Use of formalin-fixed paraffin-embedded samples for gene expression studies in breast cancer patients

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

Research output: Contribution to journalArticlepeer-review

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 formalinfixed, 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

Original languageEnglish
Article numbere123194
JournalPLoS One
Volume10
Issue number4
DOIs
Publication statusPublished - Apr 6 2015

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

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