Critical appraisal of quantitative PCR results in colorectal cancer research: Can we rely on published qPCR results?

Molecular Oncology

Volumn 8, Issue 4, 2014, Pages 813-818

  Dijkstra, J R ^a   van Kempen, L C ^b   Nagtegaal, I D ^a   Bustin, S A ^c  

^a RADBOUD UNIVERSITY MEDICAL CENTER   (Netherlands)

^b MCGILL UNIVERSITY   (Canada)

^c ANGLIA RUSKIN UNIVERSITY   (United Kingdom)

Author keywords

Colorectal cancer; MIQE; PCR; QPCR; Real time

Indexed keywords

MESSENGER RNA; TUMOR MARKER;

CANCER RESEARCH; COLORECTAL CANCER; COST EFFECTIVENESS ANALYSIS; GENE EXPRESSION; HUMAN; PRACTICE GUIDELINE; PUBLICATION; QUANTITATIVE ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; REVIEW; COLORECTAL NEOPLASMS; EVALUATION STUDY; GENETICS; MEDICAL RESEARCH; PROCEDURES; PROGNOSIS; REPRODUCIBILITY; STANDARDS;

BIOMEDICAL RESEARCH; COLORECTAL NEOPLASMS; HUMANS; PROGNOSIS; PUBLICATIONS; REAL-TIME POLYMERASE CHAIN REACTION; REPRODUCIBILITY OF RESULTS; TUMOR MARKERS, BIOLOGICAL;

EID: 84919340380     PISSN: 15747891     EISSN: 18780261     Source Type: Journal    
DOI: 10.1016/j.molonc.2013.12.016     Document Type: Review

References (32)

1. Andersen C.L., Lamy P., Thorsen K., Kjeldsen E., Wikman F., Villesen P., Oster B., Laurberg S., Orntoft T.F. Frequent genomic loss at chr16p13.2 is associated with poor prognosis in colorectal cancer. Int. J. Cancer 2011, 129:1848-1858.
2. Artells R., Moreno I., Diaz T., Martinez F., Gel B., Navarro A., Ibeas R., Moreno J., Monzo M. Tumour CD133 mRNA expression and clinical outcome in surgically resected colorectal cancer patients. Eur. J. Cancer 2010, 46:642-649.
3. Bustin S.A. Absolute quantification of mRNA using real-time reverse transcription polymerase chain reaction assays. J.Mol. Endocrinol. 2000, 25:169-193.
4. Bustin S.A. Why the need for qPCR publication guidelines?-The case for MIQE. Methods 2010, 50:217-226.
5. Bustin S.A., Benes V., Garson J., Hellemans J., Huggett J., Kubista M., Mueller R., Nolan T., Pfaffl M.W., Shipley G., Wittwer C.T., Schjerling P., Day P.J., Abreu M., Aguado B., Beaulieu J.F., Beckers A., Bogaert S., Browne J.A., Carrasco-Ramiro F., Ceelen L., Ciborowski K., Cornillie P., Coulon S., Cuypers A., De Brouwer S., De Ceuninck L., De Craene J., De Naeyer H., De Spiegelaere W., Deckers K., Dheedene A., Durinck K., Ferreira-Teixeira M., Fieuw A., Gallup J.M., Gonzalo-Flores S., Goossens K., Heindryckx F., Herring E., Hoenicka H., Icardi L., Jaggi R., Javad F., Karampelias M., Kibenge F., Kibenge M., Kumps C., Lambertz I., Lammens T., Markey A., Messiaen P., Mets E., Morais S., Mudarra-Rubio A., Nakiwala J., Nelis H., Olsvik P.A., Perez-Novo C., Plusquin M., Remans T., Rihani A., Rodrigues-Santos P., Rondou P., Sanders R., Schmidt-Bleek K., Skovgaard K., Smeets K., Tabera L., Toegel S., Van Acker T., Van den Broeck W., Van der Meulen J., Van Gele M., Van Peer G., Van Poucke M., Van Roy N., Vergult S., Wauman J., Tshuikina-Wiklander M., Willems E., Zaccara S., Zeka F., Vandesompele J. The need for transparency and good practices in the qPCR literature. Nat. Methods 2013, 10:1063-1067.
6. 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. The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin. Chem. 2009, 55:611-622.
7. Caradec J., Sirab N., Keumeugni C., Moutereau S., Chimingqi M., Matar C., Revaud D., Bah M., Manivet P., Conti M., Loric S. 'Desperate house genes': the dramatic example of hypoxia. Br. J. Cancer 2010, 102:1037-1043.
8. Ceelen L., De Craene J., De Spiegelaere W. Evaluation of normalization strategies used in real-time quantitative PCR experiments in HepaRG cell line studies. Clin. Chem. 2013, 60:1-4.
9. de Kok J.B., Roelofs R.W., Giesendorf B.A., Pennings J.L., Waas E.T., Feuth T., Swinkels D.W., Span P.N. Normalization of gene expression measurements in tumor tissues: comparison of 13 endogenous control genes. Lab. Invest. a J. Tech. Methods Pathol. 2005, 85:154-159.
10. Derveaux S., Vandesompele J., Hellemans J. How to do successful gene expression analysis using real-time PCR. Methods 2010, 50:227-230.
11. Dijkstra J.R., Mekenkamp L.J., Teerenstra S., De Krijger I., Nagtegaal I.D. MicroRNA expression in formalin-fixed paraffin embedded tissue using real time quantitative PCR: the strengths and pitfalls. J.Cell. Mol. Med. 2012, 16:683-690.
12. Greer S., Honeywell R., Geletu M., Arulanandam R., Raptis L. Housekeeping genes; expression levels may change with density of cultured cells. J.Immunol. Methods 2010, 355:76-79.
13. Herath N.I., Doecke J., Spanevello M.D., Leggett B.A., Boyd A.W. Epigenetic silencing of EphA1 expression in colorectal cancer is correlated with poor survival. Br. J. Cancer 2009, 100:1095-1102.
14. Higuchi R., Dollinger G., Walsh P.S., Griffith R. Simultaneous amplification and detection of specific DNA sequences. Bio/technology 1992, 10:413-417.
15. Koga Y., Yasunaga M., Moriya Y., Akasu T., Fujita S., Yamamoto S., Kozu T., Baba H., Matsumura Y. Detection of colorectal cancer cells from feces using quantitative real-time RT-PCR for colorectal cancer diagnosis. Cancer Sci. 2008, 99:1977-1983.
16. Mazzoccoli G., Panza A., Valvano M.R., Palumbo O., Carella M., Pazienza V., Biscaglia G., Tavano F., Di Sebastiano P., Andriulli A., Piepoli A. Clock gene expression levels and relationship with clinical and pathological features in colorectal cancer patients. Chronobiol. Int. 2011, 28:841-851.
17. Mestdagh P., Van Vlierberghe P., De Weer A., Muth D., Westermann F., Speleman F., Vandesompele J. A novel and universal method for microRNA RT-qPCR data normalization. Genome Biol. 2009, 10:R64.
18. Meyer S.U., Pfaffl M.W., Ulbrich S.E. Normalization strategies for microRNA profiling experiments: a 'normal' way to a hidden layer of complexity?. Biotechnol. Lett. 2010, 32:1777-1788.
19. Prinz F., Schlange T., Asadullah K. Believe it or not: how much can we rely on published data on potential drug targets? Nature reviews. Drug Discov. 2011, 10:712.
20. Radonic A., Thulke S., Mackay I.M., Landt O., Siegert W., Nitsche A. Guideline to reference gene selection for quantitative real-time PCR. Biochem. Biophys. Res. Commun. 2004, 313:856-862.
21. Rubie C., Frick V.O., Ghadjar P., Wagner M., Justinger C., Faust S.K., Vicinus B., Graber S., Kollmar O., Schilling M.K. CXC receptor-4 mRNA silencing abrogates CXCL12-induced migration of colorectal cancer cells. J.Translational Med. 2011, 9:22.
22. Rubie C., Kollmar O., Frick V.O., Wagner M., Brittner B., Graber S., Schilling M.K. Differential CXC receptor expression in colorectal carcinomas. Scand. J. Immunol. 2008, 68:635-644.
23. Schmittgen T.D., Livak K.J. Analyzing real-time PCR data by the comparative C(T) method. Nat. Protoc. 2008, 3:1101-1108.
24. Sorby L.A., Andersen S.N., Bukholm I.R., Jacobsen M.B. Evaluation of suitable reference genes for normalization of real-time reverse transcription PCR analysis in colon cancer. J.Exp. Clin. Cancer Res. CR 2010, 29:144.
25. Suzuki T., Higgins P.J., Crawford D.R. Control selection for RNA quantitation. BioTechniques 2000, 29:332-337.
26. Thellin O., Zorzi W., Lakaye B., De Borman B., Coumans B., Hennen G., Grisar T., Igout A., Heinen E. Housekeeping genes as internal standards: use and limits. J.Biotechnol. 1999, 75:291-295.
27. Tichopad A., Didier A., Pfaffl M.W. Inhibition of real-time RT-PCR quantification due to tissue-specific contaminants. Mol. Cell. Probes 2004, 18:45-50.
28. Tichopad A., Dilger M., Schwarz G., Pfaffl M.W. Standardized determination of real-time PCR efficiency from a single reaction set-up. Nucleic Acids Res. 2003, 31:e122.
29. Tichopad A., Kitchen R., Riedmaier I., Becker C., Stahlberg A., Kubista M. Design and optimization of reverse-transcription quantitative PCR experiments. Clin. Chem. 2009, 55:1816-1823.
30. Tsuji N., Kamagata C., Furuya M., Kobayashi D., Yagihashi A., Morita T., Horita S., Watanabe N. Selection of an internal control gene for quantitation of mRNA in colonic tissues. Anticancer Res. 2002, 22:4173-4178.
31. Vandesompele J., De Preter K., Pattyn F., Poppe B., Van Roy N., De Paepe A., Speleman F. Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol. 2002, 3. RESEARCH0034.
32. Warrington J.A., Nair A., Mahadevappa M., Tsyganskaya M. Comparison of human adult and fetal expression and identification of 535 housekeeping/maintenance genes. Physiol. Genomics 2000, 2:143-147.