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DNA degrades during storage in formalin-fixed and paraffin-embedded tissue blocks

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Abstract

Formalin-fixed paraffin-embedded (FFPE) tissue blocks are widely used to identify clinically actionable molecular alterations or perform retrospective molecular studies. Our goal was to quantify degradation of DNA occurring during mid to long-term storage of samples in usual conditions. We selected 46 FFPE samples of surgically resected carcinomas of lung, colon, and urothelial tract, of which DNA had been previously extracted. We performed a second DNA extraction on the same blocks under identical conditions after a median period of storage of 5.5 years. Quantitation of DNA by fluorimetry showed a 53% decrease in DNA quantity after storage. Quantitative PCR (qPCR) targeting KRAS exon 2 showed delayed amplification of DNA extracted after storage in all samples but one. The qPCR/fluorimetry quantification ratio decreased from 56 to 15% after storage (p < 0.001). Overall, remaining proportion of DNA analyzable by qPCR represented only 11% of the amount obtained at first extraction. Maximal length of amplifiable DNA fragments assessed with a multiplex PCR was reduced in DNA extracted from stored tissue, indicating that DNA fragmentation had increased in the paraffin blocks during storage. Next-generation sequencing was performed on 12 samples and showed a mean 3.3-fold decrease in library yield and a mean 4.5-fold increase in the number of single-nucleotide variants detected after storage. In conclusion, we observed significant degradation of DNA extracted from the same FFPE block after 4 to 6 years of storage. Better preservation strategies should be considered for storage of FFPE biopsy specimens.

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Acknowledgements

We thank the technicians of molecular biology and tissue bank from the department of pathology for their technical participation.

Author information

Author notes

  1. Alice Guyard and Alice Boyez equally contributed to this study

Authors and Affiliations

  1. Département de pathologie, AP-HP, Groupe Hospitalier Henri Mondor-Albert Chenevier, 94010, Créteil, France

    Alice Guyard, Alice Boyez, Anaïs Pujals, Jeanne Tran Van Nhieu, Yves Allory, Julien Moroch & Elie-Serge Zafrani

  2. Faculté de médecine de Créteil, Université Paris-Est Créteil, 94010, Créteil, France

    Anaïs Pujals, Jeanne Tran Van Nhieu, Yves Allory & Elie-Serge Zafrani

  3. INSERM U955, 94010, Créteil, France

    Cyrielle Robe

  4. Cabinet d’anatomie pathologique, 75012, Paris, France

    Odette Georges & Jean-Christophe Fournet

  5. AP-HP, Groupe Hospitalier Paris-Centre, hôpital Cochin, 75014, Paris, France

    Karen Leroy

  6. Faculté de médecine, Université Paris Descartes, 75000, Paris, France

    Karen Leroy

Authors
  1. Alice Guyard
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  2. Alice Boyez
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  11. Karen Leroy
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Corresponding author

Correspondence to Karen Leroy.

Ethics declarations

DNA was extracted from FFPE tissue blocks for medical diagnosis in compliance with French regulations.

Funding

This study was supported by institutional funding (AP-HP, hospital Henri Mondor, departement de Pathologie).

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The authors declare that they have no conflict of interest.

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Guyard, A., Boyez, A., Pujals, A. et al. DNA degrades during storage in formalin-fixed and paraffin-embedded tissue blocks. Virchows Arch 471, 491–500 (2017). https://doi.org/10.1007/s00428-017-2213-0

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  • DOI: https://doi.org/10.1007/s00428-017-2213-0

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