Validating a Computable Phenotype for Nephrotic Syndrome in Children and Adults Using PCORnet Data.

Background: Primary nephrotic syndromes are rare diseases which can impede adequate sample size for observational patient-oriented research and clinical trial enrollment. A computable phenotype may be powerful in identifying patients with these diseases for research across multiple institutions.
Methods: A comprehensive algorithm of inclusion and exclusion ICD-9 and ICD-10 codes to identify patients with primary nephrotic syndrome was developed. The algorithm was executed against the PCORnet CDM at three institutions from January 1, 2009 to January 1, 2018, where a random selection of 50 cases and 50 noncases (individuals not meeting case criteria seen within the same calendar year and within 5 years of age of a case) were reviewed by a nephrologist, for a total of 150 cases and 150 noncases reviewed. The classification accuracy (sensitivity, specificity, positive and negative predictive value, F1 score) of the computable phenotype was determined.
Results: The algorithm identified a total of 2708 patients with nephrotic syndrome from 4,305,092 distinct patients in the CDM at all sites from 2009 to 2018. For all sites, the sensitivity, specificity, and area under the curve of the algorithm were 99% (95% CI, 97% to 99%), 79% (95% CI, 74% to 85%), and 0.9 (0.84 to 0.97), respectively. The most common causes of false positive classification were secondary FSGS (nine out of 39) and lupus nephritis (nine out of 39).
Conclusion: This computable phenotype had good classification in identifying both children and adults with primary nephrotic syndrome utilizing only ICD-9 and ICD-10 codes, which are available across institutions in the United States. This may facilitate future screening and enrollment for research studies and enable comparative effectiveness research. Further refinements to the algorithm including use of laboratory data or addition of natural language processing may help better distinguish primary and secondary causes of nephrotic syndrome.
Competing Interests: C. Tran reports being a scientific advisor or member of Frontiers in Pediatrics Review Editor on the Editorial Board of Pediatric Nephrology. D. Gipson reports having consultancy agreements, through the University of Michigan, with AstraZeneca, Boehringer Ingelheim, Roche/Genentech, and Vertex Pharmaceuticals; reports receiving research funding, through the University of Michigan, from Atrium Health Medical Foundation, Boehringer Ingelheim, Centers for Disease Control, Food and Drug Administration, Goldfinch Bio, National Institutes of Health, Novartis, Reata, and Travere; and reports being a scientific advisor or member of the American Society of Pediatric Nephrology, American Society of Nephrology, and International Society of Pediatric Nephrology. H. Desmond reports receiving research funding through a percentage of salary from the University of Michigan, funded by Boehringer Ingelheim. I. Ayoub reports receiving honoraria from the American College of Rheumatology; reports being a scientific advisor or member of the Journal of Clinical Nephrology (Editorial Board) and the Lupus Foundation of America (advisory board). L. Mariani reports having consultancy agreements with, and receiving honoraria from, Calliditas Therapeutics Advisory Board, CKD Advisory Committee, Reata Pharmaceuticals, and Travere Therapeutics Advisory Board; reports receiving research funding from Boehringer Ingelheim; reports receiving honoraria from American Society of Nephrology Board Review Course and Update; and reports being a scientific advisor or member of Calliditas Therapeutics, Reata Pharmaceuticals, and Travere Therapeutics. M. Denburg reports having consultancy agreements with Trisalus Life Sciences (spouse); reports having an ownership interest in In-Bore LLC (spouse) and Precision Guided Interventions LLC (spouse); reports receiving research funding from Mallinckrodt; reports being a scientific advisor or member of NKF Delaware Valley Medical Advisory Board and Trisalus Life Sciences Scientific Advisory Board (spouse); and reports other interests/relationships with the American Society of Pediatric Nephrology Research and Program Committees and the National Kidney Foundation Pediatric Education Planning Committee. M. Matheny reports consultancy agreements with National Institutes of Health- Veterans Affairs- Department of Defense Pain Management Grant Consortium (PMC3); reports being a scientific advisor or member of Scientific Merit Review Board Study Section, VA Health Services Research and Development (HSR&D), Informatics and Methods Section, the Steering Committee of Indianapolis VA HSR&D Center of Innovation; and the Steering Committee of VA HSR&D VA Information Resource Center. S. Almaani reports having consultancy agreements with Aurinia Pharmaceuticals and Kezar Life Sciences; reports receiving research funding from Gilead Sciences; reports being a scientific advisor or member Clinical Nephrology Editorial Board; and reports speakers bureau from Aurinia Pharmaceuticals. S. Massengill reports having consultancy agreements with Guidepoint Group; reports being a scientific advisor or member of the Editorial Board of online Glomerular Disease Journal (Karger Publishers). All remaining authors have nothing to disclose.
(Copyright © 2021 by the American Society of Nephrology.)