Polymorphisms of EHF-ELF5 genomic region and its association with pediatric asthma in the Taiwanese population

BackgroundThe EHF and ELF5 genes, located on chromosome 11p and linked to asthma phenotypes, are high-potential candidate genes conferring asthma susceptibility. The purpose of this study was to investigate the genetic association among single nucleotide polymorphisms (SNPs) of EHF and ELF5, and their relationship with asthma in the Taiwanese population.MethodsWe selected and performed genotyping on 16 SNPs that encompass the genomic region of EHF and ELF5 in Taiwanese children with or without asthma. A total of 1983 children, 523 in the test group and 619 and 842 in two validation groups, were recruited for this study.ResultsThe SNP rs3910901, located in the 5′ upstream region of ELF5, was found to have a weak association (p = 0.043) with asthma in the odds ratio analysis. The genotype distribution was similar in all comparison groups, but the CC genotype was more frequent in asthma patients. Logistic regression adjusted allergy comorbidity showed obviously diluted association.ConclusionThe results indicated that SNP rs3910901 may have a minor impact on pediatric asthma in the Taiwanese population

Dopamine D2 receptor polymorphisms and susceptibility to alcohol dependence in Indian males: a preliminary study

<p>Abstract</p> <p>Background</p> <p>Dopamine is an important neurotransmitter involved in reward mechanism in the brain and thereby influences development and relapse of alcohol dependence. The dopamine D2 receptor (<it>DRD2</it>) gene on chromosome 11 (q22-q23) has been found to be associated with increased alcohol consumption through mechanisms involving incentive salience attributions and craving in alcoholic patients. Therefore, we investigated the association of three single nucleotide polymorphisms (SNP) in <it>DRD2 </it>gene with alcohol dependence in the north Indian subjects.</p> <p>Methods</p> <p>In a retrospective analysis, genetic association of three polymorphisms from <it>DRD2 </it>gene with alcohol dependence was investigated using a case-control approach. Alcohol dependence was determined by DSM-IV criteria and a total of 90 alcoholics and 60 healthy unrelated age-matched control subjects were recruited. Odds ratio and confidence interval was calculated to determine risk conferred by a predisposing allele/genotype/haplotype. Logistic regression analysis was carried out to correlate various clinical parameters with genotypes, and to study pair-wise interactions between SNPs.</p> <p>Results</p> <p>The study showed a significant association of -141C Ins allele and a trend of association of TaqI A1 allele of <it>DRD2 </it>with alcohol dependence. Haplotype with the predisposing -141C Ins and TaqI A1 alleles (-141C Ins-A-A1) seems to confer ≈ 2.5 times more risk to develop alcohol dependence.</p> <p>Conclusions</p> <p>The study provides preliminary insight into genetic risk to alcohol dependence in Indian males. Two polymorphisms namely, -141C Ins/Del and TaqI A in <it>DRD2 </it>gene may have clinical implications among Indian alcoholic subjects.</p

Design considerations in a sib-pair study of linkage for susceptibility loci in cancer

<p>Abstract</p> <p>Background</p> <p>Modern approaches to identifying new genes associated with disease allow very fine analysis of associaton and can be performed in population based case-control studies. However, the sibpair design is still valuable because it requires few assumptions other than acceptably high penetrance to identify genetic loci.</p> <p>Methods</p> <p>We conducted simulation studies to assess the impact of design factors on relative efficiency for a linkage study of colorectal cancer. We considered two test statistics, one comparing the mean IBD probability in affected pairs to its null value of 0.5, and one comparing the mean IBD probabilities between affected and discordant pairs. We varied numbers of parents available, numbers of affected and unaffected siblings, reconstructing the genotype of an unavailable affected sibling by a spouse and offspring, and elimination of sibships where the proband carries a mutation at another locus.</p> <p>Results</p> <p>Power and efficiency were most affected by the number of affected sibs, the number of sib pairs genotyped, and the risk attributable to linked and unlinked loci. Genotyping unaffected siblings added little power for low penetrance models, but improved validity of tests when there was genetic heterogeneity and for multipoint testing. The efficiency of the concordant-only test was nearly always better than the concordant-discordant test. Replacement of an unavailable affected sibling by a spouse and offspring recovered some linkage information, particularly if several offspring were available. In multipoint analysis, the concordant-only test was showed a small anticonservative bias at 5 cM, while the multipoint concordant-discordant test was generally the most powerful test, and was not biased away from the null at 5 cM.</p> <p>Conclusion</p> <p>Genotyping parents and unaffected siblings is useful for detecting genotyping errors and if allele frequencies are uncertain. If adequate allele frequency data are available, we suggest a single-point affecteds-only analysis for an initial scan, followed by a multipoint analysis of affected and unaffected members of all available sibships with additional markers around initial hits.</p

Association of TGFβ1, TNFα, CCR2 and CCR5 gene polymorphisms in type-2 diabetes and renal insufficiency among Asian Indians

BACKGROUND: Cytokines play an important role in the development of diabetic chronic renal insufficiency (CRI). Transforming growth factor β1 (TGF β1) induces renal hypertrophy and fibrosis, and cytokines like tumor necrosis factor-alpha (TNFα), chemoattractant protein-1 (MCP-1), and regulated upon activation and normal T cell expressed and secreted (RANTES) mediate macrophage infiltration into kidney. Over expression of these chemokines leads to glomerulosclerosis and interstitial fibrosis. The effect of MCP-1 and RANTES on kidney is conferred by their receptors i.e., chemokine receptor (CCR)-2 and CCR-5 respectively. We tested association of nine single nucleotide polymorphisms (SNPs) from TGFβ1, TNFα, CCR2 and CCR5 genes among individuals with type-2 diabetes with and without renal insufficiency. METHODS: Type-2 diabetes subjects with chronic renal insufficiency (serum creatinine ≥ 3.0 mg/dl) constituted the cases, and matched individuals with diabetes of duration ≥ 10 years and normoalbuminuria were evaluated as controls from four centres in India. Allelic and genotypic contributions of nine SNPs from TGFβ1, TNFα, CCR2 and CCR5 genes to diabetic CRI were tested by computing odds ratio (OR) and 95% confidence intervals (CI). Sub-analysis of CRI cases diabetic retinopathy status as dependent variable and SNP genotypes as independent variable in a univariate logistic regression was also performed. RESULTS: SNPs Tyr81His and Thr263Ile in TGF β1 gene were monomorphic, and Arg25Pro in TGF β1 gene and Δ32 polymorphism in CCR5 gene were minor variants (minor allele frequency <0.05) and therefore were not considered for case-control analysis. A significant allelic association of 59029G>A SNP of CCR5 gene has been observed and the allele 59029A seems to confer predisposition to development of diabetic CRI (OR 1.39; CI 1.04–1.84). In CRI subjects a compound group of genotypes "GA and AA" of SNP G>A -800 was found to confer predisposition for proliferative retinopathy (OR 3.03; CI 1.08–8.50, p = 0.035). CONCLUSION: Of the various cytokine gene polymorphisms tested, allele 59029A of CCR5 gene is significantly associated with diabetic renal insufficiency among Asian Indians. Result obtained for 59029G>A SNP of CCR5 gene is in conformity with reports from a Japanese population but due to sub-optimal power of the sample, replication in larger sample set is warranted

Common Variants of Inflammatory Cytokine Genes Are Associated with Risk of Nephropathy in Type 2 Diabetes among Asian Indians

BACKGROUND: Inflammatory cytokine genes have been proposed as good candidate genes for conferring susceptibility to diabetic nephropathy. In the present study, we examined the combined effect of multiple alleles of pro inflammatory cytokine genes for determining the risk of nephropathy in type 2 diabetic patients. METHODOLOGY/PRINCIPAL FINDINGS: Eight single nucleotide polymorphisms (SNPs) of pro-inflammatory cytokine genes (CCL2, TGFB1, IL8, CCR5, and MMP9) were genotyped in two independently ascertained type 2 diabetic cohorts with (DN) and without nephropathy (DM); consisting of patients from North India (n = 495) and South India (n = 188). Genotyping was carried out using PCR, allele specific oligonucleotide-PCR (ASO-PCR), PCR-RFLP and TaqMan allelic discrimination assays and the gene-gene interaction among genetic variants were determined by multi dimensional reduction (MDR) software. Serum high sensitive CRP (hs-CRP) levels were measured by ELISA. The hs-CRP levels were significantly higher in DN as compared to the DM group (p<0.05). The CCL2, IL8, CCR5 and MMP9 polymorphisms were found to be associated with the risk of diabetic nephropathy. Frequency of CCL2 II, IL8 -251AA, CCR5 59029AA and MMP9 279Gln/Gln genotypes were significantly higher in DN than in DM group (p<0.05) and associated with an increased risk of nephropathy in both North and South Indian cohorts. CCR5 DD and IL8 -251AA genotypes were more prevalent in North Indian DN group only. The co-occurrence of risk associated genotypes (II, -2518GG (CCL2), DD (CCR5) and 279Gln/Gln (MMP9) conferred a tenfold increased risk of nephropathy among type 2 diabetics (p<0.0002). CONCLUSION: The present study highlights that common variants of inflammatory cytokine genes exert a modest effect on risk of DN and a combination of risk alleles confer a substantial increased risk of nephropathy in type 2 diabetes among Asian Indians

Association analysis of ADPRT1, AKR1B1, RAGE, GFPT2 and PAI-1 gene polymorphisms with chronic renal insufficiency among Asian Indians with type-2 diabetes

<p>Abstract</p> <p>Background</p> <p>To determine association of nine single nucleotide polymorphisms (SNPs) in ADP ribosyltransferase-1 (ADPRT1), aldo-keto reductase family 1 member B1 (AKR1B1), receptor for advanced glycation end-products (RAGE), glutamine:fructose-6-phosphate amidotransferase-2 (GFPT2), and plasminogen activator inhibitor-1 (PAI-1) genes with chronic renal insufficiency (CRI) among Asian Indians with type 2 diabetes; and to identify epistatic interactionss between genes from the present study and those from renin-angiotensin-aldosterone system (RAAS), and chemokine-cytokine, dopaminergic and oxidative stress pathways (previously investigated using the same sample set).</p> <p>Methods</p> <p>Type 2 diabetes subjects with CRI (serum creatinine ≥3.0 mg/dl) constituted the cases (n = 196), and ethnicity and age matched individuals with diabetes for a duration of ≥ 10 years, normal renal functions and normoalbuminuria recruited as controls (n = 225). Allelic and genotypic constitution of 10 polymorphisms (SNPs) from five genes namely- <it>ADPRT1</it>, <it>AKR1B1, RAGE, GFPT2 </it>and <it>PAI-1 </it>with diabetic CRI was investigated. The genetic associations were evaluated by computation of odds ratio and 95% confidence interval. Multiple logistic regression analysis was carried out to correlate various clinical parameters with genotypes, and to study epistatic interactions between SNPs in different genes.</p> <p>Results</p> <p>Single nucleotide polymorphisms -429 T>C in <it>RAGE </it>and rs7725 C>T SNP in 3' UTR in <it>GFPT2 </it>gene showed a trend towards association with diabetic CRI. Investigation using miRBase statistical tool revealed that rs7725 in <it>GFPT2 </it>was a perfect target for predicted miRNA (hsa miR-378) suggesting the presence of the variant 'T' allele may result in an upregulation of GFPT2 contributing to diabetic renal complication. Epistatic interaction between SNPs in transforming growth factor <it>TGF-β1 </it>(investigated using the same sample set and reported elsewhere) and <it>GFPT2 </it>genotype was observed.</p> <p>Conclusions</p> <p>Association of SNPs in <it>RAGE </it>and <it>GFPT2 </it>suggest that the genes involved in modulation of oxidative pathway could be major contributor to diabetic chronic renal insufficiency. In addition, GFPT2 mediated overproduction of TGF-β1 leading to endothelial expansion and thereby CRI seems likely, suggested by our observation of a significant interaction between GFPT2 with TGF-β1 genes. Further, identification of predicted miRNA targets spanning the associated SNP in <it>GFPT2 </it>implicates the rs7725 SNP in transcriptional regulation of the gene, and suggests <it>GFPT2 </it>could be a relevant target for pharmacological intervention. Larger replication studies are needed to confirm these observations.</p

Investigating genetic determinants of ankylosing spondylitis

Ankylosing spondylitis (AS) is a common form of inflammatory arthritis, occurring in approximately 0.1% of the British and Finnish populations. The genetic contribution to the disease susceptibility accounts for >90% of the population variance, and the disease severity is also predominantly genetically determined. HLA-B27 has been strongly associated with the disease world-wide, but although it is almost essential for the inheritance of AS, the attributable risk of HLA-B27 has been estimated to be 16-50%, leaving a large component of the genetic variance to be discovered. The influence of a positional and biological candidate gene, transforming growth factor β1 (TGFB1), was investigated in a Finnish and British population. A weak association between the rare TGFB1 1627 T allele and susceptibility to, and age of symptom onset of, AS was noted. However the lack of association of TGFB1 promoter polymorphisms, which are in LD with the TGFB1 1627 alleles, with AS in families with positive non-parametric linkage scores at the locus indicates that these polymorphisms do not explain the observed linkage of disease susceptibility to chromosome 19. A novel high throughput HLA-DRB1 genotyping method based on multiplex primer extension reactions was developed. This method allows rapid and cost-effective screening of a large number of samples. The effect of HLA genes and haplotypes in susceptibility to, and severity of, AS was investigated in the Finnish population. An overrepresentation of HLA-B27 homozygotes was noted in cases with AS compared with the expected number of HLAB27 homozygotes under Hardy-Weinberg equilibrium. Significant associations between both HLA-B27 and HLA-DRB1*08 and a younger age of symptom onset was noted suggesting that genes within the MHC are involved in determining the age of symptom onset. A haplotype-based case-control study noted no association between HLA-DRB1-B27 haplotypes and AS susceptibility, but this study was underpowered. The effect of CYP2D6*4 poor metaboliser allele was investigated in the Finnish AS families. No association was noted, but due to lack of power this study could not exclude a true positive association with the disease. In summary, a novel HLA-DRB1 genotyping technique was developed to enable the assessment of the contribution of HLA-DRB1 genes in a large number of AS samples. HLA-B27 homozygosity was increased in cases with AS compared with the expected number of HLA-B27 homozygotes. HLA-B27 and HLA-DRB1*08 alleles were significantly associated with a younger age of symptom onset in AS. TGFB1 gene polymorphisms do not appear to have a major impact in AS

Adaptation from standing genetic variation and from mutation

Dissertation presented to obtain the Ph.D degree in Evolutionary BiologyUnderstanding the genetic basis of adaptation is crucial to explain the emergence and maintenance of the multitude of life forms we find on Earth today. Perhaps even more importantly, gaining knowledge about how fast organisms can cope with environmental changes may prove crucial in a world being altered at increasing speed due to the human actions. The study of adaptive evolution may therefore have major implications (and applications) in Agriculture, Conservation of endangered species and even Human Health. Natural selection has long been appreciated as one of the predominant evolutionary mechanisms and it enjoys a solid theoretical framework regarding its requirements, its effects and its limitations. Empirically, however, it has proved quite challenging to study. In wild populations natural selection is particularly difficult to characterize and measure since in these settings other evolutionary mechanisms (such as genetic drift or gene flow) often occur simultaneously. In addition to this, the different evolutionary mechanisms may vary greatly in time and in space with respect to their relative influences on the evolutionary dynamics of populations.(...