Results of a direct numerical simulation (DNS) of hypersonic boundary-layer transition induced by a cylindrical isolated roughness element are presented. High-order, low dissi- pation inviscid fluxes are used and the simulation conditions match experiments performed at the von Karman Institute Mach 6 H3 facility. Freestream disturbances are treated as planar and acoustic; a novel method is used to recover the freestream pressure fluctuations from the experimentally measured stagnation pressure spectrum. The principal natural frequency of the flow near the roughness element in the high Reynolds number case is observed to be near 50 kHz and breakdown is observed downstream of the roughness element. The quiet simulation is characterized by the amplification of a series of discrete frequencies (corresponding to harmonics of the natural roughness frequency) and the noisy simulation is characterized by the amplification of a broad range of frequencies.