Abstract: A method for performing an analysis related to potential rejection of an organ after transplantation in a subject is provided. The method involves identifying alloreactive/expanded CD8 T cell clones in either an allograft biopsy or a urine sample from the subject, wherein the T cell clones are identified using a single cell RNASeq (scRNAseq)/TCRseq test. In one embodiment, the analysis is selected from the group consisting of detection of rejection, diagnosis of rejection, treatment selection, therapeutic monitoring for rejection, identification of resistance to rejection treatment, and combinations thereof.