705 research outputs found
A Bayesian Method for Detecting and Characterizing Allelic Heterogeneity and Boosting Signals in Genome-Wide Association Studies
The standard paradigm for the analysis of genome-wide association studies
involves carrying out association tests at both typed and imputed SNPs. These
methods will not be optimal for detecting the signal of association at SNPs
that are not currently known or in regions where allelic heterogeneity occurs.
We propose a novel association test, complementary to the SNP-based approaches,
that attempts to extract further signals of association by explicitly modeling
and estimating both unknown SNPs and allelic heterogeneity at a locus. At each
site we estimate the genealogy of the case-control sample by taking advantage
of the HapMap haplotypes across the genome. Allelic heterogeneity is modeled by
allowing more than one mutation on the branches of the genealogy. Our use of
Bayesian methods allows us to assess directly the evidence for a causative SNP
not well correlated with known SNPs and for allelic heterogeneity at each
locus. Using simulated data and real data from the WTCCC project, we show that
our method (i) produces a significant boost in signal and accurately identifies
the form of the allelic heterogeneity in regions where it is known to exist,
(ii) can suggest new signals that are not found by testing typed or imputed
SNPs and (iii) can provide more accurate estimates of effect sizes in regions
of association.Comment: Published in at http://dx.doi.org/10.1214/09-STS311 the Statistical
Science (http://www.imstat.org/sts/) by the Institute of Mathematical
Statistics (http://www.imstat.org
A Powerful Approach to Sub-Phenotype Analysis in Population-Based Genetic Association Studies
The ultimate goal of genome-wide association (GWA) studies is to identify genetic variants contributing effects to complex phenotypes in order to improve our understanding of the biological architecture underlying the trait. One approach to allow us to meet this challenge is to consider more refined sub-phenotypes of disease, defined by pattern of symptoms, for example, which may be physiologically distinct, and thus may have different underlying genetic causes. The disadvantage of sub-phenotype analysis is that large disease cohorts are sub-divided into smaller case categories, thus reducing power to detect association. To address this issue, we have developed a novel test of association within a multinomial regression modeling framework, allowing for heterogeneity of genetic effects between sub-phenotypes. The modeling framework is extremely flexible, and can be generalized to any number of distinct sub-phenotypes. Simulations demonstrate the power of the multinomial regression-based analysis over existing methods when genetic effects differ between sub-phenotypes, with minimal loss of power when these effects are homogenous for the unified phenotype. Application of the multinomial regression analysis to a genome-wide association study of type 2 diabetes, with cases categorized according to body mass index, highlights previously recognized differential mechanisms underlying obese and non-obese forms of the disease, and provides evidence of a potential novel association that warrants follow-up in independent replication cohorts
Recessive mutations in the cancer gene <i>Ataxia Telangiectasia Mutated (ATM)</i>, at a locus previously associated with metformin response, cause dysglycaemia and insulin resistance
Aim:
To investigate glucose and insulin metabolism in participants with ataxia telangiectasia in the absence of a diagnosis of diabetes.
Methods:
A standard oral glucose tolerance test was performed in participants with ataxia telangiectasia (n = 10) and in a control cohort (n = 10). Serial glucose and insulin measurements were taken to permit cohort comparisons of glucose‐insulin homeostasis and indices of insulin secretion and sensitivity.
Results:
During the oral glucose tolerance test, the 2‐h glucose (6.75 vs 4.93 mmol/l; P = 0.029), insulin concentrations (285.6 vs 148.5 pmol/l; P = 0.043), incremental area under the curve for glucose (314 vs 161 mmol/l/min; P = 0.036) and incremental area under the curve for insulin (37,720 vs 18,080 pmol/l/min; P = 0.03) were higher in participants with ataxia telangiectasia than in the controls. There were no significant differences between groups in fasting glucose, insulin concentrations or insulinogenic index measurement (0.94 vs 0.95; P = 0.95). The Matsuda index, reflecting whole‐body insulin sensitivity, was lower in participants with ataxia telangiectasia (5.96 vs 11.03; P = 0.019) than in control subjects.
Conclusions:
Mutations in Ataxia Telangiectasia Mutated (ATM) that cause ataxia telangiectasia are associated with elevated glycaemia and low insulin sensitivity in participants without diabetes. This indicates a role of ATM in glucose and insulin metabolic pathway
Hardy-Weinberg Equilibrium Testing of Biological Ascertainment for Mendelian Randomization Studies
Mendelian randomization (MR) permits causal inference between exposures and a disease. It can be compared with randomized controlled trials. Whereas in a randomized controlled trial the randomization occurs at entry into the trial, in MR the randomization occurs during gamete formation and conception. Several factors, including time since conception and sampling variation, are relevant to the interpretation of an MR test. Particularly important is consideration of the “missingness” of genotypes that can be originated by chance, genotyping errors, or clinical ascertainment. Testing for Hardy-Weinberg equilibrium (HWE) is a genetic approach that permits evaluation of missingness. In this paper, the authors demonstrate evidence of nonconformity with HWE in real data. They also perform simulations to characterize the sensitivity of HWE tests to missingness. Unresolved missingness could lead to a false rejection of causality in an MR investigation of trait-disease association. These results indicate that large-scale studies, very high quality genotyping data, and detailed knowledge of the life-course genetics of the alleles/genotypes studied will largely mitigate this risk. The authors also present a Web program (http://www.oege.org/software/hwe-mr-calc.shtml) for estimating possible missingness and an approach to evaluating missingness under different genetic models
Another tool in the genome-wide association study arsenal: population-based detection of somatic gene conversion
The hunt for the genetic contributors to complex disease has used a number of strategies, resulting in the identification of variants associated with many of the common diseases affecting society. However most of the genetic variants detected to date are single nucleotide polymorphisms (SNPs) and copy number variants (CNVs) and fall far short of explaining the full genetic component of any given disease. An as yet untapped genomic mechanism is somatic gene conversion and deletion, which could be complicit in disease risk but has been challenging to detect in genome-wide datasets. In a recent publication in BMC Medicine by Kenneth Ross, the author uses existing datasets to look at somatic gene conversion and deletion in human disease. Here, we describe how Ross's recent efforts to detect such occurrences could impact the field going forward
The UK DNA banking network: a “fair access” biobank
The UK DNA Banking Network (UDBN) is a secondary biobank: it aggregates and manages resources (samples and data) originated by others. The network comprises, on the one hand, investigator groups led by clinicians each with a distinct disease specialism and, on the other hand, a research infrastructure to manage samples and data. The infrastructure addresses the problem of providing secure quality-assured accrual, storage, replenishment and distribution capacities for samples and of facilitating access to DNA aliquots and data for new peer-reviewed studies in genetic epidemiology. ‘Fair access’ principles and practices have been pragmatically developed that, unlike open access policies in this area, are not cumbersome but, rather, are fit for the purpose of expediting new study designs and their implementation. UDBN has so far distributed >60,000 samples for major genotyping studies yielding >10 billion genotypes. It provides a working model that can inform progress in biobanking nationally, across Europe and internationally
Linkage Disequilibrium in Wild Mice
Crosses between laboratory strains of mice provide a powerful way of detecting quantitative trait loci for complex traits related to human disease. Hundreds of these loci have been detected, but only a small number of the underlying causative genes have been identified. The main difficulty is the extensive linkage disequilibrium (LD) in intercross progeny and the slow process of fine-scale mapping by traditional methods. Recently, new approaches have been introduced, such as association studies with inbred lines and multigenerational crosses. These approaches are very useful for interval reduction, but generally do not provide single-gene resolution because of strong LD extending over one to several megabases. Here, we investigate the genetic structure of a natural population of mice in Arizona to determine its suitability for fine-scale LD mapping and association studies. There are three main findings: (1) Arizona mice have a high level of genetic variation, which includes a large fraction of the sequence variation present in classical strains of laboratory mice; (2) they show clear evidence of local inbreeding but appear to lack stable population structure across the study area; and (3) LD decays with distance at a rate similar to human populations, which is considerably more rapid than in laboratory populations of mice. Strong associations in Arizona mice are limited primarily to markers less than 100 kb apart, which provides the possibility of fine-scale association mapping at the level of one or a few genes. Although other considerations, such as sample size requirements and marker discovery, are serious issues in the implementation of association studies, the genetic variation and LD results indicate that wild mice could provide a useful tool for identifying genes that cause variation in complex traits
SNPsyn: detection and exploration of SNP–SNP interactions
SNPsyn (http://snpsyn.biolab.si) is an interactive software tool for the discovery of synergistic pairs of single nucleotide polymorphisms (SNPs) from large genome-wide case-control association studies (GWAS) data on complex diseases. Synergy among SNPs is estimated using an information-theoretic approach called interaction analysis. SNPsyn is both a stand-alone C++/Flash application and a web server. The computationally intensive part is implemented in C++ and can run in parallel on a dedicated cluster or grid. The graphical user interface is written in Adobe Flash Builder 4 and can run in most web browsers or as a stand-alone application. The SNPsyn web server hosts the Flash application, receives GWAS data submissions, invokes the interaction analysis and serves result files. The user can explore details on identified synergistic pairs of SNPs, perform gene set enrichment analysis and interact with the constructed SNP synergy network
The Social Licence for Research:Why care.data Ran Into Trouble
In this article we draw on the concept of a social licence to explain public concern at the introduction of care.data, a recent English initiative designed to extract data from primary care medical records for commissioning and other purposes, including research. The concept of a social licence describes how the expectations of society regarding some activities may go beyond compliance with the requirements of formal regulation; those who do not fulfil the conditions for the social licence (even if formally compliant) may experience ongoing challenge and contestation. Previous work suggests that people's cooperation with specific research studies depends on their perceptions that their participation is voluntary and is governed by values of reciprocity, non-exploitation and service of the public good. When these conditions are not seen to obtain, threats to the social licence for research may emerge. We propose that care.data failed to adequately secure a social licence because of: (i) defects in the warrants of trust provided for care.data, (ii) the implied rupture in the traditional role, expectations and duties of general practitioners, and (iii) uncertainty about the status of care.data as a public good. The concept of a social licence may be useful in explaining the specifics of care.data, and also in reinforcing the more general lesson for policy-makers that legal authority does not necessarily command social legitimacy
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