Correcting false gene expression measurements from degraded RNA using RTQ-PCR

Diagnostic Molecular Pathology

Volumn 16, Issue 1, 2007, Pages 38-49

  Port, Matthias ^a,b   Schmelz, Hans Ulrich ^a,c,e   Stassen, Tanja ^d   Müeller, Kerstin ^a   Stockinger, Marcus ^a   Obermair, Richard ^a   Abend, Michael ^a  

^a Bundeswehr Institute of Radiobiology   (Germany)

^b HANNOVER MEDICAL SCHOOL   (Germany)

^c BUNDESWEHRZENTRALKRANKENHAUS KOBLENZ   (Germany)

^d UNIVERSITY OF MUNICH   (Germany)

^e Institut fur Radiobiologie der Bundeswehr   (Germany)

Author keywords

Correction of false gene expression measurements; House keeping genes; RNA degradation; RTQ PCR; Simulation of RNA degradation

Indexed keywords

PROTEIN BAX; PROTEIN BCL 2; RIBONUCLEASE; RNA;

ADULT; AGED; ANIMAL CELL; ARTICLE; CONTROLLED STUDY; FEMALE; GENE EXPRESSION; HISTOLOGY; HOUSEKEEPING GENE; HUMAN; HUMAN CELL; HUMAN TISSUE; IN VITRO STUDY; IN VIVO STUDY; MALE; MOLECULAR MODEL; MOUSE; NONHUMAN; PRIORITY JOURNAL; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA DEGRADATION; RNA ISOLATION;

ANIMALS; CELL LINE, TUMOR; DOGS; ETHANOL; GENE EXPRESSION; HUMANS; KINETICS; MICE; NEOPLASMS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RIBONUCLEASES; RNA STABILITY; RNA, NEOPLASM; SENSITIVITY AND SPECIFICITY;

EID: 34247563337     PISSN: 10529551     EISSN: None     Source Type: Journal    
DOI: 10.1097/01.pdm.0000213472.70054.94     Document Type: Article

References (17)

1. Mizuno T, Nagamura H, Iwamoto KS, et al. RNA from decades-old archival tissue blocks for retrospective studies. Diagn Mol Pathol. 1998;7:202-208.
2. Akyol G, Dash S, Shieh YS, et al. Detection of hepatitis C virus RNA sequences by polymerase chain reaction in fixed liver tissue. Mod Pathol. 1992;5:501-504.
3. Anderson J, Renshaw J, McManus A, et al. Amplification of the t(2; 13) and t(1; 13) translocations of alveolar rhabdomyosarcoma in small formalin-fixed biopsies using a modified reverse transcriptase polymerase chain reaction. Am J Pathol. 1997;150:477-482.
4. Auerbach C, Moutschen-Dahmen M, Moutschen J. Genetic and cytogenetical effects of formaldehyde and related compounds. Mutat Res. 1977;39:317-361.
5. Ben Ezra J, Johnson DA, Rossi J, et al. Effect of fixation on the amplification of nucleic acids from paraffin-embedded material by the polymerase chain reaction. J Histochem Cytochem. 1991;39:351-354.
6. Bresters D, Schipper ME, Reesink HW, et al. The duration of fixation influences the yield of HCV cDNA-PCR products from formalin-fixed, paraffin-embedded liver tissue. J Virol Methods. 1994;48:267-272.
7. Almeida A, Paul TJ, Magdelenat H, et al. Gene expression analysis by real-time reverse transcription polymerase chain reaction: influence of tissue handling. Anal Biochem. 2004;328:101-108.
8. Port M, Schmelz HU, Stockinger M, et al. Gene expression profiling in seminoma and nonseminoma. J Clin Oncol. 2005;23:58-69.
9. Finke J, Fritzen R, Ternes P, et al. An improved strategy and a useful housekeeping gene for RNA analysis from formalin-fixed, paraffin-embedded tissues by PCR. Biotechniques. 1993;14:448-453.
10. Foss RD, Guha-Thakurta N, Conran RM, et al. Effects of fixative and fixation time on the extraction and polymerase chain reaction amplification of RNA from paraffin-embedded tissue. Comparison of two housekeeping gene mRNA controls. Diagn Mol Pathol. 1994;3:148-155.
11. Greer CE, Peterson SL, Kiviat NB, et al. PCR amplification from paraffin-embedded tissues. Effects of fixative and fixation time. Am J Clin Pathol. 1991;95:117-124.
12. Laguna MP, Pizzocaro G, Kleep O, et al. EAU guidelines on testicular cancer. Eur Ural. 2001;40:102-110.
13. Stassen T, Port M, Nuyken I, et al. Radiation-induced gene expression in MCF-7 cells. Int J Radiat Biol. 2003;79:319-331.
14. Specht K, Richter T, Muller U, et al. Quantitative gene expression analysis in microdissected archival formalin-fixed and paraffin-embedded tumor tissue. Am J Pathol. 2001;158:419-429.
15. Perlmutter MA, Best CJ, Gillespie JW, et al. Comparison of snap freezing versus ethanol fixation for gene expression profiling of tissue specimens. J Mol Diagn. 2004;6:371-377.
16. Antonov J, Goldstein DR, Oberli A, et al. Reliable gene expression measurements from degraded RNA by quantitative real-time PCR depend on short amplicons and a proper normalization. Lab Invest. 2005;85:1040-1050.
17. Vandesompele J, De Preter K, 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:RESEARCH0034.