Standardization of gene expression quantification by absolute real-time qRT-PCR system using a single standard for marker and reference genes

Biomarker Insights

Volumn 2010, Issue 5, 2010, Pages 79-85

  Zhou, Yi Hong ^a   Raj, Vinay R ^b   Siegel, Eric ^c   Yu, Liping ^d  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF ARKANSAS FOR MEDICAL SCIENCES   (United States)

^c UNIVERSITY OF ARKANSAS FOR MEDICAL SCIENCES   (United States)

^d Ziren Research LLC   (United States)

Author keywords

Biomarkers; Gene expression; qRT PCR; Quantification

Indexed keywords

BETA ACTIN; COMPLEMENTARY DNA; MESSENGER RNA; PHOSPHATIDYLINOSITOL 3,4,5 TRISPHOSPHATE 3 PHOSPHATASE; RIBOSOME PROTEIN; TRANSCRIPTION FACTOR PAX6; TUMOR MARKER;

ARTICLE; BRAIN TUMOR; CONTROLLED STUDY; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENETIC ANALYSIS; GENETIC VARIABILITY; HISTOPATHOLOGY; HUMAN; HUMAN TISSUE; INTERMETHOD COMPARISON; MARKER GENE; PREDICTION; QUANTITATIVE ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; SINGLE STANDARD FOR MARKER AND REFERENCE GENE; STANDARDIZATION;

EID: 77957134390     PISSN: None     EISSN: 11772719     Source Type: Journal    
DOI: 10.4137/bmi.s5596     Document Type: Article

References (19)

1. Zhou YH, et al. The expression of PAX6, PTEN, vascular endothelial growth factor, and epidermal growth factor receptor in gliomas: relationship to tumor grade and survival. Clin Cancer Res. 2003;9(9):3369-75.
2. Zhou YH, et al. Modeling prognosis for patients with malignant astrocytic gliomas: quantifying the expression of multiple genetic markers and clinical variables. Neuro Oncol. 2005;7(4):485-94.
3. Vera-Ramirez L, et al. Gene-expression profiles, tumor microenvironment, and cancer stem cells in breast cancer: Latest advances towards an integrated approach. Cancer Treat Rev. 2010.
4. Hou J, et al. Gene expression-based classification of non-small cell lung carcinomas and survival prediction. PLoS One. 2010;5(4):p. e10312.
5. Varambally S, et al. Integrative genomic and proteomic analysis of prostate cancer reveals signatures of metastatic progression. Cancer Cell. 2005;8(5): 393-406.
6. Verhaak RG, et al. Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1. Cancer Cell. 2010;17(1):98-110.
7. Shi L, et al. The MicroArray Quality Control (MAQC) project shows interand intraplatform reproducibility of gene expression measurements. Nat Biotechnol. 2006;24(9):1151-61.
8. Kuo WP, et al. Analysis of matched mRNA measurements from two different microarray technologies. Bioinformatics. 2002;18(3):405-12.
9. Larsson O, Sandberg R. Lack of correct data format and comparability limits future integrative microarray research. Nat Biotechnol. 2006;24(11):1322-3.
10. katz MH. Multivariable Analysis. 1999, Cambridge: Cambridge University Press.
11. Wong ML, Medrano JF. Real-time PCR for mRNA quantitation. Biotechniques. 2005;39(1):75-85.
12. Canales RD, et al. Evaluation of DNA microarray results with quantitative gene expression platforms. Nat Biotechnol. 2006;24(9):1115-22.
13. Pfaffl MW. A new mathematical model for relative quantification in realtime RT-PCR. Nucleic Acids Res. 2001;29(9):e45.
14. Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods. 2001;25(4):402-8.
15. Rutledge RG, Cote C. Mathematics of quantitative kinetic PCR and the application of standard curves. Nucleic Acids Res. 2003;31(16):e93.
16. Sano T, et al. Differential expression of MMAC/PTEN in glioblastoma multiforme: relationship to localization and prognosis. Cancer Res. 1999;59(8): 1820-4.
17. Schuirmann DJ. A comparison of the two one-sided tests procedure and the power approach for assessing the equivalence of average bioavailability. J Pharmacokinet Biopharm. 1987;15(6):657-80.
18. Berger R, Hsu J. Bioequivalence Trials, Intersection-Union Tests and Equivalence Confidence Sets. Statistical Science. 1996;11:283-319.
19. Hodges JL, Lehmann EL Jr. Hodges-Lehmann Estimators. Encyclopedia of Statistical Sciences. 1983;3(Kotz S, Johnson NL, Read CB, editors):463-5.