Predictive Modeling of Type 1 Diabetes Stages Using Disparate Data Sources

• Published in: Diabetes (New York, N.Y.) Vol. 69; no. 2; pp. 238 - 248
• Main Authors: Frohnert, Brigitte I., Webb-Robertson, Bobbie-Jo, Bramer, Lisa M., Reehl, Sara M., Waugh, Kathy, Steck, Andrea K., Norris, Jill M., Rewers, Marian
• Format: Journal Article
• Language: English
• Published: United States American Diabetes Association 01.02.2020
• Subjects: Adenosine Diphosphate - metabolism; Adolescent; Ascorbic acid; Ascorbic Acid - blood; Autoimmunity; Biomarkers; Biomarkers - blood; Butyrates - blood; Case-Control Studies; Child; Child, Preschool; Diabetes; Diabetes mellitus (insulin dependent); Diabetes Mellitus, Type 1 - blood; Diabetes Mellitus, Type 1 - immunology; Female; Fibrinogen; Fibrinogen - metabolism; Genetics/Genomes/Proteomics/Metabolomics; Humans; Infant; Learning algorithms; Machine learning; Male; Mannose; Mannose - blood; Metabolomics; Models, Biological; Polymorphism, Genetic; Protein Tyrosine Phosphatase, Non-Receptor Type 22 - genetics; Protein-tyrosine-phosphatase; Young Adult
• ISSN: 0012-1797; 1939-327X; 1939-327X
• DOI: 10.2337/db18-1263

This study aims to model genetic, immunologic, metabolomics, and proteomic biomarkers for development of islet autoimmunity (IA) and progression to type 1 diabetes in a prospective high-risk cohort. We studied 67 children: 42 who developed IA (20 of 42 progressed to diabetes) and 25 control subjects matched for sex and age. Biomarkers were assessed at four time points: earliest available sample, just prior to IA, just after IA, and just prior to diabetes onset. Predictors of IA and progression to diabetes were identified across disparate sources using an integrative machine learning algorithm and optimization-based feature selection. Our integrative approach was predictive of IA (area under the receiver operating characteristic curve [AUC] 0.91) and progression to diabetes (AUC 0.92) based on standard cross-validation (CV). Among the strongest predictors of IA were change in serum ascorbate, 3-methyl-oxobutyrate, and the PTPN22 (rs2476601) polymorphism. Serum glucose, ADP fibrinogen, and mannose were among the strongest predictors of progression to diabetes. This proof-of-principle analysis is the first study to integrate large, diverse biomarker data sets into a limited number of features, highlighting differences in pathways leading to IA from those predicting progression to diabetes. Integrated models, if validated in independent populations, could provide novel clues concerning the pathways leading to IA and type 1 diabetes.