HIV-infected patients undergoing kidney transplantation are a unique patient subset with significantly increased episodes of graft rejection compared to non-infected transplant recipients. Biomarker development for monitoring of transplant rejection is a critically unmet need, particularly in HIV-infected individuals. Epigenetic mechanisms, including changes in DNA 5-methylcytosine (5mC), contribute to AR and can be used for HIV-infected kidney transplant recipients (HIVKT). screening. In addition to 5mC, another epigenetic modification involves oxidation of 5mC to yield 5-hydroxymethylcytosine (5hmC). 5hmC modifications also carry important epigenetic information signals that affect gene expression in a fashion distinct from 5mC. In this regard, it has been recently shown that 5hmC modifications are important in cell differentiation. The 5hmC modification has provided a tractable target that can be covalently labeled and isolated. Once isolated, 5hmC enriched loci can be mapped within the human genome using next-generation sequencing. The power of this approach involves its sensitivity to determine the distribution of 5hmC modifications using <1 ng DNA. Because of the high sensitivity, robustness, clinical convenience (non-invasive, blood-based) and cost-efficiency, this novel technology could uncover sensitive and specific biomarkers for acute rejection (AR) diagnosis, prognosis, treatment response, and relapse detection. In addition to AR in HIVKT, this technology could be broadly applied for diagnosis and prognosis of AR in other non-HIVKT patients and in other solid organ transplant patients.