1. Effect of cross-platform gene-expression, computational methods on breast cancer subtyping in PALOMA-2 and PALLET studies.
- Author
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Cheang, Maggie, Rimawi, Mothaffar, Johnston, Stephen, Jacobs, Samuel, Bliss, Judith, Pogue-Geile, Katherine, Kilburn, Lucy, Zhu, Zhou, Schuster, Eugene, Xiao, Hui, Swaim, Lisa, Deng, Shibing, Lu, Dongrui, Gauthier, Eric, Tursi, Jennifer, Slamon, Dennis, Rugo, Hope, Finn, Richard, and Liu, Yuan
- 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.
- Published
- 2024