Regional fat depot masses are influenced by protein-coding gene variants

Fig 1. The effect size and direction of effect of meta-analysis findings. Effect size and direction of effect of the three exome-wide significant missense variants: A. rs11057401 in CCDC92 (EAF = 0.32), B. rs62621401 in SPATA20 (EAF = 0.016) and C. rs4911494 in UQCC1 (EAF = 0.62). Data is presented for the 6 DXA measures under investigation and is presented as the beta value ± SD. The meta-analysis significance level using an additive model for gender combined (All) as well as for gender stratified analysis, together with the N indicated to the right of the data in parentheses. DXA measures are Arm fat mass (Arm), Total android fat mass (Android), Subcutaneous android fat mass (Abdominal subcut), Visceral android fat mass (Abdominal visceral), Gluteal fat mass (Gynoid) and Leg fat mass (Leg). Exome-wide significant data (p<2E-7) are in bold and underlined.

Fig 2. Expression of candidate genes across a human primary adipocyte differentiation time course. cDNA expression of CCDC92 (A), ZNF664 (B), SPATA20 (C), UQCC1 (D) and GDF5 (E) was measured over a 14-day adipogenic differentiation time-course using primary preadipocytes from abdominal subcutaneous adipose tissue (ASAT) and gluteal subcutaneous adipose tissue (GSAT) fat depots[40]. Data are shown as DDCt values (normalized to PPIA and PGK1; n = 6, mean ± SEM). A multivariate general linear model was used to test for statistical significance between depots and time, and to assess depot x time interactions. p-values are presented in the shaded boxes, NS: non-significant.

Fig 3. eQTL assessment of exome-wide significant loci by allele-specific qPCR expression. Allelic expression was measured on 4 candidate transcripts in our three exome-wide significant regions using allele-specific qPCR. Data is presented as the % of the minor allele detected compared to the major allele, as described in the methods, with a line indicating the mean and 95%CIs. To assess the rs11057401 eQTL haplotype the proxy SNP rs9863 was assessed for CCDC92 (A) and the transcribed region proxy SNP rs1054852 for ZNF664 (B). The index SNP rs62621401 was used to assess the SPATA20 transcript (C) and the index SNP rs4911494 for UQCC1. Paired samples were compared between abdominal subcutaneous adipose tissue (ASAT) and gluteal subcutaneous adipose tissue (GSAT) and genomic DNA (gDNA). For each transcript ABI Taqman genotyping assays were selected that fall within the transcribed sequence. gDNA selected from the same individuals as the cDNAs acts as a paired control with presumed equal allele expression. Deviation from 50% for gDNA, particularly pronounced in SPATA20 (C), represents inherent imbalance in assay technical performance and position of optimal Ct between Vic and Fam…