Open-array analysis of genetic variants in Egyptian patients with type 2 diabetes and obesity

Open-array analysis of genetic variants in Egyptian patients with type 2 diabetes and obesity

Diabetes mellitus is considered a major public health problem worldwide. Susceptibility to diabetes is influenced by both genetic and environmental determinants. The aim of the present study was to test for 16 independent single nucleotide polymorphisms (SNPs) in established Type 2 diabetes (T2D) an...

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Bibliographic Details
Published in:The Egyptian journal of medical human genetics Vol. 18; no. 4; pp. 341 - 348
Main Authors: Attia, Hanaa R.M., Kamel, Solaf A., Ibrahim, Mona H., Farouk, Heba A., Rahman, Amany H.A., Sayed, Ghada H., Musa, Nevine I.
Format: Journal Article
Language:English
Published: Cairo, Egypt Elsevier B.V 01-10-2017
Egyptian Society of Human Genetics
Springer Nature B.V
SpringerOpen
Subjects:
Age
Body mass index
Cardiovascular disease
Cyclin-dependent kinases
Deoxyribonucleic acid
Diabetes
Diabetes mellitus
DNA
Family medical history
Fasting
Genes
Genetic testing
Genomes
Genotyping
Gluconeogenesis
Glycolysis
Homeostasis
Hyperglycemia
Immune response
Insulin
Insulin resistance
Laboratories
Lipids
Obesity
OpenArray
Peroxisome proliferator-activated receptors
Public health
Real-Time PCR System
Risk gene variants
Single-nucleotide polymorphism
Stat4 protein
Studies
Thermal cycling
Type 2 diabetes
Type 2 diabetes
Obesity
Real-Time PCR System
Risk gene variants
OpenArray
Genotyping
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Summary:Diabetes mellitus is considered a major public health problem worldwide. Susceptibility to diabetes is influenced by both genetic and environmental determinants. The aim of the present study was to test for 16 independent single nucleotide polymorphisms (SNPs) in established Type 2 diabetes (T2D) and obesity susceptibility loci by GWAS in a sample of Egyptian patients to find out if there is shared genetic background underlying both disease entities. Genotyping was performed using OpenArray® protocol on the QuantStudio™ 12K Flex Real-Time PCR System. In the present case control study a custom array was designed to facilitate cost-effective analysis of selected SNPs related to glycolysis, gluconeogenesis, inflammation, insulin signalling, and immune function. Seven gene variants showed significant association with the risk of T2D patients including FCGRA2, STAT4, CELSR2, PPARG, EXT2 rs3740878, GCKR, PTGS1. Factors that significantly affect T2D were obesity (p<0.001) and GCKR (p=0.001) and PTGS1 (p=0.001) gene variants. Gene variants that showed significant or borderline effect on obesity were MTHFD1, EXT2 rs3740878, GCKR and PTGS1 (p=0.03, 0.017, 0.059, 0.006) respectively. Overlapping genetic aspects should be considered and the presence of risk alleles of different genes together could contribute to the risk of T2D or obesity or both. The MTHFD1 and EXT2rs3740878 gene variants significantly affect obesity and not shared with T2D. Gene variants that showed combined effect on both disease entities were GCKR and PTGS1. These findings provide a basis for future studies on a larger scale. More stress on the risk gene variants that have a combined impact on both diabetes and obesity is recommended to improve risk prediction and preventive strategies.
ISSN:1110-8630
2090-2441
DOI:10.1016/j.ejmhg.2017.03.002