Association Study Of Type Research Articles

Structural basis of ethnic-specific variants of PAX4 associated with type 2 diabetes

Recently, we conducted genome-wide association studies of type 2 diabetes (T2D) in a Japanese population, which identified 20 novel T2D loci that were not associated with T2D in Europeans. Moreover, nine novel missense risk variants, such as those of PAX4, were not rare in the Japanese population, but rare in Europeans. We report in silico structural analysis of ethnic-specific variants of PAX4, which suggests the pathogenic effect of these variants.

Differential risk factors and morbidity/mortality pattern in type 2 diabetes: A study among two Mendelian populations with different ancestry (India)

Background and aims:Association studies of type 2 diabetes mellitus (T2DM) with risk factors have shown variable results. Moreover, population-specific comparative investigations are negligible. Therefore, the present study aimed to evaluate the association of dyslipidemia and obesity with impaired fasting glucose (IFG) and T2DM among two ethnically, geographically and culturally different populations in India.Methods:This was a cross-sectional study among Jats and Meiteis, each inhabiting a separate geographical region. A total of 2371 individuals, age ≥30 years were recruited through household survey. Obesity variables were captured using anthropometric measurements while fasting blood (2.5 mL) was drawn to measure lipid and glucose levels using enzymatic assay by spectrophotometer. Participants were categorized under normal, IFG and T2DM groups, indicative of diabetes progression stages. Statistical analysis was performed using SPSS 16.0 version.Results:Significant differential distribution of lipid and obesity variables among IFG and T2DM in both populations were observed. Odds ratio revealed high TC and all obesity variables except BMI posed significant increased risk for T2DM among Jats. Abnormal TG, VLDL, WC, and WHtR posed significant increased risk for T2DM among Meiteis. Age-cohort wise prevalence of T2DM showed increasing trend at ≥60 years among Jats and decreasing trend at ≥60 years among Meiteis, suggesting a potential higher morbidity in the former and mortality in latter because of T2DM.Conclusions:The present study observed a differential association of risk factors for T2DM among Jats and Meiteis. This study emphasize the need to implement community-specific intervention programs for prevention, treatment and management of T2DM.

242-OR: Rare Genetic Variants in the Islet Regulome Contribute to the Heritability of Type 2 Diabetes Risk

Genome-wide association studies of type 2 diabetes (T2D) show common variant heritability is enriched within gene regulatory regions of pancreatic islets. Whole genome sequence (WGS) data in cohorts allows us to determine the contribution of the complete spectrum of genetic variation to the heritability of T2D risk, including rare alleles that have recently arisen in the human population. A variant-based heritability analysis can partition disease risk into environmental and genetic components, and the genetic components can be further decomposed by variant frequency (a proxy of variant age) and pancreatic islets regulatory annotation (a proxy of functional relevance to T2D risk). We hypothesized that rare, non-protein coding variants would have a significant contribution to the heritability of T2D risk and that further restricting to gene regulatory regions active in pancreatic islets would also produce significant heritability estimates. We conducted a WGS heritability analysis (GREML method in GCTA software) of T2D risk in 15109 unrelated individuals (2215 with T2D; 12894 controls) of European ancestry from the NHLBI’s TOPMed study. We partitioned variants with allele count > 5 by minor allele frequency (MAF): rare variants [MAF<0.1%], and annotation: all non-coding variants, and non-coding variants in pancreatic islets regulatory regions. We further partitioned variants by linkage disequilibrium properties to reduce estimate bias. One of the rare, "all non-coding" variants sets showed a relatively large liability-scale heritability estimate (h2=0.6, P< 0.001). Further significant estimates in rare variants were from active transcription start sites (h2=0.1, P<0.01); active promoters (three variant sets with h2=0.07, 0.08 and 0.1, P<0.05, after body mass index adjustment) and active enhancers from promotor capture Hi-C models (h2=0.07, P<0.05). These findings show a role for rare, non-coding variants in the genetic architecture of type 2 diabetes. Disclosure A. Manning: None. Funding National Institutes of Health (K01DK107836)

303-OR: ADA Presidents' Select Abstract: Transethnic Association Study of Type 2 Diabetes in More than a Million Individuals

We conducted the largest trans-ethnic meta-analysis of genome-wide association studies of type 2 diabetes (T2D) by aggregating 171,262 cases and 1,075,072 controls from diverse populations (doubling the effective sample size from recently published European-specific analysis). We identified 250 loci associated with T2D at genome-wide significance (p<5x10-8; 59 novel), which were delineated to 475 distinct signals (p<10-5). Allelic effects on T2D at index variants for most signals were homogenous across populations: only 17% displayed evidence of effect-size heterogeneity related to ancestry (pHET <1.4x10-4, Bonferroni correction). T2D-associated variants were jointly enriched (p<0.00023, correction for 220 annotations) in coding exons, pancreatic islet enhancers and promoters, adipose enhancers, liver enhancers, and binding sites for transcription factors (NKX2.2, PDX1, FOXA2, EZH2). Compared to previous efforts, increased sample size, population diversity, and annotation-informed fine-mapping appreciably improved localisation of causal variants achieving single variant resolution at 217 signals (>50% of the posterior probability of association assigned to a single variant). Through co-localisation of these high-confidence causal variants with protein and RNA QTLs (in disease-relevant tissues), and chromatin conformation capture data (in human islets), we identified >80 candidate effector genes including several not previously implicated e.g., CARD9, PDE8B, ABCB10, SIX3, INHBB. Genetic risk scores derived from ethnic-specific effect sizes at lead variants were transferrable across populations, with minimum liability-scale variance explained from Europeans into Africans. T2D-associated variants displayed evidence of directional adaptation through time, indicating selection for increased T2D risk in African populations, relative to elsewhere in the world. These analyses represent the most comprehensive view of the genetic contribution to T2D to date. Disclosure A. Mahajan: None. X. Sim: None. W. Zhang: None. J.E. Below: None. H. Kitajima: None. L. Speidel: None. A. Morris: None.

A Low-Frequency Amerindian Specific Variant in PALD1, a Negative Regulator of Insulin Signaling, Associates with Type 2 Diabetes

We recently completed a genome wide association study for type 2 diabetes (T2D) in 7659 American Indians who are predominantly of Pima Indian heritage using a custom designed Axiom array. A novel intronic variant (hg19 chr10:72276664 G>C) in PALD1 was identified that associated with T2D (risk allele frequency (RAF)=0.01, OR=2.19[1.49-3.22] per risk allele [C], P=6.6×10-5 adjusted for age, sex, birthyear, PCs 1-5 and accounting for genetic relatedness). Further analysis in a dataset of Urban American Indians (N=3029) representing several tribal groups living in the Phoenix area, identified a directionally consistent association (OR=2.32, P=0.12), but this variant was rare among the entire Urban American Indian sample (RAF=0.003). A meta-analysis of both datasets resulted in a summary OR of 2.15[1.49-3.13], P=4.9×10-5. In Pima Indians, this variant is highly concordant (r2=0.92) with a novel missense variant (hg19 chr10:72298980 C>T, p.[P568S]) in PALD1. The missense variant also had a significant association with T2D in Pima Indians (RAF=0.02, OR=1.80[1.25-2.60], P=0.002) and in Urban American Indians (RAF=0.008, OR=2.29[1.03-5.12], P=0.04). However, after conditional analysis, only the intronic variant remains significant in the Pima Indian dataset. PALD1 is a predicted phosphatase and acts as a negative regulator of insulin signaling. Overexpression of PALD1 leads to lower insulin stimulated AKT phosphorylation and insulin receptor abundance. For preliminary functional studies, a short fragment (100bp) containing each allele of the PALD1 intronic variant (C or G) was cloned upstream of a SV40 promoter luciferase vector and transfected into C2C12 myoblasts. The T2D risk allele (C) fragment had significantly (P=0.004) higher SV40 promoter mediated luciferase activity as compared to the non-risk (G) allele. This result is consistent with the possible role of PALD1 in T2D pathogenesis. Further mechanistic studies are currently ongoing. Disclosure A.K. Nair: None. J.R. Sutherland: None. G.R. Elson: None. P. Piaggi: None. S. Kobes: None. R.L. Hanson: None. C. Bogardus: None. L. Baier: None.

Sumoylation Modulates the Susceptibility to Type 1 Diabetes.

Susceptibility to type 1 diabetes (T1D) is determined by interactions of multiple genes with environmental triggers. Thus far, more than 50 T1D susceptibility regions have been suggested from genetic studies by employing either genome-wide or candidate gene approaches. Because the lack of a linear correlation between the presence of risk genes and the onset of disease, the exact susceptible genes encoded in these regions remain largely elusive. In 2004, we first reported the cloning of a novel small ubiquitin -like modifier (SUMO) gene, SUMO4, in the IDDM5 region on chromosome 6q25, and presented strong genetic and functional evidence suggesting that SUMO4 could be a novel T1D susceptibility gene. Follow up studies have consistently confirmed this association in multiple Asian populations despite controversial observations in Caucasians, which could be caused by genetic heterogeneity. In this chapter, we will summarize and validate genetic data for SUMO4 association studies in type 1 diabetes. The functional properties and possible molecular mechanisms by which altered sumoylation function modulates the development of type 1 diabetes will be also discussed based on published data.

Co-localization of the zinc transporter ZnT8 (slc30A8) with ghrelin and motilin in the gastrointestinal tract of pigs.

Zinc is an important co-factor for insulin storage in pancreatic β-cells of different species and the uptake of this ion into insulin containing secretory vesicles is managed by the zinc transporter, ZnT8, a member of the slc30A gene family. Recent studies indicate that this protein is a major autoimmune target in human type 1A diabetes and has also been implicated by genome-wide association studies in type 2 diabetes. Since individuals suffering from type 1 diabetes often develop gastrointestinal motility disorders, we investigated the expression of ZnT8 in the porcine gastrointestinal tract. For this purpose, we studied the cell-type specific expression of ZnT8 in the gut and its co-expression with endocrine hormones that are closely linked to intestinal motility regulation. Nested RT-PCR and immunostaining of sequential serial sections, as well as double-immunostaining using antibodies directed against ZnT8, ghrelin, motilin, neurotensin, serotonin and glucagon-like peptide 1, indicated that ZnT8 is co-localized with ghrelin and motilin. Our findings provide important information about the cell-type specific expression of ZnT8 in the porcine gastrointestinal system. The selective and exclusive expression of ZnT8 in two endocrine cell-types that are engaged in motility functions may be of particular interest for further investigations into type I diabetes-associated gastrointestinal dysfunctions.

Double trouble: T2DM genetic risk factors play a causal role in CAD.

Double trouble: T2DM genetic risk factors play a causal role in CAD.

A multi-functional analyzer uses parameter constraints to improve the efficiency of model-based gene-set analysis

We develop a model-based methodology for integrating gene-set information with an experimentally-derived gene list. The methodology uses a previously reported sampling model, but takes advantage of natural constraints in the high-dimensional discrete parameter space in order to work from a more structured prior distribution than is currently available. We show how the natural constraints are expressed in terms of linear inequality constraints within a set of binary latent variables. Further, the currently available prior gives low probability to these constraints in complex systems, such as Gene Ontology (GO), thus reducing the efficiency of statistical inference. We develop two computational advances to enable posterior inference within the constrained parameter space: one using integer linear programming for optimization and one using a penalized Markov chain sampler. Numerical experiments demonstrate the utility of the new methodology for a multivariate integration of genomic data with GO or related information systems. Compared to available methods, the proposed multi-functional analyzer covers more reported genes without mis-covering nonreported genes, as demonstrated on genome-wide data from association studies of type 2 diabetes and from RNA interference studies of influenza.

From Markers to Molecular Mechanisms: Type 1 Diabetes in the Post-GWAS Era

By the year 2000, a draft of the human genome sequence was completed. Millions of single-nucleotide polymorphisms (SNPs) had been deposited into public databases, and high throughput technologies were under development for SNP genotyping. At that time, it was predicted that large case control association studies would provide far better resolution and power than genome-wide linkage studies. Type 1 diabetes was one of the first phenotypes to be examined by genome-wide association studies (GWAS), and to date over 50 genomic regions have been associated with the disease. In general, the great majority of these loci individually contribute a relatively small degree of risk, and most loci lie outside of coding sequences. The identification of molecular mechanisms from these genomic data therefore remains a significant challenge. Here, we summarize genetic candidate, linkage, and association studies of type 1 diabetes and discuss a potential strategy to identify mechanisms of disease from genomic data.

Genome-wide association studies of Type 2 diabetes: are these ready to make an impact in the clinic?

SUMMARY Genome-wide association studies have facilitated a substantial and rapid rise in the number of confirmed susceptibility variants for Type 2 diabetes. This has inevitably led to widespread hope that these findings will translate into improved clinical care for the growing numbers of patients with diabetes. This article summarizes recent discoveries in the field of Type 2 diabetes genetics and will discuss their importance and the current obstacles to clinical translation.

Association study of type 2 diabetes genetic susceptibility variants and risk of pancreatic cancer: an analysis of PanScan-I data

To examine associations between recently identified common type 2 diabetes (T2D) susceptibility genetic variants and pancreatic cancer risk. Using data on individuals of European ancestry from the Cancer Genetic Markers of Susceptibility PanScan-I study (1,763 pancreatic cancer cases and 1,802 controls), we tested associations for 37 T2D susceptibility variants with pancreatic cancer risk. Associations with pancreatic cancer were also tested for three composite T2D susceptibility measures, incorporating data on all 37 variants, and for ten additional variants related to T2D-related phenotypes, including fasting glucose and beta-cell function. Of the 37 T2D risk alleles, two showed nominally significant positive associations with pancreatic cancer risk (FTO rs8050136 per-allele OR = 1.12; CI: 1.02-1.23; MTNR1B rs1387153 OR = 1.11; CI: 1.00-1.23) and one showed an inverse association (BCL11A rs243021 OR = 0.88; CI: 0.80-0.97). The composite T2D susceptibility measures were not associated with pancreatic cancer. The glucose-raising allele of MADD rs11039149 was associated with increased risk of pancreatic cancer (OR = 1.14; CI: 1.03-1.27). Overall, these results do not provide strong evidence that common variants underling T2D or related phenotypes also affect pancreatic cancer risk; however, associations for FTO, MTNR1B, BCL11A, and MADD variants warrant further investigation in larger studies. Hypothesis-driven analyses of existing genome-wide genetic data can be cost-efficient and promising approaches for investigating genetic susceptibility to complex diseases.

Genome-wide association studies in type 2 diabetes

Despite numerous candidate gene and linkage studies, the field of type 2 diabetes (T2D) genetics had until recently succeeded in identifying few genuine disease-susceptibility loci. The advent of genome-wide association (GWA) scans has transformed the situation, leading to an expansion in the number of established, robustly replicating T2D loci to almost 20. These novel findings offer unique insights into the pathogenesis of T2D and in the main point toward the etiologic importance of disorders of beta-cell development and function. All associated variants have common allele frequencies in the discovery populations, and exert modest to small effects on the risk of disease, characteristics that limit their prognostic and diagnostic potential. However, ongoing studies focusing on the role of copy number variation and targeting low-frequency polymorphisms should identify additional T2D susceptibility loci, some of which may have larger effect sizes and offer better individual prediction of disease risk.

Genome-wide association studies in type 1 diabetes

Type 1 diabetes (T1D) is a chronic disease that typically manifests itself in childhood through the autoimmune destruction of pancreatic beta cells, resulting in a lack of production of insulin. T1D is a multifactorial disease with a strong genetic component that is thought to interact with specific environmental triggers. Several genetic determinants of T1D were already established before the era of genome-wide association studies, primarily with the HLA class II genes, encoding highly polymorphic antigen-presenting proteins that account for almost 50% of the genetic risk for T1D. The recent development of high-throughput single nucleotide polymorphism genotyping array technologies has enabled investigators to perform high-density genome-wide association studies in search of the remaining T1D loci. Combined with the well-established genes known for many years, 16 loci have now been uncovered to date as being robustly associated with the pathogenesis of this phenotype.

Variants of the adiponectin gene and type 2 diabetes in a Polish population

Several association studies of type 2 diabetes mellitus (T2DM) and adiponectin gene polymorphisms have been reported with conflicting results. Our aim was to search for the association of three polymorphisms (-11.391G>A, +45T>G, and +276G>T) in the adiponectin gene with T2DM and prediabetic quantitative traits in Polish Caucasians. The study groups comprised 495 unrelated T2DM cases and 435 controls. We compared the distribution of genotypes between study groups. In addition, genotype-quantitative trait analyses were also done in the controls. The study subjects were genotyped using the restriction fragment length polymorphism technique. The frequencies of the minor alleles were as follows: 10.6 versus 8.2% for -11.391G>A (p = 0.0722), 7.0 versus 8.0% for +45T>G (p = 0.48), and 15.5% in T2DM versus 19.8% in controls (p = 0.0145) for +276G>T, respectively. The difference for genotype distribution between the groups was statistically significant (p = 0.0247) for the +276G>T variant: 71.31 versus 62.99%, 26.46 versus 34.48% and 2.22 versus 2.53%, respectively, for GG, GT and TT. In quantitative traits analysis, the T allele of +276G>T was associated (p < 0.05) with lower insulin resistance (HOMA-IR, fasting insulin) among controls. Additionally, the A allele at position -11.391 was associated (p < 0.05) with higher insulin resistance (HOMA-IR, fasting insulin). In multiple regression analysis, all identified association remained significant after the inclusion in the model of gender, BMI and age. In addition, in this model, -11.391G>A and +276G>T were independently associated with T2DM. Finally, we conclude that the adiponectin gene polymorphisms are associated with T2DM and prediabetic quantitative traits in Polish Caucasians.

The Genetics of Type 2 Diabetes: A Realistic Appraisal in 2008

Over the last few months, genome-wide association studies have contributed significantly to our understanding of the genetic architecture of type 2 diabetes. If and how this information will impact clinical practice is not yet clear. Primary papers reporting genome-wide association studies in type 2 diabetes or establishing a reproducible association for specific candidate genes were compiled. Further information was obtained from background articles, authoritative reviews, and relevant meeting conferences and abstracts. As many as 17 genetic loci have been convincingly associated with type 2 diabetes; 14 of these were not previously known, and most of them were unsuspected. The associated polymorphisms are common in populations of European descent but have modest effects on risk. These loci highlight new areas for biological exploration and allow the initiation of experiments designed to develop prediction models and test possible pharmacogenetic and other applications. Although substantial progress in our knowledge of the genetic basis of type 2 diabetes is taking place, these new discoveries represent but a small proportion of the genetic variation underlying the susceptibility to this disorder. Major work is still required to identify the causal variants, test their role in disease prediction and ascertain their therapeutic implications.

All we need is GWAS: Genome-Wide Association Studies in Type 2 Diabetes Mellitus presented on the 2008 EASD Meeting in Rome

Several lines of evidence suggest that genetic susceptibility plays a major role in the pathogenesis of type 2 diabetes mellitus (T2DM). Limited success of candidate gene approach and linkage analysis in identifying the genetic background of T2DM has caused many research groups to apply the genome-wide association studies (GWAS) approach. Recently, several GWAS have identified and validated novel gene variants highly associated with T2DM. Unfortunately, most of the genetic variance in risk of T2DM still remains undiscovered. The main topic for discussion concerning genetics of T2DM during the 2008 EASD sessions was how to get more data from existing GWAS, and how to improve GWAS for the future. The presentations and subsequent discussions highlighted some clear weaknesses of GWAS that need to be overcome before further progress can be made. One recognized minefield is the inability to pick up the signals from true diabetes susceptibility variants, against the background statistical noise produced by a large number of other analyzed markers. Also, there are the problems of low sensitivity in identifying the signals from relatively rare variants, and the low effectiveness in identifying epistatic gene-gene interactions.

IL4 in the 5q31 context: association studies of type 1 diabetes and rheumatoid arthritis in the Spanish population

IL4, the gene coding the prototypic Th2 cytokine, has been frequently studied in the context of several inflammatory conditions, but conclusive results have not been obtained. This gene is located in the 5q31-33 complex genetic region, which shows some susceptibility factors to type 1 diabetes (T1D) and rheumatoid arthritis (RA) among other inflammatory conditions. Our aim was to assess the involvement on T1D and RA of IL4 polymorphisms considered individually and in combination with other polymorphisms in 5q31-33, specifically in the OCTN locus, where the L503F polymorphism has been associated with Crohn's disease and other Th1 diseases. We performed a case-control study including 316 T1D patients, 599 RA patients and 540 healthy controls, all of them corresponding to white Spanish individuals. The IL4 single-nucleotide polymorphisms (SNPs) -590C/T (rs2243250) and the OCTN1 exonic SNP L503F (rs1050152) were analysed in all samples. Frequency comparisons of -590C/T and stratified analysis including both cited SNPs were performed using chi-square tests. The -590C/T IL4 SNP was not found associated with T1D or RA when individual analyses were performed. However, a significant association with T1D emerged after stratification by L503F [p=0.02, odds ratio=1.95, 95% CI=1.07-3.55]. The location of the IL4 gene in the complex 5q31-33 genetic region, which contains many genes involved in immunological responses and presents linkage disequilibrium extended along many kilobases, makes necessary to interpret cautiously the previous IL4-association studies.

Adiponectin receptor genes: mutation screening in syndromes of insulin resistance and association studies for type 2 diabetes and metabolic traits in UK populations

Aims/hypothesisAdiponectin is an adipokine with insulin-sensitising and anti-atherogenic properties. Several reports suggest that genetic variants in the adiponectin gene are associated with circulating levels of adiponectin, insulin sensitivity and type 2 diabetes risk. Recently two receptors for adiponectin have been cloned. Genetic studies have yielded conflicting results on the role of these genes and type 2 diabetes predisposition. In this study we aimed to evaluate the potential role of genetic variation in these genes in syndromes of severe insulin resistance, type 2 diabetes and in related metabolic traits in UK Europid populations.Materials and methodsExons and splice junctions of the adiponectin receptor 1 and 2 genes (ADIPOR1; ADIPOR2) were sequenced in patients from our severe insulin resistance cohort (n=129). Subsequently, 24 polymorphisms were tested for association with type 2 diabetes in population-based type 2 diabetes case–control studies (n=2,127) and with quantitative traits in a population-based longitudinal study (n=1,721).ResultsNo missense or nonsense mutations in ADIPOR1 and ADIPOR2 were detected in the cohort of patients with severe insulin resistance. None of the 24 polymorphisms (allele frequency 2.3–48.3%) tested was associated with type 2 diabetes in the case–control study. Similarly, none of the polymorphisms was associated with fasting plasma insulin, fasting and 2-h post-load plasma glucose, 30-min insulin increment or BMI.Conclusions/interpretationGenetic variation in ADIPOR1 and ADIPOR2 is not a major cause of extreme insulin resistance in humans, nor does it contribute in a significant manner to type 2 diabetes risk and related traits in UK Europid populations.Electronic supplementary materialThe online version of this article (doi:10.1007/s00125-006-0534-7) contains supplementary material, which is accessible to authorised users.

Polymorphisms in the gene encoding hepatocyte nuclear factor-4&dgr; and susceptibility to type 2 diabetes in a Polish population

Recently, several association studies of type 2 diabetes mellitus (T2DM) and the hepatocyte nuclear factor (HNF)-4alpha gene were reported with conflicting results. Our aim was to search for association between two polymorphisms of HNF-4alpha and T2DM in Polish Caucasians. The study groups comprised of 461 T2DM cases and 366 controls. Genotype-quantitative trait analyses were based on the oral glucose tolerance test (OGTT), glucose and insulin results, and comprised 310 glucose-tolerant subjects. All individuals were genotyped for two HNF-4alpha polymorphisms. The frequencies of the minor alleles were as follows: 19.2% in T2DM vs. 17.6% in controls for rs2144908; and 20.6% vs. 20.1% for rs4810424, respectively. The distributions of alleles, genotypes, and haplotypes of the HNF-4alpha polymorphisms did not differ between the study groups (lowest P = 0.41). None of the examined SNPs showed an association in control subjects with quantitative traits of fasting plasma glucose, fasting insulin, as well as plasma glucose and insulin 2 hours after glucose load in OGTT. We conclude that both examined polymorphisms in HNF-4alpha are not associated with T2DM and prediabetic phenotypes in Polish Caucasian study groups of this size.