Background: Genomic tests, such as MammaPrint (MP) and Oncotype DX Breast Recurrence Score (RS), assess risk of recurrence in patients with early breast cancer (EBC). Using both assays may yield discordant results which leads to uncertainty in treatment recommendations. The assays differ in technology and genes analyzed. RS relies on RT-PCR to query 16 cancer-related genes and 5 controls. MP uses a microarray to query 70 cancer-related genes and 465 normalization controls. Here we explore the genetic basis for discordance by using the FLEX whole transcriptome database to examine differentially expressed genes among patients who received discordant RS and MP results. Methods: Patients with EBC enrolled in the FLEX study (NCT03053193) undergo standard of care MP and BluePrint (BP) tests, and consent to clinically annotated whole transcriptome data collection. MP stratifies risk of recurrence as Low risk and High. RS classifies patients as Low Risk (RS 0-10), Intermediate (RS 11-25), and High Risk (RS 26-100). Due to low representation of BP Basal and BP HER2-type tumors in this data set, we only examined BP Luminal-type tumors (N = 705). We used full genome transcriptomes to compare gene expression among discordant cases. Gene expression data were quantile normalized and analyzed using R package ‘limma’. Genes were considered differentially expressed at a fold change of at least 1.7 and an adjusted p-value of lower than 0.05. To keep the analysis as unbiased as possible, comparisons between RS categories only included tumors within the same MP score range and similarly comparisons of MP categories only contained tumors within the same RS score range. Results: The comparisons between discordant cases, their numbers and the amount of differentially expressed genes (DEGs) are shown below. Sample sizes are shown in parentheses. Of the 49 DEGs found in the RS Intermediate group, several are associated with increased proliferation or increased metastatic potential. SCUBE2 and MMP9 were among the 49 genes and are among the 70-genes assayed by MP. Conclusions: The comparisons highlight the genomic diversity of the RS Intermediate (RS11-25) group, as seen with the high number of DEGs. MP separates cases into more genomically distinct categories, as reflected by fewer DEGs. Clinical trial information: NCT03053193.