Research Paper Multiple Sclerosis 0(00) 1–12 ! The Author(s) 2010 Reprints and permissions: sagepub.co.uk/journalsPermissions.nav DOI: 10.1177/1352458510364633 msj.sagepub.com Analysis of multiple candidate genes in association with phenotypes of multiple sclerosis Madeleine H Sombekke 1 *, David Arteta 2 *, Mark A van de Wiel 3,4 , J Bart A Crusius 5 , Diego Tejedor 2 , Joep Killestein 1 , Antonio Martı ´nez 2 , A Salvador Pen ˜a 5 , Chris H Polman 1 and Bernard MJ Uitdehaag 1,3 Abstract Multiple sclerosis is a heterogeneous neurological disease with varying degrees of severity. The common hypothesis is that susceptibility to multiple sclerosis and its phenotype are caused by a combination of environmental and genetic factors. The genetic part exerts its effect through several genes, each having modest effects. We evaluated whether disease severity could be predicted by a model based on clinical data and data from a DNA chip. The DNA chip was designed containing several single nucleotide polymorphisms in 44 genes, previously described to be associated with multiple sclerosis. A total of 605 patients with multiple sclerosis were included in this analysis, using gender, onset type and age at onset as clinical covariates. We correlated 80 single nucleotide polymorphisms to the degree of disease severity using the following three outcome measures: linear Multiple Sclerosis Severity Score, dichotomous Multiple Sclerosis Severity Score (using a cut-off point of 2.5) and time to reach Expanded Disability Status Scale score 6. Sixty-nine single nucleotide polymorphisms were included in the analysis. No individual single nucleotide polymorph- ism showed a significant association; however, a combination of single nucleotide polymorphisms significantly improved the prediction of disease severity in addition to the clinical variables. In all three models the Interleukin 2 gene was included, confirming a previously reported modest effect on disease severity. The highest power was obtained using the dichotomized Multiple Sclerosis Severity Score as outcome. Several single nucleotide polymorphisms showed their added predictive value over the clinical data in the predictive models. These results support our hypothesis that disease severity is determined by clinical variables and genetic influences (through several genes with small effects) in concert. Keywords genetics, multiple sclerosis, outcome, Interleukin 2 Date received: 26th November 2009; accepted: 3rd February 2010 Introduction Multiple sclerosis (MS) is a presumed autoimmune dis- ease affecting the central nervous system, characterized by demyelination and neurodegeneration. The clinical disease course is highly variable; some patients remain without significant functional loss for many years, while others become wheelchair-bound within a short period of time. 1 As different treatment options have become available (with varying efficacy and side- effects), the identification of patients prone to develop high disability within a short period has become highly relevant. However, predictors for future disability are scarce. *These authors contributed equally to this study. 1 Department of Neurology, VU University Medical Center, Amsterdam, The Netherlands. 2 Progenika Biopharma, S.A., Derio, Spain. 3 Department of Epidemiology and Biostatistics, VU University Medical Center, Amsterdam, The Netherlands. 4 Department of Mathematics, VU University, Amsterdam, The Netherlands. 5 Laboratory of Immunogenetics, Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands. Corresponding author: MH Sombekke, Department of Neurology, VU University Medical Center, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands. Email: m.sombekke@vumc.nl Mult Scler OnlineFirst, published on April 8, 2010 as doi:10.1177/1352458510364633