El-Sayed Moustafa, Julia S., Eleftherohorinou, Hariklia, de Smith, Adam J., Andersson-Assarsson, Johanna C., Couto Alves, Alexessander, Hadjigeorgiou, Eleni, Walters, Robin G., Asher, Julian E., Bottolo, Leonardo, Buxton, Jessica L., Sladek, Rob, Meyre, David, Dina, Christian, Visvikis-Siest, Sophie, Jacobson, Peter, Sjöström, Lars, Carlsson, Lena M.S., Walley, Andrew, Falchi, Mario, Froguel, Philippe, Blakemore, Alexandra I.F. and Coin, Lachlan J.M. (2012) Novel association approach for variable number tandem repeats (VNTRs) identifies DOCK5 as a susceptibility gene for severe obesity. Human Molecular Genetics, 21(16), pp. 3727-3738. ISSN (print) 0964-6906

Abstract

Variable number tandem repeats (VNTRs) constitute a relatively under-examined class of genomic variants in the context of complex disease because of their sequence complexity and the challenges in assaying them. Recent large-scale genome-wide copy number variant mapping and association efforts have highlighted the need for improved methodology for association studies using these complex polymorphisms. Here we describe the in-depth investigation of a complex region on chromosome 8p21.2 encompassing the dedicator of cytokinesis 5 (DOCK5) gene. The region includes two VNTRs of complex sequence composition which flank a common 3975 bp deletion, all three of which were genotyped by polymerase chain reaction and fragment analysis in a total of 2744 subjects. We have developed a novel VNTR association method named VNTRtest, suitable for association analysis of multi-allelic loci with binary and quantitative outcomes, and have used this approach to show significant association of the DOCK5 VNTRs with childhood and adult severe obesity (P(empirical)= 8.9 × 10(-8) and P= 3.1 × 10(-3), respectively) which we estimate explains ~0.8% of the phenotypic variance. We also identified an independent association between the 3975 base pair (bp) deletion and obesity, explaining a further 0.46% of the variance (P(combined)= 1.6 × 10(-3)). Evidence for association between DOCK5 transcript levels and the 3975 bp deletion (P= 0.027) and both VNTRs (P(empirical)= 0.015) was also identified in adipose tissue from a Swedish family sample, providing support for a functional effect of the DOCK5 deletion and VNTRs. These findings highlight the potential role of DOCK5 in human obesity and illustrate a novel approach for analysis of the contribution of VNTRs to disease susceptibility through association studies.

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