Computational protocol: Predicting Progression of IgA Nephropathy: New Clinical Progression Risk Score

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Protocol publication

[…] The distributions of quantitative variables were assessed for normality and summarized as means and standard deviations (or medians and ranges for non-normally distributed variables). Statistical testing of continuous variables was performed using Student’s t-test (or Mann-Whitney U-test if appropriate). All categorical variables were expressed as frequencies or percentages (%) and comparison of proportions was performed using a standard X2 test. Baseline clinical variables included sex, age, family history, BMI, baseline serum creatinine, eGFR, SBP, DBP, mean arterial pressure, pulse pressure, urine protein, gross hematuria, serum UA, serum albumin, serum triglycerides, serum cholesterol, hemoglobin, platelets, WBC, serum IgA, Haas classification, and treatment type. All slides of kidney biopsies were reviewed by a single experienced renal pathologist. The primary outcome was defined as occurrence of ESRD defined by a need for renal replacement therapy (dialysis or renal transplantation). The association of baseline variables with the primary outcome was tested using Cox regression proportional hazards models. A two sided P<0.05 was considered statistically significant. To identify independent predictors of progression, we performed a multivariate Cox regression analysis with a stepwise selection of variables (entry and elimination P<0.05). Patients were censored at the time of death or loss to follow-up. The proportional hazards assumption was formally tested for each of the outcomes using the method proposed by Grambsch and Therneau and implemented in the R survival package version 2.36 (R v.2.9). The independent predictors retained in the final model were used to derive the Risk Score. The effects of each independent predictor, as well as their cumulative effect in the form of the Risk Score were next tested using the Kaplan-Meier approach. We also scored our patients using the Japanese , the French and the RENAAL risk scores. The R2 (reflecting the fraction of variance in the primary outcome explained) was determined for each of the models . In addition, survival areas under receiver operating characteristic (ROC) curves were also assessed for the 24th, 60th and 120th month time points. These analyses were performed using Survcomp package version 1.1.6 (R v.2.9) and ROCR package version 1.0–2 (R v.2.9) . Based on the size and median follow-up of our cohort, we estimate 80% power to detect hazard ratios greater than 1.4 in this study. Our power calculations were performed with the PS software version 3.0 . […]

Pipeline specifications

Software tools survcomp, ROCR
Application Miscellaneous
Organisms Homo sapiens
Diseases Kidney Diseases, Kidney Failure, Chronic