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MammaPrint molecular diagnostics on formalin-fixed, paraffin-embedded tissue.

Anna Sapino1, Paul Roepman2, Sabine C Linn3

  • 1Department of Medical Sciences, University of Turin, Turin, Italy.

The Journal of Molecular Diagnostics : JMD
|January 1, 2014
PubMed
Summary

MammaPrint, a prognostic 70-gene profile for early-stage breast cancer, is now validated for formalin-fixed, paraffin-embedded (FFPE) tissue. This optimized assay shows high precision and reproducibility, offering results substantially equivalent to fresh tissue analysis.

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Area of Science:

  • Oncology
  • Molecular Diagnostics
  • Biotechnology

Background:

  • MammaPrint, a 70-gene prognostic profile, has been crucial for early-stage breast cancer management.
  • Traditional MammaPrint analysis required fresh tissue, limiting its application in certain clinical settings.
  • Advances in RNA processing now permit microarray diagnostics on formalin-fixed, paraffin-embedded (FFPE) tissues.

Purpose of the Study:

  • To optimize, validate, and assess the performance of the MammaPrint assay using RNA extracted from FFPE breast cancer tissues.
  • To establish the reliability and reproducibility of MammaPrint when applied to FFPE samples.
  • To determine the equivalence of MammaPrint results obtained from FFPE versus fresh tissue.

Main Methods:

  • Method optimization and assay establishment were performed using 157 and 125 matched FFPE and fresh tissue samples, respectively.
  • Independent validation involved 211 matched FFPE and fresh tumor samples from five hospitals.
  • Reproducibility, repeatability, and precision were assessed through duplicate analyses, interlaboratory testing, and longitudinal experiments over 12 months.

Main Results:

  • FFPE sample processing achieved a high success rate of 97%.
  • The MammaPrint assay on FFPE tissue demonstrated 91.5% overall equivalence compared to fresh tissue analysis in an independent cohort.
  • The FFPE assay exhibited high precision (97.3%) and repeatability (97.8%), with excellent concordance (96%) between laboratories and replicate samples.

Conclusions:

  • MammaPrint has been successfully adapted for use with FFPE tissue, expanding its clinical utility.
  • The FFPE MammaPrint assay is precise, reproducible, and yields results substantially equivalent to those from fresh tissue.
  • This translation to FFPE tissue broadens accessibility to prognostic genomic profiling for early-stage breast cancer patients.