Comparative performances of machine learning methods for classifying Crohn Disease patients using genome-wide genotyping data

Romagnoni, Alberto, Jegou, Simon, Van Steel, Kirsten, Wainrib, Gilles, Hugot, Jean-Pierre, and International Inflammatory Bowel Disease Genetics Consortium, (2019) Comparative performances of machine learning methods for classifying Crohn Disease patients using genome-wide genotyping data. Scientific Reports, 9. 10351.

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Abstract

Crohn Disease (CD) is a complex genetic disorder for which more than 140 genes have been identified using genome wide association studies (GWAS). However, the genetic architecture of the trait remains largely unknown. The recent development of machine learning (ML) approaches incited us to apply them to classify healthy and diseased people according to their genomic information. The Immunochip dataset containing 18,227 CD patients and 34,050 healthy controls enrolled and genotyped by the international Inflammatory Bowel Disease genetic consortium (IIBDGC) has been re-analyzed using a set of ML methods: penalized logistic regression (LR), gradient boosted trees (GBT) and artificial neural networks (NN). The main score used to compare the methods was the Area Under the ROC Curve (AUC) statistics. The impact of quality control (QC), imputing and coding methods on LR results showed that QC methods and imputation of missing genotypes may artificially increase the scores. At the opposite, neither the patient/control ratio nor marker preselection or coding strategies significantly affected the results. LR methods, including Lasso, Ridge and ElasticNet provided similar results with a maximum AUC of 0.80. GBT methods like XGBoost, LightGBM and CatBoost, together with dense NN with one or more hidden layers, provided similar AUC values, suggesting limited epistatic effects in the genetic architecture of the trait. ML methods detected near all the genetic variants previously identified by GWAS among the best predictors plus additional predictors with lower effects. The robustness and complementarity of the different methods are also studied. Compared to LR, non-linear models such as GBT or NN may provide robust complementary approaches to identify and classify genetic markers

Item ID: 63186
Item Type: Article (Research - C1)
ISSN: 2045-2322
Copyright Information: Open Access. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Cre-ative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not per-mitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. © The Author(s) 2019
Additional Information:

Gillan Mahy is part of the International Inflammatory Bowel Disease Genetics Consortium (IIBDGC) Collaborators group. All collaborators are listed at the end of the article

Funders: Fondation pour la Recherche Médicale (FRM), Investissements d’Avenir Programme (IAP)
Projects and Grants: FRM DEI20151234405, IAP ANR-11-IDEX-0005-02
Date Deposited: 19 May 2020 00:48
FoR Codes: 11 MEDICAL AND HEALTH SCIENCES > 1103 Clinical Sciences > 110307 Gastroenterology and Hepatology @ 100%
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