161P MammaPrint and BluePrint diagnostic tests can be robustly assessed on Whole-Transcriptome NGS platform

Abstract

BackgroundThe MammaPrint (MP) 70-gene risk of recurrence and BluePrint (BP) 80-gene molecular subtyping tests are used in personalized treatment planning of early-stage breast cancer (EBC). MP and BP are offered both centrally, on the microarray (MA) platform and as decentralized solution based on a targeted Next Generation Sequencing (NGS) kit. Recently, we translated MP and BP to a Whole-Transcriptome (WT) -NGS based platform. Here we present the comparison between MA and WT-NGS based test results and report the performance on the equivalence.MethodsA set of 151 Formalin Fixed Paraffin Embedded (FFPE) EBC samples was processed both on WT-NGS and on standard MA diagnostics platform. Libraries were prepared with the TruSeq Total RNA stranded 75 bp single-read protocol on a NextSeq machine. A set of 709 FFPE samples from patients with stage II-III HER2 positive EBC, partly treated were available for WT-NGS and MA processing to confirm the validation. Comparisons of the MP (High-, Low-risk) and BP (Basal-, Luminal-, HER2-type) results from WT-NGS and MA were based on the overall concordance and index correlation.ResultsWT-NGS MP results are highly comparable with the MA predicate [96% concordance, positive percent agreement (PPA)= 99% (95%CI: 93.5 – 99.8), negative percent agreement (NPA) = 93% (95%CI: 83.9 – 96.8)]. Similarly, high concordance of 96.7 % is observed between WT-NGS and MA BP results. MP and BP indices are highly correlating between MA and WT-NGS results (Pearson correlation coefficient () of 0.97 for MP, Basal, Luminal, and 0.88 for HER2). Concordance is also confirmed in the HER2 set (MP =97.9%, PPA = 99.1 % (95 % CI: 98.0 – 99.6), NPA = 81.3% (95 % CI: 68.1 – 89.8) and BP = 92.0%), with high index correlation = 0.92 for MP and Basal, = 0.97 for Luminal and = 0.81 for HER2).ConclusionsWT-NGS test results are highly comparable with the predicate MA as also independently confirmed on a large set of clinical samples. The successful translation of the MA to an WT-NGS-based test highlights the robustness of the biology behind the MP/BP test, which prove to be reliable tool for personalized medical care, irrespective of the technology platform used.Legal entity responsible for the studyAgendia NV.FundingAgendia NV.DisclosureR. Bhaskaran, Y. Bijl, D. Israeli, S. Jong-Raadsen, E. van montfort, A. Gallagher, T. Piel, A. Witteveen, M. Kleijn, A. Glas, L. Mittempergher: Financial Interests, Personal, Full or part-time Employment: Agendia NV. S. Bao, S. Mee, T. Cavness, J. Falk: Financial Interests, Personal, Full or part-time Employment: Agendia Inc. All other authors have declared no conflicts of interest. BackgroundThe MammaPrint (MP) 70-gene risk of recurrence and BluePrint (BP) 80-gene molecular subtyping tests are used in personalized treatment planning of early-stage breast cancer (EBC). MP and BP are offered both centrally, on the microarray (MA) platform and as decentralized solution based on a targeted Next Generation Sequencing (NGS) kit. Recently, we translated MP and BP to a Whole-Transcriptome (WT) -NGS based platform. Here we present the comparison between MA and WT-NGS based test results and report the performance on the equivalence. The MammaPrint (MP) 70-gene risk of recurrence and BluePrint (BP) 80-gene molecular subtyping tests are used in personalized treatment planning of early-stage breast cancer (EBC). MP and BP are offered both centrally, on the microarray (MA) platform and as decentralized solution based on a targeted Next Generation Sequencing (NGS) kit. Recently, we translated MP and BP to a Whole-Transcriptome (WT) -NGS based platform. Here we present the comparison between MA and WT-NGS based test results and report the performance on the equivalence. MethodsA set of 151 Formalin Fixed Paraffin Embedded (FFPE) EBC samples was processed both on WT-NGS and on standard MA diagnostics platform. Libraries were prepared with the TruSeq Total RNA stranded 75 bp single-read protocol on a NextSeq machine. A set of 709 FFPE samples from patients with stage II-III HER2 positive EBC, partly treated were available for WT-NGS and MA processing to confirm the validation. Comparisons of the MP (High-, Low-risk) and BP (Basal-, Luminal-, HER2-type) results from WT-NGS and MA were based on the overall concordance and index correlation. A set of 151 Formalin Fixed Paraffin Embedded (FFPE) EBC samples was processed both on WT-NGS and on standard MA diagnostics platform. Libraries were prepared with the TruSeq Total RNA stranded 75 bp single-read protocol on a NextSeq machine. A set of 709 FFPE samples from patients with stage II-III HER2 positive EBC, partly treated were available for WT-NGS and MA processing to confirm the validation. Comparisons of the MP (High-, Low-risk) and BP (Basal-, Luminal-, HER2-type) results from WT-NGS and MA were based on the overall concordance and index correlation. ResultsWT-NGS MP results are highly comparable with the MA predicate [96% concordance, positive percent agreement (PPA)= 99% (95%CI: 93.5 – 99.8), negative percent agreement (NPA) = 93% (95%CI: 83.9 – 96.8)]. Similarly, high concordance of 96.7 % is observed between WT-NGS and MA BP results. MP and BP indices are highly correlating between MA and WT-NGS results (Pearson correlation coefficient () of 0.97 for MP, Basal, Luminal, and 0.88 for HER2). Concordance is also confirmed in the HER2 set (MP =97.9%, PPA = 99.1 % (95 % CI: 98.0 – 99.6), NPA = 81.3% (95 % CI: 68.1 – 89.8) and BP = 92.0%), with high index correlation = 0.92 for MP and Basal, = 0.97 for Luminal and = 0.81 for HER2). WT-NGS MP results are highly comparable with the MA predicate [96% concordance, positive percent agreement (PPA)= 99% (95%CI: 93.5 – 99.8), negative percent agreement (NPA) = 93% (95%CI: 83.9 – 96.8)]. Similarly, high concordance of 96.7 % is observed between WT-NGS and MA BP results. MP and BP indices are highly correlating between MA and WT-NGS results (Pearson correlation coefficient () of 0.97 for MP, Basal, Luminal, and 0.88 for HER2). Concordance is also confirmed in the HER2 set (MP =97.9%, PPA = 99.1 % (95 % CI: 98.0 – 99.6), NPA = 81.3% (95 % CI: 68.1 – 89.8) and BP = 92.0%), with high index correlation = 0.92 for MP and Basal, = 0.97 for Luminal and = 0.81 for HER2). ConclusionsWT-NGS test results are highly comparable with the predicate MA as also independently confirmed on a large set of clinical samples. The successful translation of the MA to an WT-NGS-based test highlights the robustness of the biology behind the MP/BP test, which prove to be reliable tool for personalized medical care, irrespective of the technology platform used. WT-NGS test results are highly comparable with the predicate MA as also independently confirmed on a large set of clinical samples. The successful translation of the MA to an WT-NGS-based test highlights the robustness of the biology behind the MP/BP test, which prove to be reliable tool for personalized medical care, irrespective of the technology platform used.