A genome-wide search for type 2 diabetes susceptibility genes in an extended Arab family.

Twenty percent of people aged 20 to 79 have type 2 diabetes (T2D) in the United Arab Emirates (UAE). Genome-wide association studies (GWAS) to identify genes for T2D have not been reported for Arab countries. We performed a discovery GWAS in an extended UAE family (N=178; 66 diabetic; 112 healthy) genotyped on the Illumina Human 660 Quad Beadchip, with independent replication of top hits in 116 cases and 199 controls. Power to achieve genome-wide significance (commonly P=5×10(-8)) was therefore limited. Nevertheless, transmission disequilibrium testing in FBAT identified top hits at Chromosome 4p12-p13 (KCTD8: rs4407541, P=9.70×10(-6); GABRB1: rs10517178/rs1372491, P=4.19×10(-6)) and 14q13 (PRKD1: rs10144903, 3.92×10(-6)), supported by analysis using a linear mixed model approximation in GenABEL (4p12-p13 GABRG1/GABRA2: rs7662743, Padj-agesex=2.06×10(-5); KCTD8: rs4407541, Padj-agesex=1.42×10(-4); GABRB1: rs10517178/rs1372491, Padj-agesex=0.027; 14q13 PRKD1: rs10144903, Padj-agesex=6.95×10(-5)). SNPs across GABRG1/GABRA2 did not replicate, whereas more proximal SNPs rs7679715 (Padj-agesex=0.030) and rs2055942 (Padj-agesex=0.022) at COX7B2/GABRA4 did, in addition to a trend distally at KCTD8 (rs4695718: Padj-agesex=0.096). Modelling of discovery and replication data support independent signals at GABRA4 (rs2055942: Padj-agesex-combined=3×10(-4)) and at KCTD8 (rs4695718: Padj-agesex-combined=2×10(-4)). Replication was observed for PRKD1 rs1953722 (proxy for rs10144903; Padj-agesex=0.031; Padj-agesex-combined=2×10(-4)). These genes may provide important functional leads in understanding disease pathogenesis in this population.

Evaluation of different sources of DNA for use in genome wide studies and forensic application.

In the field of epidemiology, Genome-Wide Association Studies (GWAS) are commonly used to identify genetic predispositions of many human diseases. Large repositories housing biological specimens for clinical and genetic investigations have been established to store material and data for these studies. The logistics of specimen collection and sample storage can be onerous, and new strategies have to be explored. This study examines three different DNA sources (namely, degraded genomic DNA, amplified degraded genomic DNA and amplified extracted DNA from FTA card) for GWAS using the Illumina platform. No significant difference in call rate was detected between amplified degraded genomic DNA extracted from whole blood and amplified DNA retrieved from FTA™ cards. However, using unamplified-degraded genomic DNA reduced the call rate to a mean of 42.6% compared to amplified DNA extracted from FTA card (mean of 96.6%). This study establishes the utility of FTA™ cards as a viable storage matrix for cells from which DNA can be extracted to perform GWAS analysis.

A Population-Specific Major Allele Reference Genome From The United Arab Emirates Population.

The ethnic composition of the population of a country contributes to the uniqueness of each national DNA sequencing project and, ideally, individual reference genomes are required to reduce the confounding nature of ethnic bias. This work represents a representative Whole Genome Sequencing effort of an understudied population. Specifically, high coverage consensus sequences from 120 whole genomes and 33 whole exomes were used to construct the first ever population specific major allele reference genome for the United Arab Emirates (UAE). When this was applied and compared to the archetype hg19 reference, assembly of local Emirati genomes was reduced by ∼19% (i.e., some 1 million fewer calls). In compiling the United Arab Emirates Reference Genome (UAERG), sets of annotated 23,038,090 short (novel: 1,790,171) and 137,713 structural (novel: 8,462) variants; their allele frequencies (AFs) and distribution across the genome were identified. Population-specific genetic characteristics including loss-of-function variants, admixture, and ancestral haplogroup distribution were identified and reported here. We also detect a strong correlation between F ST and admixture components in the UAE. This baseline study was conceived to establish a high-quality reference genome and a genetic variations resource to enable the development of regional population specific initiatives and thus inform the application of population studies and precision medicine in the UAE.

Genetic Diversity and Low Stratification of the Population of the United Arab Emirates.

With high consanguinity rates on the Arabian Peninsula, it would not have been unexpected if the population of the United Arab Emirates (UAE) was shown to be relatively homogenous. However, this study of 1000 UAE nationals provided a contrasting perspective, one of a relatively heterogeneous population. Located at the apex of Europe, Asia, and Africa, the observed diversity could be explained by a plethora of migration patterns since the first Out-of-Africa movement. A strategy to explore the extent of genetic variation of the population of the UAE is presented. The first step involved a comprehensive population stratification study that was instructive for subsequent whole genome sequencing (WGS) of suitable representatives (which is described elsewhere). When these UAE data were compared to previous smaller studies from the region, the findings were consistent with a population that is a diverse and admixed group of people. However, rather than sharp and distinctive clusters, cluster analysis reveals low levels of stratification throughout the population. UAE emirates exhibit high within-Emirate-distance/among-Emirate distance ratios. Supervised admixture analysis showed a continuous gradient of ancestral populations, suggesting that admixture on the south eastern tip of the Arabian Peninsula occurred gradually. When visualized using a unique technique that combined admixture ratios and principal component analysis (PCA), unappreciated diversity was revealed while mitigating projection bias of conventional PCA. We observe low population stratification in the UAE in terms of homozygosity versus separation cluster coefficients. This holds for the UAE in a global context as well as for isolated cluster analysis of the Emirati birthplaces. However, the subtle clustering observed in the Emirates reflects geographic proximity and historic migration events. The analytical strategy used here highlights the complementary nature of data from genotype array and WGS for anthropological studies. Specifically, genotype array data were instructive to select representative subjects for WGS. Furthermore, from the 2.3 million allele frequencies obtained from genotype arrays, we identified 46,481 loci with allele frequencies that were significantly different with respect to other world populations. This comparison of allele frequencies facilitates variant prioritization in common diseases. In addition, these loci bear great potential as biomarkers in anthropological and forensic studies.

Whole Genome Sequencing of Four Representatives From the Admixed Population of the United Arab Emirates.

Whole genome sequences (WGS) of four nationals of the United Arab Emirates (UAE) at an average coverage of 33X have been completed and described. The selection of suitable subpopulation representatives was informed by a preceding comprehensive population structure analysis. Representatives were chosen based on their central location within the subpopulation on a principal component analysis (PCA) and the degree to which they were admixed. Novel genomic variations among the different subgroups of the UAE population are reported here. Specifically, the WGS analysis identified 4,161,067-4,798,806 variants in the four individual samples, where approximately 80% were single nucleotide polymorphisms (SNPs) and 20% were insertions or deletions (indels). An average of 2.75% was found to be novel variants according to dbSNP (build 151). This is the first report of structural variants (SV) from WGS data from UAE nationals. There were 15,677-20,339 called SVs, of which around 13.5% were novel. The four samples shared 1,399,178 variants, each with distinct variants as follows: 1,085,524 (for the individual denoted as UAE S011), 1,228,559 (UAE S012), 791,072 (UAE S013), and 906,818 (UAE S014). These results show a previously unappreciated population diversity in the region. The synergy of WGS and genotype array data was demonstrated through variant annotation of the former using 2.3 million allele frequencies for the local population derived from the latter technology platform. This novel approach of combining breadth and depth of array and WGS technologies has guided the choice of population genetic representatives and provides complementary, regionalized allele frequency annotation to new genomes comprising millions of loci.

Genetic Associations With Diabetic Retinopathy and Coronary Artery Disease in Emirati Patients With Type-2 Diabetes Mellitus.

Aim: Type 2 Diabetes Mellitus (T2DM) is associated with both microvascular complications such as diabetic retinopathy (DR), and macrovascular complications like coronary artery disease (CAD). Genetic risk factors have a role in the development of these complications. In the present case-control study, we investigated genetic variations associated with DR and CAD in T2DM patients from the United Arab Emirates. Methods: A total of 407 Emirati patients with T2DM were recruited. Categorization of the study population was performed based on the presence or absence of DR and CAD. Seventeen Single Nucleotide Polymorphisms (SNPs), were selected for association analyses through search of publicly available databases, namely GWAS catalog, infinome genome interpretation platform and GWAS Central database. A multivariate logistic regression test was performed to evaluate the association between the 17 SNPs and DR, CAD, or both. To account for multiple testing, significance was set at p < 0.00294 using the Bonferroni correction. Results: The SNPs rs9362054 near the CEP162 gene and rs4462262 near the UBE2D1 gene were associated with DR (OR = 1.66, p = 0.001; OR = 1.37, p = 0.031; respectively), and rs12219125 near the PLXDC2 gene was associated (suggestive) with CAD (OR = 2.26, p = 0.034). Furthermore, rs9362054 near the CEP162 gene was significantly associated with both complications (OR = 2.27, p = 0.0021). The susceptibility genes for CAD (PLXDC2) and DR (UBE2D1) have a role in angiogenesis and neovascularization. Moreover, association between the ciliary gene CEP162 and DR was established in terms of retinal neural processing, confirming previous reports. Conclusions: The present study reports associations of different genetic loci with DR and CAD. We report new associations between CAD and PLXDC2, and DR with UBE2D1 using data from T2DM Emirati patients.

Association of Diabetes Related Complications with Heart Rate Variability among a Diabetic Population in the UAE.

Microvascular, macrovascular and neurological complications are the key causes of morbidity and mortality among type II diabetes mellitus (T2DM) patients. The aim of this study was to investigate the alterations of cardiac autonomic function of diabetic patients in relation to three types of diabetes-related complications. ECG recordings were collected and analyzed from 169 T2DM patients in supine position who were diagnosed with nephropathy (n = 55), peripheral neuropathy (n = 64) and retinopathy (n = 106) at two hospitals in the UAE. Comparison between combinations of patients with complications and a control diabetic group (CONT) with no complication (n = 34) was performed using time, frequency and multi-lag entropy measures of heart rate variability (HRV). The results show that these measures decreased significantly (p<0.05) depending on the presence and type of diabetic complications. Entropy, (median, 1st- 3rd interquartile range) for the group combining all complications (1.74,1.37-2.09) was significantly lower than the corresponding values for the CONT group (1.77, 1.39-2.24) with lag-1 for sequential beat-to-beat changes. Odds ratios (OR) from the entropy analysis further demonstrated a significantly higher association with the combination of retinopathy and peripheral neuropathy versus CONT (OR: 1.42 at lag 8) and an even OR for the combination of retinopathy and nephropathy (OR: 2.46 at lag 8) compared to the other groups with complications. Also, the OR of low frequency power to high frequency power ratio (LF/HF) showed a higher association with these diabetic-related complications compared to CONT, especially for the patient group combining all complications (OR: 4.92). This study confirms that the type of microvascular or peripheral neuropathy complication present in T2DM patients have different effects on heart rate entropy, implying disorders of multi-organ connectivity are directly associated with autonomic nervous system dysfunction. Clinical practice may benefit from including multi-lag entropy for cardiac rhythm analysis in conjunction with traditional screening methods in patients with diabetic complications to ensure better preventive and treatment outcomes in the Emirati Arab population.

Novel dynamic peak and distribution plantar pressure measures on diabetic patients during walking.

Diabetic peripheral neuropathy (DPN) is a common complication leading to foot ulceration and amputation. Several kinematic, kinetic and plantar pressure measures have been proposed for DPN detection, however findings have been inconsistent. In this work, we present new shape features that capture variations in the plantar pressure using shape and entropy measures to the study of patients with retinopathy, DPN and nephropathy, and a control diabetic group with no complications. The change in the peak plantar pressure (PPP) position with each step for both feet was represented as a convex polygon, asymmetry index, area of the convex polygon, 2nd wavelet moment (WM2) and sample entropy (SamEn). WM2 and the SamEn were more sensitive in capturing variations due to presence of complications than the area and asymmetry measures. WM2 of the left heel (median: 1st IQ, 3rd IQ): 8.27 (4.6,14.8) and left forefoot: 9.2 (2.4,16) were significantly lower for the DPN group compared to the control (CONT) group (heel 11.9 (5.0,16.4); forefoot: 10.3 (4.4,21.3), p < 0.05). SamEn for the DPN group was significantly lower in the right foot compared to the left foot (1.3 (1.26, 1.37) and 1.33 (1.26,1.4), p < 0.01) compared to CONT (right foot: 1.37 (1.24,1.45) and left foot: 1.34 (1.25,1.42), P < 0.05). These new shape and regularity features have shown promising results in detecting diabetic peripheral neuropathy and warrant further investigation.

Gait alterations in the UAE population with and without diabetic complications using both traditional and entropy measures.

Diabetic foot, one of the most common and debilitating manifestations of type 2 diabetes mellitus (T2DM), is the leading cause of worldwide non-traumatic lower extremity amputations. Diabetics who are at risk of ulceration are currently mainly identified by a thorough clinical examination of the feet, which typically does not show clear symptoms during the early stages of disease progression. In this study, we used a non-linear dynamics tool, gait entropy (GaitEN), in addition to traditional linear gait analysis methods, to investigate gait alterations amongst diabetic patients with combinations of three types of T2DM related complications: retinopathy, diabetic peripheral neuropathy (DPN) and nephropathy. Peak plantar pressure (PPP) was not significantly different in the group with DPN as compared to the control group (diabetics with no complications, CONT) in the forefoot region (DPN: mean±SD: 396±69.4kPa, CONT: 409±68.9kPa), although it was significantly lower in the heel region (DPN: mean±SD: 285±43.1.4kPa, CONT: 295±61.8kPa). On the other hand, gait entropy was significantly lower for the DPN compared to CONT group (DPN: 0.95±0.34, CONT: 1.03±0.28, p<0.05). The significant low entropy was maintained when neuropathy was combined with either retinopathy or nephropathy. For the group with all three complications (ALL-C), the entropy was higher than CONT (ALL-C: 1.07±0.26). This may indicate an intrinsic sensorimotor feedback mechanism for the DPN patients to regulate their gait. However, this feedback gets weaker as patients develop multiple complications. Further analysis with longer walking time and different speeds is needed to verify the entropy results.

Relationship between MTHFR C677T and A1298C gene polymorphisms and complications of type 2 diabetes mellitus in an Emirati population.

PURPOSE: Type 2 diabetes mellitus (T2DM) is the most common form of diabetes with clinical consequences giving rise to chronic multiple organ complications. Methylenetetrahydrofolate reductase (MTHFR) polymorphisms are genetic variations that have been linked to T2DM, and micro/macrovascular complications. The link between MTHFR and T2DM however is strongly dependent on the ethnic group studied. The objective of this study was to investigate the possible association between two MTHFR polymorphisms (C677T and A1298C) and T2DM and specifically examine if there are any associations with clinical and demographic characteristics among patients in the United Arab Emirates (UAE). METHODS: The study included 169 T2DM patients and 209 healthy controls. Genomic DNA was isolated and genotyped using TaqMan real-Time PCR assays for the MTHFR C677T and A1298C polymorphisms. RESULTS: There were no significant differences in genotype and haplotype distributions observed between groups. A significant association was observed between the C677T polymorphism and history of cerebrovascular accident (CVA) (p = 0.0330), history of nephropathy (p = 0.0280) and levels of LDL cholesterol (p = 0.0409). Also, the A1298C polymorphism was associated with hypertriglyceridemia (p = 0.0305) in T2DM patients. CONCLUSION: These findings demonstrate that the MTHFR gene polymorphisms are not related to T2DM in the Emirati population. However, these polymorphisms can be used as risk markers for CVA, nephropathy, high LDL cholesterol and triglycerides in T2DM patients and allow timely treatment.