Evaluation of reference genes and normalization strategy for quantitative real-time PCR in human pancreatic carcinoma

Disease Markers

Volumn 32, Issue 3, 2012, Pages 203-210

  Mohelnikova Duchonova, Beatrice ^a,b   Oliverius, Martin ^c   Honsova, Eva ^c   Soucek, Pavel ^a  

^a NATIONAL INSTITUTE OF PUBLIC HEALTH   (Czech Republic)

^b CHARLES UNIVERSITY   (Czech Republic)

^c INSTITUTE FOR CLINICAL AND EXPERIMENTAL MEDICINE   (Czech Republic)

Author keywords

carcinoma; normalization; Pancreas; quantification; reference gene; transcript

Indexed keywords

INITIATION FACTOR 2; TRANSCRIPTION FACTOR ELF 1;

ADULT; AGED; ARTICLE; CLINICAL ARTICLE; COMPUTER PROGRAM; CONTROLLED STUDY; EIF2B1 GENE; FEMALE; GENE; GENE CONTROL; GENE EXPRESSION; GENE IDENTIFICATION; GENETIC STABILITY; HUMAN; HUMAN TISSUE; MALE; MRPL19 GENE; PANCREAS CARCINOMA; POP4 GENE; PRIORITY JOURNAL; REAL TIME POLYMERASE CHAIN REACTION; REFERENCE GENE; RNA DEGRADATION;

EID: 84858266162     PISSN: 02780240     EISSN: 18758630     Source Type: Journal    
DOI: 10.3233/DMA-2011-0875     Document Type: Article

References (28)

1. A. Jemal, R. Seigel, J. Xu et al., Cancer statistics 2010, CA Cancer J Clin 60 (2010), 277-300.
2. IHIS CR, Cancer Incidence 2006 in the Czech Republic, Czech Republic, 2009.
3. M. Hidalgo, Pancreatic cancer, New Engl J Med 362 (2010), 1605-1617.
4. M.J. Moore, D. Goldstein, J. Hamm et al., Erlotinib plus gem-citabine compared with gemcitabine alone in patients with advanced pancreatic cancer, a phase III trial of the National Cancer Institute of Canada Clinical Trials Group, J Clin Oncol 25 (2007), 1960-1966. (Pubitemid 46972777)
5. C. Rosty, T. Ueki, P Argani et al., Overexpression of S100A4 in pancreatic ductal adenocarcinomas is associated with poor differentiation and DNA hypomethylation, Am J Pathol 160 (2002), 45-50. (Pubitemid 34052264)
6. S. Fleige, V. Walf, S. Huch et al., Comparison of relative mRNA quantification models and the impact of RNA integrity in quantitative real-time RT-PCR, Biotechnol Lett 28 (2006), 1601-1613. (Pubitemid 44306128)
7. M. Hubackova, R. Vaclavikova, M. Mrhalova et al., NAD(P) H, quinone oxidoreductase 1 Pro187Ser polymorphism and expression do not co-segregate with clinico-pathological char-acteristcs of human mammary tumors, Pharmacogenet Ge-nomics 19 (2009), 505-512.
8. M. Hubackova, R. Vaclavikova, M. Ehrlichova et al., Association of superoxide dismutases and NAD(P)H oxidoreduc-tases with prognosis of patients with breast carcinomas, Int J Cancer (2011), Feb 23. doi, 10.1002/ijc.26006.
9. S.A. Bustin, V. Benes, J.A. Garson et al., The MIQE guidelines, minimum information for publication of quantitative real-time PCR experiments, Clin Chem 55 (2009), 611-622.
10. C. Sharma, K.M. Eltawil, P.D. Renfrew et al., Advances in diagnosis, treatment and palliation of pancreatic carcinoma: 1990-2010, World J Gastroenterol 17 (2011), 867-897.
11. F. Vilardell and C.A. Iacobuzio-Donahue, Cancer gene profiling in pancreatic cancer, Methods Mol Biol 576 (2010), 279-292.
12. H. Zhong and J.W. Simons, Direct comparison of GAPDH, beta-actin, cyclophilin, and 28S rRNA as internal standards for quantifying RNA levels under hypoxia, Biochem Biophys Res Commun 259 (1999), 523-526. (Pubitemid 29335566)
13. C. Blanquicett, M.R. Johnson, M. Heslin et al., Housekeeping gene variability in normal and carcinomatous colorectal and liver tissues, applications in pharmacogenomic gene expression studies, Anal Biochem 303 (2002), 209-214. (Pubitemid 34407587)
14. V.P. Mane, M.A. Heuer, P. Hillyer et al., Systematic method for determining an ideal housekeeping gene for real-time PCR analysis, J Biomol Tech 19 (2008), 342-347.
15. F.L. Greene, A. Trotti III, A.G. Fritz, C.C. Compton, D.R. Byrd and S.B. Edge, eds, AJCC Cancer Staging Handbook-7th ed., 2010, American Joint Committee on Cancer, Chicago, IL, USA, 2009.
16. P. Soucek, P. Anzenbacher, I. Skoumalova et al., Expression of cytochrome P450 genes in CD34+ hematopoietic stem and progenitor cells, Stem Cells 23 (2005), 1417-1422. (Pubitemid 41504929)
17. J. Vandesompele, K. De Preter, F. Pattyn et al., Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes, Genome Biol 3 (2002), research0034.1-0034.11.
18. C.L. Andersen, J.L. Jensen and T.F. Ørntoft, Normalization of Real-Time Quantitative Reverse Transcription-PCR Data, A Model-Based Variance Estimation Approach to Identify Genes Suited for Normalization, Applied to Bladder and Colon Cancer Data Sets, Cancer Res 64 (2004), 5245-5250. (Pubitemid 39006544)
19. S.T. Mees, W.A. Mardin, C. Wendel et al., EP300-a miRNA-regulated metastasis suppressor gene in ductal adenocarcino-mas of the pancreas, Int J Cancer 126 (2010), 114-124.
20. D. Li, W. Ren, X. Wang etal., A modified method using TRIzol reagent and liquid nitrogen produces high-quality RNA from rat pancreas, Appl Biochem Biotechnol 158 (2009), 253-261.
21. U. Rudloff, U. Bhanot, W. Gerald et al., Biobanking of human pancreas cancer tissue: impact of ex-vivo procurement times on RNA quality, Ann Surg Oncol 17 (2010), 2229-2236.
22. S. Fleige and M.W. Pfaffl, RNA integrity and the effect on the real-time qRT-PCR performance, Mol Aspects Med 27 (2006), 126-139.
23. J. Antonov, D.R. Goldstein, A. Oberli et al., Reliable gene expression measurements from degraded RNA by quantitative real-time PCR depend on short amplicons and a proper normalization, Lab Invest 85 (2005), 1040-1050. (Pubitemid 41486428)
24. K.J. Livak and T.D. Schmittgen, Analysis of relative gene expression data using real time quantitative PCR and the 2-deltaCt methods, Methods 25 (2001), 402-408. (Pubitemid 34164012)
25. C. Rubie, K. Kempf, J. Hans et al., Housekeeping gene variability in normal and cancerous colorectal, pancreatic, esophageal, gastric and hepatic tissues, Mol Cell Probes 19 (2005), 101-109. (Pubitemid 40174728)
26. C.W. Chang, W.C. Cheng, C.R. Chen et al., Identification of human housekeeping genes and tissue-selective genes by microarray meta-analysis, PLoS One 6 (2011), e22859.
27. E. Gadaleta, R.J. Cutts, G.P. Kelly et al., A global insight into a cancer transcriptional space using pancreatic data: importance, findings and flaws, Nucleic Acids Res 39 (2011), 7900-7907.
28. J.P. Ioannidis, D.B. Allison, C.A. Ball et al., Repeatability of published microarray gene expression analyses, Nat Genet 41 (2009), 149-155.