npj Breast Cancer (Jun 2024)

Effect of cross-platform gene-expression, computational methods on breast cancer subtyping in PALOMA-2 and PALLET studies

  • Maggie Chon U Cheang,
  • Mothaffar Rimawi,
  • Stephen Johnston,
  • Samuel A. Jacobs,
  • Judith Bliss,
  • Katherine Pogue-Geile,
  • Lucy Kilburn,
  • Zhou Zhu,
  • Eugene F. Schuster,
  • Hui Xiao,
  • Lisa Swaim,
  • Shibing Deng,
  • Dongrui R. Lu,
  • Eric Gauthier,
  • Jennifer Tursi,
  • Dennis J. Slamon,
  • Hope S. Rugo,
  • Richard S. Finn,
  • Yuan Liu

DOI
https://doi.org/10.1038/s41523-024-00658-y
Journal volume & issue
Vol. 10, no. 1
pp. 1 – 9

Abstract

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Abstract Intrinsic breast cancer molecular subtyping (IBCMS) provides significant prognostic information for patients with breast cancer and helps determine treatment. This study compared IBCMS methods on various gene-expression platforms in PALOMA-2 and PALLET trials. PALOMA-2 tumor samples were profiled using EdgeSeq and nanostring and subtyped with AIMS, PAM50, and research-use-only (ruo)Prosigna. PALLET tumor biopsies were profiled using mRNA sequencing and subtyped with AIMS and PAM50. In PALOMA-2 (n = 222), a 54% agreement was observed between results from AIMS and gold-standard ruoProsigna, with AIMS assigning 67% basal-like to HER2-enriched. In PALLET (n = 224), a 69% agreement was observed between results from PAM50 and AIMS. Different IBCMS methods may lead to different results and could misguide treatment selection; hence, a standardized clinical PAM50 assay and computational approach should be used. Trial number: NCT01740427