ORIGINAL INVESTIGATION Linkage and heritability analysis of migraine symptom groupings: a comparison of three different clustering methods on twin data Carla C. M. Chen Æ Kerrie L. Mengersen Æ Jonathan M. Keith Æ Nicholas G. Martin Æ Dale R. Nyholt Received: 11 January 2009 / Accepted: 6 March 2009 / Published online: 19 March 2009 Ó Springer-Verlag 2009 Abstract Migraine is a painful disorder for which the etiology remains obscure. Diagnosis is largely based on International Headache Society criteria. However, no fea- ture occurs in all patients who meet these criteria, and no single symptom is required for diagnosis. Consequently, this definition may not accurately reflect the phenotypic heterogeneity or genetic basis of the disorder. Such phe- notypic uncertainty is typical for complex genetic disorders and has encouraged interest in multivariate statistical methods for classifying disease phenotypes. We applied three popular statistical phenotyping methods—latent class analysis, grade of membership and grade of membership ‘‘fuzzy’’ clustering (Fanny)—to migraine symptom data, and compared heritability and genome-wide linkage results obtained using each approach. Our results demonstrate that different methodologies produce different clustering structures and non-negligible differences in subsequent analyses. We therefore urge caution in the use of any single approach and suggest that multiple phenotyping methods be used. Introduction The essential first step for linkage analysis or association studies is to accurately identify the phenotype. For com- plex diseases such as migraine, identification of the phenotype is challenging due to the lack of objective markers and uncertainty about the etiology of the disease. The diagnosis of this type of disorder is often based on satisfaction of clinically accepted criteria. Although they may not be useful for diagnosis and treatment, these clinical-based phenotypes may not be optimal for genetic research, in particular finding genetic loci contributing to disease inheritance (eg., Hallmayer et al. 2003) and this has led to a call for the development and use of new phenotyping strategies in genetic research (e.g., Wessman et al. 2007). Migraine is a common, painful and debilitating disorder. Numerous researchers have shown that there is a significant genetic component to risk of this disorder (Ziegler et al. 1998; Mulder et al. 2003; Svensson et al. 2003, 2004; Nyholt et al. 2004, 2005), with estimates of heritability ranging between 34 and 57% in twin-cohort studies across six countries (Mulder et al. 2003). The diagnosis of migraine is found to be difficult due to lack of biological markers and overlap with other types of neurological dis- orders, such as tension type headache and brain tumour. C. C. M. Chen (&)  K. L. Mengersen  J. M. Keith School of Mathematical Sciences, Queensland University of Technology, Brisbane, QLD 4001, Australia e-mail: carla.chen@qut.edu.au K. L. Mengersen e-mail: k.mengersen@qut.edu.au J. M. Keith e-mail: j.keith@qut.edu.au N. G. Martin Genetic Epidemiology Laboratory, Queensland Institute of Medical Research, PO Royal Brisbane Hospital, Brisbane, QLD 4029, Australia e-mail: Nick.Martin@qimr.edu.au D. R. Nyholt Neurogenetics Laboratory and Genetic Epidemiology Laboratory, Queensland Institute of Medical Research, PO Royal Brisbane Hospital, Brisbane, QLD 4029, Australia e-mail: daleN@qimr.edu.au 123 Hum Genet (2009) 125:591–604 DOI 10.1007/s00439-009-0652-7