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 features, 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 investigate 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 macrodissected 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 macrodissected 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, intermediate, 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.