Advertisement

Analytical and Bioanalytical Chemistry

, Volume 378, Issue 6, pp 1616–1623 | Cite as

Analysis and interpretation of data from real-time PCR trace detection methods using quantitation of GM soya as a model system

  • Malcolm J. BurnsEmail author
  • Hernan Valdivia
  • Neil Harris
Original Paper

Abstract

Recent years have seen an increased interest in DNA trace detection methods involved in many areas of bioanalytical research, such as quantitation of genetically modified (GM) ingredients in food products. There is little in the way of standardisation of data handling from these methods, and the data generated needs to be analysed appropriately if the results are to be interpreted correctly. This paper describes particular aspects of real-time PCR trace detection methods in order to increase the understanding of data generated using this bioanalytical technique. Using the specific example of GM soya detection and quantitation, it focuses on the production of calibration curves based on the mean and individual data values, the interpretation of correlation coefficients, regression techniques, and discusses suitable data analysis arising from simple and more complex experimental designs following transformation. By using the approaches outlined in this paper, more accurate analysis of data from real-time PCR and GM trace detection methods could be achieved.

Keywords

Real-time PCR Trace detection Data analysis Quality assurance 

Notes

Acknowledgements

The authors thank the Department of Trade and Industry for funding this work, and Mike Griffiths for his valuable additional advice with the statistical analyses.

References

  1. 1.
    Artlett CM, Gennaro Dito C, Christner PJ (2003) Biol Proc Online 5:103–107CrossRefGoogle Scholar
  2. 2.
    Hahn S, Zhong XY, Burk MR, Troeger C, Holzgreve W (2000) Ann NY Acad Sci 906:148–152PubMedGoogle Scholar
  3. 3.
    Quesada MA, Rye HS, Gingrich JC, Glazer AN, Mathies RA (1991) BioTechniques 10(5):616–622;624–625PubMedGoogle Scholar
  4. 4.
    Saghatelian A, Guckian KM, Thayer DA, Reza Ghadiri M (2003) J Am Chem Soc 125 (2):344–345Google Scholar
  5. 5.
    Schweitzer B, Kingsmore S (2001) Curr Opin Biotechnol 12:21–27CrossRefPubMedGoogle Scholar
  6. 6.
    Yang CX, Li YF, Feng P, Huang CZ (2002) Fenxi-Huaxue 30(4):473–477Google Scholar
  7. 7.
    Palecek E (2002) Talanta 56(5):809–819CrossRefGoogle Scholar
  8. 8.
    Aberasturi FJ, Jimenez AI, Arias JJ, Jimenez F (2002) Anal Lett 35(10):1677–1691CrossRefGoogle Scholar
  9. 9.
    Liu ZY (2002) Lihua Jianyan Huaxue Fence 38(8):413Google Scholar
  10. 10.
    Prichard E (2001) Analytical measurement terminology. The Royal Society of Chemistry, ISBN 0–85404–443–4Google Scholar
  11. 11.
    Rao KS, Balaji T, Rao TP, Babu Y, Naidu GRK (2002) Spectrochim Acta Part B At Spectrosc 57B(8):1333–1338Google Scholar
  12. 12.
    Fowler J, Cohen L, Jarvis P (1998) practical statistics for field biology, 2nd edn. Wiley, ISBN 0–471–98296–2Google Scholar
  13. 13.
    Freedman D, Pisani R, Purves R (1998) Statistics, 3rd edn. Norton, ISBN 0–393–97083–3Google Scholar
  14. 14.
    Hill ARC, von Holst C (2001) Analyst (Cambridge, UK) 126(11):2044–2052Google Scholar
  15. 15.
    Han J (2002) How can data mining help bio-data analysis? BIOKDD02: Workshop on data mining in bioinformatics, international conference on knowledge discovery and data mining July 23–26, 2002, Edmonton, Alberta, CanadaGoogle Scholar
  16. 16.
    Welch SJ (2000) Rev Sci Instrum 71(11):4286–4293CrossRefGoogle Scholar
  17. 17.
    Wolkenstein MG, Hutter H, Grasserbauer M (1998) Fresenius J Anal Chem 361(6–7):722–724Google Scholar
  18. 18.
    Grove DS (1999) J Biomol Tech 10:11–16Google Scholar
  19. 19.
    Holst-Jensen A, Rønning SB, Løvseth A, Berdal KG (2003) Anal Bioanal Chem 375:985–993PubMedGoogle Scholar
  20. 20.
    Anon (1997) User bulletin ABI Prism 7700 sequence detection system, 2:1–36Google Scholar
  21. 21.
    Vaïtilingom M, Pijneburg H, Gendre F, Brignon P (1999) J Agric Food Chem 47:5261–5266PubMedGoogle Scholar
  22. 22.
    Hübner Ph, Waiblinger H-U, Pietsch K, Brodmann P (2001) J AOAC Int 84:1855–1864PubMedGoogle Scholar
  23. 23.
    Pauli U, Liniger M, Schrott M, Schouwey B, Hübner Ph, Brodmann P, Eugster A (2001) Mitt Lebens Und Hyg 92:145–158Google Scholar
  24. 24.
    Terry C, Harris N (2001) Eur Food Res Technol 213:425–431Google Scholar
  25. 25.
    Hird H, Powell J, Johnson M-L, Oehlschlager S (2003) J AOAC Int 86:66–71PubMedGoogle Scholar
  26. 26.
    ABI PRISM 7700 (1998) Sequence detection system, user’s manual. PE Applied BiosystemsGoogle Scholar
  27. 27.
    Deng AP, Kolar V, Ulrich R, Franek M (2002) Anal Bioanal Chem 373(8):685–690CrossRefPubMedGoogle Scholar
  28. 28.
    Favetta P, Guitton J, Bleyzac N, Dufresne C, Bureau J (2001) J Chromatogr B Biomed Appl 751(2):377–382CrossRefGoogle Scholar
  29. 29.
    Kolb N, Herrera JL, Ferreyra DJ, Uliana RF (2001) J Agric Food Chem 49(10):4538–4541CrossRefPubMedGoogle Scholar
  30. 30.
    Ridtitid W, Wongnawa M, Mahatthanatrakul W, Punyo J, Sunbhanich M (2002) J Pharm Biomed Anal 28(1):181–186CrossRefPubMedGoogle Scholar
  31. 31.
    Eurachem guide (1998) The fitness for purpose of analytical methods: a laboratory guide to method validation and related topics. LGC, TeddingtonGoogle Scholar
  32. 32.
    Almeida AM, Castel Branco MM, Falcao AC (2002) J Chromatogr B Anal Technol Biomed Life Sci 774(2):215–222CrossRefGoogle Scholar
  33. 33.
    Limonard CBG (1979) Clin Chim Acta 95(2):353–367CrossRefPubMedGoogle Scholar
  34. 34.
    Wachter G, Kleiner J, Lernhardt U (1998) CLB Chemie Labor Biotechnik 49(11):421–424Google Scholar
  35. 35.
    van Loco J, Elskens M, Croux C, Beernaert H (2002) Accred Qual Assur 7(7):281–285CrossRefGoogle Scholar
  36. 36.
    USDA, office of agricultural affairs. US mission to the European Union. Proposal for the regulation on genetically modified food and feed and labeling and traceability for genetically modified organisms. http://www.useu.be/agri/GMOs.html. Cited 13 Aug 2003Google Scholar
  37. 37.
    Miller JN, Miller JC (2000) Statistics and chemometrics for analytical chemistry, 4th edn. Pearson Education Limited, ISBN 0130228885Google Scholar
  38. 38.
    Mendenhall W, Sincich T (1996) A second course in statistics: regression analysis, 5th edn. Prentice-all, ISBN 0133968219Google Scholar
  39. 39.
    Bevington P, Robinson D (eds) (1991) Data reduction and error analysis for the physical sciences. McGraw-Hill, ISBN 0079112439Google Scholar

Copyright information

© Springer-Verlag 2004

Authors and Affiliations

  • Malcolm J. Burns
    • 1
    Email author
  • Hernan Valdivia
    • 1
  • Neil Harris
    • 1
  1. 1.BioAnalytical Innovation TeamLGC LimitedTeddingtonUK

Personalised recommendations