Single Nucleotide Polymorphims Research Articles

Bone marrow stromal antigen 2 (BST-2) genetic variants influence expression levels and disease outcome in HIV-1 chronically infected patients

BackgroundBone marrow stromal antigen 2 (BST-2) also known as Tetherin (CD317/HM1.24), is a host restriction factor that blocks the release of HIV-1 virions from infected cells. Previous studies reported that BST-2 genetic variants or single nucleotide polymorphims (SNPs) have a preventative role during HIV-1 infection. However, the influence of BST-2 SNPs on expression levels remains unknown. In this study, we investigated the influence of BST-2 SNPs on expression levels and disease outcome in HIV-1 subtype C chronically infected antiretroviral therapy naïve individuals.ResultsWe quantified BST-2 mRNA levels in peripheral blood mononuclear cells (PBMCs), determined BST-2 protein expression on the surface of CD4+ T cells using flow cytometry and genotyped two intronic single nucleotide polymorphisms (SNPs) rs919267 and rs919266 together with one SNP rs9576 located in the 3’ untranslated region (UTR) of bst-2 gene using TaqMan assays from HIV-1 uninfected and infected participants. Subsequently, we determined the ability of plasma antibody levels to mediate antibody-dependent cellular phagocytosis (ADCP) using gp120 consensus C and p24 subtype B/C protein. Fc receptor-mediated NK cell degranulation was evaluated as a surrogate for ADCC activity using plasma from HIV-1 positive participants. BST-2 mRNA expression levels in PBMCs and protein levels on CD4+ T cells were lower in HIV-1 infected compared to uninfected participants (p = 0.075 and p < 0.001, respectively). rs919267CT (p = 0.042) and rs919267TT (p = 0.045) were associated with lower BST-2 mRNA expression levels compared to rs919267CC in HIV-1 uninfected participants. In HIV-1 infected participants, rs919267CT associated with lower CD4 counts, (p = 0.003), gp120-IgG1 (p = 0.040), gp120-IgG3 (p = 0.016) levels but higher viral loads (p = 0.001) while rs919267TT was associated with lower BST-2 mRNA levels (p = 0.046), CD4 counts (p = 0.001), gp120-IgG1 levels (p = 0.033) but higher plasma viral loads (p = 0.007). Conversely, rs9576CA was associated with higher BST-2 mRNA expression levels (p = 0.027), CD4 counts (p = 0.079), gp120-IgG1 (p = 0.009), gp120-IgG3 (p = 0.039) levels but with lower viral loads (p = 0.037).ConclusionOur findings show that bst-2 SNPs mediate BST-2 expression and disease outcome, correlate with gp120-IgG1, gp120-IgG3 levels but not p24-IgG levels, ADCC and ADCP activity.Graphical

The Gly82Ser polymorphism in the receptor for advanced glycation end products is associated with increased risk for coronary events in the general population

Abstract Background/Introduction Activation of the receptor for advanced glycation end products (RAGE) by AGEs and various immune mediators has pro-inflammatory and pro-atherogenic effects. RAGE also exists in a soluble form, sRAGE, that acts as a decoy receptor for RAGE ligands. Low plasma sRAGE has previously been found to be associated with a higher risk for major adverse coronary events (MACE) in the population. Purpose The purpose of our study was to examine the causality of the association, by exploring whether genetic variants that influence sRAGE are associated with atherosclerosis progression and incident MACE and mortality in the population. Methods We performed a genome-wide association study (GWAS) in 4192 individuals from a randomly selected subgroup of a population-based cohort. Subsequently, we explored the associations between the identified single nucleotide polymorphims (SNPs) associated with plasma sRAGE levels, baseline intima media thickness (IMT) and IMT progression in the common carotid artery during a median follow-up of 16.5 years. Further, we analyzed the prospective relationships between the sRAGE-associated SNPs, incident MACE and mortality in the entire population-based cohort of 29245 individuals. The median follow-up time from baseline was 21.2 years for MACE and 21.6 years for total mortality (time to event or end of follow-up). Results We found the minor alleles of two single nucleotide polymorphisms (SNPs), rs2070600 and rs204993, to be independently associated with lower plasma sRAGE. While rs204993 is a silent intronic mutation, rs2070600 is known to cause a Gly82Ser polymorphism in the ligand binding domain, enhancing RAGE propensity for activation. In Cox regression analyses, we found an association between the minor T (vs. C) allele of rs2070600 and increased risk for first-time MACE [HR 1.12 (1.02–1.23); P=0.023]. The association was independent of traditional cardiovascular risk factors, blood pressure-lowering medication and lipid-lowering medication at baseline. rs204993 was not associated with MACE. Neither SNP was associated with carotid IMT at baseline or with IMT progression. We did not identify any relationships with total mortality. Conclusions We demonstrate for the first time an independent link between a genetic RAGE determinant and the risk for MACE in the population. Despite both identified SNPs being associated with lower sRAGE levels, only the functional rs2070600 mutation was associated with MACE, suggesting that the link is probably due to the enhancement of RAGE function rather than to the sRAGE lowering effect. Funding Acknowledgement Type of funding source: Public Institution(s). Main funding source(s): This study was supported by grants from the Swedish Research Council and the Swedish Heart and Lung foundation.

Genome-wide association study and predictive ability for growth traits in Nellore cattle

This study aimed to identify genomic regions influencing growth traits in Nellore cattle and evaluate the predictive ability of each trait based on results obtained from single-step genome-wide association analyzes (ssGWAS) considering different single nucleotide polymorphims (SNP) densities of markers. The National Association of Breeders and Researchers provided the dataset, from eighteen Nellore herds participating of the Nellore Brazilian breeding program. The traits birth weight (BW), adjusted weight at 210 (W210) and at 450 (W450) days of age and adult cow weight (ACW) were considered. A total of 963 animals, genotyped using the Illumina BovineHD BeadChip, were used as a reference population to impute genotypes of 7,689 animals, genotyped in low-density panel. Genotype imputation was performed using the FImpute 2.2 software. The ssGWAS was used to identify genomic regions associated to growth traits. Several genes in enrichment analysis were related to muscle and adipose tissue development and metabolism, feed efficiency, milk composition and maternal behavior. The predictive ability varied from low (0.10) to moderate (0.68). The predictive ability and bias for both panels were similar for all traits. The results found in this study should improve the understanding of genetic and physiologic mechanism associated with growth traits. However, the association of these results with other approaches, like system biologic and other omics information should improve the identification of causative genetic variants in growth traits in indicine cattle.

Identification of novel drought-tolerant-associated SNPs in common bean (Phaseolus vulgaris).

Common bean (Phaseolus vulgaris L.) is a leguminous in high demand for human nutrition and a very important agricultural product. Production of common bean is constrained by environmental stresses such as drought. Although conventional plant selection has been used to increase production yield and stress tolerance, drought tolerance selection based on phenotype is complicated by associated physiological, anatomical, cellular, biochemical, and molecular changes. These changes are modulated by differential gene expression. A common method to identify genes associated with phenotypes of interest is the characterization of Single Nucleotide Polymorphims (SNPs) to link them to specific functions. In this work, we selected two drought-tolerant parental lines from Mesoamerica, Pinto Villa, and Pinto Saltillo. The parental lines were used to generate a population of 282 families (F3:5) and characterized by 169 SNPs. We associated the segregation of the molecular markers in our population with phenotypes including flowering time, physiological maturity, reproductive period, plant, seed and total biomass, reuse index, seed yield, weight of 100 seeds, and harvest index in three cultivation cycles. We observed 83 SNPs with significant association (p < 0.0003 after Bonferroni correction) with our quantified phenotypes. Phenotypes most associated were days to flowering and seed biomass with 58 and 44 associated SNPs, respectively. Thirty-seven out of the 83 SNPs were annotated to a gene with a potential function related to drought tolerance or relevant molecular/biochemical functions. Some SNPs such as SNP28 and SNP128 are related to starch biosynthesis, a common osmotic protector; and SNP18 is related to proline biosynthesis, another well-known osmotic protector.

A whole genome analyses of genetic variants in two Kelantan Malay individuals.

BackgroundThe sequencing of two members of the Royal Kelantan Malay family genomes will provide insights on the Kelantan Malay whole genome sequences. The two Kelantan Malay genomes were analyzed for the SNP markers associated with thalassemia and Helicobacter pylori infection. Helicobacter pylori infection was reported to be low prevalence in the north-east as compared to the west coast of the Peninsular Malaysia and beta-thalassemia was known to be one of the most common inherited and genetic disorder in Malaysia.ResultBy combining SNP information from literatures, GWAS study and NCBI ClinVar, 18 unique SNPs were selected for further analysis. From these 18 SNPs, 10 SNPs came from previous study of Helicobacter pylori infection among Malay patients, 6 SNPs were from NCBI ClinVar and 2 SNPs from GWAS studies. The analysis reveals that both Royal Kelantan Malay genomes shared all the 10 SNPs identified by Maran (Single Nucleotide Polymorphims (SNPs) genotypic profiling of Malay patients with and without Helicobacter pylori infection in Kelantan, 2011) and one SNP from GWAS study. In addition, the analysis also reveals that both Royal Kelantan Malay genomes shared 3 SNP markers; HBG1 (rs1061234), HBB (rs1609812) and BCL11A (rs766432) where all three markers were associated with beta-thalassemia.ConclusionsOur findings suggest that the Royal Kelantan Malays carry the SNPs which are associated with protection to Helicobacter pylori infection. In addition they also carry SNPs which are associated with beta-thalassemia. These findings are in line with the findings by other researchers who conducted studies on thalassemia and Helicobacter pylori infection in the non-royal Malay population.

Identification of differential selection traces in two Polish cattle breeds.

Genetic improvement of animals based on artificial selection is leading to changes in the frequency of genes related to desirable production traits. The changes are reflected by the neutral, intergenic single nucleotide polymorphims (SNPs) being in long-range linkage disequilibrium with functional polymorphisms. Genome-wide SNP analysis tools designed for cattle, allow for scanning divergences in allelic frequencies between distinct breeds and thus for identification of genomic regions which were divergently selected in breeds' histories. In this study, by using Bovine SNP50 assay, we attempted to identify genomic regions showing the highest differences in allele frequencies between two distinct cattle breeds - preserved, unselected Polish Red breed and highly selected Holstein cattle. Our study revealed 19 genomic regions encompassing 55 protein-coding genes and numerous quantitative trait loci which potentially may underlie some of the phenotypic traits distinguishing the breeds.

Genetic Structure and Linkage Disequilibrium in a Diverse, Representative Collection of the C4 Model Plant, Sorghum bicolor

To facilitate the mapping of genes in sorghum [Sorghum bicolor (L.) Moench] underlying economically important traits, we analyzed the genetic structure and linkage disequilibrium in a sorghum mini core collection of 242 landraces with 13,390 single-nucleotide polymorphims. The single-nucleotide polymorphisms were produced using a highly multiplexed genotyping-by-sequencing methodology. Genetic structure was established using principal component, Neighbor-Joining phylogenetic, and Bayesian cluster analyses. These analyses indicated that the mini-core collection was structured along both geographic origin and sorghum race classification. Examples of the former were accessions from Southern Africa, East Asia, and Yemen. Examples of the latter were caudatums with widespread geographical distribution, durras from India, and guineas from West Africa. Race bicolor, the most primitive and the least clearly defined sorghum race, clustered among other races and formed only one clear bicolor-centric cluster. Genome-wide linkage disequilibrium analyses showed linkage disequilibrium decayed, on average, within 10−30 kb, whereas the short arm of SBI-06 contained a linkage disequilibrium block of 20.33 Mb, confirming a previous report of low recombination on this chromosome arm. Four smaller but equally significant linkage disequilibrium blocks of 3.5−35.5 kb were detected on chromosomes 1, 2, 9, and 10. We examined the genes encoded within each block to provide a first look at candidates such as homologs of GS3 and FT that may indicate a selective sweep during sorghum domestication.

Abstract 18: Predictive value of BRCA1 haplotype for trabectedin efficacy in patients with advanced soft-tissue sarcoma.

Abstract Background: Trabectedin (T) has shown objective response and disease stabilisation in 5%-10% and 30-40% of unselected patients with advanced soft tissue sarcoma (STS) failing prior anthracyclines and/or ifosfamide chemotherapy. Although the precise mechanism of action of T is not fully elucidated, this drug has been found to be more active in tumor cells with a deficient homologous recombination (HR) repair system. BRCA1 is a key player of the HER system. Our aim was to determine whether the status of 4 single nucleotide polymorphims (SNPs) was associated with clinical activity of T in advanced STS patients. Methods: We analyzed SNPs (rs16941, rs16942, rs 1799966, and rs 799917) of BRCA1 in two independent cohort of patients (training cohort: 113 patients, validation cohort: 84 patients) with advanced STS from nine major referral European centres for STS. All patients were treated between 1999 and 2011 in phase I-II clinical trials or in the context of a compassionate-use programme that was open to advanced STS patients who had failed conventional chemotherapy. T was given at different doses (0.5-3 mg/m2) with the use of two different schedules: a 3-h infusion or a 24-h continuous infusion. Results: Median age of the patients in the training set was 49 years (range 17-77). The two most frequent histological subtypes were: leiomyosarcoma (non-uterine: 21, uterine: 10) and liposarcoma (myxoid round cell: 21, other: 17). 632 cycles of T were administered, with a median of 4 cycles per patient (range 1-25). The median follow-up was 10 months (range, 0.6-96 months). One complete response, 18 partial responses, and 26 disease stabilizations that lasted for &amp;gt;6 months were observed. The median PFS was 3.5 months (95% confidence interval [CI], 2.7-4.4 months). The median OS was 13.6 months (95% CI, 8.7-18.5 months). PFS was significantly higher for patients who had at least 1 allele of the most frequent BRCA1 AAAG haplotype (median PFS: 5.6 months [95% CI, 1.4-9.8 months] vs 2.5 months [95% CI, 1.3-3.6 months]; P = .03). The same trend was observed for OS (median OS: 14.1 months [95% CI, 4.4-23.8 months] vs 5.4 months [95% CI, 1.7-9.0 months]; P = .0095). We observed a similar association between BRCA1 haptlotype and PFS in the independent validation cohort (median PFS: 5.2 vs 2.7 months, P = .02). Conclusion: BRCA1 haplotype may represent a predictive DNA-based biomarker for trabectedin efficacy in advanced STS patients. Such a biomarker assessable form paraffin-embedded tumor material could be easily used into routine practice provided it is validated in a prospective setting. Citation Format: Audrey Laroche-Clary, Vanessa Chaire, Valérie Le Morvan, Agnès Neuville, Sébastien Salas, François Bertucci, Philippe Pourquier, Antoine Italiano. Predictive value of BRCA1 haplotype for trabectedin efficacy in patients with advanced soft-tissue sarcoma. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 18. doi:10.1158/1538-7445.AM2013-18

Association betweenIL17A/IL17RAGene Polymorphisms and Susceptibility to Alopecia Areata in the Korean Population

BackgroundAlopecia areata is marked by autoimmune assault on the hair follicle resulting in hair loss. T helper 17 cell subset has important roles in protecting the host against extracellular pathogens, however, also promotes inflammatory pathology in autoimmune disease, and it expresses both interleukin (IL)-17A and IL-17F, which can signal via the IL-17 receptor A.ObjectiveTo investigate the significance of IL17A and IL17RA gene polymorphisms in the susceptibility to alopecia areata.MethodsWe conducted case-control association study of 238 alopecia areata patients and 270 matched healthy controls. Allele frequency of total 2 single nucleotide polymorphims in the IL17A gene and 4 single nucleotide polymorphims in the IL17RA gene were studied. The statistical analyses were performed according to onset age, the presence of familyhistory, clinical subtypes, and presence of nail involvement or body hair involvement.ResultsOne single nucleotide polymorphim (rs879577) of IL17RA gene showed significant difference between alopecia areata patients group and controls group (p= 0.0288). One single nucleotide polymorphim (rs4819554) of IL17RA gene showed significant difference between the early onset and late onset alopecia areata (p=0.0421).ConclusionIL17RA gene polymorphism might contribute to the increased susceptibility to alopecia areata in Korean population, and IL17RA gene polymorphism may be associated with onset age.

Species Discrimination, Population Structure and Linkage Disequilibrium in Eucalyptus camaldulensis and Eucalyptus tereticornis Using SSR Markers

Eucalyptus camaldulensis and E. tereticornis are closely related species commonly cultivated for pulp wood in many tropical countries including India. Understanding the genetic structure and linkage disequilibrium (LD) existing in these species is essential for the improvement of industrially important traits. Our goal was to evaluate the use of simple sequence repeat (SSR) loci for species discrimination, population structure and LD analysis in these species. Investigations were carried out with the most common alleles in 93 accessions belonging to these two species using 62 SSR markers through cross amplification. The polymorphic information content (PIC) ranged from 0.44 to 0.93 and 0.36 to 0.93 in E. camaldulensis and E. tereticornis respectively. A clear delineation between the two species was evident based on the analysis of population structure and species-specific alleles. Significant genotypic LD was found in E. camaldulensis, wherein out of 135 significant pairs, 17 pairs showed r2≥0.1. Similarly, in E. tereticornis, out of 136 significant pairs, 18 pairs showed r2≥0.1. The extent of LD decayed rapidly showing the significance of association analyses in eucalypts with higher resolution markers. The availability of whole genome sequence for E. grandis and the synteny and co-linearity in the genome of eucalypts, will allow genome-wide genotyping using microsatellites or single nucleotide polymorphims.

Role of BMI‐Associated Loci Identified in GWAS Meta‐Analyses in the Context of Common Childhood Obesity in European Americans

Obesity is a serious health concern for children and adolescents, particularly in Western societies, where its incidence is now considered to have reached epidemic proportions. A number of genetic determinants of adult BMI have already been established through genome wide association studies (GWAS), most recently from the GIANT meta-analysis of such datasets combined. In this current study of European Americans, we examined the 32 loci detected in that GIANT study in the context of common childhood obesity within a cohort of 1,097 cases (defined as BMI ≥95th percentile), together with 2,760 lean controls (defined as BMI <50th percentile), aged between 2 and 18 years old. Nine of these single-nucleotide polymorphims (SNPs) yielded at least nominal evidence for association with common childhood obesity, namely at the FTO, TMEM18, NRXN3, MC4R, SEC16B, GNPDA2, TNNI3K, QPCTL, and BDNF loci. However, overall 28 of the 32 loci showed directionally consistent effects to that of the adult BMI meta-analysis. We conclude that among the 32 loci that have been reported to associate with adult BMI in the largest meta-analysis of BMI to date, at least nine also contribute to the determination of common obesity in childhood in European Americans, as demonstrated by their associations in our pediatric cohort.

Genetic studies of the protein kinase AKT1 in Parkinson's disease

The protein kinase AKT1 belongs to the Akt family and is a potent mediator of cell growth and survival and fully activated when phosphorylated. The AKT family has been found to be phosphorylated to a lesser extent in the dopaminergic cells of Parkinson's disease patients compared to control individuals, which might influence cell survival. Several publications support the implication of AKT1 in disorders of the dopaminergic system including bipolar disease and schizophrenia. In 2008 an association study performed in a Greek Parkinson's disease case–control material reported the identification of a protective AKT1 haplotype. Based on their work we have performed a replication study in a Swedish Parkinson's disease cohort. We genotyped the four single nucleotide polymorphims (SNPs): rs2494743, rs2498788, rs2494746 and rs1130214 in a case–control material consisting of 243 Parkinson patients and 315 controls. We did not find any associations with Parkinson's disease for either the individual SNPs or any of the haplotypes. In contrast to previously published results, our data do not support the hypothesis of genetic variants in AKT1 confering protection against Parkinson's disease.

A machine learning pipeline for quantitative phenotype prediction from genotype data

BackgroundQuantitative phenotypes emerge everywhere in systems biology and biomedicine due to a direct interest for quantitative traits, or to high individual variability that makes hard or impossible to classify samples into distinct categories, often the case with complex common diseases. Machine learning approaches to genotype-phenotype mapping may significantly improve Genome-Wide Association Studies (GWAS) results by explicitly focusing on predictivity and optimal feature selection in a multivariate setting. It is however essential that stringent and well documented Data Analysis Protocols (DAP) are used to control sources of variability and ensure reproducibility of results. We present a genome-to-phenotype pipeline of machine learning modules for quantitative phenotype prediction. The pipeline can be applied for the direct use of whole-genome information in functional studies. As a realistic example, the problem of fitting complex phenotypic traits in heterogeneous stock mice from single nucleotide polymorphims (SNPs) is here considered.MethodsThe core element in the pipeline is the L1L2 regularization method based on the naïve elastic net. The method gives at the same time a regression model and a dimensionality reduction procedure suitable for correlated features. Model and SNP markers are selected through a DAP originally developed in the MAQC-II collaborative initiative of the U.S. FDA for the identification of clinical biomarkers from microarray data. The L1L2 approach is compared with standard Support Vector Regression (SVR) and with Recursive Jump Monte Carlo Markov Chain (MCMC). Algebraic indicators of stability of partial lists are used for model selection; the final panel of markers is obtained by a procedure at the chromosome scale, termed ’saturation’, to recover SNPs in Linkage Disequilibrium with those selected.ResultsWith respect to both MCMC and SVR, comparable accuracies are obtained by the L1L2 pipeline. Good agreement is also found between SNPs selected by the L1L2 algorithms and candidate loci previously identified by a standard GWAS. The combination of L1L2-based feature selection with a saturation procedure tackles the issue of neglecting highly correlated features that affects many feature selection algorithms.ConclusionsThe L1L2 pipeline has proven effective in terms of marker selection and prediction accuracy. This study indicates that machine learning techniques may support quantitative phenotype prediction, provided that adequate DAPs are employed to control bias in model selection.

Allelic variation of the Waxy gene in foxtail millet [Setaria italica (L.) P. Beauv.] by single nucleotide polymorphisms

The Waxy (Wx) gene product controls the formation of a straight chain polymer of amylose in the starch pathway. Dominance/recessiveness of the Wx allele is associated with amylose content, leading to non-waxy/waxy phenotypes. For a total of 113 foxtail millet accessions, agronomic traits and the molecular differences of the Wx gene were surveyed to evaluate genetic diversities. Molecular types were associated with phenotypes determined by four specific primer sets (non-waxy, Type I; low amylose, Type VI; waxy, Type IV or V). Additionally, the insertion of transposable element in waxy was confirmed by ex1/TSI2R, TSI2F/ex2, ex2int2/TSI7R and TSI7F/ex4r. Seventeen single nucleotide polymorphims (SNPs) were observed from non-coding regions, while three SNPs from coding regions were non-synonymous. Interestingly, the phenotype of No. 88 was still non-waxy, although seven nucleotides (AATTGGT) insertion at 2,993 bp led to 78 amino acids shorter. The rapid decline of r (2) in the sequenced region (exon 1-intron 1-exon 2) suggested a low level of linkage disequilibrium and limited haplotype structure. K (s) values and estimation of evolutionary events indicate early divergence of S. italica among cereal crops. This study suggested the Wx gene was one of the targets in the selection process during domestication.

Evidence That Rho Guanine Nucleotide Exchange Factor 11 (ARHGEF11) on 1q21 is a Type 2 Diabetes Susceptibility Gene in the Old Order Amish

Rho guanine nucleotide exchange factor 11 (ARHGEF11), located on chromosome 1q21, is involved in G protein signaling and is a pathway known to play a role in both insulin secretion and action. We genotyped 52 single nucleotide polymorphims (SNPs) in ARHGEF11 and compared the genotype frequencies of subjects with type 2 diabetes (n = 145) or type 2 diabetes/impaired glucose tolerance (IGT) (n = 293) with those of control subjects with normal glucose tolerance (NGT) (n = 358). Thirty SNPs, spanning the entire gene, were significantly associated with type 2 diabetes or type 2 diabetes/IGT. The most significantly associated SNP was rs6427340 (intron 2), in which the less common allele was the risk allele (odds ratio [OR] 1.82 [95% CI 1.20-2.70], P = 0.005 for type 2 diabetes vs. NGT and 1.79 [1.27-2.50], P = 0.0008 for type 2 diabetes/IGT vs. NGT). In an expanded set of nondiabetic subjects (n = 754), most of the type 2 diabetes-and IGT-associated SNPs were significantly associated with glucose levels during an oral glucose tolerance test, with the same SNP (rs6427340) showing the most significant associations (P = 0.007). All type 2 diabetes-and IGT-associated SNPs were in high linkage disequilibrium and constitute a single 133-kb haplotype block. These results, coupled with similar findings in Pima Indians, suggest that sequence variation in ARHGEF11 may influence risk of type 2 diabetes.

Single nucleotide polymorphisms in the promoter and coding region of the FSH receptor gene determine four haplotypes differently distributed in normozoospermic and azoospermic men

The human follicle-stimulating hormone (FSH) receptor possesses single nucleotide polymorphims (SNPs) in exon 10 (at codons 307 and 680) which influence serum FSH levels in women but not in men. In the present study we extended our previous analysis to 438 men with non-obstructive azoospermia and 304 controls. In addition, we analysed a novel, common SNP in the core promoter of the FSHR gene (at position –29). SNPs were determined by the Taqman allelic discrimination assay. No significant difference in the frequency of the polymorphism at position 680 (Asn/Asn, Asn/Ser, Ser/Ser) between azoo- and normozoospermic men was found. As for the SNP at position –29 (A/G), the A–29 was less frequent than the G–29 allele both in controls (25% vs. 75%) and in patients (30% vs. 70%) (p=NS). Considering the three SNPs together, the four most common allelic variants were found, i.e. A-Thr-Asn, G-Thr-Asn, A-Ala-Ser and G-Ala-Ser, combined into the 10 major combinations. A statistically significant difference in the allelic distribution between controls and azoospermic men was found (p<0.01 by Fisher's exact test) and the A-Ala-Ser haplotype was more frequent in patients (9.1%) than in controls (5.4%), while the G-Thr-Asn haplotype was less frequent in patients (33.1%) than in controls (40.6%). No significant correlation between serum FSH levels and FSHR allele was found. This study shows that the SNPs in the FSHR gene do not influence serum FSH levels in normal and azoospermic men. However, the different distribution of the FSHR alleles between controls and azoospermic men suggests that the A-Ala-Ser haplotype might represent a genetic factor contributing to phenotypic expression of severe spermatogenetic impairment.

SNPs, haplotypes, and model selection in a candidate gene region: The SIMPle analysis for multilocus data

Modern molecular techniques make discovery of numerous single nucleotide polymorphims (SNPs) in candidate gene regions feasible. Conventional analysis relies on either independent tests with each variant or the use of haplotypes in association analysis. The first technique ignores the dependencies between SNPs. The second, though it may increase power, often introduces uncertainty by estimating haplotypes from population data. Additionally, as the number of loci expands for a haplotype, ambiguity in interpretation increases for determining the underlying genetic components driving a detected association. Here, we present a genotype-level analysis to jointly model the SNPs via a SNP interaction model with phase information (SIMPle) to capture the underlying haplotype structure. This analysis estimates both the risk associated with each variant and the importance of phase between pairwise combinations of SNPs. Thus, rather than selecting between genotype- or haplotype-level approaches, the SIMPle method frames the analysis of multilocus data in a model selection paradigm, the aim to determine which SNPs, phase terms, and linear combinations best describe the relation between genetic variation and a trait of interest. To avoid unstable estimation due to sparse data and to incorporate both the dependencies among terms and the uncertainty in model selection, we propose a Bayes model averaging procedure. This highlights key SNPs and phase terms and yields a set of best representative models. Using simulations, we demonstrate the utility of the SIMPle model to identify crucial SNPs and underlying haplotype structures across a variety of causal models and genetic architectures.

Genetic variants of WNK4 in whites and African Americans with hypertension.

Human chromosome 17q has been implicated to contain a gene that influences hypertension susceptibility. This region contains the WNK4 gene that causes the mendelian disorder pseudohypoaldosteronism type II, characterized by high potassium levels and hypertension. The goal of this study was to identify genetic variants in all exons of WNK4 in hypertensive individuals and to examine the association of these variants with essential hypertension. Single-nucleotide polymorphims (SNPs) were identified by sequencing the entire coding region in 32 whites and 32 African Americans with hypertension. A single SNP in whites and 8 SNPs in African Americans were genotyped in a larger cohort of whites (165 hypertensives; 91 normotensives) and African Americans (120 hypertensives; 98 normotensives). The frequency of the rare allele differed significantly between hypertensive whites (13.0%) and normotensive whites (7.1%, P=0.040) for the single intronic SNP (bp 1 156 666). This difference remained significant after adjusting for body mass index and sex (P=0.035). Genotypic frequencies differed significantly between hypertensive and normotensive individuals when a dominant model either with (P=0.027) or without (P=0.028) covariate adjustment was assumed. The odds ratio for hypertension was 2.28 for AA or AG individuals vs those with the GG genotype (95% confidence interval, 1.09 to 4.75). No significant differences in allelic or genotypic frequencies were observed in African Americans for any SNPs. The finding in whites is consistent with the hypothesis that polymorphisms in WNK4 influence the risk of hypertension. However, because the associated SNP does not appear to be a functional variant and the limitations of case/control association studies, confirmation of these results in additional cohorts is warranted.

Expressed variants of Δ12-fatty acid desaturase for the high oleate trait in spanish market-type peanut lines

Increasing the oleic to linoleic acid ratio (O/L) in peanut has positiveeffects on peanut quality and its nutritional value. Δ12-Fattyacid desaturases (Δ12-Fad) have been targeted as logicalcandidates controlling the high oleate trait. A previous study using genomicDNA identified an insertion and a polymorphism resulting in an amino acid changeassociated with the high oleate trait in Spanish-type peanut cultivars. Theobjectives of this research were to use RT-PCR to confirm that the SingleNucleotide Polymorphims (SNPs) identified by analysis of genomic DNA wereexpressed, and to determine if expression patterns for Δ12-Fadwere the same in both seeds and leaves. A polymorphic region of theΔ12-Fad containing a series of nucleotide changes wasamplified, cloned, and sequenced from mRNA of 155 clones of two parental linesand their independent derived backcross lines (IDBLs). The latter differed intheir oleic to linoleic ratio. Data indicated that the “A”insertion and the amino acid change were expressed in both leaf and seed tissue of thehigh and low-intermediate O/L genotypes. It is postulated that several copiesof the Δ12-Fad are present in the genome. It is reasonable toconclude that total activity, and ultimately the O/L ratio, is dependent on thenumber of functional copies. The results provide the basis for an assay toscreen for the high O/L ratio at the molecular level. We also report thepresence of another isozyme of Δ12-Fad with high homology tosoybean isozyme 2 that was expressed in seeds.