Intra- and Interlaboratory Reproducibility of the Sensitivity to Endocrine Therapy Assay for Stage II/III Breast Cancer

Abstract

Background The sensitivity to endocrine therapy assay (SET2,3) predicts treatment outcomes in Stage II-III breast cancer. SET2,3 measures transcription related to estrogen and progesterone receptors (SETER/PR index) and the molecular subtype (RNA4: ESR1, PGR, ERBB2, AURKA) from formalin-fixed paraffin-embedded (FFPE) tissue sections. Methods We designed a nested study across 3 pathology laboratories, each testing 60 breast cancers twice in controlled batches. Laboratories macrodissected and directly homogenized the unstained FFPE tumor sections, then performed the QuantiGene Plex bead-based hybridization assay. SET2,3 was calculated centrally using predefined statistical R-scripts and applying pre-defined cutpoints. Concordance correlation coefficient (CCC) was calculated from continuous measurements and Kappa statistic from categorical results. A mixed-effects model estimated contributions to bias (fixed effects) and variance (random effects) from the replicated design. Results Intralaboratory (CCC 0.96–0.99) and interlaboratory (CCC 0.98–0.99) SET2,3 results were concordant, with rates of agreement for high/low categorization within (Kappa 0.83–0.93) and between laboratories (Kappa 0.87–0.88). The relative contributions to overall variance of SET2,3 measurements were 96.90% from biological differences between cancers, 0.67% from interlaboratory variability, and 2.44% from residual causes including intralaboratory replicates. Similar results were obtained with SETER/PR, the baseline prognostic index calculated using pathological or clinical tumor and nodal staging information, and the 4 individual genes (ESR1, PGR, ERBB2, and AURKA). Conclusion Intra- and interpathology laboratory measurements of SET2,3 and its components were highly reproducible when tested from FFPE tumor sections.

Evaluation of Sensitivity to Endocrine Therapy Index (SET2,3) for Response to Neoadjuvant Endocrine Therapy and Longer-Term Breast Cancer Patient Outcomes (Alliance Z1031)

“…Another limitation is that SET2,3 results were inferred from Agilent microarray gene expression measurements rather than the platform used to develop or to perform this test (7,26). It is likely that this introduces some technical inaccuracy, although we had calibrated SET2,3 between genomic platforms to measure SET2,3 from a similar microarray platform to evaluate the I-SPY2 trial (7).…”

Evaluation of the Sensitivity to Endocrine Therapy Index and 21-Gene Breast Recurrence Score in the SWOG S8814 Trial

“…1 The sensitivity to endocrine therapy (SET2,3) index is a customized assay for formalin-fixed paraffin-embedded tumor tissues, which yields reproducible results within and between different laboratories, offering prognostic information for patients receiving endocrine therapy. [6][7][8] It combines the SET index of transcription related to estrogen and progesterone receptors (SET ER/PR ) with a baseline prognostic index (BPI) derived from pathologic tumor size, nodal involvement, and molecular subtype by RNA4 (ESR1, PGR, ERBB2, and AURKA). [7][8][9] Each component, SET ER/PR index and BPI, added independent prognostic information in prior studies 8,10 and multivariable Cox models of SET2,3 demonstrated that the RNA4 within the BPI could be substituted by contemporary prognostic signatures, but the SET ER/PR index could not be substituted.…”

“…[6][7][8] It combines the SET index of transcription related to estrogen and progesterone receptors (SET ER/PR ) with a baseline prognostic index (BPI) derived from pathologic tumor size, nodal involvement, and molecular subtype by RNA4 (ESR1, PGR, ERBB2, and AURKA). [7][8][9] Each component, SET ER/PR index and BPI, added independent prognostic information in prior studies 8,10 and multivariable Cox models of SET2,3 demonstrated that the RNA4 within the BPI could be substituted by contemporary prognostic signatures, but the SET ER/PR index could not be substituted. 8 High SET2,3 scores are associated with endocrine sensitivity and more favorable prognosis, and low SET2,3 scores with endocrine therapy resistance and less-favorable outcomes.…”

Prognostic Tests in Early-Stage Hormone Receptor–Positive Breast Cancer: An Opportunity to Refine Personalized Cancer Care

“…It should also be noted that the model provided valuable prognostic information for the first 5 years, but not beyond, although this may be in part explained by the fact that endocrine therapy was discontinued after 5 years. In addition, although the authors previously demonstrated reproducibility of this assay with high interlaboratory and interlaboratory concordance, 23 the practical aspect and associated costs are important factors as we navigate the increasing costs of cancer care and cost-effectiveness of gene expression profiling. 24 It is likely that without additional predictive merit, the prognostic aspect would not justify the means or the cost to be routinely used in practice at present.…”