eliminate-contamination-problems-real-time-rt-pcr-detection-noroviruses36840

Links
[1] http://dx.doi.org/10.1016/j.mimet.2009.01.018 [2] https://www.sciensano.be/en/biblio?f%5Bauthor%5D=1488&f%5Bsearch%5D=Stals%2CA. [3] https://www.sciensano.be/en/biblio?f%5Bauthor%5D=2733&f%5Bsearch%5D=Werbrouck%2CH. [4] https://www.sciensano.be/en/biblio?f%5Bauthor%5D=1482&f%5Bsearch%5D=Baert%2CL. [5] https://www.sciensano.be/en/biblio?f%5Bauthor%5D=666&f%5Bsearch%5D=N%20Botteldoorn [6] https://www.sciensano.be/en/biblio?f%5Bauthor%5D=2727&f%5Bsearch%5D=Herman%2CL. [7] https://www.sciensano.be/en/biblio?f%5Bauthor%5D=1485&f%5Bsearch%5D=Uyttendaele%2CM. [8] https://www.sciensano.be/en/biblio?f%5Bauthor%5D=1491&f%5Bsearch%5D=E.%20Van%20Coillie [9] https://www.sciensano.be/en/biblio?f%5Bkeyword%5D=1029&f%5Bsearch%5D=a [10] https://www.sciensano.be/en/biblio?f%5Bkeyword%5D=4818&f%5Bsearch%5D=Absence [11] https://www.sciensano.be/en/biblio?f%5Bkeyword%5D=843&f%5Bsearch%5D=an [12] https://www.sciensano.be/en/biblio?f%5Bkeyword%5D=618&f%5Bsearch%5D=article [13] https://www.sciensano.be/en/biblio?f%5Bkeyword%5D=846&f%5Bsearch%5D=AS [14] https://www.sciensano.be/en/biblio?f%5Bkeyword%5D=444&f%5Bsearch%5D=Belgium [15] https://www.sciensano.be/en/biblio?f%5Bkeyword%5D=1518&f%5Bsearch%5D=Case [16] https://www.sciensano.be/en/biblio?f%5Bkeyword%5D=1323&f%5Bsearch%5D=cause [17] https://www.sciensano.be/en/biblio?f%5Bkeyword%5D=1332&f%5Bsearch%5D=Control [18] https://www.sciensano.be/en/biblio?f%5Bkeyword%5D=2262&f%5Bsearch%5D=Correlation [19] https://www.sciensano.be/en/biblio?f%5Bkeyword%5D=1335&f%5Bsearch%5D=data [20] https://www.sciensano.be/en/biblio?f%5Bkeyword%5D=540&f%5Bsearch%5D=detection [21] https://www.sciensano.be/en/biblio?f%5Bkeyword%5D=1149&f%5Bsearch%5D=Dna [22] https://www.sciensano.be/en/biblio?f%5Bkeyword%5D=1344&f%5Bsearch%5D=effect [23] https://www.sciensano.be/en/biblio?f%5Bkeyword%5D=1347&f%5Bsearch%5D=effects [24] https://www.sciensano.be/en/biblio?f%5Bkeyword%5D=2169&f%5Bsearch%5D=electronic [25] https://www.sciensano.be/en/biblio?f%5Bkeyword%5D=1491&f%5Bsearch%5D=EVALUATION [26] https://www.sciensano.be/en/biblio?f%5Bkeyword%5D=4470&f%5Bsearch%5D=Flemish [27] https://www.sciensano.be/en/biblio?f%5Bkeyword%5D=1008&f%5Bsearch%5D=food [28] https://www.sciensano.be/en/biblio?f%5Bkeyword%5D=4791&f%5Bsearch%5D=Frequency [29] https://www.sciensano.be/en/biblio?f%5Bkeyword%5D=3960&f%5Bsearch%5D=function [30] https://www.sciensano.be/en/biblio?f%5Bkeyword%5D=1269&f%5Bsearch%5D=general [31] https://www.sciensano.be/en/biblio?f%5Bkeyword%5D=2433&f%5Bsearch%5D=genetics [32] https://www.sciensano.be/en/biblio?f%5Bkeyword%5D=1155&f%5Bsearch%5D=genomic [33] https://www.sciensano.be/en/biblio?f%5Bkeyword%5D=2184&f%5Bsearch%5D=im [34] https://www.sciensano.be/en/biblio?f%5Bkeyword%5D=954&f%5Bsearch%5D=Institute [35] https://www.sciensano.be/en/biblio?f%5Bkeyword%5D=525&f%5Bsearch%5D=IS [36] https://www.sciensano.be/en/biblio?f%5Bkeyword%5D=2190&f%5Bsearch%5D=journal [37] https://www.sciensano.be/en/biblio?f%5Bkeyword%5D=543&f%5Bsearch%5D=Laboratories [38] https://www.sciensano.be/en/biblio?f%5Bkeyword%5D=1359&f%5Bsearch%5D=methods [39] https://www.sciensano.be/en/biblio?f%5Bkeyword%5D=774&f%5Bsearch%5D=Migration [40] https://www.sciensano.be/en/biblio?f%5Bkeyword%5D=3705&f%5Bsearch%5D=Norovirus [41] https://www.sciensano.be/en/biblio?f%5Bkeyword%5D=912&f%5Bsearch%5D=ON [42] https://www.sciensano.be/en/biblio?f%5Bkeyword%5D=396&f%5Bsearch%5D=PCR [43] https://www.sciensano.be/en/biblio?f%5Bkeyword%5D=2205&f%5Bsearch%5D=performance [44] 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