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Reproducibility and intratumoral heterogeneity of the PAM50 breast cancer assay.

Publication ,  Journal Article
Hurson, AN; Hamilton, AM; Olsson, LT; Kirk, EL; Sherman, ME; Calhoun, BC; Geradts, J; Troester, MA
Published in: Breast Cancer Res Treat
May 2023

BACKGROUND: The PAM50 assay is used routinely in clinical practice to determine breast cancer prognosis and management; however, research assessing how technical variation and intratumoral heterogeneity contribute to misclassification and reproducibility of these tests is limited. METHODS: We evaluated the impact of intratumoral heterogeneity on the reproducibility of results for the PAM50 assay by testing RNA extracted from formalin-fixed paraffin embedded breast cancer blocks sampled at distinct spatial locations. Samples were classified according to intrinsic subtype (Luminal A, Luminal B, HER2-enriched, Basal-like, or Normal-like) and risk of recurrence with proliferation score (ROR-P, high, medium, or low). Intratumoral heterogeneity and technical reproducibility (replicate assays on the same RNA) were assessed as percent categorical agreement between paired intratumoral and replicate samples. Euclidean distances between samples, calculated across the PAM50 genes and the ROR-P score, were compared for concordant vs. discordant samples. RESULTS: Technical replicates (N = 144) achieved 93% agreement for ROR-P group and 90% agreement on PAM50 subtype. For spatially distinct biological replicates (N = 40 intratumoral replicates), agreement was lower (81% for ROR-P and 76% for PAM50 subtype). The Euclidean distances between discordant technical replicates were bimodal, with discordant samples showing higher Euclidian distance and biologic heterogeneity. CONCLUSION: The PAM50 assay achieved very high technical reproducibility for breast cancer subtyping and ROR-P, but intratumoral heterogeneity is revealed by the assay in a small proportion of cases.

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Published In

Breast Cancer Res Treat

DOI

EISSN

1573-7217

Publication Date

May 2023

Volume

199

Issue

1

Start / End Page

147 / 154

Location

Netherlands

Related Subject Headings

  • Reproducibility of Results
  • Receptor, erbB-2
  • Receptor, ErbB-2
  • RNA
  • Prognosis
  • Oncology & Carcinogenesis
  • Humans
  • Female
  • Breast Neoplasms
  • Breast
 

Citation

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Hurson, A. N., Hamilton, A. M., Olsson, L. T., Kirk, E. L., Sherman, M. E., Calhoun, B. C., … Troester, M. A. (2023). Reproducibility and intratumoral heterogeneity of the PAM50 breast cancer assay. Breast Cancer Res Treat, 199(1), 147–154. https://doi.org/10.1007/s10549-023-06888-1
Hurson, Amber N., Alina M. Hamilton, Linnea T. Olsson, Erin L. Kirk, Mark E. Sherman, Benjamin C. Calhoun, Joseph Geradts, and Melissa A. Troester. “Reproducibility and intratumoral heterogeneity of the PAM50 breast cancer assay.Breast Cancer Res Treat 199, no. 1 (May 2023): 147–54. https://doi.org/10.1007/s10549-023-06888-1.
Hurson AN, Hamilton AM, Olsson LT, Kirk EL, Sherman ME, Calhoun BC, et al. Reproducibility and intratumoral heterogeneity of the PAM50 breast cancer assay. Breast Cancer Res Treat. 2023 May;199(1):147–54.
Hurson, Amber N., et al. “Reproducibility and intratumoral heterogeneity of the PAM50 breast cancer assay.Breast Cancer Res Treat, vol. 199, no. 1, May 2023, pp. 147–54. Pubmed, doi:10.1007/s10549-023-06888-1.
Hurson AN, Hamilton AM, Olsson LT, Kirk EL, Sherman ME, Calhoun BC, Geradts J, Troester MA. Reproducibility and intratumoral heterogeneity of the PAM50 breast cancer assay. Breast Cancer Res Treat. 2023 May;199(1):147–154.
Journal cover image

Published In

Breast Cancer Res Treat

DOI

EISSN

1573-7217

Publication Date

May 2023

Volume

199

Issue

1

Start / End Page

147 / 154

Location

Netherlands

Related Subject Headings

  • Reproducibility of Results
  • Receptor, erbB-2
  • Receptor, ErbB-2
  • RNA
  • Prognosis
  • Oncology & Carcinogenesis
  • Humans
  • Female
  • Breast Neoplasms
  • Breast