This article is part of the supplement: Genetic Analysis Workshop 17: Unraveling Human Exome Data
Disease risk prediction with rare and common variants
Department of Epidemiology and Public Health, Yale University, 60 College Street, New Haven, CT 06510, USA
BMC Proceedings 2011, 5(Suppl 9):S61 doi:10.1186/1753-6561-5-S9-S61Published: 29 November 2011
A number of studies have been conducted to investigate the predictive value of common genetic variants for complex diseases. To date, these studies have generally shown that common variants have no appreciable added predictive value over classical risk factors. New sequencing technology has enhanced the ability to identify rare variants that may have larger functional effects than common variants. One would expect rare variants to improve the discrimination power for disease risk by permitting more detailed quantification of genetic risk. Using the Genetic Analysis Workshop 17 simulated data sets for unrelated individuals, we evaluate the predictive value of rare variants by comparing prediction models built using the support vector machine algorithm with or without rare variants. Empirical results suggest that rare variants have appreciable effects on disease risk prediction.