Evaluation of qPCR curve analysis methods for reliable biomarker discovery: Bias, resolution, precision, and implications

Methods

Volumn 59, Issue 1, 2013, Pages 32-46

  Ruijter, Jan M ^a   Pfaffl, Michael W ^b   Zhao, Sheng ^c   Spiess, Andrej N ^d   Boggy, Gregory ^e   Blom, Jochen ^f   Rutledge, Robert G ^g   Sisti, Davide ^h   Lievens, Antoon ⁱ   De Preter, Katleen ^j   Derveaux, Stefaan ^j,l   Hellemans, Jan ^j,k   Vandesompele, Jo ^j,k  

^a ACADEMIC MEDICAL CENTER   (Netherlands)

^b TECHNICAL UNIVERSITY OF MUNICH   (Germany)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d UNIVERSITY MEDICAL CENTER HAMBURG EPPENDORF   (Germany)

^e DNA Software Inc   (United States)

^f BIELEFELD UNIVERSITY   (Germany)

^g LAURENTIAN FORESTRY CENTRE   (Canada)

^h UNIVERSITY OF URBINO   (Italy)

ⁱ GHENT UNIVERSITY   (Belgium)

^j GHENT UNIVERSITY HOSPITAL   (Belgium)

^k Biogazelle NV   (Belgium)

^l Wafergen   (United States)

more..

Author keywords

Benchmark; Bias; Precision; QPCR curve analysis; Resolution; Transcriptional biomarker

Indexed keywords

BIOLOGICAL MARKER;

ACCURACY; ALGORITHM; ARTICLE; CONCEPTUAL FRAMEWORK; GENE EXPRESSION; PATIENT CODING; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL;

AREA UNDER CURVE; BIAS (EPIDEMIOLOGY); CHILD; GENE EXPRESSION; GENE EXPRESSION PROFILING; HUMANS; KINETICS; NEUROBLASTOMA; REAL-TIME POLYMERASE CHAIN REACTION; REFERENCE STANDARDS; ROC CURVE; TUMOR MARKERS, BIOLOGICAL;

EID: 84872186528     PISSN: 10462023     EISSN: 10959130     Source Type: Journal    
DOI: 10.1016/j.ymeth.2012.08.011     Document Type: Article

References (49)

1. Bustin S.A., Benes V., Garson J.A., Hellemans J., Huggett J., Kubista M., Mueller R., Nolan T., Pfaffl M.W., Shipley G.L., Vandesompele J., Wittwer C.T. Clin. Chem. 2009, 55:611-622.
2. Higuchi R., Fockler C., Dollinger G., Watson R. Biotechnology (N.Y.) 1993, 11:1026-1030.
3. Bustin S.A., Benes V., Nolan T., Pfaffl M.W. J. Mol. Endocrinol. 2005, 34:597-601.
4. VanGuilder H.D., Vrana K.E., Freeman W.M. Biotechniques 2008, 44:619-626.
5. Creemers E.E., Tijsen A.J., Pinto Y.M. Circ. Res. 2012, 110:483-495.
6. Tijsen A.J., Creemers E.E., Moerland P.D., De Windt L.J. Circ. Res. 2010, 106:1035-1039.
7. Fendler A., Jung M., Stephan C., Honey R.J., Stewart R.J., Pace K.T., Erbersdobler A., Samaan S., Jung K., Yousef G.M. Int. J. Oncol. 2011, 39:1183-1192.
8. de Preter K., Mestdagh P., Vermeulen J., Zeka F., Naranjo A., Bray I., Castel V., Chen C., Drozynska E., Eggert A., Hogarty M.D., Izycka-Swieszewska E., London W.B., Noguera R., Piqueras M., Bryan K., Schowe B., van R.R., Molenaar J.J., Schramm A., Schulte J.H., Stallings R.L., Versteeg R., Laureys G., Van R.N., Speleman F., Vandesompele J. Clin. Cancer Res. 2011, 17:7684-7692.
9. Belzeaux R., Formisano-Treziny C., Loundou A., Boyer L., Gabert J., Samuelian J.C., Feron F., Naudin J., Ibrahim E.C. J. Psychiatr. Res. 2010, 44:1205-1213.
10. Larkin S.E., Holmes S., Cree I.A., Walker T., Basketter V., Bickers B., Harris S., Garbis S.D., Townsend P.A., Aukim-Hastie C. Br. J. Cancer 2012, 106:157-165.
11. Vermeulen J., De Preter K., Naranjo A., Vercruysse L., Van R.N., Hellemans J., Swerts K., Bravo S., Scaruffi P., Tonini G.P., De B.B., Noguera R., Piqueras M., Canete A., Castel V., Janoueix-Lerosey I., Delattre O., Schleiermacher G., Michon J., Combaret V., Fischer M., Oberthuer A., Ambros P.F., Beiske K., Benard J., Marques B., Rubie H., Kohler J., Potschger U., Ladenstein R., Hogarty M.D., McGrady P., London W.B., Laureys G., Speleman F., Vandesompele J. Lancet Oncol. 2009, 10:663-671.
12. de Boer M.E., Berg S., Timmermans M.E., den Dunnen M.E., van Straalen N.M., Ellers J., Roelofs D. BMC Mol. Biol. 2011, 12:11.
13. Izzo M., Kirkland P., Gu X., Lele Y., Gunn A., House J. Aus. Vet. J. 2012, 90:122-129.
14. Livak K.J., Schmittgen T.D. Methods 2001, 25:402-408.
15. Rutledge R.G., Cote C. Nucleic Acids Res. 2003, 31:e93.
16. Walker N.J. Science 2002, 296:557-559.
17. Nolan T., Hands R.E., Bustin S.A. Nat. Protoc. 2006, 1:1559-1582.
18. Ginzinger D.G. Exp. Hematol. 2002, 30:503-512.
19. Freeman W.M., Walker S.J., Vrana K.E. Biotechniques 1999, 26:112-115.
20. Pfaffl M.W., Hageleit M. Biotechnol. Lett. 2001, 23:275-282.
21. Vandesompele J., De Preter K., Pattyn F., Poppe B., Van R.N., De P.A., Speleman F. Genome Biol. 2002, 3. RESEARCH0034.
22. Fleige S., Walf V., Huch S., Prgomet C., Sehm J., Pfaffl M.W. Biotechnol. Lett. 2006, 28:1601-1613.
23. Karlen Y., McNair A., Perseguers S., Mazza C., Mermod N. BMC Bioinformatics 2007, 8:131.
24. Hellemans J., Mortier G., De P.A., Speleman F., Vandesompele J. Genome Biol. 2007, 8:R19.
25. Stolovitzky G., Cecchi G. Natl. Acad. Sci. USA 1996, 93:12947-12952.
26. Peccoud J., Jacob C. Biophys. J. 1996, 71:101-108.
27. Rutledge R.G., Stewart D. Mol. Biol. 2008, 9:96.
28. Alvarez M.J., Vila-Ortiz G.J., Salibe M.C., Podhajcer O.L., Pitossi F.J. BMC Bioinformatics 2007, 8:85.
29. Boggy G.J., Woolf P.J. PLoS ONE 2010, 5:e12355.
30. Lievens A., Van Aelst S., Van den Bulcke M., Goetghebeur E. Nucleic Acids Res. 2012, 40:e10.
31. Gentle A., Anastasopoulos F., McBrien N.A. BioTechniques 2001, 31:502. 504-506, 508.
32. Tichopad A., Dilger M., Schwarz G., Pfaffl M.W. Nucleic Acids Res. 2003, 31:e122.
33. Zhao S., Fernald R.D. J. Comput. Biol. 2005, 12:1047-1064.
34. Peirson S.N., Butler J.N., Foster R.G. Nucleic Acids Res. 2003, 31:e73.
35. Ramakers C., Ruijter J.M., Lekanne Deprez R.H., Moorman A.F.M. Neurosci. Lett. 2003, 339:62-66.
36. Liu W., Saint D.A. Anal. Biochem. 2002, 302:52-59.
37. Spiess A.N., Feig C., Ritz C. BMC Bioinformatics 2008, 9:221.
38. Ruijter J.M., Ramakers C., Hoogaars W.M., Karlen Y., Bakker O. Nucleic Acids Res. 2009, 37:e45.
39. Liu W., Saint D.A. Biochem. Biophys. Res. Commun. 2002, 294:347-353.
40. Larionov A., Krause A., Miller W. BMC Bioinformatics 2005, 6:62.
41. Guescini M., Sisti D., Rocchi M.B., Stocchi L., Stocchi V. BMC Bioinformatics 2008, 9:326.
42. Rutledge R.G. PLoS ONE 2011, 6:e17636.
43. Markham N.R., Zuker M. Methods Mol. Biol. 2008, 453:3-31.
44. Vermeulen J., De Preter K., Lefever S., Nuytens J., De V.F., Derveaux S., Hellemans J., Speleman F., Vandesompele J. Nucleic Acids Res. 2011, 39:e63.
45. Conover W.J. Practical Nonparametric Statistics 1980, J Wiley, New York.
46. Tichopad A., Kitchen R., Riedmaier I., Becker C., Stahlberg A., Kubista M. Clin. Chem. 2009, 55:1816-1823.
47. Rutledge R.G., Stewart D. BMC Biotechnol. 2008, 8:47.
48. Rutledge R.G., Stewart D. PLoS ONE 2010, 5:e9731.
49. Sisti D., Guescini M., Rocchi M.B., Tibollo P., D'Atri M., Stocchi V. BMC Bioinformatics 2010, 11:186.