SHORT DESCRIPTION: In this article, we introduced the method of pooled DNA samples for the GWAS analysis and introduced all the bioinformatic and statistical analyzes associated with genomic data across the entire genome, which was an important part of the first strand of the project. The following is a full article abstract: ABSTRACT: Background: Recently, we witnessed great progress in the discovery of genetic variants associated with obesity and type 2 diabetes (T2D), especially in adults. Much less is known regarding genetic variants associated with insulin resistance (IR). We hypothesized that novel IR genes could be efficiently detected in a population of obese children and adolescents who may not exhibit comorbidities and other confounding factors. Objectives: This study aimed to determine whether a genome-wide association study (GWAS), using a DNA-pooling approach, could identify novel genes associated with IR. SUBJECTS: The pooled-DNA GWAS analysis included Slovenian obese children and adolescents with and without IR matched for body mass index, gender and age. A replication study was conducted in another independent cohort with or without IR. METHODS: For the pooled-DNA GWAS, we used HumanOmni5-Quad SNP array (Illumina). Allele frequency distributions were compared with modified t-tests and χ2-tests and ranked using PLINK. Top single nucleotide polymorphisms (SNPs) were validated using individual genotyping by high-resolution melting analysis and TaqMan assay. RESULTS: We identified five top-ranking SNPs from the pooled-DNA GWAS analysis within the ECE1, IL1R2, GNPDA1, HLA-J and PYGB loci. All except SNP rs9261108 (HLA-J locus) were confirmed in the validation phase using individual genotyping. The SNP rs2258617 within PYGB remained statistically significant for both recessive and additive models in both cohorts and in a merged analysis of both cohorts and present the strongest novel candidate gene for IR. CONCLUSION: We report for the first time a pooled-DNA GWAS approach to identify five novel SNPs or genes for IR in a paediatric population. The four loci confirmed in the second validation phase study warrant further studies, especially the strongest SNP rs2258617 within PYGB, and provide targets for further basic research of IR mechanisms and for the development of potential new IR and T2D therapies.
COBISS.SI-ID: 4003720
SHORT DESCRIPTION: In this analysis, the EFFECTS of the candidate Deptor gene on various metabolic parameters including cholesterol blood levels were examined in the population of obese children and adolescent. Effects on the cholesterol-related parameters were insignificant, while they were significant on some traits related to insulin resistance, the results were therefore focused on these traits. The original abstract follows: ABSTRACT: Background: Insulin resistance (IR) is one of the major metabolic complications of obesity in children and adolescents. DEP domain-containing mammalian target of rapamycin interacting protein (DEPTOR) is involved in downstream insulin signaling and DEPTOR’s effects are regulated by its level of expression. Objectives: To analyze promoter region of DEPTOR for genetic variants associated with altered IR in obese children and adolescents. Subjects and methods: IR was determined in 322 normoglycemic obese subjects [173 females, 149 males; mean age 13.3}3.5 yr, mean BMI-SDS 2.85}0.83, HbA1C 5.2}0.2% (33}2.5 mmol/mol)] using homeostatic model assessment – insulin resistance [HOMA-IR ()2 prepubertal and )3 pubertal)] and whole body insulin sensitivity index [WBISI ((6.5 prepubertal and (4.5 pubertal)]. Genetic variants, determined by high resolution melting analysis, were confirmed by Sanger sequencing, whereas population allele distribution was determined by TaqMan genotyping probes. Results: Genetic variant c.-143T)C (rs7840156) was associated with a significant 2-fold decreased risk to present with IR, determined by HOMA-IR [odds ratio (OR)=0.614, 95% confidence interval (CI)=0.435–0.867, p=0.0057) and WBISI (OR=0.582, 95% CI=0.414–0.817, p=0.0018). The CC genotype had lower mean HOMA-IR value (2.47}0.44 vs. 3.04}0.14, p=0.0177) and higher mean WBISI value (7.00}0.71 vs. 5.27}0.33, p=0.0235) than TT genotype. Variant c.-143T)C was located in evolutionary highly conserved region in DEPTOR promoter region. Conclusion: Presented results on association between insulin sensitivity and genetic variants in DEPTOR gene suggest DEPTOR and mammalian target of rapamycin signaling pathway to be potential target for future research and pharmacological interventions.
COBISS.SI-ID: 2775980