Institute of Medical Informatics, Biometry and Epidemiology, University of Duisburg-Essen, Essen, Germany.
PLoS One. 2010 Nov 15;5(11):e13967. doi: 10.1371/journal.pone.0013967.
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.
METHODOLOGY/PRINCIPAL FINDINGS: 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/SIGNIFICANCE: 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.
独立的全基因组关联研究（GWAS）表明，在黑皮质素 4 受体基因（MC4R）下游 150kb 以上的两个单核苷酸多态性（SNP；rs12970134 和 rs17782313）对肥胖有影响。目前尚不清楚这些 SNP 是否直接影响 MC4R 的功能或表达，或者这些 SNP 是否位于易肥胖的单倍型上，或者是否包含具有功能相关性的遗传变异（合成关联）。由于这两种情况都存在，MC4R 编码区的功能相关突变和多态性以及基因下游的稳健关联，MC4R 是探索合成关联的理想模型。
方法/主要发现：我们分析了 GWAS 数据中包含 MC4R 的一个基因组区域（364.9kb），该区域包含 424 个肥胖三体型（极度肥胖的儿童/青少年和父母双方）。SNP rs12970134 显示出最低的 p 值（p=0.004；肥胖效应等位基因的相对风险：1.37）；对该 SNP 的条件分析表明，在分析的 78 个 SNP 中有 7 个提供了独立的信号（p≤0.05）。这 8 个 SNP 用于推导两个标记的单倍型。根据 p 值选择了三个最佳的单倍型组合，在 363 个独立的肥胖三体型中进行了验证。证实的肥胖效应单倍型包括 MC4R 的 3'和 5'端的 SNP。在联合模型中纳入 MC4R 编码变异对合成关联下预期的效应大小估计值几乎没有影响。
结论/意义：从 MC4R 5'端到基因 3'端至少 150kb 的区域延伸的单倍型与肥胖的相关性比单个 SNP 更强。合成关联分析表明，MC4R 编码变异对关联信号几乎没有影响。携带该单倍型的个体应该在 MC4R 编码区之外富集相关突变，因此可以用于重新测序方法。我们的数据还强调了 GWAS 衍生 SNP 所描述的识别相关突变所面临的问题。
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