Disease Liability Prediction from Large Scale Genotyping Data Using Classifiers with a Reject Option

Authors:
Jose R. Quevedo;Antonio Bahamonde;Miguel Perez-Enciso;Oscar Luaces
Affiliations:
Oviedo University, Gijón;Oviedo University, Gijón;Universitat Autònoma de Barcelona and Institut Català de Recerca i Estudis Avançats, Barcelona;Oviedo University, Gijón
Venue:
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Year:
2012

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Abstract

Genome-wide association studies (GWA) try to identify the genetic polymorphisms associated with variation in phenotypes. However, the most significant genetic variants may have a small predictive power to forecast the future development of common diseases. We study the prediction of the risk of developing a disease given genome-wide genotypic data using classifiers with a reject option, which only make a prediction when they are sufficiently certain, but in doubtful situations may reject making a classification. To test the reliability of our proposal, we used the Wellcome Trust Case Control Consortium (WTCCC) data set, comprising 14,000 cases of seven common human diseases and 3,000 shared controls.