PAM50 breast cancer subtyping by RT-qPCR and concordance with standard clinical molecular markers

Roy Rl Bastien, Álvaro Rodríguez-Lescure, Mark Tw Ebbert, Aleix Prat, Blanca Munárriz, Leslie Rowe, Patricia Miller, Manuel Ruiz-Borrego, Daniel Anderson, Bradley Lyons, Isabel Álvarez, Tracy Dowell, David Wall, Miguel Ángel Seguí, Lee Barley, Kenneth M. Boucher, Emilio Alba, Lisa Pappas, Carole A. Davis, Ignacio ArandaChristiane Fauron, Inge J. Stijleman, José Palacios, Antonio Antán, Eva Carrasco, Rosalía Caballero, Matthew J. Ellis, Torsten O. Nielsen, Charles M. Perou, Mark Astill, Philip S. Bernard, Miguel Martín

Research output: Contribution to journalArticlepeer-review

234 Scopus citations


Background: Many methodologies have been used in research to identify the intrinsic subtypes of breast cancer commonly known as Luminal A, Luminal B, HER2-Enriched (HER2-E) and Basal-like. The PAM50 gene set is often used for gene expression-based subtyping; however, surrogate subtyping using panels of immunohistochemical (IHC) markers are still widely used clinically. Discrepancies between these methods may lead to different treatment decisions. Methods. We used the PAM50 RT-qPCR assay to expression profile 814 tumors from the GEICAM/9906 phase III clinical trial that enrolled women with locally advanced primary invasive breast cancer. All samples were scored at a single site by IHC for estrogen receptor (ER), progesterone receptor (PR), and Her2/neu (HER2) protein expression. Equivocal HER2 cases were confirmed by chromogenic in situ hybridization (CISH). Single gene scores by IHC/CISH were compared with RT-qPCR continuous gene expression values and intrinsic subtype assignment by the PAM50. High, medium, and low expression for ESR1, PGR, ERBB2, and proliferation were selected using quartile cut-points from the continuous RT-qPCR data across the PAM50 subtype assignments. Results: ESR1, PGR, and ERBB2 gene expression had high agreement with established binary IHC cut-points (area under the curve (AUC)0.9). Estrogen receptor positivity by IHC was strongly associated with Luminal (A and B) subtypes (92%), but only 75% of ER negative tumors were classified into the HER2-E and Basal-like subtypes. Luminal A tumors more frequently expressed PR than Luminal B (94% vs 74%) and Luminal A tumors were less likely to have high proliferation (11% vs 77%). Seventy-seven percent (30/39) of ER-/HER2+ tumors by IHC were classified as the HER2-E subtype. Triple negative tumors were mainly comprised of Basal-like (57%) and HER2-E (30%) subtypes. Single gene scoring for ESR1, PGR, and ERBB2 was more prognostic than the corresponding IHC markers as shown in a multivariate analysis. Conclusions: The standard immunohistochemical panel for breast cancer (ER, PR, and HER2) does not adequately identify the PAM50 gene expression subtypes. Although there is high agreement between biomarker scoring by protein immunohistochemistry and gene expression, the gene expression determinations for ESR1 and ERBB2 status was more prognostic.

Original languageEnglish
Article number44
JournalBMC Medical Genomics
StatePublished - 2012

Bibliographical note

Funding Information:
This work was supported by the Huntsman Cancer Institute (HCI)/ Foundation, the ARUP Institute for Clinical and Experimental Pathology, and NCI grants U01 CA114722-01 and P30 CA42014-19. A. Prat is supported by the Translational Oncology fellowship of the Sociedad Española de Oncologia Médica (SEOM). We thank the TRAC facility and Research Informatics at HCI, and the UNC Tissue Procurement Facility for contributing samples. We also appreciate the guidance of Dr. Joel S. Parker.

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)


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