Sample preparation approach influences pam50 risk of recurrence score in early breast cancer

Tonje G. Lien, Hege Oma Ohnstad, Ole Christian Lingjærde, Johan Vallon-Christersson, Marit Aaserud, My Anh Tu Sveli, Åke Borg, Øystein Garred, Elin Borgen, Bjørn Naume, Hege Russnes, Therese Sørlie, on behalf of OSBREAC

Research output: Contribution to journalArticlepeer-review


The PAM50 gene expression subtypes and the associated risk of recurrence (ROR) score are used to predict the risk of recurrence and the benefits of adjuvant therapy in early-stage breast cancer. The Prosigna assay includes the PAM50 subtypes along with their clinicopathological fea-tures, and is approved for treatment recommendations for adjuvant hormonal therapy and chemotherapy in hormone-receptor-positive early breast cancer. The Prosigna test utilizes RNA extracted from macrodissected tumor cells obtained from formalin-fixed, paraffin-embedded (FFPE) tissue sections. However, RNA extracted from fresh-frozen (FF) bulk tissue without macrodissection is widely used for research purposes, and yields high-quality RNA for downstream analyses. To in-vestigate the impact of the sample preparation approach on ROR scores, we analyzed 94 breast carcinomas included in an observational study that had available gene expression data from macro-dissected FFPE tissue and FF bulk tumor tissue, along with the clinically approved Prosigna scores for the node-negative, hormone-receptor-positive, HER2-negative cases (n = 54). ROR scores were calculated in R; the resulting two sets of scores from FFPE and FF samples were compared, and treatment recommendations were evaluated. Overall, ROR scores calculated based on the macro-dissected FFPE tissue were consistent with the Prosigna scores. However, analyses from bulk tissue yielded a higher proportion of cases classified as normal-like; these were samples with relatively low tumor cellularity, leading to lower ROR scores. When comparing ROR scores (low, intermedi-ate, and high), discordant cases between the two preparation approaches were revealed among the luminal tumors; the recommended treatment would have changed in a minority of cases.

Original languageEnglish
Article number6118
Issue number23
Publication statusPublished - 2021 Dec

Subject classification (UKÄ)

  • Cancer and Oncology

Free keywords

  • Breast cancer
  • Bulk
  • FFPE
  • Fresh-frozen
  • Macrodissection
  • PAM50
  • Prosigna
  • Risk of recurrence score


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