The disclosure provides methods, devices, compositions and kits for diagnosing or predicting transplant status or outcome in a subject who has received a transplant. The methods comprise determining the presence or absence of one or more nucleic acids from a donor transplant, wherein said one or more nucleic acids from said donor are identified based on a predetermined marker profile, and diagnosing or predicting transplant status or outcome based on the presence or absence of said one or more nucleic acids.