Kidney_nHM_score

Non-classical HLA and MIC risk score in kidney transplantation

Publication: Tammi S, Markkinen S, Helanterä I, Lempinen M, Partanen J, Hyvärinen K, Ritari J. Non-Classical HLA and MIC Risk Score Is Associated With Acute Kidney Transplant Rejection Beyond Classical HLA Matching. HLA. 2026 Apr;107(4):e70698. doi: 10.1111/tan.70698. PMID: 41925073; PMCID: PMC13044989.

Code (./src)

cl_HLA_imputation.R Imputation of classical HLA alleles
Non_cl_HLA_MIC_imputation.R Imputation of non-classical HLA and MIC alleles
Mismatch_calculations.R Calculation of allelic and eplet mismatching between recipient and donor
Cox_analysis_AR.R Cox proportional hazards analysis for the association of non-classical HLA and MIC with acute rejection after kidney transplantation
Added_value_of_nHM_score.R Evaluation of the added value of nHM score beyond classical HLA matching
competing_risks_analysis.R Cumulative incidence using Aalen-Johansen method and competing risks analysis using Fine-Gray subdistribution hazards models

Model evaluation:
Model_evaluation_non-linearity.R Evaluation of non-linearity of the models
Model_evaluation_AUC_Brier.R Evaluation of model discrimination by time-dependent AUC and Brier scores
Model_evaluation_Unos_C.R Uno's C index for higly censored data

Functions:
functions.R Functions for Cox ph modeling, Kaplan-Meier plotting and standardization of nHM score
dosage_function.R function to convert imputed posterior probabilities to dosages
mismatch_functions.R functions to calculate mismatches between recipient and donor