Automated extraction of DNA and RNA from a single formalin-fixed paraffin-embedded tissue section for analysis of both single-nucleotide polymorphisms and mRNA expression

Clinical Chemistry

Volumn 56, Issue 12, 2010, Pages 1845-1853

  Hennig, Guido ^a,b   Gehrmann, Mathias ^a   Stropp, Udo ^a   Brauch, Hiltrud ^c,d   Fritz, Peter ^c,d   Eichelbaum, Michel ^c,d   Schwab, Matthias ^c,d,e   Schroth, Werner ^c,d  

^a SIEMENS AG   (Germany)

^b Siemens Healthcare Diagnostics   (Germany)

^c DR MARGARETE FISCHER BOSCH INSTITUTE OF CLINICAL PHARMACOLOGY   (Germany)

^d UNIVERSITY OF TÜBINGEN   (Germany)

^e UNIVERSITY HOSPITAL TÜBINGEN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; DNA TOPOISOMERASE (ATP HYDROLYSING); EPIDERMAL GROWTH FACTOR RECEPTOR 2; EPOXIDE HYDROLASE; ESTROGEN RECEPTOR ALPHA; MATRILYSIN; PROGESTERONE RECEPTOR; RNA; VASCULOTROPIN A;

ARTICLE; AUTOMATION; BIRC5 GENE; BREAST CANCER; CANCER GENETICS; DNA DETERMINATION; DNA EXTRACTION; GENE; GENE EXPRESSION; HUMAN; HUMAN TISSUE; MAJOR CLINICAL STUDY; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA ANALYSIS; RNA EXTRACTION; SINGLE NUCLEOTIDE POLYMORPHISM; TISSUE SECTION;

AUTOMATION, LABORATORY; BREAST NEOPLASMS; CELL LINE, TUMOR; DNA; FEMALE; FIXATIVES; FORMALDEHYDE; GENE EXPRESSION PROFILING; GENOTYPE; HUMANS; PARAFFIN EMBEDDING; POLYMERASE CHAIN REACTION; POLYMORPHISM, SINGLE NUCLEOTIDE; RNA; RNA, MESSENGER; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION; TISSUE FIXATION; TUMOR MARKERS, BIOLOGICAL;

AVES;

EID: 78649897310     PISSN: 00099147     EISSN: 15308561     Source Type: Journal    
DOI: 10.1373/clinchem.2010.151233     Document Type: Article

References (19)

1. Harris L, Fritsche H, Mennel R, Norton L, Ravdin P, Taube S, et al. American Society of Clinical Oncology 2007 update of recommendations for the use of tumor markers in breast cancer. J Clin Oncol 2007;25:5287-312.
2. Wang HL, Lopategui J, Amin MB, Patterson S. KRAS mutation testing in human cancers: the pathologist's role in the era of personalized medicine. Adv Anat Pathol 2010;17:23-32.
3. Mizuno T, Nagamura H, Iwamoto KS, Ito T, Fukuhara T, Tokunaga M, et al. RNA from decades-old archival tissue blocks for retrospective studies. Diagn Mol Pathol 1998;7:202-8. (Pubitemid 29152166)
4. Masuda N, Ohnishi T, Kawamoto S, Monden M, Okubo K. Analysis of chemical modification of RNA from formalin-fixed samples and optimization of molecular biology applications for such samples. Nucleic Acids Res 1999;27:4436-43.
5. Jaremko M, Justenhoven C, Abraham BK, Schroth W, Fritz P, Brod S, et al. MALDI-TOF MS and TaqMan assisted SNP genotyping of DNA isolated from formalin-fixed and paraffin-embedded tissues (FFPET). Hum Mutat 2005;25:232-8.
6. Ribeiro-Silva A, Zhang H, Jeffrey SS. RNA extraction from ten year old formalin-fixed paraffin-embedded breast cancer samples: a comparison of column purification and magnetic bead-based technologies. BMC Mol Biol 2007;8:118-28.
7. Specht K, Richter T, Müller U, Walch A, Werner M, Höfler H. Quantitative gene expression analysis in microdissected archival formalin-fixed and paraffin-embedded tumor tissue. Am J Pathol 2001;158:419-29. (Pubitemid 32158605)
8. Rupp GM, Locker J. Purification and analysis of RNA from paraffin-embedded tissues. Biotechniques 1988;6:56-60.
9. Stanta G, Schneider C. RNA extracted from paraffin-embedded human tissues is amenable to analysis by PCR amplification. Biotechniques 1991;11:304-8.
10. Bohmann K, Hennig G, Rogel U, Poremba C, Mueller BM, Fritz P, et al. RNA extraction from archival formalin-fixed paraffin-embedded tissue: a comparison of manual, semiautomated, and fully automated purification methods. Clin Chem 2009;55:1719-27.
11. Schwers S, Reifenberger E, Gehrmann M, Izmailov A, Bohmann K. A high-sensitivity, medium-density, and target amplification-free planar waveguide microarray system for gene expression analysis of formalin-fixed and paraffin-embedded tissue. Clin Chem 2009;55: 1995-2003.
12. Mueller BM, Kronenwett R, Hennig G, Euting H, Weber K, Bohmann K, et al. Quantitative determination of estrogen receptor, progesterone receptor, and HER2 mRNA in formalin-fixed paraffin-embedded tissue - a new option for predictive biomarker assessment in breast cancer. Diagn Mol Path. Forthcoming.
13. Oeth P, Beaulieu M, Park C, Kosman, D, del Mistro G, van den Boom H, Jurinke C. iPLEXTM assay: increased plexing efficiency and flexibility for MassARRAY® system through single base primer extension with mass-modified terminators. 2007 Sep 27. Sequenom application note. http://www.sequenom.com/ getdoc/52ad1d40- ff33-421f-a26f-58ca91b86364/iPLEX-Application- Note (Accessed November 2010).
14. Tan SH, Lee SC, Goh BC, Wong J. Pharmacogenetics in breast cancer therapy. Clin Cancer Res 2008;14:8027-41.
15. Wirtenberger M, Tchatchou S, Hemminki K, Schmutzhard J, Sutter C, Schmutzler RK, et al. Associations of genetic variants in the estrogen receptor coactivators PPAGC1A, PPARGC1B and EP300 with familial breast cancer. Carcinogenesis 2006;27:2201-8.
16. Rokavec M, Schroth W, Amaral SM, Fritz P, Antoniadou L, Glavac D, et al. A polymrphism in the TC21 promoter associates with an unfavorable tamoxifen treatment outcome in breast cancer. Cancer Res 2008;68:9799-808.
17. Li J, Wang K, Li S, Timmermans-Wielenga V, Rank F, Wiuf C, et al. DNA copy number aberrations in breast cancer by array comparative genomic hybridization. Genomics Proteomics Bioinformatics 2009;7:13-24.
18. Lichy JH, Dalbegue F, Zavar M, Washington C, Tsai MM, Sheng ZM, Taubenberger JK. Genetic heterogeneity in ductal carcinoma of the breast. Lab Invest 2000;80:291-301.
19. Goetz MP, Suman VJ, Couch FJ, Ames MM, Rae JM, Erlander MG, et al. Cytochrome P450 2D6 and homeobox 13/interleukin-17B receptor: combining inherited and tumor gene markers for prediction of tamoxifen resistance. Clin Cancer Res 2008;14:5864-8.