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

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.

Transferring MINDACT to Daily Routine: Implementation of the 70-Gene Signature in Luminal Early Breast Cancer – Results from a Prospective Registry of the Austrian Group Medical Tumor Therapy (AGMT)

“…Currently, Agendia has developed an FFPE-based next-generation sequencing kit for the implementation of 70-GS in a decentralized setting, which allows central laboratories to process the samples within country borders [24]. Recently reported validation results are promising and select laboratories in Belgium and Germany have implemented this process already [25].…”

The Future of Precision Oncology

“…Solutions to these limitations are not generalizable and may differ from one region to another [ 130 ]. To ensure consistency and accuracy, some molecular profiling assessments may only be available at specialized centers of excellence, whereas the cost of specialized laboratory infrastructures may limit the testing capabilities of local centers [ 130 , 131 ]. However, reductions in the cost of specialist equipment, as well as the development of kit-based genomic, transcriptomic, and proteomic assays with robust bioinformatic algorithms that mitigate the need for specialized expertise, may facilitate the implementation of decentralized molecular diagnostics and increase patient access to testing [ 130 , 131 , 132 ].…”

“…To ensure consistency and accuracy, some molecular profiling assessments may only be available at specialized centers of excellence, whereas the cost of specialized laboratory infrastructures may limit the testing capabilities of local centers [ 130 , 131 ]. However, reductions in the cost of specialist equipment, as well as the development of kit-based genomic, transcriptomic, and proteomic assays with robust bioinformatic algorithms that mitigate the need for specialized expertise, may facilitate the implementation of decentralized molecular diagnostics and increase patient access to testing [ 130 , 131 , 132 ]. Whether testing is centralized or localized, clinical diagnostics will benefit from the digital exchange of molecular profiling data that can be viewed by a multidisciplinary team of experts (such as molecular tumor boards) to derive accurate and timely diagnoses [ 5 , 90 ].…”

Genomic Signatures in Luminal Breast Cancer

“…Recently, the MammaPrint® and BluePrint® RNA sequencing test was found to be equivalent to the clinically validated microarray test [68]. It was also demonstrated that the MammaPrint RNA-sequencing test can be used as a decentralized platform with results equivalent to those derived from the predicated diagnostic device [68, 69]. Independent intra-assay reproducibility was also shown for the Prosigna® and EndoPredict® assays [70, 71].…”