Two-Stage Two-Locus Models in Genome-Wide Association

Studies in model organisms suggest that epistasis may play an important role in the etiology of complex diseases and traits in humans. With the era of large-scale genome-wide association studies fast approaching, it is important to quantify whether it will be possible to detect interacting loci using realistic sample sizes in humans and to what extent undetected epistasis will adversely affect power to detect association when single-locus approaches are employed. We therefore investigated the power to detect association for an extensive range of two-locus quantitative trait models that incorporated varying degrees of epistasis. We compared the power to detect association using a single-locus model that ignored interaction effects, a full two-locus model that allowed for interactions, and, most important, two two-stage strategies whereby a subset of loci initially identified using single-locus tests were analyzed using the full two-locus model. Despite the penalty introduced by multiple testing, fitting the full two-locus model performed better than single-locus tests for many of the situations considered, particularly when compared with attempts to detect both individual loci. Using a two-stage strategy reduced the computational burden associated with performing an exhaustive two-locus search across the genome but was not as powerful as the exhaustive search when loci interacted. Two-stage approaches also increased the risk of missing interacting loci that contributed little effect at the margins. Based on our extensive simulations, our results suggest that an exhaustive search involving all pairwise combinations of markers across the genome might provide a useful complement to single-locus scans in identifying interacting loci that contribute to moderate proportions of the phenotypic variance

GLIDERS - A web-based search engine for genome-wide linkage disequilibrium between HapMap SNPs

<p>Abstract</p> <p>Background</p> <p>A number of tools for the examination of linkage disequilibrium (LD) patterns between nearby alleles exist, but none are available for quickly and easily investigating LD at longer ranges (>500 kb). We have developed a web-based query tool (GLIDERS: Genome-wide LInkage DisEquilibrium Repository and Search engine) that enables the retrieval of pairwise associations with r²≥ 0.3 across the human genome for any SNP genotyped within HapMap phase 2 and 3, regardless of distance between the markers.</p> <p>Description</p> <p>GLIDERS is an easy to use web tool that only requires the user to enter rs numbers of SNPs they want to retrieve genome-wide LD for (both nearby and long-range). The intuitive web interface handles both manual entry of SNP IDs as well as allowing users to upload files of SNP IDs. The user can limit the resulting inter SNP associations with easy to use menu options. These include MAF limit (5-45%), distance limits between SNPs (minimum and maximum), r²(0.3 to 1), HapMap population sample (CEU, YRI and JPT+CHB combined) and HapMap build/release. All resulting genome-wide inter-SNP associations are displayed on a single output page, which has a link to a downloadable tab delimited text file.</p> <p>Conclusion</p> <p>GLIDERS is a quick and easy way to retrieve genome-wide inter-SNP associations and to explore LD patterns for any number of SNPs of interest. GLIDERS can be useful in identifying SNPs with long-range LD. This can highlight mis-mapping or other potential association signal localisation problems.</p

Linkage Disequilibrium Mapping via Cladistic Analysis of Single-Nucleotide Polymorphism Haplotypes

We present a novel approach to disease-gene mapping via cladistic analysis of single-nucleotide polymorphism (SNP) haplotypes obtained from large-scale, population-based association studies, applicable to whole-genome screens, candidate-gene studies, or fine-scale mapping. Clades of haplotypes are tested for association with disease, exploiting the expected similarity of chromosomes with recent shared ancestry in the region flanking the disease gene. The method is developed in a logistic-regression framework and can easily incorporate covariates such as environmental risk factors or additional unlinked loci to allow for population structure. To evaluate the power of this approach to detect disease-marker association, we have developed a simulation algorithm to generate high-density SNP data with short-range linkage disequilibrium based on empirical patterns of haplotype diversity. The results of the simulation study highlight substantial gains in power over single-locus tests for a wide range of disease models, despite overcorrection for multiple testing

Evaluation and monitoring of terrestrial and aquatic insect biodiversity in forested and cleared watersheds at Camp Atterbury, Indiana.

Executive Summary Camp Atterbury is a 33,132 ha military installation near Edinburgh, Indiana. Construction of a 80 ha (4,550 ha with safety fan) Multi-Purpose Training Range (MPTR) began in 1998, and supports training for military vehicles and dismounted infantry, with a variety of stationary and moving targets. This study provides a baseline for long term monitoring and evaluation of natural communities to assess the impacts of construction of, and training in, the MPTR. We assessed both aquatic macroinvertebrate and terrestrial insect community diversity, abundance, and richness and similarity at a series of study plots using quantifiable, repeatable and replicated methods. These data provide baseline data facilitating long-term monitoring and assessment as a measure of ecosystem health, and allow evaluation of relationships between community composition and habitat metrics. Methods Eight terrestrial study sites, each comprised of a 30 m square plot, were randomly selected, with four of these placed in the cleared portions of the MPTR and four placed in adjacent upland forest. We used several sampling methods, with focus on three groups of taxa (all insect taxa, ants, and leafhoppers and kin) and compared the efficacy of both the methods and the groups as monitoring tools. Sampling methods included: 1) a Malaise trap (mesh tent-like device that captures flying insects) at each site; 2) four sweep sample transects at each site; 3) four leaf litter samples from each site, with invertebrates extracted using the Winkler method; and 4) Nine pitfall traps at each site. Samples were collect during Summer and Fall study periods, and this report gives results from the Summer sample period. Several habitat parameters were recorded, including a vegetation index, canopy cover, ground cover, and leaf litter depth. Dominant plant taxa were collected, and data loggers recorded soil and air temperature during the study. We sampled aquatic macroinvertebrates at three stream sites draining the MPTR. Invertebrates were collected in replicate samples with a dipnet and these were sorted and subsampled in the laboratory. Canopy cover and basic water chemistry data were collected, and data loggers recorded changes in terrestrial and aquatic temperature. An index of biotic integrity and taxon richness were used to evaluate the aquatic communities. Results and Discussion At least 409 taxa and 3776 specimens were collected at terrestrial sample sites during the Summer sampling period. In general, there were some differences among sites, among sampling methods, and among treatments (cleared MPTR versus forested) when we examined taxon richness and species diversity, but these differences could not always be fully resolved. While taxon richness and species diversity differed among treatments, and, in general, plots in the two treatments harbored different insect communities. Species accumulation curves and various estimators of taxon richness were used to evaluate the four sampling methods and the three groups of taxa (all taxa, ants, leafhoppers). Based on the performance of the different taxa (all, ants, leafhoppers) compared across the different methods (malaise sampling, Winkler extracted leaf litter samples, pitfall traps, and sweep samples), the single most effective taxon for monitoring was found to be the ants (Formicidae), and the single best method for monitoring was found to be pitfall trapping. We collected 818 specimens, primarily aquatic macroinvertebrates, from the three stream sites during Summer sampling. All three streams were dry during the fall sample period, and thus no aquatic macroinvertebrates were collected. Using Hilsenhoff’s (1988) family-level index of biotic integrity, water quality was classified as “good” at one site, and “fair” at the other two, although taxon richness was lowest at the site classified as good. In addition to invertebrates, numerous salamanders (Eurycea cirrigera, the Two-lined Salamander) were observed in the streams. 3 For aquatic invertebrates, we found that the small upstream portions that directly drained the MPTR only held water seasonally, and thus were not effective sites for monitoring of stream macroinvertebrates. There was insufficient separation between MPTR-influenced stream sites and control sites, and a lack of replication (few streams flowing away from the MPTR) precluded robust statistical analysis of the data we did obtain. The community of aquatic macroinvertebrates collected during this study appeared similar to the communities reported by Robinson (2004) elsewhere at Camp Atterbury in larger streams, and includes taxa typical of rocky bottom Midwestern forest streams. Fish were largely absent due to the intermittent nature of the streams. Salamanders were abundant in the streams, and because they are top predators in this seasonal habitat, they may be suitable subjects for studies of potential bioaccumulation of toxins. This study provides a snapshot of insect biodiversity at a point in time, thus providing baseline for any possible future monitoring of insect biodiversity. Sampling methods and analyses developed in this study could easily be implemented at a wide variety of other military installations to facilitate inventory and/or monitoring of insect biodiversity.Ope

Lack of Support for the Association between GAD2 Polymorphisms and Severe Human Obesity

The demonstration of association between common genetic variants and chronic human diseases such as obesity could have profound implications for the prediction, prevention, and treatment of these conditions. Unequivocal proof of such an association, however, requires independent replication of initial positive findings. Recently, three (−243 A>G, +61450 C>A, and +83897 T>A) single nucleotide polymorphisms (SNPs) within glutamate decarboxylase 2 (GAD2) were found to be associated with class III obesity (body mass index > 40 kg/m(2)). The association was observed among 188 families (612 individuals) segregating the condition, and a case-control study of 575 cases and 646 lean controls. Functional data supporting a pathophysiological role for one of the SNPs (−243 A>G) were also presented. The gene GAD2 encodes the 65-kDa subunit of glutamic acid decarboxylase—GAD65. In the present study, we attempted to replicate this association in larger groups of individuals, and to extend the functional studies of the −243 A>G SNP. Among 2,359 individuals comprising 693 German nuclear families with severe, early-onset obesity, we found no evidence for a relationship between the three GAD2 SNPs and obesity, whether SNPs were studied individually or as haplotypes. In two independent case-control studies (a total of 680 class III obesity cases and 1,186 lean controls), there was no significant relationship between the −243 A>G SNP and obesity (OR = 0.99, 95% CI 0.83–1.18, p = 0.89) in the pooled sample. These negative findings were recapitulated in a meta-analysis, incorporating all published data for the association between the −243G allele and class III obesity, which yielded an OR of 1.11 (95% CI 0.90–1.36, p = 0.28) in a total sample of 1,252 class III obese cases and 1,800 lean controls. Moreover, analysis of common haplotypes encompassing the GAD2 locus revealed no association with severe obesity in families with the condition. We also obtained functional data for the −243 A>G SNP that does not support a pathophysiological role for this variant in obesity. Potential confounding variables in association studies involving common variants and complex diseases (low power to detect modest genetic effects, overinterpretation of marginal data, population stratification, and biological plausibility) are also discussed in the context of GAD2 and severe obesity

The Use of Genome-Wide eQTL Associations in Lymphoblastoid Cell Lines to Identify Novel Genetic Pathways Involved in Complex Traits

Peer reviewe

Localization of type 1 diabetes susceptibility to the MHC class I genes HLA-B and HLA-A

The major histocompatibility complex (MHC) on chromosome 6 is associated with susceptibility to more common diseases than any other region of the human genome, including almost all disorders classified as autoimmune. In type 1 diabetes the major genetic susceptibility determinants have been mapped to the MHC class II genes HLA-DQB1 and HLA-DRB1 (refs 1-3), but these genes cannot completely explain the association between type 1 diabetes and the MHC region. Owing to the region's extreme gene density, the multiplicity of disease-associated alleles, strong associations between alleles, limited genotyping capability, and inadequate statistical approaches and sample sizes, which, and how many, loci within the MHC determine susceptibility remains unclear. Here, in several large type 1 diabetes data sets, we analyse a combined total of 1,729 polymorphisms, and apply statistical methods - recursive partitioning and regression - to pinpoint disease susceptibility to the MHC class I genes HLA-B and HLA-A (risk ratios >1.5; Pcombined = 2.01 × 10-19 and 2.35 × 10-13, respectively) in addition to the established associations of the MHC class II genes. Other loci with smaller and/or rarer effects might also be involved, but to find these, future searches must take into account both the HLA class II and class I genes and use even larger samples. Taken together with previous studies, we conclude that MHC-class-I-mediated events, principally involving HLA-B*39, contribute to the aetiology of type 1 diabetes. ©2007 Nature Publishing Group

Carriage of the V279F Null Allele within the Gene Encoding Lp-PLA2 Is Protective from Coronary Artery Disease in South Korean Males

The Asia-specific PLA2G7 994G-T transversion leads to V279F substitution within the lipoprotein-associated phospholipase-A2 (Lp-PLA₂) and to absence of enzyme activity in plasma. This variant offers a unique natural experiment to assess the role of Lp-PLA₂ in the pathogenesis of coronary artery disease (CAD) in humans. Given conflicting results from mostly small studies, a large two-stage case-control study was warranted.PLA2G7 V279F genotypes were initially compared in 2890 male cases diagnosed with CAD before age 60 with 3128 male controls without CAD at age 50 and above and subsequently in a second independent male dataset of 877 CAD cases and 1230 controls. In the first dataset, the prevalence of the 279F null allele was 11.5% in cases and 12.8% in controls. After adjustment for age, body mass index, diabetes, smoking, glucose and lipid levels, the OR (95% CI) for CAD for this allele was 0.80 (0.66-0.97, p = 0.02). The results were very similar in the second dataset, despite lower power, with an allele frequency of 11.2% in cases and 12.5% in controls, leading to a combined OR of 0.80 (0.69-0.92), p = 0.002. The magnitude and direction of this genetic effect were fully consistent with large epidemiological studies on plasma Lp-PLA₂ activity and CAD risk.Natural deficiency in Lp-PLA₂ activity due to carriage of PLA2G7 279F allele protects from CAD in Korean men. These results provide evidence for a causal relationship between Lp-PLA₂ and CAD, and support pharmacological inhibition of this enzyme as an innovative way to prevent CAD

Carriage of the V279F Null Allele within the Gene Encoding Lp-PLA2 Is Protective from Coronary Artery Disease in South Korean Males

The Asia-specific PLA2G7 994G-T transversion leads to V279F substitution within the lipoprotein-associated phospholipase-A2 (Lp-PLA₂) and to absence of enzyme activity in plasma. This variant offers a unique natural experiment to assess the role of Lp-PLA₂ in the pathogenesis of coronary artery disease (CAD) in humans. Given conflicting results from mostly small studies, a large two-stage case-control study was warranted.PLA2G7 V279F genotypes were initially compared in 2890 male cases diagnosed with CAD before age 60 with 3128 male controls without CAD at age 50 and above and subsequently in a second independent male dataset of 877 CAD cases and 1230 controls. In the first dataset, the prevalence of the 279F null allele was 11.5% in cases and 12.8% in controls. After adjustment for age, body mass index, diabetes, smoking, glucose and lipid levels, the OR (95% CI) for CAD for this allele was 0.80 (0.66-0.97, p = 0.02). The results were very similar in the second dataset, despite lower power, with an allele frequency of 11.2% in cases and 12.5% in controls, leading to a combined OR of 0.80 (0.69-0.92), p = 0.002. The magnitude and direction of this genetic effect were fully consistent with large epidemiological studies on plasma Lp-PLA₂ activity and CAD risk.Natural deficiency in Lp-PLA₂ activity due to carriage of PLA2G7 279F allele protects from CAD in Korean men. These results provide evidence for a causal relationship between Lp-PLA₂ and CAD, and support pharmacological inhibition of this enzyme as an innovative way to prevent CAD