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1.  Use of Genome-Wide Expression Data to Mine the “Gray Zone” of GWA Studies Leads to Novel Candidate Obesity Genes 
PLoS Genetics  2010;6(6):e1000976.
To get beyond the “low-hanging fruits” so far identified by genome-wide association (GWA) studies, new methods must be developed in order to discover the numerous remaining genes that estimates of heritability indicate should be contributing to complex human phenotypes, such as obesity. Here we describe a novel integrative method for complex disease gene identification utilizing both genome-wide transcript profiling of adipose tissue samples and consequent analysis of genome-wide association data generated in large SNP scans. We infer causality of genes with obesity by employing a unique set of monozygotic twin pairs discordant for BMI (n = 13 pairs, age 24–28 years, 15.4 kg mean weight difference) and contrast the transcript profiles with those from a larger sample of non-related adult individuals (N = 77). Using this approach, we were able to identify 27 genes with possibly causal roles in determining the degree of human adiposity. Testing for association of SNP variants in these 27 genes in the population samples of the large ENGAGE consortium (N = 21,000) revealed a significant deviation of P-values from the expected (P = 4×10−4). A total of 13 genes contained SNPs nominally associated with BMI. The top finding was blood coagulation factor F13A1 identified as a novel obesity gene also replicated in a second GWA set of ∼2,000 individuals. This study presents a new approach to utilizing gene expression studies for informing choice of candidate genes for complex human phenotypes, such as obesity.
Author Summary
Obesity has a strong genetic component and an estimated 45%–85% of the variation in adult relative weight is genetically determined. Many genes have recently been identified in genome-wide association studies. The individual effects of the identified genes, however, have been very modest, and their identification required very large sample sizes. New approaches are therefore needed to uncover further genetic variants that contribute to the development of obesity and related conditions. Much can be learned from studying the expression of genes in adipose tissue of obese and non-obese subjects, but it is very difficult to distinguish which genes' expression differences represent reactions to obesity from those related to causal processes. We studied monozygotic twin pairs discordant for obesity and contrasted the gene expression profiles of obese and lean co-twins (controlling for genetic variation) to those from unrelated individuals to try to discern the cause-and-effect relationships of the identified changes in gene expression in fat. Testing the identified genes in 21,000 individuals identified numerous new genes with possible roles in the development of obesity. Among the top findings was a gene involved in blood coagulation (Factor XIIIA1), possibly linking obesity with known complications including deep vein thrombosis, heart attack, and stroke.
doi:10.1371/journal.pgen.1000976
PMCID: PMC2880558  PMID: 20532202

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