Next generation sequencing (NGS) is increasingly being used clinically to characterize the molecular alterations found in patients’ tumors. These testing results have the potential to affect clinical care by guiding therapeutic approaches based upon genotype. NGS based testing approaches have a distinct advantage over provider-ordered single gene testing in that they can detect unexpected, yet clinically important genetic changes. Here, we illustrate this principle with the case of a 33-year-old man with myeloid sarcoma that was refractory to six different chemotherapeutic regimens. Our clinical NGS assay detected an unanticipated FIP1L1-PDGFRA rearrangement in his tumor. The patient was immediately placed on Imatinib therapy to which he responded, and remains in remission 10 months after the rearrangement was initially detected.