Translational Oncology (Dec 2019)

Decentralization of Next-Generation RNA Sequencing-Based MammaPrint® and BluePrint® Kit at University Hospitals Leuven and Curie Institute Paris

  • Laurence Slembrouck,
  • Lauren Darrigues,
  • Cecile Laurent,
  • Lorenza Mittempergher,
  • Leonie JMJ Delahaye,
  • Isabelle Vanden Bempt,
  • Sara Vander Borght,
  • Liesbet Vliegen,
  • Petra Sintubin,
  • Virginie Raynal,
  • Mylene Bohec,
  • Cécile Reyes,
  • Audrey Rapinat,
  • Céline Helsmoortel,
  • Lynn Jongen,
  • Griet Hoste,
  • Patrick Neven,
  • Hans Wildiers,
  • Ann Smeets,
  • Ines Nevelsteen,
  • Kevin Punie,
  • Els Van Nieuwenhuysen,
  • Sileny Han,
  • Anne Vincent Salomon,
  • Enora Laas Faron,
  • Timothé Cynober,
  • David Gentien,
  • Sylvain Baulande,
  • Mireille HJ Snel,
  • Anke T Witteveen,
  • Sari Neijenhuis,
  • Annuska M Glas,
  • Fabien Reyal,
  • Giuseppe Floris

Journal volume & issue
Vol. 12, no. 12
pp. 1557 – 1565

Abstract

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A previously developed and centrally validated MammaPrint® (MP) and BluePrint® (BP) targeted RNA next-generation sequencing (NGS) kit was implemented and validated in two large academic European hospitals. Additionally, breast cancer molecular subtypes by MP and BP RNA sequencing were compared with immunohistochemistry (IHC). Patients with early breast cancer diagnosed at University Hospitals Leuven and Curie Institute Paris were prospectively included between September 2017 and January 2018. Formalin-fixed paraffin-embedded tissue sections were analyzed with MP and BP NGS technology at the beta sites and with both NGS and microarray technology at Agendia. Raw NGS data generated on Illumina MiSeq instruments at the beta sites were interpreted and compared with NGS and microarray data at Agendia. MP and BP NGS molecular subtypes were compared to surrogate IHC breast cancer subtypes. Equivalence of MP and BP indices was determined by Pearson's correlation coefficient. Acceptable limits were defined a priori, based on microarray data generated at Agendia between 2012 and 2016. The concordance, the Negative Percent Agreement and the Positive Percent Agreement were calculated based on the contingency tables and had to be equal to or higher than 90%. Out of 124 included samples, 48% were MP Low and 52% High Risk with microarray. Molecular subtypes were BP luminal, HER2 or basal in 82%, 8% and 10% respectively. Concordance between MP microarray at Agendia and MP NGS at the beta sites was 91.1%. Concordance of MP High and Low Risk classification between NGS at the beta sites and NGS at Agendia was 93.9%. Concordance of MP and BP molecular subtyping using NGS at the beta sites and microarray at Agendia was 89.5%. Concordance between MP and BP NGS subtyping, and IHC was 71.8% and 76.6%, for two IHC surrogate models. The MP/BP NGS kit was successfully validated in a decentralized setting.