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. 2013 Aug 30;29(5):649–654. doi: 10.1007/s12264-013-1379-y

DNA extraction from fresh-frozen and formalin-fixed, paraffinembedded human brain tissue

Jian-Hua Wang 1,2,✉, Amany Gouda-Vossos 1, Nicolas Dzamko 1, Glenda Halliday 1, Yue Huang 1,✉
PMCID: PMC5562648  PMID: 23996594

Abstract

Both fresh-frozen and formalin-fixed, paraffinembedded (FFPE) human brain tissues are invaluable resources for molecular genetic studies of central nervous system diseases, especially neurodegenerative disorders. To identify the optimal method for DNA extraction from human brain tissue, we compared methods on differently-processed tissues. Fragments of LRRK2 and MAPT (257 bp and 483 bp/245 bp) were amplified for evaluation. We found that for FFPE samples, the success rate of DNA extraction was greater when using a commercial kit than a laboratory-based method (successful DNA extraction from 76% versus 33% of samples). PCR amplicon size and storage period were key factors influencing the success rate of DNA extraction from FFPE samples. In the fresh-frozen samples, the DNA extraction success rate was 100% using either a commercial kit (QIAamp DNA Micro) or a laboratorybased method (sample boiling in 0.1 mol/L NaOH, followed by proteinase K digestion, and then DNA extraction using Chelex-100) regardless of PCR amplicon length or tissue storage time. Although the present results demonstrate that PCR-amplifiable genomic DNA can be extracted from both fresh-frozen and FFPE samples, fresh brain tissue is recommended for DNA extraction in future neuropathological studies.

Keywords: DNA extraction, fresh-frozen human brain tissue, formalin-fixed paraffin-embedded human brain tissue, polymerase chain reaction amplification

Contributor Information

Jian-Hua Wang, Email: wangjh6304@sina.com.

Yue Huang, Email: y.huang@neura.edu.au.

References

  • [1].Andreassen CN, Sorensen FB, Overgaard J, Alsner J. Optimisation and validation of methods to assess single nucleotide polymorphisms (SNPs) in archival histological material. Radiother Oncol. 2004;72:351–356. doi: 10.1016/j.radonc.2004.07.006. [DOI] [PubMed] [Google Scholar]
  • [2].Ferrer I, Armstrong J, Capellari S, Parchi P, Arzberger T, Bell J, et al. Effects of formalin fixation, paraffin embedding, and time of storage on DNA preservation in brain tissue: a BrainNet Europe study. Brain Pathol. 2007;17:297–303. doi: 10.1111/j.1750-3639.2007.00073.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [3].Matevossian A, Akbarian S. J Vis Exp. 2008. Neuronal nuclei isolation from human postmortem brain tissue. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [4].Huang HS, Matevossian A, Jiang Y, Akbarian S. Chromatin immunoprecipitation in postmortem brain. J Neurosci Methods. 2006;156:284–292. doi: 10.1016/j.jneumeth.2006.02.018. [DOI] [PubMed] [Google Scholar]
  • [5].Saldanha J, Gannicliffe A, Itzhaki RF. An improved method for preparing DNA from human brain. J Neurosci Methods. 1984;11:275–279. doi: 10.1016/0165-0270(84)90089-X. [DOI] [PubMed] [Google Scholar]
  • [6].Jackson DP, Lewis FA, Taylor GR, Boylston AW, Quirke P. Tissue extraction of DNA and RNA and analysis by the polymerase chain reaction. J Clin Pathol. 1990;43:499–504. doi: 10.1136/jcp.43.6.499. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [7].Sepp R, Szabo I, Uda H, Sakamoto H. Rapid techniques for DNA extraction from routinely processed archival tissue for use in PCR. J Clin Pathol. 1994;47:318–323. doi: 10.1136/jcp.47.4.318. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [8].Morgan K, Lam L, Kalsheker N. A rapid and efficient method for DNA extraction from paraffin wax embedded tissue for PCR amplification. Clin Mol Pathol. 1996;49:M179–180. doi: 10.1136/mp.49.3.M179. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [9].Bonin S, Petrera F, Niccolini B, Stanta G. PCR analysis in archival postmortem tissues. Mol Pathol. 2003;56:184–186. doi: 10.1136/mp.56.3.184. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [10].Shi SR, Cote RJ, Wu L, Liu C, Datar R, Shi Y, et al. 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. 2002;50:1005–1011. doi: 10.1177/002215540205000802. [DOI] [PubMed] [Google Scholar]
  • [11].Schiffner LA, Bajda EJ, Prinz M, Sebestyen J, Shaler R, Caragine TA. Optimization of a simple, automatable extraction method to recover sufficient DNA from low copy number DNA samples for generation of short tandem repeat profiles. Croat Med J. 2005;46:578–586. [PubMed] [Google Scholar]
  • [12].Funabashi KS, Barcelos D, Visona I, Silva MS, Sousa ML, de Franco MF, 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. 2012;208:584–591. doi: 10.1016/j.prp.2012.07.001. [DOI] [PubMed] [Google Scholar]
  • [13].Coombs NJ, Gough AC, Primrose JN. Optimisation of DNA and RNA extraction from archival formalin-fixed tissue. Nucleic Acids Res. 1999;27:e12. doi: 10.1093/nar/27.16.e12. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [14].Gilks WP, Abou-Sleiman PM, Gandhi S, Jain S, Singleton A, Lees AJ, et al. A common LRRK2 mutation in idiopathic Parkinson’s disease. Lancet. 2005;365:415–416. doi: 10.1016/S0140-6736(05)17830-1. [DOI] [PubMed] [Google Scholar]
  • [15].Baker M, Litvan I, Houlden H, Adamson J, Dickson D, Perez-Tur J, et al. Association of an extended haplotype in the tau gene with progressive supranuclear palsy. Hum Mol Genet. 1999;8:711–715. doi: 10.1093/hmg/8.4.711. [DOI] [PubMed] [Google Scholar]
  • [16].Huang Y, Halliday GM, Vandebona H, Mellick GD, Mastaglia F, Stevens J, et al. Prevalence and clinical features of common LRRK2 mutations in Australians with Parkinson’s disease. Mov Disord. 2007;22:982–989. doi: 10.1002/mds.21477. [DOI] [PubMed] [Google Scholar]
  • [17].Savioz A, Blouin JL, Guidi S, Antonarakis SE, Bouras C. A method for the extraction of genomic DNA from human brain tissue fixed and stored in formalin for many years. Acta Neuropathol. 1997;93:408–413. doi: 10.1007/s004010050632. [DOI] [PubMed] [Google Scholar]
  • [18].Cotter FE, Hall PA, Young BD. Extraction of DNA from small sections of frozen tissue with simultaneous histological examination. J Clin Pathol. 1988;41:1125–1126. doi: 10.1136/jcp.41.10.1125. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [19].Serth J, Kuczyk MA, Paeslack U, Lichtinghagen R, Jonas U. Quantitation of DNA extracted after micropreparation of cells from frozen and formalin-fixed tissue sections. Am J Pathol. 2000;156:1189–1196. doi: 10.1016/S0002-9440(10)64989-9. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [20].Coura R, Prolla JC, Meurer L, Ashton-Prolla P. An alternative protocol for DNA extraction from formalin fixed and paraffin wax embedded tissue. J Clin Pathol. 2005;58:894–895. doi: 10.1136/jcp.2004.021352. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [21].Shi SR, Datar R, Liu C, Wu L, Zhang Z, Cote RJ, et al. DNA extraction from archival formalin-fixed, paraffin-embedded tissues: heat-induced retrieval in alkaline solution. Histochem Cell Biol. 2004;122:211–218. doi: 10.1007/s00418-004-0693-x. [DOI] [PubMed] [Google Scholar]

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