Selection of reference genes for normalization of qRT-PCR data derived from FFPE breast tumors

Diagnostic Molecular Pathology

Volumn 18, Issue 2, 2009, Pages 103-107

  Drury, Suzanne ^a,b   Anderson, Helen ^a   Dowsett, Mitch ^a  

^a Breakthrough Breast Cancer Research Centre   (United Kingdom)

^b ROYAL MARSDEN HOSPITAL   (United Kingdom)

Author keywords

FFPE; qPCR; Reference gene; RNA

Indexed keywords

39 S RIBOSOMAL PROTEIN L19; BETA ACTIN; BETA GLUCURONIDASE; CD71 ANTIGEN; EPIDERMAL GROWTH FACTOR RECEPTOR 2; ESTROGEN RECEPTOR ALPHA; FK 506 BINDING PROTEIN; GLYCERALDEHYDE 3 PHOSPHATE DEHYDROGENASE; NUCLEAR PROTEIN; PLAKOGLOBIN; PROTEIN PUM1; PROTEIN RPLPO; RIBOSOME PROTEIN; RNA BINDING PROTEIN; TATA BINDING PROTEIN; UNCLASSIFIED DRUG; PARAFFIN;

ARTICLE; BREAST TUMOR; CONTROLLED STUDY; GENE EXPRESSION; GENE TARGETING; HORMONAL THERAPY; HUMAN; HUMAN TISSUE; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; REAL TIME POLYMERASE CHAIN REACTION; RNA DEGRADATION; RNA EXTRACTION; FEMALE; METHODOLOGY; PROTO ONCOGENE; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; STANDARD; TISSUE FIXATION;

BREAST NEOPLASMS; FEMALE; GENES, ERBB-2; HUMANS; PARAFFIN EMBEDDING; REFERENCE STANDARDS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; TISSUE FIXATION;

EID: 67649989073     PISSN: 10529551     EISSN: None     Source Type: Journal    
DOI: 10.1097/PDM.0b013e31817c1ae2     Document Type: Article

References (20)

1. Goelz SE, Hamilton SR, Vogelstein B. Purification of DNA from formaldehyde fixed and paraffin embedded human tissue. Biochem Biophys Res Commun. 1985;130:118-126. (Pubitemid 15249008)
2. Paik S, Kim C, Song Y, et al. Technology insight: application of molecular techniques to formalin-fixed paraffin-embedded tissues from breast cancer. Nat Clin Prac. 2005;2:246-254. (Pubitemid 40812455)
3. 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. (Pubitemid 34164013)
4. Hodges E, Smith J. Isolation of nucleic acid from paraffin embedded tissue for PCR amplification and sequencing of TcR Vβ genes. Leuk Res. 1995;19:183-186.
5. Stanta G, Bonin S. RNA quantitative analysis from fixed and paraffin-embedded tissues: membrane hybridisation and capillary electrophoresis. BioTechniques. 1998;24:271-276. (Pubitemid 28113104)
6. Masuda N, Ohnishi T, Kawamoto S, et al. Analysis of chemical modification of RNA from formalin-fixed samples and optimisation of molecular biology applications for such samples. Nuc Acids Res. 1999;27:4436-4443. (Pubitemid 29533185)
7. Penland SK, Keku TO, Torrice C, et al. RNA expression analysis of formalin-fixed paraffin-embedded tumors. Lab Invest. 2007;87: 383-391. (Pubitemid 46474570)
8. Paik S, Shak S, Tang G, et al. A multigene assay to predict recurrence of tamoxifen-treated, node-negative breast cancer. NEJM. 2004;351:2817-2826. (Pubitemid 40051905)
9. Arcturus Paradise® Sample Quality Assessment Kit. Available at: http://www.bucher.ch/en/products/Arcturus-Bioscience/Paradise- RNA-Isolation-Amplification-Kits/mainColumnParagraphs/04/document/ Paradise%20QC%20Kit-0313-101905.pdf. Accessed on: February 21, 2008.
10. Pérez-Novo CA, Claeys C, Speleman F, et al. Impact of RNA quality on reference gene expression stability. BioTechniques. 2005; 39:52-56.
11. 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: research 0034.1-0034.11.
12. Cronin M, Pho M, Dutta D, et al. Measurement of gene expression in archival paraffin-embedded tissues. Am J Pathol. 2004;164: 35-42.
13. Larionov AA, Dixon JM, Krause A, et al. Validation of reference genes for relative real time PCR to study hormone-dependent gene expression in breast cancer biopsies. Breast Cancer Res Treat. 2005;94:S253.
14. Naora H, Naora H. Differential expression patterns of b-actin mRNA in cells undergoing apoptosis. Biochem Biophys Res Comm. 1995;211:491-496.
15. Rondinelli RH, Epner DE, Tricoli JV. Increased glyceraldehyde-3- phosphate gene expression in late pathological stage human prostate cancer. Prostate Cancer Prostatic Dis. 1995;1:66-72.
16. Szabo A, Perou CM, Karaca M, et al. Statistical modelling for selecting housekeeper genes. Genome Biol. 2004;5:R59.
17. van Wezel T, Lombaerts M, van Roon EH, et al. Expression analysis of candidate breast tumor suppressor genes on chromosome 16q. Breast Cancer Res. 2005;7:R998-R1004.
18. de Kok JB, Roelofs RW, Giesendorf BA, et al. Normalization of gene expression measurements in tumor tissues: comparison of 13 endogenous control genes. Lab Invest. 2005;85:154-159.
19. 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. (Pubitemid 23086133)
20. geNorm [software] Version 3.4. Available at: http://medgen.ugent.be/ Bjvdesomp/genorm/.