Signatures of natural selection at the FTO (fat mass and obesity associated) locus in human populations.

Polymorphisms in the first intron of FTO have been robustly replicated for associations with obesity. In the Sorbs, a Slavic population resident in Germany, the strongest effect on body mass index (BMI) was found for a variant in the third intron of FTO (rs17818902). Since this may indicate population specific effects of FTO variants, we initiated studies testing FTO for signatures of selection in vertebrate species and human populations.First, we analyzed the coding region of 35 vertebrate FTO orthologs with Phylogenetic Analysis by Maximum Likelihood (PAML, ω = dN/dS) to screen for signatures of selection among species. Second, we investigated human population (Europeans/CEU, Yoruba/YRI, Chinese/CHB, Japanese/JPT, Sorbs) SNP data for footprints of selection using DnaSP version 4.5 and the Haplotter/PhaseII. Finally, using ConSite we compared transcription factor (TF) binding sites at sequences harbouring FTO SNPs in intron three.PAML analyses revealed strong conservation in coding region of FTO (ω<1). Sliding-window results from population genetic analyses provided highly significant (p<0.001) signatures for balancing selection specifically in the third intron (e.g. Tajima's D in Sorbs = 2.77). We observed several alterations in TF binding sites, e.g. TCF3 binding site introduced by the rs17818902 minor allele.Population genetic analysis revealed signatures of balancing selection at the FTO locus with a prominent signal in intron three, a genomic region with strong association with BMI in the Sorbs. Our data support the hypothesis that genes associated with obesity may have been under evolutionary selective pressure

Population genetic measures on unstandardized iHS and Fst.

<p><i>p</i> = <i>p</i>-value for association to BMI in the Sorbs; iHS = integrated Haplotype score; CEU = Central Europeans; CHB = Han Chinese from Beijing; JPT = Japanese from Tokyo; YRI = Yoruba from Ibadan; n. a. = not available</p><p>Population genetic measures on unstandardized iHS and Fst.</p

Results of the DnaSP Analyses.

<p>n = number of haplotypes</p><p>* <i>p</i><0,05</p><p>** <i>p</i><0,02</p><p>*** <i>p</i><0,001</p><p>^# 0,1><i>p</i>>0,05</p><p><i>FTO</i>: 52.297.274–52.696.065 bp; rs1421091 - rs2689269 on Human May 2004 (NCBI35/hg17), Intron 1: 52.326.794–52401034bp; rs7203521 - rs6499646, Intron 3: 52.421.901–52.434.067 bp; rs7204916 - rs7205213</p><p>Results of the DnaSP Analyses.</p

Tajima’s D within the <i>FTO</i> locus from five populations showing signals of selection.

<p>Sliding window analysis of Tajima’s D in the whole gene locus (∼ 1 Mb) was conducted with DnaSP version 4.50.0.3. Populations of European, African, Chinese, Japanese and Sorbs were included in the analysis. Closely related individuals were removed, i.e. trios from Chinese and Japanese populations and individuals with IBD > 0.05 from Sorbs. Higher values of Tajima’s D were observed at the intron 3.</p

Neighbor-joining phylogenetic tree of 35 species on <i>FTO</i> coding sequences showing the evolutionary relationship.

<p>The bootstrap consensus tree inferred from 1000 replicates is generated to present the evolutionary relationship among 35 species on <i>FTO</i> coding sequences which were retrieved from Ensembl or NCBI. Accession numbers are listed at <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0117093#pone.0117093.s001" target="_blank">S1 Table</a>. Alignment was carried out by ClustalW (1581 nucleotides left) and phylogenetic tree is constructed by neighbor-joining method in MEGA6. Branches corresponding to partitions reproduced in less than 50% bootstrap replicates did no display. This tree works as the initial tree for further PAML analysis.</p

THOC5 : A novel gene involved in HDL-cholesterol metabolism

Although numerous genes are known to regulate serum lipid traits, identified variants explain only a small proportion of the expected heritability. We intended to identify further genetic variants associated with lipid phenotypes in a self-contained population of Sorbs in Germany. We performed a genome-wide association study (GWAS) on LDL-cholesterol, HDL-cholesterol (HDL-C), and triglyceride (TG) levels in 839 Sorbs. All single-nucleotide polymorphisms with a P value <0.01 were subjected to a meta-analysis, including an independent Swedish cohort (Diabetes Genetics Initiative; n = ∼ 3,100). Novel association signals with the strongest effects were subjected to replication studies in an additional German cohort (Berlin, n = 2,031). In the initial GWAS in the Sorbs, we identified 14 loci associated with lipid phenotypes reaching P values <10 -5 and confirmed significant effects for 18 previously reported loci. The combined meta-analysis of the three study cohorts (n(HDL) = 6041; n (LDL) = 5,995; n(TG) = 6,087) revealed a novel association for a variant in THOC5 (rs8135828) with serum HDL-C levels (P = 1.78 × 10-7; Z -score = -5.221). Consistently, the variant was also associated with circulating APOA1 levels in Sorbs. The small interfering RNA-mediated mRNA silencing of THOC5 in HepG2 cells resulted in lower mRNA levels of APOA1, SCARB1, and ABCG8 (all P < 0.05). We propose THOC5 to be a novel gene involved in the regulation of serum HDL-C levels