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

doi:10.1016/j.tranon.2019.08.008

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

Transl Oncol. 2019 Dec;12(12):1557-1565. doi: 10.1016/j.tranon.2019.08.008. Epub 2019 Sep 9.

Authors

Laurence Slembrouck¹, Lauren Darrigues², Cecile Laurent³, Lorenza Mittempergher⁴, Leonie Jmj Delahaye⁴, Isabelle Vanden Bempt⁵, Sara Vander Borght⁶, Liesbet Vliegen⁵, Petra Sintubin⁵, Virginie Raynal⁷, Mylene Bohec⁷, Cécile Reyes⁸, Audrey Rapinat⁸, Céline Helsmoortel⁹, Lynn Jongen¹⁰, Griet Hoste¹¹, Patrick Neven¹², Hans Wildiers¹³, Ann Smeets¹⁴, Ines Nevelsteen¹⁴, Kevin Punie¹³, Els Van Nieuwenhuysen¹², Sileny Han¹², Anne Vincent Salomon¹⁵, Enora Laas Faron², Timothé Cynober¹⁶, David Gentien⁸, Sylvain Baulande⁷, Mireille Hj Snel⁴, Anke T Witteveen⁴, Sari Neijenhuis⁴, Annuska M Glas⁴, Fabien Reyal¹⁷, Giuseppe Floris¹⁸

Affiliations

¹ KU Leuven - University of Leuven, Department of Oncology, B-3000 Leuven, Belgium. Electronic address: laurence.slembrouck@kuleuven.be.
² Curie Institute, Department of Surgery, Paris Descartes University, F-75248, France.
³ Curie Institute, Residual Tumor & Response to Treatment Laboratory, RT2Lab, Paris Descartes University, INSERM, U932 Immunity and Cancer, Paris, F-75248, France.
⁴ Agendia, Department of Research and Development, Medical Affairs, Amsterdam, The Netherlands.
⁵ KU Leuven - University of Leuven, University Hospitals Leuven, Department of Human Genetics, B-3000 Leuven, Belgium.
⁶ KU Leuven - University of Leuven, University Hospitals Leuven, Department of Human Genetics, B-3000 Leuven, Belgium; KU Leuven - University Hospitals Leuven, Department of Pathology, B-3000 Leuven, Belgium.
⁷ Curie Institute, PSL Research University, Genomics of Excellence (ICGex) Platform, Paris, F-75248, France.
⁸ Curie Institute, PSL Research University, Translational Research Department, Genomics Platform, Paris, F-75248, France.
⁹ KU Leuven - University of Leuven, University Hospitals Leuven, Genomics Core, B-3000 Leuven, Belgium.
¹⁰ KU Leuven - University of Leuven, Department of Oncology, B-3000 Leuven, Belgium.
¹¹ KU Leuven - University of Leuven, University Hospitals Leuven, Department of Gynaecology and Obstetrics, B-3000 Leuven, Belgium.
¹² KU Leuven - University of Leuven, Department of Oncology, B-3000 Leuven, Belgium; KU Leuven - University of Leuven, University Hospitals Leuven, Department of Gynaecology and Obstetrics, B-3000 Leuven, Belgium.
¹³ KU Leuven - University of Leuven, Department of Oncology, B-3000 Leuven, Belgium; KU Leuven - University of Leuven, University Hospitals Leuven, Department of General Medical Oncology, B-3000 Leuven, Belgium.
¹⁴ KU Leuven - University of Leuven, Department of Oncology, B-3000 Leuven, Belgium; KU Leuven - University of Leuven, University Hospitals Leuven, Department of Surgical Oncology, B-3000 Leuven, Belgium.
¹⁵ Curie Institute, Department of Tumor Biology, Paris, F-75248, France.
¹⁶ Curie Institute, Administration and General Services, Paris, F-75248, France.
¹⁷ Curie Institute, Department of Surgery, Paris Descartes University, F-75248, France; Curie Institute, Residual Tumor & Response to Treatment Laboratory, RT2Lab, Paris Descartes University, INSERM, U932 Immunity and Cancer, Paris, F-75248, France.
¹⁸ KU Leuven - University Hospitals Leuven, Department of Pathology, B-3000 Leuven, Belgium; KU Leuven - University of Leuven, Department of Imaging and Pathology, Laboratory of Translational Cell & Tissue Research.

Abstract

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.