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Use of Formalin-Fixed Paraffin-Embedded Samples for Gene Expression Studies in Breast Cancer Patients

Author

Listed:
  • Valeria Musella
  • Maurizio Callari
  • Eleonora Di Buduo
  • Manuela Scuro
  • Matteo Dugo
  • Patrizia Miodini
  • Giampaolo Bianchini
  • Biagio Paolini
  • Luca Gianni
  • Maria Grazia Daidone
  • Vera Cappelletti

Abstract

To obtain gene expression profiles from samples collected in clinical trials, we conducted a pilot study to assess feasibility and estimate sample attrition rates when profiling formalin-fixed, paraffin-embedded specimens. Ten matched fresh-frozen and fixed breast cancer samples were profiled using the Illumina HT-12 and Ref-8 chips, respectively. The profiles obtained with Ref 8, were neither technically nor biologically reliable since they failed to yield the expected separation between estrogen receptor positive and negative samples. With the use of Affymetrix HG-U133 2.0 Plus chips on fixed samples and a quantitative polymerase chain reaction -based sample pre-assessment step, results were satisfactory in terms of biological reliability, despite the low number of present calls (M = 21%±5). Compared with the Illumina DASL WG platform, Affymetrix data showed a wider interquartile range (1.32 vs 0.57, P

Suggested Citation

  • Valeria Musella & Maurizio Callari & Eleonora Di Buduo & Manuela Scuro & Matteo Dugo & Patrizia Miodini & Giampaolo Bianchini & Biagio Paolini & Luca Gianni & Maria Grazia Daidone & Vera Cappelletti, 2015. "Use of Formalin-Fixed Paraffin-Embedded Samples for Gene Expression Studies in Breast Cancer Patients," PLOS ONE, Public Library of Science, vol. 10(4), pages 1-20, April.
    • Handle: RePEc:plo:pone00:0123194
    DOI: 10.1371/journal.pone.0123194
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