Nucleic acid extraction methods from fixed and paraffin-embedded tissues in cancer diagnostics

Expert Review of Molecular Diagnostics

Volumn 13, Issue 3, 2013, Pages 271-282

  Bonin, Serena ^a   Stanta, Giorgio ^a  

^a UNIVERSITY OF TRIESTE   (Italy)

Author keywords

quality control; RNA; tissue processing

Indexed keywords

FORMALDEHYDE; NUCLEIC ACID; PARAFFIN;

AUTOMATION; CANCER DIAGNOSIS; CHEMICAL MODIFICATION; CLINICAL PRACTICE; CROSS LINKING; CULTURE MEDIUM; DNA EXTRACTION; FALSE NEGATIVE RESULT; HEAT TREATMENT; HOSPITAL ORGANIZATION; HUMAN; IMMUNOHISTOCHEMISTRY; INCUBATION TEMPERATURE; ISCHEMIA; MOLECULAR DIAGNOSTICS; MOLECULAR PATHOLOGY; PERSONALIZED MEDICINE; PROTEIN DEGRADATION; PROTEIN EXPRESSION; QUALITY CONTROL; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; REVIEW; RNA EXTRACTION; RNA ISOLATION; TISSUE FIXATION; TISSUE SECTION; TREATMENT RESPONSE; WORKFLOW;

AUTOMATION, LABORATORY; DNA; HUMANS; MOLECULAR DIAGNOSTIC TECHNIQUES; NEOPLASMS; PARAFFIN EMBEDDING; RNA; TISSUE FIXATION;

EID: 84876105335     PISSN: 14737159     EISSN: 17448352     Source Type: Journal    
DOI: 10.1586/erm.13.14     Document Type: Review

References (99)

1. Oktay MH, Hui P. Molecular pathology as the driving force for personalized oncology. Expert Rev. Mol. Diagn. 12(8), 811-813 (2012
2. Anderson SM. Laboratory methods for KRAS mutation analysis. Expert Rev. Mol. Diagn. 11(6), 635-642 (2011
3. Lade-Keller J, Romer KM, Guldberg P et al. Evaluation of BRAF mutation testing methodologies in formalin-fixed paraffinembedded cutaneous melanomas. JMD 15(1), 70-80 (2012
4. Ellison G, Zhu G, Moulis A, Dearden S, Speake G, McCormack R. EGFR mutation testing in lung cancer: a review of available methods and their use for analysis of tumour tissue and cytology samples. J. Clin. Pathol. 66(2), 79-89 (2013
5. Stanta G. Guidelines for Molecular Analysis in Archive Tissues. Springer-Verlag, Berlin Heidelberg, Germany 21-29 (2011
6. Burgemeister R. Laser capture microdissection of FFPE tissue sections bridging the gap between microscopy and molecular analysis. Methods Mol. Biol. 724, 105-115 (2011
7. Espinosa E, Vara JA, Navarro IS et al. Gene profiling in breast cancer: time to move forward. Cancer Treat. Rev. 37(6), 416-421 (2011
8. Farragher SM, Tanney A, Kennedy RD, Paul Harkin D. RNA expression analysis from formalin fixed paraffin embedded tissues. Histochem. Cell Biol. 130(3), 435-445 (2008
9. Nair VS, Maeda LS, Ioannidis JP. Clinical outcome prediction by microRNAs in human cancer: a systematic review. J. Natl Cancer Inst. 104(7), 528-540 (2012
10. Takano EA, Mikeska T, Dobrovic A, Byrne DJ, Fox SB. A multiplex endpoint RT-PCR assay for quality assessment of RNA extracted from formalin-fixed paraffinembedded tissues. BMC Biotechnol. 10, 89 (2010
11. Gohlmann H. Formalin-Fixed Paraffin- Embedded Tissues: Methods and Protocols. Al-Mulla F (Ed.). Humana Press, USA, (2011
12. Turashvili G, Yang W, McKinney S et al. Nucleic acid quantity and quality from paraffin blocks: defining optimal fixation, processing and DNA/RNA extraction techniques. Exp. Mol. Pathol. 92(1), 33-43 (2012
13. 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. 131(12), 1805-1816 (2007
14. Chung JY, Braunschweig T, Williams R et al. Factors in tissue handling and processing that impact RNA obtained from formalin-fixed, paraffin-embedded tissue. J. Histochem. Cytochem. 56(11), 1033-1042 (2008
15. Dotti I, Bonin S, Basili G et al. Effects of formalin, methacarn, and FineFIX fixatives on RNA preservation. Diagn. Mol. Pathol. 19(2), 112-122 (2010
16. 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. 27(22), 4436-4443 (1999
17. Meuse CW, Barker PE. Quantitative infrared spectroscopy of formalin-fixed, paraffin-embedded tissue specimens: paraffin wax removal with organic solvents. Appl. Immunohistochem. Mol. Morphol. 17(6), 547-552 (2009
18. Roberts L, Bowers J, Sensinger K, Lisowski A, Getts R, Anderson MG. Identification of methods for use of formalin-fixed, paraffin-embedded tissue samples in RNA expression profiling. Genomics 94(5), 341-348 (2009
19. Gilbert MT, Haselkorn T, Bunce M et al. The isolation of nucleic acids from fixed, paraffin-embedded tissues-which methods are useful when? PLoS ONE 2(6), e537 (2007
20. Banerjee SK, Makdisi WF, Weston AP, Mitchell SM, Campbell DR. Microwavebased DNA extraction from paraffinembedded tissue for PCR amplification. BioTechniques 18(5), 768-770, 772 (1995
21. Lin J, Kennedy SH, Svarovsky T et al. High-quality genomic DNA extraction from formalin-fixed and paraffin-embedded samples deparaffinized using mineral oil. Anal. Biochem. 395(2), 265-267 (2009
22. Okello JB, Zurek J, Devault AM et al. Comparison of methods in the recovery of nucleic acids from archival formalin-fixed paraffin-embedded autopsy tissues. Anal. Biochem. 400(1), 110-117 (2010
23. Gilbert MT, Sanchez JJ, Haselkorn T et al. Multiplex PCR with minisequencing as an effective high-throughput SNP typing method for formalin-fixed tissue. Electrophoresis 28(14), 2361-2367 (2007
24. Chung JY, Braunschweig T, Hewitt SM. Optimization of recovery of RNA from formalin-fixed, paraffin-embedded tissue. Diagn. Mol. Pathol. 15(4), 229-236 (2006
25. Bonin S, Hlubek F, Benhattar J et al. Multicentre validation study of nucleic acids extraction from FFPE tissues. Virchows Arch. 457(3), 309-317 (2010
26. Funabashi KS, Barcelos D, Visona I et al. DNA extraction and molecular analysis of non-tumoral liver, spleen, and brain from autopsy samples: the effect of formalin fixation and paraffin embedding. Pathol. Res. Pract. 208(10), 584-591 (2012
27. Huijsmans CJ, Damen J, van der Linden JC, Savelkoul PH, Hermans MH. Comparative analysis of four methods to extract DNA from paraffin-embedded tissues: effect on downstream molecular applications. BMC Res. Notes 3, 239 (2010
28. Ludyga N, Grunwald B, Azimzadeh O et al. Nucleic acids from long-term preserved FFPE tissues are suitable for downstream analyses. Virchows Arch. 460(2), 131-140 (2012
29. Munoz-Cadavid C, Rudd S, Zaki SR et al. Improving molecular detection of fungal DNA in formalin-fixed paraffin-embedded tissues: comparison of five tissue DNA extraction methods using panfungal PCR. J. Clin. Microbiol. 48(6), 2147-2153 (2010
30. Kotorashvili A, Ramnauth A, Liu C et al. Effective DNA/RNA Coextraction for analysis of microRNAs, mRNAs, and genomic DNA from formalin-fixed paraffin-embedded specimens. PLoS ONE 7(4), e34683 (2012
31. Huang WY, Sheehy TM, Moore LE, Hsing AW, Purdue MP. Simultaneous recovery of DNA and RNA from formalin-fixed paraffin-embedded tissue and application in epidemiologic studies. Cancer Epidemiol. Biomarkers Prev. 19(4), 973-977 (2010
32. Chung JY, Yi JM, Xie R et al. A pressure cooking-based DNA extraction from archival formalin-fixed, paraffin-embedded tissue. Anal. Biochem. 425(2), 128-134 (2012
33. von Ahlfen S, Missel A, Bendrat K, Schlumpberger M. Determinants of RNA quality from FFPE samples. PLoS ONE 2(12), e1261 (2007
34. Doleshal M, Magotra AA, Choudhury B, Cannon BD, Labourier E, Szafranska AE. Evaluation and validation of total RNA extraction methods for microRNA expression analyses in formalin-fixed, paraffin-embedded tissues. J. Mol. Diagn. 10(3), 203-211 (2008
35. Rupp GM, Locker J. Purification and analysis of RNA from paraffin-embedded tissues. BioTechniques 6(1), 56-60 (1988
36. Stanta G, Schneider C. RNA extracted from paraffin-embedded human tissues is amenable to analysis by PCR amplification. BioTechniques 11(3), 304, 306, 308 (1991
37. 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. 8, 118 (2007
38. Li J, Smyth P, Cahill S et al. Improved RNA quality and TaqMan Pre-amplification method (PreAmp) to enhance expression analysis from formalin fixed paraffin embedded (FFPE) materials. BMC Biotechnol. 8, 10 (2008
39. Oberli A, Popovici V, Delorenzi M et al. Expression profiling with RNA from formalin-fixed, paraffin-embedded material. BMC Med. Genomics 1, 9 (2008
40. van Maldegem F, de Wit M, Morsink F, Musler A, Weegenaar J, van Noesel CJ. Effects of processing delay, formalin fixation, and immunohistochemistry on RNA recovery from formalin-fixed paraffin-embedded tissue sections. Diagn. Mol. Pathol. 17(1), 51-58 (2008
41. Abramovitz M, Ordanic-Kodani M, Wang Y et al. Optimization of RNA extraction from FFPE tissues for expression profiling in the DASL assay. BioTechniques 44(3), 417-423 (2008
42. Ton CC, Vartanian N, Chai X et al. Gene expression array testing of FFPE archival breast tumor samples: an optimized protocol for WG-DASL sample preparation. Breast Cancer Res. Treat. 125(3), 879-883 (2011
43. Hewitt SM, Lewis FA, Cao Y et al. Tissue handling and specimen preparation in surgical pathology: issues concerning the recovery of nucleic acids from formalinfixed, paraffin-embedded tissue. Arch. Pathol. Lab. Med. 132(12), 1929-1935 (2008
44. Khokhar SK, Mitui M, Leos NK, Rogers BB, Park JY. Evaluation of Maxwell® 16 for automated DNA extraction from whole blood and formalin-fixed paraffin embedded (FFPE) tissue. Clin. Chem. Lab. Med. 50(2), 267-272 (2012
45. van Eijk R, Stevens L, Morreau H, van Wezel T. Assessment of a fully automated high-throughput DNA extraction method from formalin-fixed, paraffin-embedded tissue for KRAS, and BRAF somatic mutation analysis. Exp. Mol. Pathol. 94(1), 121-125 (2013
46. Bohmann K, Hennig G, Rogel U et al. RNA extraction from archival formalinfixed paraffin-embedded tissue: a comparison of manual, semiautomated, and fully automated purification methods. Clin. Chem. 55(9), 1719-1727 (2009
47. Dundas N, Leos NK, Mitui M, Revell P, Rogers BB. Comparison of automated nucleic acid extraction methods with manual extraction. J. Mol. Diagn. 10(4), 311-316 (2008
48. Duval K, Aubin RA, Elliott J et al. Optimized manual and automated recovery of amplifiable DNA from tissues preserved in buffered formalin and alcohol-based fixative. Forensic Sci. Int. Genet. 4(2), 80-88 (2010
49. Niland EE, McGuire A, Cox MH, Sandusky GE. High quality DNA obtained with an automated DNA extraction method with 70+ year old formalin-fixed celloidin-embedded (FFCE) blocks from the indiana medical history museum. Am. J. Transl. Res. 4(2), 198-205 (2012
50. Sam SS, Lebel KA, Bissaillon CL, Tafe LJ, Tsongalis GJ, Lefferts JA. Automation of genomic DNA isolation from formalinfixed, paraffin-embedded tissues. Pathol. Res. Pract. 208(12), 705-707 (2012
51. Hennig G, Gehrmann M, Stropp U et al. Automated extraction of DNA and RNA from a single formalin-fixed paraffinembedded tissue section for analysis of both single-nucleotide polymorphisms and mRNA expression. Clin. Chem. 56(12), 1845-1853 (2010
52. Lehmann A, Schewe C, Hennig G et al. Applicability of a system for fully automated nucleic acid extraction from formalin-fixed paraffin-embedded sections for routine KRAS mutation testing. Diagn. Mol. Pathol. 21(2), 114-119 (2012
53. Dedhia P, Tarale S, Dhongde G, Khadapkar R, Das B. Evaluation of DNA extraction methods and real time PCR optimization on formalin-fixed paraffinembedded tissues. Asian Pac. J. Cancer Prev. 8(1), 55-59 (2007
54. King C, Debruyne R, Kuch M, Schwarz C, Poinar H. A quantitative approach to detect and overcome PCR inhibition in ancient DNA extracts. BioTechniques 47(5), 941-949 (2009
55. Hebeda KM, Van Altena MC, Rombout P, Van Krieken JH, Groenen PJ. PCR clonality detection in Hodgkin lymphoma. J. Hematop. 2(1), 34-41 (2009
56. Dotti I, Bonin S. Integrity of nucleic acids. In: Guidelines for Molecular Analysis in Archive Tissues. Stanta G (Ed.). Springer- Verlag, Berlin, Heidelberg, Germany 81-86 (2011
57. Abramovitz M, Barwick BG, Willis S et al. Molecular characterisation of formalinfixed paraffin-embedded (FFPE) breast tumour specimens using a custom 512-gene breast cancer bead array-based platform. Br. J. Cancer 105(10), 1574-1581 (2011
58. Bibikova M, Yeakley JM, Wang-Rodriguez J, Fan JB. Quantitative expression profiling of RNA from formalin-fixed, paraffinembedded tissues using randomly assembled bead arrays. Methods Mol. Biol. 439, 159-177 (2008
59. Mittempergher L, de Ronde JJ, Nieuwland M et al. Gene expression profiles from formalin fixed paraffin embedded breast cancer tissue are largely comparable to fresh frozen matched tissue. PLoS ONE 6(2), e17163 (2011
60. Rentoft M, Coates PJ, Laurell G, Nylander K. Transcriptional profiling of formalin fixed paraffin embedded tissue: pitfalls and recommendations for identifying biologically relevant changes. PLoS ONE 7(4), e35276 (2012
61. Waddell N, Cocciardi S, Johnson J et al.; kConFab Investigators. Gene expression profiling of formalin-fixed, paraffin-embedded familial breast tumours using the whole genome-DASL assay. J. Pathol. 221(4), 452-461 (2010
62. Nardon E, Donada M, Bonin S, Dotti I, Stanta G. Higher random oligo concentration improves reverse transcription yield of cDNA from bioptic tissues and quantitative RT-PCR reliability. Exp. Mol. Pathol. 87(2), 146-151 (2009
63. Penland SK, Keku TO, Torrice C et al. RNA expression analysis of formalin-fixed paraffin-embedded tumors. Lab. Invest. 87(4), 383-391 (2007
64. Bussolati G, Annaratone L, Medico E, D'Armento G, Sapino A. Formalin fixation at low temperature better preserves nucleic acid integrity. PLoS ONE 6(6), e21043 (2011
65. Viertler C, Groelz D, Gundisch S et al. A new technology for stabilization of biomolecules in tissues for combined histological and molecular analyses. J. Mol. Diagn. 14(5), 458-466 (2012
66. Daniele L, D'armento G, Bussolati G. Preanalytical time interval (PATI) and fixation. In: Guidelines for Molecular Analysis in Archive Tissues. Stanta G (Ed.). Springer-Verlag, Berlin, Heidelberg, Germany UK, 5-11 (2011
67. Xie R, Chung JY, Ylaya K et al. Factors influencing the degradation of archival formalin-fixed paraffin-embedded tissue sections. J. Histochem. Cytochem. 59(4), 356-365 (2011
68. Spruessel A, Steimann G, Jung M et al. Tissue ischemia time affects gene and protein expression patterns within minutes following surgical tumor excision. BioTechniques 36(6), 1030-1037 (2004
69. Bray SE, Paulin FE, Fong SC et al. Gene expression in colorectal neoplasia: modifications induced by tissue ischaemic time and tissue handling protocol. Histopathology 56(2), 240-250 (2010
70. Di Novi C, Minniti D, Barbaro S, Zampirolo MG, Cimino A, Bussolati G. Vacuum-based preservation of surgical specimens: an environmentally-safe step towards a formalin-free hospital. Sci. Total Environ. 408(16), 3092-3095 (2010
71. Bussolati G, Chiusa L, Cimino A, D'Armento G. Tissue transfer to pathology labs: under vacuum is the safe alternative to formalin. Virchows Arch. 452(2), 229-231 (2008
72. Groenen PJ, Blokx WA, Diepenbroek C et al. Preparing pathology for personalized medicine: possibilities for improvement of the pre-analytical phase. Histopathology 59(1), 1-7 (2011
73. Comanescu M, Arsene D, Ardeleanu C, Bussolati G. The mandate for a proper preservation in histopathological tissues. Rom. J. Morphol. Embryol. 53(2), 233-242 (2012
74. Moggio A, D'Armento G, Bussolati B. Efficient stem cell isolation from under vacuum preserved tissue samples. Organogenesis 8(3), 71-75 (2012
75. Milcheva R, Janega P, Celec P, Russev R, Babal P. Alcohol based fixatives provide excellent tissue morphology, protein immunoreactivity and RNA integrity in paraffin embedded tissue specimens. Acta Histochem. 115(3), 279-289(2012
76. van Essen HF, Verdaasdonk MA, Elshof SM, de Weger RA, van Diest PJ. Alcohol based tissue fixation as an alternative for formaldehyde: influence on immunohistochemistry. J. Clin. Pathol. 63(12), 1090-1094 (2010
77. Boon ME, Kok LP. Theory and practice of combining coagulant fixation and microwave histoprocessing. Biotech. Histochem. 83(6), 261-277 (2008
78. Zanini C, Gerbaudo E, Ercole E, Vendramin A, Forni M. Evaluation of two commercial and three home-made fixatives for the substitution of formalin: a formaldehyde-free laboratory is possible. Environ. Health 11, 59 (2012
79. Masir N, Ghoddoosi M, Mansor S et al. RCL2, a potential formalin substitute for tissue fixation in routine pathological specimens. Histopathology 60(5), 804-815 (2012
80. Moelans CB, Oostenrijk D, Moons MJ, van Diest PJ. Formaldehyde substitute fixatives: effects on nucleic acid preservation. J. Clin. Pathol. 64(11), 960-967 (2011
81. Moelans CB, ter Hoeve N, van Ginkel JW, ten Kate FJ, van Diest PJ. Formaldehyde substitute fixatives. Analysis of macroscopy, morphologic analysis, and immunohistochemical analysis. Am. J. Clin. Pathol. 136(4), 548-556 (2011
82. Kothmaier H, Rohrer D, Stacher E, Quehenberger F, Becker KF, Popper HH. Comparison of formalin-free tissue fixatives: a proteomic study testing their application for routine pathology and research. Arch. Pathol. Lab. Med. 135(6), 744-752 (2011
83. Nietner T, Jarutat T, Mertens A. Systematic comparison of tissue fixation with alternative fixatives to conventional tissue fixation with buffered formalin in a xenograft-based model. Virchows Arch. 461(3), 259-269 (2012
84. Nassiri M, Ramos S, Zohourian H, Vincek V, Morales AR, Nadji M. Preservation of biomolecules in breast cancer tissue by a formalin-free histology system. BMC Clin. Pathol. 8, 1 (2008
85. Mahjoub F, Zarei A, Jahanzad I, Shahsiah R, Derakhshandeh S, Najafi M. Comparison of formalin and FineFIX in preserving DNA material in small biopsies. Pathol. Int. 58(10), 678-680 (2008
86. Kahler D, Alexander C, Schultz H et al. Proteomics out of the archive: two-dimensional electrophoresis and mass spectrometry using HOPE-fixed, paraffin-embedded tissues. J. Histochem. Cytochem. 58(3), 221-228 (2010
87. Bellet V, Boissière F, Bibeau F et al. Proteomic analysis of RCL2 paraffinembedded tissues. J. Cell. Mol. Med. 12(5B), 2027-2036 (2008
88. Ergin B, Meding S, Langer R et al. Proteomic analysis of PAX gene-fixed tissues. J. Proteome Res. 9(10), 5188-5196 (2010
89. Mange A, Chaurand P, Perrochia H, Roger P, Caprioli RM, Solassol J. Liquid chromatography-tandem and MALDI imaging mass spectrometry analyses of RCL2/CS100-fixed, paraffin-embedded tissues: proteomics evaluation of an alternate fixative for biomarker discovery. J. Proteome Res. 8(12), 5619-5628 (2009
90. Stanta G, Mucelli SP, Petrera F, Bonin S, Bussolati G. A novel fixative improves opportunities of nucleic acids and proteomic analysis in human archive's tissues. Diagn. Mol. Pathol. 15(2), 115-123 (2006
91. Dabbs DJ. Immunohistochemical protocols: back to the future. Am. J. Clin. Pathol. 129(3), 355-356 (2008
92. Engel KB, Moore HM. Effects of preanalytical variables on the detection of proteins by immunohistochemistry in formalin-fixed, paraffin-embedded tissue. Arch. Pathol. Lab. Med. 135(5), 537-543 (2011
93. Torrente MC, Rios C, Misad C, Ramirez R, Acuna M, Cifuentes L. DNA extraction from formalin-fixed laryngeal biopsies: Comparison of techniques. Acta Otolaryngol. 131(3), 330-333 (2011
94. Jacobson TA, Lundahl J, Mellstedt H, Moshfegh A. Gene expression analysis using long-term preserved formalin-fixed and paraffin-embedded tissue of non-small cell lung cancer. Int. J. Oncol. 38(4), 1075-1081 (2011
95. Linton K, Hey Y, Dibben S et al. Methods comparison for high-resolution transcriptional analysis of archival material on Affymetrix Plus 2.0 and Exon 1.0 microarrays. BioTechniques 47(1), 587-596 (2009
96. Paraffin Sample DNA Extraction (WaxFree DNA). www.trimgen.com/docs/ Flyers/WF-Flyer. pdf
97. Paraffin Sample RNA Extraction (WaxFree RNA). www.trimgen.com/docs/ Flyers/WR-Flyer. pdf
98. Oncotype DX®: Breast Cancer Assay, Oncotype DX®: Colon Cancer Assay. www.oncotypedx.com
99. Bio Theranostics: solutions for metastsatic cancer (2013). www.biotheranostics.com/healthcareprofessionals/hcp