title: MammaPrint molecular diagnostics on formalin-fixed, paraffin-embedded tissue.
abstract: MammaPrint, a prognostic 70-gene profile for early-stage breast cancer, has been available for fresh tissue. Improvements in RNA processing have enabled microarray diagnostics for formalin-fixed, paraffin-embedded (FFPE) tissue. Here, we describe method optimization, validation, and performance of MammaPrint using analyte from FFPE tissue. Laboratory procedures for enabling the assay to be run on FFPE tissue were determined using 157 samples, and the assay was established using 125 matched FFPE and fresh tissues. Validation of MammaPrint-FFPE, compared with MammaPrint-fresh, was performed on an independent series of matched tissue from five hospitals (n = 211). Reproducibility, repeatability, and precision of the FFPE assay (n = 87) was established for duplicate analysis of the same tumor, interlaboratory performance, 20-day repeat experiments, and repeated analyses over 12 months. FFPE sample processing had a success rate of 97%. The MammaPrint assay using FFPE analyte demonstrated an overall equivalence of 91.5% (95% confidence interval, 86.9% to 94.5%) between the 211 independent matched FFPE and fresh tumor samples. Precision was 97.3%, and repeatability was 97.8%, with highly reproducible results between replicate samples of the same tumor and between two laboratories (concordance, 96%). Thus, with 580 tumor samples, MammaPrint was successfully translated to FFPE tissue. The assay has high precision and reproducibility, and FFPE results are substantially equivalent to results derived from fresh tissue.
authors.affiliation: Department of Medical Sciences, University of Turin, Turin, Italy. Electronic address: anna.sapino@unito.it.
authors.forename: Anna
authors.initials: A
authors.lastname: Sapino
authors.affiliation: Department of Research and Development, Agendia, Amsterdam, the Netherlands.
authors.forename: Paul
authors.initials: P
authors.lastname: Roepman
authors.affiliation: Department of Medical Oncology, Netherlands Cancer Institute, Amsterdam, the Netherlands; Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands.
authors.forename: Sabine C
authors.initials: SC
authors.lastname: Linn
authors.affiliation: Department of Research and Development, Agendia, Amsterdam, the Netherlands.
authors.forename: Mireille H J
authors.initials: MH
authors.lastname: Snel
authors.affiliation: Department of Product Development and Support, Agendia, Amsterdam, the Netherlands.
authors.forename: Leonie J M J
authors.initials: LJ
authors.lastname: Delahaye
authors.affiliation: Department of Product Development and Support, Agendia, Amsterdam, the Netherlands.
authors.forename: Jeroen
authors.initials: J
authors.lastname: van den Akker
authors.affiliation: Department of Product Development and Support, Agendia, Amsterdam, the Netherlands.
authors.forename: Annuska M
authors.initials: AM
authors.lastname: Glas
authors.affiliation: Department of Research and Development, Agendia, Amsterdam, the Netherlands.
authors.forename: Iris M
authors.initials: IM
authors.lastname: Simon
authors.affiliation: Department of Medical Affairs, Agendia, Irvine, California.
authors.forename: Neil
authors.initials: N
authors.lastname: Barth
authors.affiliation: Department of Medical Affairs, Agendia, Amsterdam, the Netherlands.
authors.forename: Femke A
authors.initials: FA
authors.lastname: de Snoo
authors.affiliation: Department of Research and Development, Agendia, Amsterdam, the Netherlands.
authors.forename: Laura J
authors.initials: LJ
authors.lastname: van 't Veer
authors.affiliation: Department of Medical Sciences, University of Turin, Turin, Italy.
authors.forename: Luca
authors.initials: L
authors.lastname: Molinaro
authors.affiliation: Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands.
authors.forename: Els M J J
authors.initials: EM
authors.lastname: Berns
authors.affiliation: Department of Medical Oncology, Netherlands Cancer Institute, Amsterdam, the Netherlands.
authors.forename: Jelle
authors.initials: J
authors.lastname: Wesseling
authors.affiliation: Department of Surgical Oncology, St. Luke's Hospital and Health Network, Bethlehem, Pennsylvania.
authors.forename: Lee B
authors.initials: LB
authors.lastname: Riley
authors.affiliation: Department of Pathology, St. Luke's Hospital and Health Network, Bethlehem, Pennsylvania.
authors.forename: David
authors.initials: D
authors.lastname: Anderson
authors.affiliation: Department of Medicine, Todd Cancer Institute, Long Beach Memorial Medical Center, Long Beach, California.
authors.forename: Bichlien
authors.initials: B
authors.lastname: Nguyen
authors.affiliation: Department of Surgery, University of South Florida, Tampa, Florida.
authors.forename: Charles E
authors.initials: CE
authors.lastname: Cox
mesh_terms: D055088:Early Detection of Cancer / Q000379:methods* / Q000592:standards; D005557:Formaldehyde; D020869:Gene Expression Profiling / Q000379:methods* / Q000592:standards; D006801:Humans; D009369:Neoplasms / Q000175:diagnosis / Q000235:genetics; D016612:Paraffin Embedding; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D016707:Tissue Fixation
chemical_list: D005557:Formaldehyde