title: Investigation of a genome wide association signal for obesity: synthetic association and haplotype analyses at the melanocortin 4 receptor gene locus.
abstract: BACKGROUND
  Independent genome-wide association studies (GWAS) showed an obesogenic effect of two single nucleotide polymorphisms (SNP; rs12970134 and rs17782313) more than 150 kb downstream of the melanocortin 4 receptor gene (MC4R). It is unclear if the SNPs directly influence MC4R function or expression, or if the SNPs are on a haplotype that predisposes to obesity or includes functionally relevant genetic variation (synthetic association). As both exist, functionally relevant mutations and polymorphisms in the MC4R coding region and a robust association downstream of the gene, MC4R is an ideal model to explore synthetic association.
  
  
  RESULTS
  We analyzed a genomic region (364.9 kb) encompassing the MC4R in GWAS data of 424 obesity trios (extremely obese child/adolescent and both parents). SNP rs12970134 showed the lowest p-value (p = 0.004; relative risk for the obesity effect allele: 1.37); conditional analyses on this SNP revealed that 7 of 78 analyzed SNPs provided independent signals (p≤0.05). These 8 SNPs were used to derive two-marker haplotypes. The three best (according to p-value) haplotype combinations were chosen for confirmation in 363 independent obesity trios. The confirmed obesity effect haplotype includes SNPs 3' and 5' of the MC4R. Including MC4R coding variants in a joint model had almost no impact on the effect size estimators expected under synthetic association.
  
  
  CONCLUSIONS
  A haplotype reaching from a region 5' of the MC4R to a region at least 150 kb from the 3' end of the gene showed a stronger association to obesity than single SNPs. Synthetic association analyses revealed that MC4R coding variants had almost no impact on the association signal. Carriers of the haplotype should be enriched for relevant mutations outside the MC4R coding region and could thus be used for re-sequencing approaches. Our data also underscore the problems underlying the identification of relevant mutations depicted by GWAS derived SNPs.
authors.affiliation: Institute of Medical Informatics, Biometry and Epidemiology, University of Duisburg-Essen, Essen, Germany.
authors.forename: André
authors.initials: A
authors.lastname: Scherag
authors.forename: Ivonne
authors.initials: I
authors.lastname: Jarick
authors.forename: Jessica
authors.initials: J
authors.lastname: Grothe
authors.forename: Heike
authors.initials: H
authors.lastname: Biebermann
authors.forename: Susann
authors.initials: S
authors.lastname: Scherag
authors.forename: Anna-Lena
authors.initials: AL
authors.lastname: Volckmar
authors.forename: Carla Ivane Ganz
authors.initials: CI
authors.lastname: Vogel
authors.forename: Brandon
authors.initials: B
authors.lastname: Greene
authors.forename: Johannes
authors.initials: J
authors.lastname: Hebebrand
authors.forename: Anke
authors.initials: A
authors.lastname: Hinney
mesh_terms: D024509:3' Flanking Region / Q000235:genetics; D024506:5' Flanking Region / Q000235:genetics; D000293:Adolescent; D002648:Child; D005260:Female; D005787:Gene Frequency; D020022:Genetic Predisposition to Disease / Q000235:genetics; D055106:Genome-Wide Association Study / Q000379:methods*; D005838:Genotype; D006239:Haplotypes; D006801:Humans; D016015:Logistic Models; D008297:Male; D009154:Mutation; D009765:Obesity / Q000235:genetics*; D016366:Open Reading Frames / Q000235:genetics; D020641:Polymorphism, Single Nucleotide; D044105:Receptor, Melanocortin, Type 4 / Q000235:genetics*; D012307:Risk Factors
chemical_list: D044105:Receptor, Melanocortin, Type 4