A multiplex endpoint RT-PCR assay for quality assessment of RNA extracted from formalin-fixed paraffin-embedded tissues

BMC Biotechnology

Volumn 10, Issue , 2010, Pages

  Takano, Elena A ^a   Mikeska, Thomas ^a,b   Dobrovic, Alexander ^a,b   Byrne, David J ^a   Fox, Stephen B ^a,b  

^a PETER MACCALLUM CANCER CENTRE   (Australia)

^b UNIVERSITY OF MELBOURNE   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

AMPLICONS; AMPLIFICATION PRODUCTS; BREAST TUMOUR; CHEMICALLY MODIFIED; DIFFERENT PROTOCOLS; FORMALIN; GEL ELECTROPHORESIS; PCR ASSAY; QUALITY ASSESSMENT; QUANTITATIVE REAL TIME PCR; REVERSE TRANSCRIPTION; RNA EXTRACTION; RNA QUALITY; TARGET SEQUENCES;

ASSAYS; ELECTROPHORESIS; EXTRACTION; FORMALDEHYDE; GENES; HISTOLOGY; MULTIPLEXING; PARAFFIN WAXES; PARAFFINS; QUALITY CONTROL; RATING; RNA; TRANSCRIPTION;

POLYMERASE CHAIN REACTION;

COMPLEMENTARY DNA; FORMALDEHYDE; MESSENGER RNA; PARAFFIN; RNA;

ARTICLE; BREAST TUMOR; CONTROLLED STUDY; GENE EXPRESSION; QUALITY CONTROL; REAL TIME POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA ANALYSIS; RNA DEGRADATION; RNA EXTRACTION; CHEMISTRY; COMPARATIVE STUDY; FEMALE; GENETICS; HUMAN; METHODOLOGY;

BREAST NEOPLASMS; FEMALE; FORMALDEHYDE; HUMANS; PARAFFIN EMBEDDING; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA; RNA, NEOPLASM;

EID: 78650085766     PISSN: None     EISSN: 14726750     Source Type: Journal    
DOI: 10.1186/1472-6750-10-89     Document Type: Article

References (42)

1. Farragher SM, Tanney A, Kennedy RD, Harkin DP. RNA expression analysis from formalin fixed paraffin embedded tissues. Histochem Cell Biol 2008, 130:435-445. 10.1007/s00418-008-0479-7, 18679706.
2. Medeiros F, Rigl CT, Anderson GG, Becker SH, Halling KC. Tissue handling for genome-wide expression analysis: a review of the issues, evidence, and opportunities. Arch Pathol Lab Med 2007, 131:1805-1816.
3. von Ahlfen S, Missel A, Bendrat K, Schlumpberger M. Determinants of RNA quality from FFPE samples. PLoS One 2007, 2:e1261. 10.1371/journal.pone.0001261, 2092395, 18060057.
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, 27:4436-4443. 10.1093/nar/27.22.4436, 148727, 10536153.
5. Park YN, Abe K, Li H, Hsuih T, Thung SN, Zhang DY. Detection of hepatitis C virus RNA using ligation-dependent polymerase chain reaction in formalin-fixed, paraffin-embedded liver tissues. Am J Pathol 1996, 149:1485-1491. 1865282, 8909238.
6. Cronin M, Pho M, Dutta D, Stephans JC, Shak S, Kiefer MC, Esteban JM, Baker JB. 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. 1602211, 14695316.
7. Antonov J, Goldstein DR, Oberli A, Baltzer A, Pirotta M, Fleischmann A, Altermatt HJ, Jaggi R. 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. 10.1038/labinvest.3700303, 15951835.
8. Waddell N, Cocciardi S, Johnson J, Healey S, Marsh A, Riley J, Silva L, Vargas AC, Reid L, , et al. kConFab Investigators Gene expression profiling of formalin-fixed, paraffin-embedded familial breast tumours using the whole genome-DASL assay. J Pathol 2010, 221:452-461. kConFab Investigators.
9. Bibikova M, Talantov D, Chudin E, Yeakley JM, Chen J, Doucet D, Wickham E, Atkins D, Barker D, Chee M, et al. Quantitative gene expression profiling in formalin-fixed, paraffin-embedded tissues using universal bead arrays. Am J Pathol 2004, 165:1799-1807. 1618650, 15509548.
10. Specht K, Richter T, Muller U, Walch A, Werner M, Hofler H. Quantitative gene expression analysis in microdissected archival formalin-fixed and paraffin-embedded tumor tissue. Am J Pathol 2001, 158:419-429. 1850313, 11159180.
11. Fleige S, Pfaffl MW. RNA integrity and the effect on the real-time qRT-PCR performance. Mol Aspects Med 2006, 27:126-139. 10.1016/j.mam.2005.12.003, 16469371.
12. Penland SK, Keku TO, Torrice C, He X, Krishnamurthy J, Hoadley KA, Woosley JT, Thomas NE, Perou CM, Sandler RS, et al. RNA expression analysis of formalin-fixed paraffin-embedded tumors. Lab Invest 2007, 87:383-391.
13. Glasel JA. Validity of nucleic acid purities monitored by 260 nm/280 nm absorbance ratios. Biotechniques 1995, 18:62-63.
14. Manchester KL. Value of A260/A280 ratios for measurement of purity of nucleic acids. Biotechniques 1995, 19:208-210.
15. Manchester KL. Use of UV methods for measurement of protein and nucleic acid concentrations. Biotechniques 1996, 20:968-970.
16. 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. 10.1093/nar/gni054, 1072807, 15800207.
17. Schroeder A, Mueller O, Stocker S, Salowsky R, Leiber M, Gassmann M, Lightfoot S, Menzel W, Granzow M, Ragg T, et al. The RIN: an RNA integrity number for assigning integrity values to RNA measurements. BMC Mol Biol 2006, 7:3. 10.1186/1471-2199-7-3, 1413964, 16448564.
18. 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. 10.1038/ng1203-292, 14647279.
19. Nolan T, Hands RE, Bustin SA. Quantification of mRNA using real-time RT-PCR. Nat Protoc 2006, 1:1559-1582. 10.1038/nprot.2006.236, 17406449.
20. Liu H, Huang X, Zhang Y, Ye H, El Hamidi A, Kocjan G, Dogan A, Isaacson PG, Du M-Q. Archival fixed histologic and cytologic specimens including stained and unstained materials are amenable to RT-PCR. Diagn Mol Pathol 2002, 11:222-227. 10.1097/00019606-200212000-00005, 12459638.
21. van Maldegem F, de Wit M, Morsink F, Musler A, Weegenaar J, van N, Carel JM. Effects of processing delay, formalin fixation, and immunohistochemistry on RNA Recovery From Formalin-fixed Paraffin-embedded Tissue Sections. Diagn Mol Pathol 2008, 17:51-58.
22. Fedorowicz G, Guerrero S, Wu TD, Modrusan Z. Microarray analysis of RNA extracted from formalin-fixed, paraffin-embedded and matched fresh-frozen ovarian adenocarcinomas. BMC Med Genomics 2009, 2:23. 10.1186/1755-8794-2-23, 2694827, 19426511.
23. 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. 10.1016/j.bbrc.2003.11.177, 14706621.
24. Ohl F, Jung M, Radonic A, Sachs M, Loening SA, Jung K. Identification and validation of suitable endogenous reference genes for gene expression studies of human bladder cancer. J Urol 2006, 175:1915-1920. 10.1016/S0022-5347(05)00919-5, 16600798.
25. Jung M, Ramankulov A, Roigas J, Johannsen M, Ringsdorf M, Kristiansen G, Jung K. In search of suitable reference genes for gene expression studies of human renal cell carcinoma by real-time PCR. BMC Mol Biol 2007, 8:47. 10.1186/1471-2199-8-47, 1913536, 17559644.
26. Gao Q, Wang X-Y, Fan J, Qiu S-J, Zhou J, Shi Y-H, Xiao Y-S, Xu Y, Huang XW, Sun J, et al. Selection of reference genes for real-time PCR in human hepatocellular carcinoma tissues. J Cancer Res Clin Oncol 2008, 134:979-986. 10.1007/s00432-008-0369-3, 18317805.
27. Valente V, Teixeira SA, Neder L, Okamoto OK, Oba-Shinjo SM, Marie SKN, Scrideli CA, Paco-Larson ML, Carlotti CGJ. Selection of suitable housekeeping genes for expression analysis in glioblastoma using quantitative RT-PCR. BMC Mol Biol 2009, 10:17. 10.1186/1471-2199-10-17, 2661085, 19257903.
28. Drury S, Anderson H, Dowsett M. Selection of REFERENCE genes for normalization of qRT-PCR data derived from FFPE breast tumors. Diagn Mol Pathol 2009, 18:103-107. 10.1097/PDM.0b013e31817c1ae2, 19430294.
29. Kreth S, Heyn J, Grau S, Kretzschmar HA, Egensperger R, Kreth FW. Identification of valid endogenous control genes for determining gene expression in human glioma. Neuro Oncol 2010, 12:570-579. 10.1093/neuonc/nop072, 20511187.
30. Wilfinger WW, Mackey K, Chomczynski P. Effect of pH and ionic strength on the spectrophotometric assessment of nucleic acid purity. Biotechniques 1997, 22:474-6-478-81.
31. Mouritzen P, Nielsen PS, Jacobsen N, Noerholm M, Lomholt C, Pfundheller HM, Ramsing NB, Kauppinen S, Tolstrup N. ProbeLibrary - Expression profiling 99% of all human genes using only 90 dual-labeled real-time PCR Probes. Biotechniques 2004, 37:492-495.
32. Mikeska T, Dobrovic A. Validation of a primer optimisation matrix to improve the performance of reverse transcription - quantitative real-time PCR assays. BMC Res Notes 2009, 2:112. 10.1186/1756-0500-2-112, 2706253, 19549292.
33. Bustin SA, Benes V, Garson JA, Hellemans J, Huggett J, Kubista M, Mueller R, Nolan T, Pfaffl MW, Shipley GL, et al. The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin Chem 2009, 55:611-622. 10.1373/clinchem.2008.112797, 19246619.
34. Gallup JM, Ackermann MR. The 'PREXCEL-Q Method' for qPCR. Int J Biomed Sci 2008, 4:273-293. 2744046, 19759920.
35. Mestdagh P, Feys T, Bernard N, Guenther S, Chen C, Speleman F, Vandesompele J. High-throughput stem-loop RT-qPCR miRNA expression profiling using minute amounts of input RNA. Nucleic Acids Res 2008, 36:e143. 10.1093/nar/gkn725, 2588502, 18940866.
36. 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. 10.1186/1471-2199-8-118, 2233637, 18154675.
37. van Dongen JJM, Langerak AW, Bruggemann M, Evans PAS, Hummel M, Lavender FL, Delabesse E, Davi F, Schuuring E, Garcia-Sanz R, et al. Design and standardization of PCR primers and protocols for detection of clonal immunoglobulin and T-cell receptor gene recombinations in suspect lymphoproliferations: report of the BIOMED-2 Concerted Action BMH4-CT98-3936. Leukemia 2003, 17:2257-2317. 10.1038/sj.leu.2403202, 14671650.
38. Ohl F, Jung M, Xu C, Stephan C, Rabien A, Burkhardt M, Nitsche A, Kristiansen G, Loening SA, Radonic A, et al. Gene expression studies in prostate cancer tissue: which reference gene should be selected for normalization?. J Mol Med 2005, 83:1014-1024. 10.1007/s00109-005-0703-z, 16211407.
39. Godfrey TE, Kim SH, Chavira M, Ruff DW, Warren RS, Gray JW, Jensen RH. Quantitative mRNA expression analysis from formalin-fixed, paraffin-embedded tissues using 5' nuclease quantitative reverse transcription-polymerase chain reaction. J Mol Diagn 2000, 2:84-91. 1906896, 11272893.
40. Paik S, Shak S, Tang G, Kim C, Baker J, Cronin M, Baehner FL, Walker MG, Watson D, Park T, et al. A multigene assay to predict recurrence of tamoxifen-treated, node-negative breast cancer. N Engl J Med 2004, 351:2817-2826. 10.1056/NEJMoa041588, 15591335.
41. Cronin M, Sangli C, Liu M-L, Pho M, Dutta D, Nguyen A, Jeong J, Wu J, Langone KC, Watson D, et al. Analytical validation of the Oncotype DX genomic diagnostic test for recurrence prognosis and therapeutic response prediction in node-negative, estrogen receptor-positive breast cancer. Clin Chem 2007, 53:1084-1091. 10.1373/clinchem.2006.076497, 17463177.
42. Rasmussen R. Quantification on the LightCycler. Rapid Cycle Real-Time PCR: Methods and Applications 2001, 21-34. Springer, Heidelberg, Germany, Meuer SC, Wittwer C, Nakagawara K.