Validation of putative reference genes for normalization of q-rt-pcr data from paraffin-embedded lymphoid tissue

Diagnostic Molecular Pathology

Volumn 18, Issue 4, 2009, Pages 243-249

  Green, Tina Marie ^a   De Stricker, Karin ^a   Møller, Michael Boe ^a  

^a ODENSE UNIVERSITY HOSPITAL   (Denmark)

Author keywords

Formalin fixation; Lymphoid tissue; Lymphoma; Quantitative real time PCR; Reference genes

Indexed keywords

BETA GLUCURONIDASE; PARAFFIN; TATA BINDING PROTEIN;

AMPLICON; ARTICLE; CONTROLLED STUDY; GENE EXPRESSION; GENE TARGETING; HUMAN; HUMAN TISSUE; LYMPHOID TISSUE; LYMPHOMA; PRIORITY JOURNAL; REAL TIME POLYMERASE CHAIN REACTION; VIRUS ONCOGENE;

DNA, COMPLEMENTARY; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; GENES, NEOPLASM; HUMANS; LYMPH NODES; LYMPHOMA, LARGE B-CELL, DIFFUSE; MOLECULAR DIAGNOSTIC TECHNIQUES; PARAFFIN EMBEDDING; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, MESSENGER;

EID: 74549115838     PISSN: 10529551     EISSN: None     Source Type: Journal    
DOI: 10.1097/PDM.0b013e3181a06f42     Document Type: Article

References (31)

1. Cohen CD, Frach K, Schlondorff D, et al. Quantitative gene expression analysis in renal biopsies: A novel protocol for a highthroughput multicenter application. Kidney Int. 2002;61:133-140.
2. Heid CA, Stevens J, Livak KJ, et al. Real time quantitative PCR. Genome Res. 1996;6:986-994.
3. Paik S, Shak S, Tang G, et al. A multigene assay to predict recurrence of tamoxifen-treated, node-negative breast cancer. N Engl J Med. 2004;351:2817-2826.
4. Cronin M, Pho M, Dutta D, et al. Measurement of gene expression in archival paraffin-embedded tissues: development and performance of a 92-gene reverse transcriptase-polymerase chain reaction assay. Am J Pathol. 2004;164:35-42.
5. Glenn ST, Jones CA, Liang P, et al. Expression profiling of archival renal tumors by quantitative PCR to validate prognostic markers. Biotechniques. 2007;43:639-647.
6. Lehmann U, Kreipe H. Real-time PCR analysis of DNA and RNA extracted from formalin-fixed and paraffin-embedded biopsies. Methods. 2001;25:409-418.
7. Godfrey TE, Kim SH, Chavira M, et al. Quantitative mRNA expression analysis from formalin-fixed, paraffin-embedded tissues using 50 nuclease quantitative reverse transcription-polymerase chain reaction. J Mol Diagn. 2000;2:84-91.
8. Chen J, Byrne GE Jr, Lossos IS. Optimization of RNA extraction from formalin-fixed, paraffin-embedded lymphoid tissues. Diagn Mol Pathol. 2007;16:61-72.
9. 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.
10. Bustin SA. Absolute quantification of mRNA using real-time reverse transcription polymerase chain reaction assays. J Mol Endocrinol. 2000;25:169-193.
11. Lossos IS, Czerwinski DK, Wechser MA, et al. Optimization of quantitative real-time RT-PCR parameters for the study of lymphoid malignancies. Leukemia. 2003;17:789-795.
12. Vandesompele J, De PK, Pattyn F, et al. Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol. 2002;3:RESEARCH-0034.
13. Tricarico C, Pinzani P, Bianchi S, et al. 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.
14. Suzuki T, Higgins PJ, Crawford DR. Control selection for RNA quantitation. Biotechniques. 2000;29:332-337.
15. Dheda K, Huggett JF, Chang JS, et al. The implications of using an inappropriate reference gene for real-time reverse transcription PCR data normalization. Anal Biochem. 2005;344:141-143.
16. Skovgaard K, Mortensen S, Poulsen KT, et al. Validation of putative reference genes for qRT-PCR normalization in tissues and blood from pigs infected with Actinobacillus pleuropneumoniae. Vet Immunol Immunopathol. 2007;118:140-146.
17. Beillard E, Pallisgaard N, van der Velden V, et al. Evaluation of candidate control genes for diagnosis and residual disease detection in leukemic patients using "real-time" quantitative reverse-transcriptase polymerase chain reaction (RQ-PCR)-a Europe against cancer program. Leukemia. 2003;17:2474-2486.
18. geNorm Version 3.5. Ghent, Belgium: Center of Medical Genetics, Ghent University Hospital; 2002.
19. NormFinder Version 2004. Aarhus, Denmark: Molecular Diagnostic Laboratory, Department of Clinical Biochemistry, Aarhus University Hospital, Skejby Sygehus, Denmark; 2004.
20. 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;25:402-408.
21. NanoDrop Technologies I. NanoDrop user's manual, v3.5. rev 7, 2007. 2007.
22. Goldsworthy SM, Stockton PS, Trempus CS, et al. Effects of fixation on RNA extraction and amplification from laser capture microdissected tissue. Mol Carcinog. 1999;25:86-91.
23. Masuda N, Ohnishi T, Kawamoto S, et al. Analysis of chemical modification of RNA from formalin-fixed samples and optimization of molecular biology applications for such samples. Nucleic Acids Res. 1999;27:4436-4443.
24. Mizuno T, Nagamura H, Iwamoto KS, et al. RNA from decadesold archival tissue blocks for retrospective studies. Diagn Mol Pathol. 1998;7:202-208.
25. Koch I, Slotta-Huspenina J, Hollweck R, et al. Real-time quantitative RT-PCR shows variable, assay-dependent sensitivity to formalin fixation: implications for direct comparison of transcript levels in paraffin-embedded tissues. Diagn Mol Pathol. 2006;15: 149-156.
26. Thomazy VA, Luthra R, Uthman MO, et al. Determination of cyclin D1 and CD20 mRNA levels by real-time quantitative RT-PCR from archival tissue sections of mantle cell lymphoma and other non-Hodgkin's lymphomas. J Mol Diagn. 2002;4:201-208.
27. Lossos IS, Czerwinski DK, Alizadeh AA, et al. Prediction of survival in diffuse large-B-cell lymphoma based on the expression of six genes. N Engl J Med. 2004;350:1828-1837.
28. Lion T. Current recommendations for positive controls in RT-PCR assays. Leukemia. 2001;15:1033-1037.
29. Gloghini A, Canal B, Klein U, et al. RT-PCR analysis of RNA extracted from Bouin-fixed and paraffin-embedded lymphoid tissues. J Mol Diagn. 2004;6:290-296.
30. Bernstein PL, Herrick DJ, Prokipcak RD, et al. Control of c-myc mRNA half-life in vitro by a protein capable of binding to a coding region stability determinant. Genes Dev. 1992;6:642-654.
31. Specht K, Richter T, Muller U, et al. Quantitative gene expression analysis in microdissected archival formalin-fixed and paraffinembedded tumor tissue. Am J Pathol. 2001;158:419-429.