Methods and Systems for Analysis of Organ Transplantation

Abstract

Disclosed herein are methods of detecting, predicting or monitoring a status or outcome of a transplant in a transplant recipient.

What is claimed is: 
     
         1 . A method of detecting or predicting a condition of a transplant recipient, the method comprising:
 a. obtaining a sample, wherein the sample comprises one or more gene expression products from the transplant recipient;   b. performing an assay to determine an expression level of the one or more gene expression products from the transplant recipient; and   c. detecting or predicting the condition of the transplant recipient by applying an algorithm to the expression level determined in step (b), wherein the algorithm is a classifier capable of distinguishing between at least two conditions that are not normal conditions, wherein one of the at least two conditions is an acute rejection, and wherein one of the at least two conditions is a transplant dysfunction with no rejection.   
     
     
         2 . (canceled) 
     
     
         3 . A method of detecting or predicting a condition of a transplant recipient, the method comprising:
 a. obtaining a sample, wherein the sample comprises one or more gene expression products from the transplant recipient;   b. performing an assay to determine an expression level of the one or more gene expression products from the transplant recipient; and detecting or predicting the condition of the transplant recipient by applying an algorithm to the expression level determined in step (b), wherein the algorithm is a three-way classifier capable of distinguishing between at least three conditions, and wherein one of the at least three conditions is transplant rejection.   
     
     
         4 - 10 . (canceled) 
     
     
         11 . The method of  claim 1 , wherein the gene expression products are RNA. 
     
     
         12 . The method of  claim 1 , wherein the gene expression products are polypeptides. 
     
     
         13 . The method of  claim 1 , wherein the gene expression products are DNA complements of RNA expression products from the transplant recipient. 
     
     
         14 . The method of  claim 1 , wherein the algorithm is a trained algorithm. 
     
     
         15 . The method of  claim 14 , wherein the trained algorithm is trained with gene expression data from biological samples from at least three different cohorts. 
     
     
         16 . The method of  claim 14 , wherein the trained algorithm comprises a linear classifier. 
     
     
         17 . The method of  claim 14 , wherein the linear classifier comprises one or more linear discriminant analysis, Fisher's linear discriminant, Naïve Bayes classifier, Logistic regression, Perceptron, Support vector machine (SVM) or a combination thereof. 
     
     
         18 . The method of  claim 1 , wherein the algorithm comprises a Diagonal Linear Discriminant Analysis (DLDA) algorithm. 
     
     
         19 . The method of  claim 1 , wherein the algorithm comprises a Nearest Centroid algorithm. 
     
     
         20 . The method of  claim 1 , wherein the algorithm comprises a Random Forest algorithm or statistical bootstrapping. 
     
     
         21 . The method of  claim 1 , wherein the algorithm comprises a Prediction Analysis of Microarrays (PAM) algorithm. 
     
     
         22 . The method of  claim 1 , wherein the algorithm is not validated by a cohort-based analysis of an entire cohort. 
     
     
         23 . The method of  claim 1 , wherein the algorithm is validated by a combined analysis with an unknown phenotype and a subset of a cohort with known phenotypes. 
     
     
         24 . The method of  claim 1 , wherein the one or more gene expression products comprises five or more gene expression products with different sequences. 
     
     
         25 . The method of  claim 24 , wherein the five or more gene expression products correspond to less than 200 genes listed in Table 1a or 1c. 
     
     
         26 . The method of  claim 15 , wherein the biological samples are differentially classified based on one or more clinical features. 
     
     
         27 . The method of  claim 26 , wherein the one or more clinical features comprise status or outcome of a transplanted organ. 
     
     
         28 . The method of  claim 1 , wherein the classifier is a three-way classifier which is generated, in part, by comparing two or more gene expression profiles from two or more control samples. 
     
     
         29 - 30 . (canceled) 
     
     
         31 . The method of  claim 28 , wherein the two or more gene expression profiles from the two or more control samples are normalized by frozen multichip average (fRMA). 
     
     
         32 - 33 . (canceled) 
     
     
         34 . The method of  claim 1 , wherein the sample is a blood sample or is derived from a blood sample. 
     
     
         35 . The method of  claim 34 , wherein the blood sample is a peripheral blood sample. 
     
     
         36 . The method of  claim 35 , wherein the blood sample is a whole blood sample. 
     
     
         37 . The method of  claim 1 , wherein the sample does not comprise tissue from a biopsy of a transplanted organ of the transplant recipient. 
     
     
         38 . The method of  claim 1 , wherein the sample is not derived from tissue from a biopsy of a transplanted organ of the transplant recipient. 
     
     
         39 . The method of  claim 1 , wherein the assay is a microarray, SAGE, blotting, RT-PCR, sequencing and/or quantitative PCR assay. 
     
     
         40 . The method of  claim 1 , wherein the assay is a microarray assay. 
     
     
         41 . The method of  claim 40 , wherein the microarray assay comprises the use of an Affymetrix Human Genome U133 Plus 2.0 GeneChip or an HT HG-U133+PM Array Plate. 
     
     
         42 . The method of  claim 1 , wherein the assay is a sequencing assay. 
     
     
         43 . The method of  claim 42 , wherein the assay is a RNA sequencing assay. 
     
     
         44 . The method of  claim 42 , wherein the assay comprises a DNA sequencing assay. 
     
     
         45 . The method of  claim 42 , wherein the assay comprises a NextGen sequencing assay or massively parallel sequencing assay. 
     
     
         46 . The method of  claim 1 , wherein the gene expression products correspond to five or more genes listed in Table 1a or 1c. 
     
     
         47 . The method of  claim 1 , wherein the method has an error rate of less than about 10%. 
     
     
         48 . The method of  claim 1 , wherein the method has an accuracy of at least about 70%. 
     
     
         49 . The method of  claim 1 , wherein the method has a sensitivity of at least about 80%. 
     
     
         50 . The method of  claim 1 , wherein the method has a specificity of at least about 80%. 
     
     
         51 . The method of  claim 1 , wherein the transplant recipient is a recipient of an organ or tissue. 
     
     
         52 . The method of  claim 1 , wherein the transplant recipient has a serum creatinine level of at least 1.5 mg/dL. 
     
     
         53 . The method of  claim 1 , wherein the transplant recipient has a serum creatinine level of at least 3 mg/dL. 
     
     
         54 . The method of  claim 1 , wherein the transplant recipient is a recipient of a transplanted organ, and the organ is an eye, lung, kidney, heart, liver, pancreas, intestines, or a combination thereof. 
     
     
         55 . The method of  claim 1 , wherein the transplant recipient is a kidney transplant recipient. 
     
     
         56 . The method of  claim 1 , wherein the transplant recipient is a liver transplant recipient. 
     
     
         57 . The method of  claim 1 , further comprising providing or terminating a treatment for the transplant recipient based on the detected or predicted condition of the transplant recipient. 
     
     
         58 . A method of detecting, diagnosing, predicting or monitoring a status or outcome of a transplant in a transplant recipient, the method comprising:
 a. determining a level of expression of one or more genes in a sample from a transplant recipient, wherein the level of expression is determined by RNA sequencing; and   b. diagnosing, predicting or monitoring a status or outcome of a transplant in the transplant recipient.   
     
     
         59 . A method comprising the steps of:
 a. determining a level of expression of one or more genes in a sample from a transplant recipient;   b. normalizing the expression level data from step (a) using a frozen robust multichip average (fRMA) algorithm to produce normalized expression level data;   c. producing one or more classifiers based on the normalized expression level data from step (b); and   d. detecting, diagnosing, predicting or monitoring a status or outcome of a transplant in the transplant recipient based on the one or more classifiers from step (c).   
     
     
         60 - 61 . (canceled) 
     
     
         62 . The method of  claim 1 , wherein the method has a negative predictive value of greater than 70%. 
     
     
         63 - 66 . (canceled) 
     
     
         67 . A non-transitory computer-readable storage media comprising:
 a. a database, in a computer memory, of one or more clinical features of two or more control samples, wherein
 i. the two or more control samples are from two or more transplant recipients; and 
 ii. the two or more control samples are differentially classified based on a classification system comprising three or more different classes; 
   b. a first software module configured to compare the one or more clinical features of the two or more control samples; and   c. a second software module configured to produce a classifier set based on the comparison of the one or more clinical features.   
     
     
         68 - 71 . (canceled) 
     
     
         72 . A system comprising:
 a. a digital processing device comprising an operating system configured to perform executable instructions and a memory device;   b. a computer program including instructions executable by the digital processing device to classify a sample from a transplant recipient comprising:
 i. a software module configured to receive a gene expression profile of one or more genes from the sample from the transplant recipient; 
 ii. a software module configured to analyze the gene expression profile from the transplant recipient; and 
 iii. a software module configured to classify the sample from the transplant recipient based on a classification system comprising three or more classes. 
   
     
     
         73 - 76 . (canceled)