Abstract: This invention describes an allogenomics mismatch scoring method that estimates the genomic incompatibility between potential organ donors and a transplant recipient. The allogenomics method addresses immunological concerns and compares genotype information from matched, or potential, donors and recipients. The allogenomics method uses genomic data available before transplantation and predicts kidney graft function for greater than three years after transplantation. The strength of the inverse correlation between pre-transplantation genomic mismatches and transplant organ function increases with the time after transplantation: a low allogenomics mismatch score correlates with better acceptance and function of a donor transplant over time.

Abstract: A method for assessing risk of losing a transplanted organ by a patient having an episode of acute rejection of the transplanted organ is described. The method includes obtaining from the patient a cell sample from the transplanted organ or peripheral blood, determining a level of FOXP3 in the cell sample, and correlating the level with the risk of loss of the transplanted organ, wherein, compared to a control level, a significantly greater level of FOXP3 in the cell sample from the transplanted organ or a significantly lower level of FOXP3 in the cell sample from the peripheral blood correlates with a decreased risk of loss of the transplanted organ.

Abstract: Measurement of mRNAs in urinary cells offers a noninvasive means of diagnosing fibrosis in kidneys. One aspect of the invention is a method that includes: (a) measuring quantities of vimentin mRNA, NKCC2 mRNA, and E-cadherin mRNA in a test sample of cells obtained from urine; and (b) determining whether the vimentin mRNA quantity is higher, the NKCC2 mRNA quantity is lower, or the E-cadherin mRNA is higher than in healthy urinary cells; and thereby detecting that the sample is a fibrotic kidney sample. Step (a) can also include measuring the quantity of RNA expressed by a housekeeping gene (e.g., 18S rRNA). The quantities of vimentin mRNA, NKCC2 mRNA, and E-cadherin mRNA can be normalized against the quantity of housekeeping gene RNA.

Abstract: Methods and assay processes are described herein for identifying and treating subjects who have or will have dysfunction or rejection of a kidney transplant. The methods and assay procedures are noninvasive.

Abstract: Non-invasive methods for detecting, predicting, and/or monitoring differential diagnosis of kidney transplant dysfunction in kidney transplant patients are described.

Abstract: The invention relates to, among other things, a method for assessing risk of organ rejection in a patient having a transplanted organ. The method includes measuring an amount of expression of a small non-coding marker RNA in a biological sample from the patient. The method further includes comparing the measured amount of expression of the small non-coding marker RNA in the patient to a reference amount of expression of the small non-coding marker RNA. In another aspect, the invention relates to kits for assessing risk of organ rejection in a patient having a transplanted organ.

Abstract: Methods for prevention and treatment of kidney transplant rejection are described that involve determination, analysis and computation of a 3-gene molecular signature of levels of specific RNAs (IP-10 mRNA, CD3? mRNA, and 18S rRNA) in urinary sample cells. The methods and devices described herein are diagnostic and prognostic of acute cellular rejection in kidney allografts.

Abstract: In some embodiments, a method to detect acute rejection in allograft from is described. In some embodiments, a method to anticipate an episode of acute rejection in allografts is also described. In some embodiments, a kit for detecting or predicting acute transplant rejection of a transplanted organ is described.

Abstract: A method for assessing risk of losing a transplanted organ by a patient having an episode of acute rejection of the transplanted organ is described. The method includes obtaining from the patient a cell sample from the transplanted organ or peripheral blood, determining a level of FOXP3 in the cell sample, and correlating the level with the risk of loss of the transplanted organ, wherein, compared to a control level, a significantly greater level of FOXP3 in the cell sample from the transplanted organ or a significantly lower level of FOXP3 in the cell sample from the peripheral blood correlates with a decreased risk of loss of the transplanted organ.

Abstract: This invention describes an allogenomics mismatch scoring method that estimates the genomic incompatibility between potential organ donors and a transplant recipient. The allogenomics method addresses immunological concerns and compares genotype information from matched, or potential, donors and recipients. The allogenomics method uses genomic data available before transplantation and predicts kidney graft function for greater than three years after transplantation. The strength of the inverse correlation between pre-transplantation genomic mismatches and transplant organ function increases with the time after transplantation: a low allogenomics mismatch score correlates with better acceptance and function of a donor transplant over time.

Abstract: Measurement of mRNAs in urinary cells offers a noninvasive means of diagnosing fibrosis in kidneys. One aspect of the invention is a method that includes: (a) measuring quantities of vimentin mRNA, NKCC2 mRNA, and E-cadherin mRNA in a test sample of cells obtained from urine; and (b) determining whether the vimentin mRNA quantity is higher, the NKCC2 mRNA quantity is lower, or the E-cadherin mRNA is higher than in healthy urinary cells; and thereby detecting that the sample is a fibrotic kidney sample. Step (a) can also include measuring the quantity of RNA expressed by a housekeeping gene (e.g., 18S rRNA). The quantities of vimentin mRNA, NKCC2 mRNA, and E-cadherin mRNA can be normalized against the quantity of housekeeping gene RNA.

Abstract: Non-invasive methods for detecting, predicting, and/or monitoring differential diagnosis of kidney transplant dysfunction in kidney transplant patients are described.

Abstract: A method for assessing risk of losing a transplanted organ by a patient having an episode of acute rejection of the transplanted organ is described. The method includes obtaining from the patient a cell sample from the transplanted organ or peripheral blood, determining a level of FOXP3 in the cell sample, and correlating the level with the risk of loss of the transplanted organ, wherein, compared to a control level, a significantly greater level of FOXP3 in the cell sample from the transplanted organ or a significantly lower level of FOXP3 in the cell sample from the peripheral blood correlates with a decreased risk of loss of the transplanted organ.

Abstract: Methods for prevention and treatment of kidney transplant rejection are described that involve determination, analysis and computation of a 3-gene molecular signature of levels of specific RNAs (IP-10 mRNA, CD3? mRNA, and 18S rRNA) in urinary sample cells. The methods and devices described herein are diagnostic and prognostic of acute cellular rejection in kidney allografts.

Abstract: The invention relates to methods of evaluating transplant rejection in a host comprising determining a heightened magnitude of gene expression of genes in rejection-associated gene clusters. The disclosed gene clusters include genes that are substantially co-expressed with cytotoxic lymphocyte pro-apoptotic genes, cytoprotective genes and several other cytokine and immune cell genes.

Abstract: In some embodiments, a method to detect acute rejection in allograft from is described. In some embodiments, a method to anticipate an episode of acute rejection in allografts is also described. In some embodiments, a kit for detecting or predicting acute transplant rejection of a transplanted organ is described.

Abstract: The invention relates to, among other things, a method for assessing risk of organ rejection in a patient having a transplanted organ. The method includes measuring an amount of expression of a small non-coding marker RNA in a biological sample from the patient. The method further includes comparing the measured amount of expression of the small non-coding marker RNA in the patient to a reference amount of expression of the small non-coding marker RNA. In another aspect, the invention relates to kits for assessing risk of organ rejection in a patient having a transplanted organ.

Abstract: The invention relates to methods of evaluating transplant rejection in a host comprising determining a heightened magnitude of gene expression of genes in rejection-associated gene clusters. The disclosed gene clusters include genes that are substantially co-expressed with cytotoxic lymphocyte pro-apoptotic genes, cytoprotective genes and several other cytokine and immune cell genes.

Abstract: A method for assessing risk of losing a transplanted organ by a patient having an episode of acute rejection of the transplanted organ is described. The method includes obtaining from the patient a cell sample from the transplanted organ or peripheral blood, determining a level of FOXP3 in the cell sample, and correlating the level with the risk of loss of the transplanted organ, wherein, compared to a control level, a significantly greater level of FOXP3 in the cell sample from the transplanted organ or a significantly lower level of FOXP3 in the cell sample from the peripheral blood correlates with a decreased risk of loss of the transplanted organ.

Abstract: The invention relates to methods of evaluating transplant rejection in a host comprising determining a heightened magnitude of gene expression of genes in rejection-associated gene clusters. The disclosed gene clusters include genes that are substantially co-expressed with cytotoxic lymphocyte pro-apoptotic genes, cytoprotective genes and several other cytokine and immune cell genes.