Comparison of methods in the recovery of nucleic acids from archival formalin-fixed paraffin-embedded autopsy tissues

Analytical Biochemistry

Volumn 400, Issue 1, 2010, Pages 110-117

  Okello, John B A ^a   Zurek, Jaymi ^a   Devault, Alison M ^a   Kuch, Melanie ^a   Okwi, Andrew L ^b   Sewankambo, Nelson K ^b   Bimenya, Gabriel S ^b   Poinar, Debi ^a   Poinar, Hendrik N ^a,c,d  

^a MCMASTER UNIVERSITY   (Canada)

^b Makerere UYniversity   (Uganda)

^c MCMASTER UNIVERSITY   (Canada)

^d MCMASTER UNIVERSITY   (Canada)

Author keywords

Archival FFPE tissues; DNA RNA extraction; Histopathology; Inhibition; Nucleic acid; Quantitative PCR

Indexed keywords

BIOMOLECULES; CHLORINE COMPOUNDS; DEVELOPING COUNTRIES; DNA; ENZYME INHIBITION; EXTRACTION; FORMALDEHYDE; HISTOLOGY; NUCLEIC ACIDS; PARAFFINS; RECOVERY; RNA; TISSUE; TISSUE ENGINEERING;

CHLOROFORM EXTRACTION; COMPARISON OF METHODS; DEVELOPING WORLD; DNA CONCENTRATION; EPIDEMIOLOGICAL STUDIES; EXTRACTION METHOD; HISTOPATHOLOGY; QUANTITATIVE PCR;

POLYMERASE CHAIN REACTION;

BETA 2 MICROGLOBULIN; CHLOROFORM; DNA; FORMALDEHYDE; MYC PROTEIN; PHENOL; RNA;

ARTICLE; AUTOPSY; CONTROLLED STUDY; DNA EXTRACTION; EMBEDDING; HUMAN; HUMAN TISSUE; INCUBATION TIME; INTERMETHOD COMPARISON; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; RNA EXTRACTION; SOLVENT EXTRACTION; TISSUE FIXATION;

EID: 77649185945     PISSN: 00032697     EISSN: 10960309     Source Type: Journal    
DOI: 10.1016/j.ab.2010.01.014     Document Type: Article

References (54)

1. Worobey M., Gemmel M., Teuwen D.E., Haselkorn T., Kunstman K., Bunce M., Muyembe J.-J., Kabongo M.J.-M., Kalengayi R.M., Van Marck E., Gilbert M.T.P., and Wolinsky S.M. Direct evidence of extensive diversity of HIV-1 in Kinshasa by 1960. Nature 455 (2008) 661-664
2. Taubenberger J.K., Reid A.H., Krafft A.E., Bijwaard K.E., and Fanning T.G. Initial genetic characterization of the 1918 "Spanish" influenza virus. Science 275 (1997) 1793-1796
3. Abramovitz M., Ordanic-Kodani M., Wang Y., Li Z., Catzavelos C., Bouzyk M., Sledge Jr. G.W., Moreno C.S., and Leyland-Jones B. Optimization of RNA extraction from FFPE tissues for expression profiling in the DASL assay. BioTechniques 44 (2008) 417-423
4. Lehmann U., and Kreipe H. Real-time PCR analysis of DNA and RNA extracted from formalin-fixed and paraffin-embedded biopsies. Methods 25 (2001) 409-418
5. Puchtler H., and Meloan S.N. On the chemistry of formaldehyde fixation and its effects on immunohistochemical reactions. Histochem. Cell Biol. 82 (1985) 201-204
6. Srinivasan M., Sedmak D., and Jewell S. Effect of fixatives and tissue processing on the content and integrity of nucleic acids. Am. J. Pathol. 161 (2002) 1961-1971
7. Romero R., Juston A., Ballantyne J., and Henry B. The applicability of formalin-fixed and formalin-fixed paraffin-embedded tissues in forensic DNA analysis. J. Forensic Sci. 42 (1997) 708-714
8. Okwi A., and Byarugaba W. The prevalence of Karposi's sarcoma (KS) in the Uganda Biopsy Service before and during the AIDS era, 1965-1995. Uganda Med. J. 17 (2000) 5-10
9. Dedhia P., Tarale S., Dhongde G., Khadapkar R., and Das B. Evaluation of DNA extraction methods and real time PCR optimization on formalin-fixed paraffin-embedded tissues. Asian Pac. J. Cancer Prev. 8 (2007) 55-59
10. Doleshal M., Magotra A.A., Choudhury B., Cannon B.D., Labourier E., and Szafranska A.E. Evaluation and validation of total RNA extraction methods for microRNA expression analyses in formalin-fixed, paraffin-embedded tissues. J. Mol. Diagn. 10 (2008) 203-211
11. Gilbert M.T.P., Haselkorn T., Bunce M., Sanchez J.J., Lucas S.B., Jewell L.D., Marck E.V., and Worobey M. The isolation of nucleic acids from fixed, paraffin-embedded tissues: which methods are useful when?. PLoS ONE 2 (2007) e537
12. Goelz S.E., Hamilton S.R., and Vogelstein B. Purification of DNA from formaldehyde fixed and paraffin embedded human tissue. Biochem. Biophys. Res. Commun. 130 (1985) 118-126
13. Rupp G., and Locker J. Purification and analysis of RNA from paraffin-embedded tissues. BioTechniques 6 (1988) 56-60
14. Sato Y., Sugie R., Tsuchiya B., Kameya T., Natori M., and Mukai K. Comparison of the DNA extraction methods for polymerase chain reaction amplification from formalin-fixed and paraffin-embedded tissues. Diagn. Mol. Pathol. 10 (2001) 265-271
15. Shi S.-R., Cote R.J., Wu L., Liu C., Datar R., Shi Y., Liu D., Lim H., and Taylor C.R. DNA extraction from archival formalin-fixed, paraffin-embedded tissue sections based on the antigen retrieval principle: Heating under the influence of pH. J. Histochem. Cytochem. 50 (2002) 1005-1011
16. Shi S.-R., Datar R., Liu C., Wu L., Zhang Z., Cote R.J., and Taylor C.R. DNA extraction from archival formalin-fixed, paraffin-embedded tissues: heat-induced retrieval in alkaline solution. Histochem. Cell Biol. 122 (2004) 211-218
17. Stanta G., Bonin S., and Perin R. In: Rapley R., and Manning D.L. (Eds). RNA Isolation and Characterization Protocols (Methods in Molecular Biology) (1998), Humana, Totowa, NJ 23-26
18. Wu L., Patten N., Yamashiro C., and Chui B. Extraction and amplification of DNA from formalin-fixed, paraffin-embedded tissues. Appl. Immunohistochem. Mol. Morph. 10 (2002) 269-274
19. Rait V.K., Zhang Q., Fabris D., Mason J.T., and O'Leary T.J. Conversions of formaldehyde-modified 2'-deoxyadenosine 5'-monophosphate in conditions modeling formalin-fixed tissue dehydration. J. Histochem. Cytochem. 54 (2006) 301-310
20. Castiglione F., Degl'Innocenti D., Taddei A., Garbini F., Buccoliero A., Raspollini M., Pepi M., Paglierani M., Asirelli G., Freschi G., Bechi P., and Taddei G. Real-time PCR analysis of RNA extracted from formalin-fixed and paraffin-embedded tissues: Effects of the fixation on outcome reliability. Appl. Immunohistochem. Mol. Morph. 15 (2006) 338-342
21. Chaw Y.F., Crane L.E., Lange P., and Shapiro R. Isolation and identification of cross-links from formaldehyde-treated nucleic acids. Biochemistry 19 (1980) 5525-5531
22. Feldman M. Reactions of nucleic acids and nucleoproteins with formaldehyde. Prog. Nucleic Acid Res. Mol. Biol. 13 (1973) 1-49
23. Williams C., Ponten F., Moberg C., Soderkvist P., Uhlen M., Ponten J., Sitbon G., and Lundeberg J. A high frequency of sequence alterations is due to formalin fixation of archival specimens. Am. J. Pathol. 155 (1999) 1467-1471
24. Finke J., Fritzen R., Ternes P., Lange W., and Dolken G. An improved strategy and a useful housekeeping gene for RNA analysis from formalin-fixed, paraffin-embedded tissues by PCR. BioTechniques 143 (1993) 448-453
25. Solomon M., and Varshavsky A. Formaldehyde-mediated DNA-protein cross-linking: a probe for in vivo chromatin structures. Proc. Natl. Acad. Sci. USA 82 (1985) 6470-6474
26. Masuda N., Ohnishi T., Kawamoto S., Monden M., and 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 (1999) 4436-4443
27. Johnson S.A., Morgan D.G., and Finch C.E. Extensive postmortem stability of RNA from rat and human brain. J. Neurosci. Res. 16 (1986) 267-280
28. Lee J., Hever A., Willhite D., Zlotnik A., and Hevezi P. Effects of RNA degradation on gene expression analysis of human postmortem tissues. FASEB J. 19 (2005) 1356-1358
29. Wickham C.L., Boyce M., Joyner M.V., Sarsfield P., Wilkins B.S., Jones D.B., and Ellard S. Amplification of PCR products in excess of 600 base pairs using DNA extracted from decalcified, paraffin wax embedded bone marrow trephine biopsies. Mol. Pathol. 53 (2000) 19-23
30. Coura R., Prolla J.C., Meurer L., and Ashton-Prolla P. An alternative protocol for DNA extraction from formalin fixed and paraffin wax embedded tissue. J. Clin. Pathol. 58 (2005) 894-895
31. Coombs N.J., Gough A.C., and Primrose J.N. Optimisation of DNA and RNA extraction from archival formalin-fixed tissue. Nucleic Acids Res. 27 (1999) e12
32. Chen J., Byrne G.E., and Lossos I.S. Optimization of RNA extraction from formalin-fixed, paraffin-embedded lymphoid tissues. Diagn. Mol. Pathol. 16 (2007) 61-72
33. Shedlock A., Haygood M., Pietsch T., and Bentzen P. Enhanced DNA extraction and PCR amplification of mitochondrial genes from formalin-fixed museum specimens. BioTechniques 22 (1997) 394-400
34. Banerjee S., Makdisi W., Weston A., Mitchell S., and Campbell D. Optimisation of DNA and RNA extraction from archival formalin-fixed tissue. BioTechniques 18 (1995) 768-773
35. Lewis F., Maughan N.J., Smith V., Hillan K., and Quirke P. Unlocking the archive-gene expression in paraffin-embedded tissue. J. Pathol. 195 (2001) 66-71
36. Emmert-Buck M.R., Strausberg R.L., Krizman D.B., Bonaldo M.F., Bonner R.F., Bostwick D.G., Brown M.R., Buetow K.H., Chuaqui R.F., Cole K.A., Duray P.H., Englert C.R., Gillespie J.W., Greenhut S., Grouse L., Hillier L.W., Katz K.S., Klausner R.D., Kuznetzov V., Lash A.E., Lennon G., Linehan W.M., Liotta L.A., Marra M.A., Munson P.J., Ornstein D.K., Prabhu V.V., Prange C., Schuler G.D., Soares M.B., Tolstoshev C.M., Vocke C.D., and Waterston R.H. Molecular profiling of clinical tissue specimens: feasibility and applications. Am. J. Pathol. 156 (2000) 1109-1115
37. Stanta G., and Schneider C. RNA extracted from paraffin-embedded human tissues is amenable to analysis by PCR amplification. BioTechniques 11 (1991) 304-308
38. Gilbert M., Sanchez J., Haselkorn T., Jewell L., Lucas S., Van Marck E., Børsting C., Morling N., and Worobey M. Multiplex PCR with minisequencing as an effective high-throughput SNP typing method for formalin-fixed tissue. Electrophoresis 28 (2007) 2361-2367
39. Benavides J., García-Pariente C., Gelmetti D., Fuertes M., Ferreras M.C., García-Marín J.F., and Pérez V. Effects of fixative type and fixation time on the detection of Maedi Visna virus by PCR and immunohistochemistry in paraffin-embedded ovine lung samples. J. Virol. Methods 137 (2006) 317-324
40. Miething F., Hering S., Hanschke B., and Dressler J. Effect of fixation to the degradation of nuclear and mitochondrial DNA in different tissues. J. Histochem. Cytochem. 54 (2006) 371-374
41. Bonin S., Petrera F., Niccolini B., Stanta G., and CR P. PCR analysis in archival postmortem tissues. Mol. Pathol. 56 (2003) 184-186
42. Hofreiter M., Serre D., Poinar H.N., Kuch M., and Paabo S. Ancient DNA. Nat. Rev. Genet. 2 (2001) 353-359
43. Smith S., Vigilant L., and Morin P.A. The effects of sequence length and oligonucleotide mismatches on 5' exonuclease assay efficiency. Nucleic Acids Res. 30 (2002) e111
44. Bustin S.A., and Nolan T. Pitfalls of quantitative real-time reverse-transcription polymerase chain reaction. J. Biomol. Tech. 15 (2004) 155-166
45. Schwarz C., Debruyne R., Kuch M., McNally E., Schwarcz H., Aubrey A.D., Bada J., and Poinar H. New insights from old bones: DNA preservation and degradation in permafrost preserved mammoth remains. Nucleic Acids Res. 37 (2009) 3215-3229
46. Poinar H.N., Schwarz C., Qi J., Shapiro B., MacPhee R.D.E., Buigues B., Tikhonov A., Huson D.H., Tomsho L.P., Auch A., Rampp M., Miller W., and Schuster S.C. Metagenomics to paleogenomics: large-scale sequencing of mammoth DNA. Science 311 (2006) 392-394
47. King C., Kuch M., Debryune R., and Poinar H. A quantitative approach to detect and overcome PCR inhibition in ancient DNA extracts. BioTechniques 47 (2009) 941-949
48. Godfrey T.E., Kim S.H., Chavira M., Ruff D.W., Warren R.S., Gray J.W., and Jensen R.H. Quantitative mRNA expression analysis from formalin-fixed, paraffin-embedded tissues using 5' nuclease quantitative reverse transcription-polymerase chain reaction. J. Mol. Diagn. 2 (2000) 84-91
49. von Ahlfen S., Missel A., Bendrat K., and Schlumpberger M. Determinants of RNA quality from FFPE samples. PLoS ONE 2 (2007) e1261
50. Cronin M., Pho M., Dutta D., Stephans J.C., Shak S., Kiefer M.C., Esteban J.M., and Baker J.B. 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. 164 (2004) 35-42
51. Sutton D.H., Conn G.L., Brown T., and Lane A.N. The dependence of DNase I activity on the conformation of oligodeoxynucleotides. Biochem. J. 321 (1997) 481-486
52. Bresters D., Schipper M.E.I., Reesink H.W., Boeser-Nunnink B.D.M., and Cuypers H.T.M. The duration of fixation influences the yield of HCV cDNA-PCR products from formalin-fixed, paraffin-embedded liver tissue. J. Virol. Methods 48 (1994) 267-272
53. Schweiger M.R., Kerick M., Timmermann B., Albrecht M.W., Borodina T., Parkhomchuk D., Zatloukal K., and Lehrach H. Genome-wide massively parallel sequencing of formaldehyde fixed-paraffin embedded (FFPE) tumor tissues for copy-number- and mutation-analysis. PLoS ONE 4 (2009) e5548
54. Coudry R.A., Meireles S.I., Stoyanova R., Cooper H.S., Carpino A., Wang X., Engstrom P.F., and Clapper M.L. Successful application of microarray technology to microdissected formalin-fixed, paraffin-embedded tissue. J. Mol. Diagn. 9 (2007) 70-79