A study demonstrating the suitability of the two housekeeping genes PPIA and …

• Abstract
• Background
• Results
• Discussion
• Conclusion
• Methods
• Abbreviations
• References
• Figures
• Tables

Biology Articles » Molecular Biology » In search of suitable reference genes for gene expression studies of human renal cell carcinoma by real-time PCR » References

References

- In search of suitable reference genes for gene expression studies of human renal cell carcinoma by real-time PCR

1.   Bustin SA: Absolute quantification of mRNA using real-time reverse transcription polymerase chain reaction assays.J Mol Endocrinol 2000, 25:169-193.       2.   Rasmussen R: Quantification on the LightCycler.In Rapid Cycle Real-time PCR, Methods and Applications. Edited by: Meuer S, Wittwer C and Nakagawara K. Heidelberg, Springer Press; 2001:21-34.       3.   Thellin O, Zorzi W, Lakaye B, De BB, Coumans B, Hennen G, Grisar T, Igout A, Heinen E: Housekeeping genes as internal standards: use and limits.J Biotechnol 1999, 75:291-295.       4.   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:RESEARCH0034.1-RESEARCH0034.11.       5.   Bustin SA: Quantification of mRNA using real-time reverse transcription PCR (RT-PCR): trends and problems.J Mol Endocrinol 2002, 29:23-39.       6.   Radonic A, Thulke S, Mackay IM, Landt O, Siegert W, Nitsche A: Guideline to reference gene selection for quantitative real-time PCR.Biochem Biophys Res Commun 2004, 313:856-862.       7.   Schmid H, Cohen CD, Henger A, Irrgang S, Schlondorff D, Kretzler M: Validation of endogenous controls for gene expression analysis in microdissected human renal biopsies.Kidney Int 2003, 64:356-360.       8.   Ohl F, Jung M, Xu C, Stephan C, Rabien A, Burkhardt M, Nitsche A, Kristiansen G, Radonic A, Jung K: Gene expression studies in prostate cancer tissue: which reference gene should be selected?J Mol Med 2005, 83:1014-1024.       9.   Ohl F, Jung M, Radonic A, Sachs M, Loening SA, Jung K: Identification and validation of suitable endogenous reference genes for gene expression studies in human bladder cancer.J Urol 2006, 175:1915-1920.       10.   Jemal A, Siegel R, Ward E, Murray T, Xu J, Thun MJ: Cancer statistics, 2007.CA Cancer J Clin 2007, 57:43-66.       11.   Rousseau T, Peyret C, Zerbib M, Thiounn N, Flam T, Debre B: Circumstances of the detection of kidney cancer. Current part of accidental discoveries.J Urol (Paris) 1994, 100:189-195.       12.   Lopez-Beltran A, Scarpelli M, Montironi R, Kirkali Z: 2004 WHO classification of the renal tumors of the adults.Eur Urol 2006, 49:798-805.       13.   Kashyap MK, Kumar A, Emelianenko N, Kashyap A, Kaushik R, Huang R, Khullar M, Sharma SK, Singh SK, Bhargave AK, Upadhyaya SK: Biochemical and molecular markers in renal cell carcinoma: an update and future prospects.Biomarkers 2005, 10:258-294.       14.   Agrawal D, Chen T, Irby R, Quackenbush J, Chambers AF, Szabo M, Cantor A, Coppola D, Yeatman TJ: Osteopontin identified as lead marker of colon cancer progression, using pooled sample expression profiling.J Natl Cancer Inst 2002, 94:513-521.       15.   Bustin SA, Benes V, Nolan T, Pfaffl MW: Quantitative real-time RT-PCR--a perspective.J Mol Endocrinol 2005, 34:597-601.       16.   Petrella BL, Lohi J, Brinckerhoff CE: Identification of membrane type-1 matrix metalloproteinase as a target of hypoxia-inducible factor-2 alpha in von Hippel-Lindau renal cell carcinoma.Oncogene 2005, 24:1043-1052.       17.   Huggett J, Dheda K, Bustin S, Zumla A: Real-time RT-PCR normalisation; strategies and considerations.Genes Immun 2005, 6:279-284.       18.   Yuan J, Takahashi A, Masumori N, Itoh N, Tsukamoto T: Peroxisome proliferator-activated receptor gamma is frequently underexpressed in renal cell carcinoma.Int J Urol 2006, 13:265-270.       19.   Biederman J, Yee J, Cortes P: Validation of internal control genes for gene expression analysis in diabetic glomerulosclerosis.Kidney Int 2004, 66:2308-2314.       20.   Brinkhof B, Spee B, Rothuizen J, Penning LC: Development and evaluation of canine reference genes for accurate quantification of gene expression.Anal Biochem 2006, 356:36-43.       21.   Jorgensen SM, Kleveland EJ, Grimholt U, Gjoen T: Validation of reference genes for real-time polymerase chain reaction studies in atlantic salmon.Mar Biotechnol (NY) 2006, 8:398-408.       22.   Nishimura M, Yaguti H, Yoshitsugu H, Naito S, Satoh T: Tissue distribution of mRNA expression of human cytochrome P450 isoforms assessed by high-sensitivity real-time reverse transcription PCR.Yakugaku Zasshi 2003, 123:369-375.       23.   Haller F, Kulle B, Schwager S, Gunawan B, von HA, Sultmann H, Fuzesi L: Equivalence test in quantitative reverse transcription polymerase chain reaction: confirmation of reference genes suitable for normalization.Anal Biochem 2004, 335:1-9.       24.   Dheda K, Huggett JF, Chang JS, Kim LU, Bustin SA, Johnson MA, Rook GA, Zumla A: The implications of using an inappropriate reference gene for real-time reverse transcription PCR data normalization.Anal Biochem 2005, 344:141-143.       25.   Glare EM, Divjak M, Bailey MJ, Walters EH: beta-Actin and GAPDH housekeeping gene expression in asthmatic airways is variable and not suitable for normalising mRNA levels.Thorax 2002, 57:765-770.       26.   Schmittgen TD, Zakrajsek BA: Effect of experimental treatment on housekeeping gene expression: validation by real-time, quantitative RT-PCR.J Biochem Biophys Methods 2000, 46:69-81.        27.   Schroeder A, Mueller O, Stocker S, Salowsky R, Leiber M, Gassmann M, Lightfoot S, Menzel W, Granzow M, Ragg T: The RIN: an RNA integrity number for assigning integrity values to RNA measurements.BMC Mol Biol 2006, 7:3.       28.   Vandesompele J, De Preter K, Pattyn F, Poppe B, Van Roy N, De Paepe A, Speleman F: GeNorm software manual, last update on March 13, 2007.[http://medgen.ugent.be/~jvdesomp/genorm/geNorm_manual.pdf] 2007.       29.   Andersen CL, Jensen JL, Orntoft TF: 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 2004, 64:5245-5250.       30.   Andersen CL, Jensen JL, Orntoft TF: Molecular Diagnostic Laboratory.[http://www.mdl.dk] 2007.       31.   Murphy RM, Watt KK, Cameron-Smith D, Gibbons CJ, Snow RJ: Effects of creatine supplementation on housekeeping genes in human skeletal muscle using real-time RT-PCR.Physiol Genomics 2003, 12:163-174.       32.   Bustin SA, Nolan T: Pitfalls of quantitative real-time reverse-transcription polymerase chain reaction.J Biomol Tech 2004, 15:155-166.       33.   Tricarico C, Pinzani P, Bianchi S, Paglierani M, Distante V, Pazzagli M, Bustin SA, Orlando C: Quantitative real-time reverse transcription polymerase chain reaction: normalization to rRNA or single housekeeping genes is inappropriate for human tissue biopsies.Anal Biochem 2002, 309:293-300.       34.   Blanquicett C, Johnson MR, Heslin M, Diasio RB: Housekeeping gene variability in normal and carcinomatous colorectal and liver tissues: applications in pharmacogenomic gene expression studies.Anal Biochem 2002, 303:209-214.       35.   Imbeaud S, Graudens E, Boulanger V, Barlet X, Zaborski P, Eveno E, Mueller O, Schroeder A, Auffray C: Towards standardization of RNA quality assessment using user-independent classifiers of microcapillary electrophoresis traces.Nucleic Acids Res 2005, 33:e56.       36.   Mueller O, Lightfoot S, Schroeder A: RNA Integrity Number (RIN) - Standardization of RNA Quality Control.Agilent Technologies 2004.       37.   Almeida A, Paul TJ, Magdelenat H, Radvanyi F: Gene expression analysis by real-time reverse transcription polymerase chain reaction: influence of tissue handling.Anal Biochem 2004, 328:101-108.       38.   Auer H, Lyianarachchi S, Newsom D, Klisovic MI, Marcucci G, Kornacker K: Chipping away at the chip bias: RNA degradation in microarray analysis.Nat Genet 2003, 35:292-293.       39.   Roos-van Groningen MC, Eikmans M, Baelde HJ, de HE, Bruijn JA: Improvement of extraction and processing of RNA from renal biopsies.Kidney Int 2004, 65:97-105.       40.   Janssens N, Janicot M, Perera T, Bakker A: Housekeeping genes as internal standards in cancer research.Mol Diagn 2004, 8:107-113.       41.   Szabo A, Perou CM, Karaca M, Perreard L, Quackenbush JF, Bernard PS: Statistical modeling for selecting housekeeper genes.Genome Biol 2004, 5:R59.       42.   Pfaffl MW, Tichopad A, Prgomet C, Neuvians TP: Determination of stable housekeeping genes, differentially regulated target genes and sample integrity: BestKeeper--Excel-based tool using pair-wise correlations.Biotechnol Lett 2004, 26:509-515.       43.   Silver N, Best S, Jiang J, Thein SL: Selection of housekeeping genes for gene expression studies in human reticulocytes using real-time PCR.BMC Mol Biol 2006, 7:33.       44.   de Kok JB, Roelofs RW, Giesendorf BA, Pennings JL, Waas ET, Feuth T, Swinkels DW, Span PN: Normalization of gene expression measurements in tumor tissues: comparison of 13 endogenous control genes.Lab Invest 2005, 85:154-159.       45.   Sobin LH, Wittekind C: TNM classification of malignant tumours. 6th ed. edition. Edited by: Sobin LH and Wittekind C. New York, Wiley-Liss; 2002:184-187.       46.   Jung M, Xu C, Ohl F, Mager AK, Jung K: Transcriptor first strand cDNA synthesis kit: efficient and fast - a comparison to other kits.Biochemica 2005, 2:16-18.