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Virchows Archiv

, Volume 471, Issue 4, pp 491–500 | Cite as

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

  • Alice Guyard
  • Alice Boyez
  • Anaïs Pujals
  • Cyrielle Robe
  • Jeanne Tran Van Nhieu
  • Yves Allory
  • Julien Moroch
  • Odette Georges
  • Jean-Christophe Fournet
  • Elie-Serge Zafrani
  • Karen LeroyEmail author
Original Article

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.

Keywords

DNA Degradation Storage  FFPE tissue blocks 

Notes

Acknowledgements

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

Compliance with ethical standards

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).

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

428_2017_2213_MOESM1_ESM.docx (222 kb)
ESM 1 (DOCX 222 kb)

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Copyright information

© Springer-Verlag GmbH Deutschland 2017

Authors and Affiliations

  • Alice Guyard
    • 1
  • Alice Boyez
    • 1
  • Anaïs Pujals
    • 1
    • 2
  • Cyrielle Robe
    • 3
  • Jeanne Tran Van Nhieu
    • 1
    • 2
  • Yves Allory
    • 1
    • 2
  • Julien Moroch
    • 1
  • Odette Georges
    • 4
  • Jean-Christophe Fournet
    • 4
  • Elie-Serge Zafrani
    • 1
    • 2
  • Karen Leroy
    • 5
    • 6
    Email author
  1. 1.Département de pathologieAP-HP, Groupe Hospitalier Henri Mondor-Albert ChenevierCréteilFrance
  2. 2.Faculté de médecine de CréteilUniversité Paris-Est CréteilCréteilFrance
  3. 3.CréteilFrance
  4. 4.Cabinet d’anatomie pathologiqueParisFrance
  5. 5.AP-HP, Groupe Hospitalier Paris-Centre, hôpital CochinParisFrance
  6. 6.Faculté de médecineUniversité Paris DescartesParisFrance

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