Identification of Novel Candidate Markers of Type 2 Diabetes and Obesity in Russia by Exome Sequencing with a Limited Sample Size

Abstract

Type 2 diabetes (T2D) and obesity are common chronic disorders with multifactorial etiology. In our study, we performed an exome sequencing analysis of 110 patients of Russian ethnicity together with a multi-perspective approach based on biologically meaningful filtering criteria to detect novel candidate variants and loci for T2D and obesity. We have identified several known single nucleotide polymorphisms (SNPs) as markers for obesity (rs11960429), T2D (rs9379084, rs1126930), and body mass index (BMI) (rs11553746, rs1956549 and rs7195386) (p < 0.05). We show that a method based on scoring of case-specific variants together with selection of protein-altering variants can allow for the interrogation of novel and known candidate markers of T2D and obesity in small samples. Using this method, we identified rs328 in LPL (p = 0.023), rs11863726 in HBQ1 (p = 8 × 10^-5), rs112984085 in VAV3 (p = 4.8 × 10^-4) for T2D and obesity, rs6271 in DBH (p = 0.043), rs62618693 in QSER1 (p = 0.021), rs61758785 in RAD51B (p = 1.7 × 10^-4), rs34042554 in PCDHA1 (p = 1 × 10^-4), and rs144183813 in PLEKHA5 (p = 1.7 × 10^-4) for obesity; and rs9379084 in RREB1 (p = 0.042), rs2233984 in C6orf15 (p = 0.030), rs61737764 in ITGB6 (p = 0.035), rs17801742 in COL2A1 (p = 8.5 × 10^-5), and rs685523 in ADAMTS13 (p = 1 × 10^-6) for T2D as important susceptibility loci in Russian population. Our results demonstrate the effectiveness of whole exome sequencing (WES) technologies for searching for novel markers of multifactorial diseases in cohorts of limited size in poorly studied populations.

Keywords: association study; exome sequencing; next-generation sequencing; obesity; single nucleotide polymorphisms; susceptibility locus; type 2 diabetes.

Figure 1

Usage of the scoring and filtering approaches to identify candidate markers of type 2 diabetes (T2D) and obesity in Russian population. (a,b). Probability of positive test outcome (Score1 > 10) (a) and the expected value of Score1 (b) for variants with different true population minor allele frequency (MAF) and true odds ratio (tOR), as estimated by in silico simulation (see Methods). (c). Distribution of values of two additive scores (Score1 and Score2, see text) under dominant inheritance model for damaging coding variants inside genes implicated in T2D and other genes n/s—non-significant difference in U-test. (d). Distributions of the random expectation numbers of case-unique protein-altering variants inside implicated (top) and non-implicated (bottom) genes. Yellow arrowheads indicate observed values. (e). Schematic representation of whole exome sequencing (WES) data analysis used in the present study. Rounded rectangles represent data manipulations.