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1.  Statistical Estimation of Correlated Genome Associations to a Quantitative Trait Network 
PLoS Genetics  2009;5(8):e1000587.
Many complex disease syndromes, such as asthma, consist of a large number of highly related, rather than independent, clinical or molecular phenotypes. This raises a new technical challenge in identifying genetic variations associated simultaneously with correlated traits. In this study, we propose a new statistical framework called graph-guided fused lasso (GFlasso) to directly and effectively incorporate the correlation structure of multiple quantitative traits such as clinical metrics and gene expressions in association analysis. Our approach represents correlation information explicitly among the quantitative traits as a quantitative trait network (QTN) and then leverages this network to encode structured regularization functions in a multivariate regression model over the genotypes and traits. The result is that the genetic markers that jointly influence subgroups of highly correlated traits can be detected jointly with high sensitivity and specificity. While most of the traditional methods examined each phenotype independently and combined the results afterwards, our approach analyzes all of the traits jointly in a single statistical framework. This allows our method to borrow information across correlated phenotypes to discover the genetic markers that perturb a subset of the correlated traits synergistically. Using simulated datasets based on the HapMap consortium and an asthma dataset, we compared the performance of our method with other methods based on single-marker analysis and regression-based methods that do not use any of the relational information in the traits. We found that our method showed an increased power in detecting causal variants affecting correlated traits. Our results showed that, when correlation patterns among traits in a QTN are considered explicitly and directly during a structured multivariate genome association analysis using our proposed methods, the power of detecting true causal SNPs with possibly pleiotropic effects increased significantly without compromising performance on non-pleiotropic SNPs.
Author Summary
An association study examines a phenotype against genotypic variations over a large set of individuals in order to find the genetic variant that gives rise to the variation in the phenotype. Many complex disease syndromes consist of a large number of highly related clinical phenotypes, and the patient cohorts are routinely surveyed with a large number of traits, such as hundreds of clinical phenotypes and genome-wide profiling of thousands of gene expressions, many of which are correlated. However, most of the conventional approaches for association mapping or eQTL analysis consider a single phenotype at a time instead of taking advantage of the relatedness of traits by analyzing them jointly. Assuming that a group of tightly correlated traits may share a common genetic basis, in this paper, we present a new framework for association analysis that searches for genetic variations influencing a group of correlated traits. We explicitly represent the correlation information in multiple quantitative traits as a quantitative trait network and directly incorporate this network information to scan the genome for association. Our results on simulated and asthma data show that our approach has a significant advantage in detecting associations when a genetic marker perturbs synergistically a group of traits.
PMCID: PMC2719086  PMID: 19680538
2.  TATES: Efficient Multivariate Genotype-Phenotype Analysis for Genome-Wide Association Studies 
PLoS Genetics  2013;9(1):e1003235.
To date, the genome-wide association study (GWAS) is the primary tool to identify genetic variants that cause phenotypic variation. As GWAS analyses are generally univariate in nature, multivariate phenotypic information is usually reduced to a single composite score. This practice often results in loss of statistical power to detect causal variants. Multivariate genotype–phenotype methods do exist but attain maximal power only in special circumstances. Here, we present a new multivariate method that we refer to as TATES (Trait-based Association Test that uses Extended Simes procedure), inspired by the GATES procedure proposed by Li et al (2011). For each component of a multivariate trait, TATES combines p-values obtained in standard univariate GWAS to acquire one trait-based p-value, while correcting for correlations between components. Extensive simulations, probing a wide variety of genotype–phenotype models, show that TATES's false positive rate is correct, and that TATES's statistical power to detect causal variants explaining 0.5% of the variance can be 2.5–9 times higher than the power of univariate tests based on composite scores and 1.5–2 times higher than the power of the standard MANOVA. Unlike other multivariate methods, TATES detects both genetic variants that are common to multiple phenotypes and genetic variants that are specific to a single phenotype, i.e. TATES provides a more complete view of the genetic architecture of complex traits. As the actual causal genotype–phenotype model is usually unknown and probably phenotypically and genetically complex, TATES, available as an open source program, constitutes a powerful new multivariate strategy that allows researchers to identify novel causal variants, while the complexity of traits is no longer a limiting factor.
Author Summary
The genome-wide association study (GWAS) is the primary tool to identify genetic variants that cause phenotypic variation. As GWAS methods are generally univariate in nature, multivariate phenotypic information is usually reduced to a single composite score, which frequently results in a considerable loss of statistical power to detect causal variants. Multivariate genotype–phenotype methods do exist but attain maximal power only in special circumstances. We present a new multivariate method called TATES (Trait-based Association Test that uses Extended Simes procedure). Extensive simulations show that TATES's false positive rate is correct, and that TATES's statistical power to detect causal variants explaining 0.5% of the variance can be 2.5–9 times higher than the power of univariate tests of composite scores and 1.5–2 times higher than the power of the standard MANOVA. Unlike other multivariate methods, TATES uncovers both genetic variants that are common to multiple phenotypes as well as phenotype specific variants. TATES thus provides a more complete view of the genetic architecture of complex traits and constitutes a powerful new multivariate strategy that allows researchers to identify novel causal variants.
PMCID: PMC3554627  PMID: 23359524
3.  Bivariate Association Analyses for the Mixture of Continuous and Binary Traits with the Use of Extended Generalized Estimating Equations 
Genetic epidemiology  2009;33(3):217-227.
Genome-wide association (GWA) study is becoming a powerful tool in deciphering genetic basis of complex human diseases/traits. Currently, the univariate analysis is the most commonly used method to identify genes associated with a certain disease/phenotype under study. A major limitation with the univariate analysis is that it may not make use of the information of multiple correlated phenotypes, which are usually measured and collected in practical studies. The multivariate analysis has proven to be a powerful approach in linkage studies of complex diseases/traits, but it has received little attention in GWA. In this study, we aim to develop a bivariate analytical method for GWAS, which can be used for a complex situation that a continuous trait and a binary trait measured are under study. Based on the modified extended generalized estimating equation (EGEE) method we proposed herein, we assessed the performance of our bivariate analyses through extensive simulations as well as real data analyses. In the study, to develop an EGEE approach for bivariate genetic analyses, we combined two different generalized linear models corresponding to phenotypic variables using a Seemingly Unrelated Regression (SUR) model. The simulation results demonstrated that our EGEE-based bivariate analytical method outperforms univariate analyses in increasing statistical power under a variety of simulation scenarios. Notably, EGEE-based bivariate analyses have consistent advantages over univariate analyses whether or not there exits a phenotypic correlation between the two traits. Our study has practical importance, as one can always use multivariate analyses as a screening tool when multiple phenotypes are available, without extra costs of statistical power and false positive rate. Analyses on empirical GWA data further affirm the advantages of our bivariate analytical method.
PMCID: PMC2745071  PMID: 18924135
4.  Multivariate generalized multifactor dimensionality reduction to detect gene-gene interactions 
BMC Systems Biology  2013;7(Suppl 6):S15.
Recently, one of the greatest challenges in genome-wide association studies is to detect gene-gene and/or gene-environment interactions for common complex human diseases. Ritchie et al. (2001) proposed multifactor dimensionality reduction (MDR) method for interaction analysis. MDR is a combinatorial approach to reduce multi-locus genotypes into high-risk and low-risk groups. Although MDR has been widely used for case-control studies with binary phenotypes, several extensions have been proposed. One of these methods, a generalized MDR (GMDR) proposed by Lou et al. (2007), allows adjusting for covariates and applying to both dichotomous and continuous phenotypes. GMDR uses the residual score of a generalized linear model of phenotypes to assign either high-risk or low-risk group, while MDR uses the ratio of cases to controls.
In this study, we propose multivariate GMDR, an extension of GMDR for multivariate phenotypes. Jointly analysing correlated multivariate phenotypes may have more power to detect susceptible genes and gene-gene interactions. We construct generalized estimating equations (GEE) with multivariate phenotypes to extend generalized linear models. Using the score vectors from GEE we discriminate high-risk from low-risk groups. We applied the multivariate GMDR method to the blood pressure data of the 7,546 subjects from the Korean Association Resource study: systolic blood pressure (SBP) and diastolic blood pressure (DBP). We compare the results of multivariate GMDR for SBP and DBP to the results from separate univariate GMDR for SBP and DBP, respectively. We also applied the multivariate GMDR method to the repeatedly measured hypertension status from 5,466 subjects and compared its result with those of univariate GMDR at each time point.
Results from the univariate GMDR and multivariate GMDR in two-locus model with both blood pressures and hypertension phenotypes indicate best combinations of SNPs whose interaction has significant association with risk for high blood pressures or hypertension. Although the test balanced accuracy (BA) of multivariate analysis was not always greater than that of univariate analysis, the multivariate BAs were more stable with smaller standard deviations.
In this study, we have developed multivariate GMDR method using GEE approach. It is useful to use multivariate GMDR with correlated multiple phenotypes of interests.
PMCID: PMC4029529  PMID: 24565370
5.  A multivariate regression approach to association analysis of a quantitative trait network 
Bioinformatics  2009;25(12):i204-i212.
Motivation: Many complex disease syndromes such as asthma consist of a large number of highly related, rather than independent, clinical phenotypes, raising a new technical challenge in identifying genetic variations associated simultaneously with correlated traits. Although a causal genetic variation may influence a group of highly correlated traits jointly, most of the previous association analyses considered each phenotype separately, or combined results from a set of single-phenotype analyses.
Results: We propose a new statistical framework called graph-guided fused lasso to address this issue in a principled way. Our approach represents the dependency structure among the quantitative traits explicitly as a network, and leverages this trait network to encode structured regularizations in a multivariate regression model over the genotypes and traits, so that the genetic markers that jointly influence subgroups of highly correlated traits can be detected with high sensitivity and specificity. While most of the traditional methods examined each phenotype independently, our approach analyzes all of the traits jointly in a single statistical method to discover the genetic markers that perturb a subset of correlated triats jointly rather than a single trait. Using simulated datasets based on the HapMap consortium data and an asthma dataset, we compare the performance of our method with the single-marker analysis, and other sparse regression methods that do not use any structural information in the traits. Our results show that there is a significant advantage in detecting the true causal single nucleotide polymorphisms when we incorporate the correlation pattern in traits using our proposed methods.
Availability: Software for GFlasso is available at
PMCID: PMC2687972  PMID: 19477989
6.  GUESS-ing Polygenic Associations with Multiple Phenotypes Using a GPU-Based Evolutionary Stochastic Search Algorithm 
PLoS Genetics  2013;9(8):e1003657.
Genome-wide association studies (GWAS) yielded significant advances in defining the genetic architecture of complex traits and disease. Still, a major hurdle of GWAS is narrowing down multiple genetic associations to a few causal variants for functional studies. This becomes critical in multi-phenotype GWAS where detection and interpretability of complex SNP(s)-trait(s) associations are complicated by complex Linkage Disequilibrium patterns between SNPs and correlation between traits. Here we propose a computationally efficient algorithm (GUESS) to explore complex genetic-association models and maximize genetic variant detection. We integrated our algorithm with a new Bayesian strategy for multi-phenotype analysis to identify the specific contribution of each SNP to different trait combinations and study genetic regulation of lipid metabolism in the Gutenberg Health Study (GHS). Despite the relatively small size of GHS (n = 3,175), when compared with the largest published meta-GWAS (n>100,000), GUESS recovered most of the major associations and was better at refining multi-trait associations than alternative methods. Amongst the new findings provided by GUESS, we revealed a strong association of SORT1 with TG-APOB and LIPC with TG-HDL phenotypic groups, which were overlooked in the larger meta-GWAS and not revealed by competing approaches, associations that we replicated in two independent cohorts. Moreover, we demonstrated the increased power of GUESS over alternative multi-phenotype approaches, both Bayesian and non-Bayesian, in a simulation study that mimics real-case scenarios. We showed that our parallel implementation based on Graphics Processing Units outperforms alternative multi-phenotype methods. Beyond multivariate modelling of multi-phenotypes, our Bayesian model employs a flexible hierarchical prior structure for genetic effects that adapts to any correlation structure of the predictors and increases the power to identify associated variants. This provides a powerful tool for the analysis of diverse genomic features, for instance including gene expression and exome sequencing data, where complex dependencies are present in the predictor space.
Author Summary
Nowadays, the availability of cheaper and accurate assays to quantify multiple (endo)phenotypes in large population cohorts allows multi-trait studies. However, these studies are limited by the lack of flexible models integrated with efficient computational tools for genome-wide multi SNPs-traits analyses. To overcome this problem, we propose a novel Bayesian analysis strategy and a new algorithmic implementation which exploits parallel processing architecture for fully multivariate modeling of groups of correlated phenotypes at the genome-wide scale. In addition to increased power of our algorithm over alternative Bayesian and well-established non-Bayesian multi-phenotype methods, we provide an application to a real case study of several blood lipid traits, and show how our method recovered most of the major associations and is better at refining multi-trait polygenic associations than alternative methods. We reveal and replicate in independent cohorts new associations with two phenotypic groups that were not detected by competing multivariate approaches and not noticed by a large meta-GWAS. We also discuss the applicability of the proposed method to large meta-analyses involving hundreds of thousands of individuals and to diverse genomic datasets where complex dependencies in the predictor space are present.
PMCID: PMC3738451  PMID: 23950726
7.  Nonparametric Covariate-Adjusted Association Tests Based on the Generalized Kendall’s Tau* 
Identifying the risk factors for comorbidity is important in psychiatric research. Empirically, studies have shown that testing multiple, correlated traits simultaneously is more powerful than testing a single trait at a time in association analysis. Furthermore, for complex diseases, especially mental illnesses and behavioral disorders, the traits are often recorded in different scales such as dichotomous, ordinal and quantitative. In the absence of covariates, nonparametric association tests have been developed for multiple complex traits to study comorbidity. However, genetic studies generally contain measurements of some covariates that may affect the relationship between the risk factors of major interest (such as genes) and the outcomes. While it is relatively easy to adjust these covariates in a parametric model for quantitative traits, it is challenging for multiple complex traits with possibly different scales. In this article, we propose a nonparametric test for multiple complex traits that can adjust for covariate effects. The test aims to achieve an optimal scheme of adjustment by using a maximum statistic calculated from multiple adjusted test statistics. We derive the asymptotic null distribution of the maximum test statistic, and also propose a resampling approach, both of which can be used to assess the significance of our test. Simulations are conducted to compare the type I error and power of the nonparametric adjusted test to the unadjusted test and other existing adjusted tests. The empirical results suggest that our proposed test increases the power through adjustment for covariates when there exist environmental effects, and is more robust to model misspecifications than some existing parametric adjusted tests. We further demonstrate the advantage of our test by analyzing a data set on genetics of alcoholism.
PMCID: PMC3381868  PMID: 22745516
Comorbidity; Environmental factor; Family-based association test; Maximum test statistic; Multiple traits; Ordinal traits
8.  Random forests on Hadoop for genome-wide association studies of multivariate neuroimaging phenotypes 
BMC Bioinformatics  2013;14(Suppl 16):S6.
Multivariate quantitative traits arise naturally in recent neuroimaging genetics studies, in which both structural and functional variability of the human brain is measured non-invasively through techniques such as magnetic resonance imaging (MRI). There is growing interest in detecting genetic variants associated with such multivariate traits, especially in genome-wide studies. Random forests (RFs) classifiers, which are ensembles of decision trees, are amongst the best performing machine learning algorithms and have been successfully employed for the prioritisation of genetic variants in case-control studies. RFs can also be applied to produce gene rankings in association studies with multivariate quantitative traits, and to estimate genetic similarities measures that are predictive of the trait. However, in studies involving hundreds of thousands of SNPs and high-dimensional traits, a very large ensemble of trees must be inferred from the data in order to obtain reliable rankings, which makes the application of these algorithms computationally prohibitive.
We have developed a parallel version of the RF algorithm for regression and genetic similarity learning tasks in large-scale population genetic association studies involving multivariate traits, called PaRFR (Parallel Random Forest Regression). Our implementation takes advantage of the MapReduce programming model and is deployed on Hadoop, an open-source software framework that supports data-intensive distributed applications. Notable speed-ups are obtained by introducing a distance-based criterion for node splitting in the tree estimation process. PaRFR has been applied to a genome-wide association study on Alzheimer's disease (AD) in which the quantitative trait consists of a high-dimensional neuroimaging phenotype describing longitudinal changes in the human brain structure. PaRFR provides a ranking of SNPs associated to this trait, and produces pair-wise measures of genetic proximity that can be directly compared to pair-wise measures of phenotypic proximity. Several known AD-related variants have been identified, including APOE4 and TOMM40. We also present experimental evidence supporting the hypothesis of a linear relationship between the number of top-ranked mutated states, or frequent mutation patterns, and an indicator of disease severity.
The Java codes are freely available at
PMCID: PMC3853073  PMID: 24564704
9.  A Rapid Genome-wide Gene-based Association Test with Multivariate Traits 
Human heredity  2013;76(2):53-63.
A gene-based genome-wide association study (GWAS) provides a powerful alternative to the traditional single SNP association analysis due to its substantial reduction in the multiple testing burden and possible gain in power due to modeling multiple SNPs within a gene. A gene-based association analysis on multivariate traits is often of interest, but imposes substantial analytical as well as computational challenges to implement it at a genome-wide level.
We have proposed a rapid implementation of multivariate multiple linear regression approach (RMMLR) in unrelated individuals as well as in families. Our approach allows for covariates. Moreover the asymptotic distribution of the test statistic is not heavily influenced by the linkage disequilibrium (LD) among the SNPs and hence can be used efficiently to perform a gene-based GWAS. We have developed corresponding R package to implement such multivariate gene-based GWAS with this RMMLR approach.
We compare through extensive simulation several approaches for both single and multivariate traits. Our RMMLR maintains correct type-I error level even for set of SNPs in strong LD. It also has substantial gain in power to detect a gene when it is associated with a subset of the traits. We have also studied their performance on Minnesota Center for Twin Family Research dataset.
In our overall comparison, our RMMLR approach provides an efficient and powerful tool to perform a gene-based GWAS with single or multivariate traits and maintains the type I error appropriately.
PMCID: PMC4228787  PMID: 24247328
Multivariate regression; Gene-based genome-wide association studies; Multivariate trait
10.  Generalized Analysis of Molecular Variance 
PLoS Genetics  2007;3(4):e51.
Many studies in the fields of genetic epidemiology and applied population genetics are predicated on, or require, an assessment of the genetic background diversity of the individuals chosen for study. A number of strategies have been developed for assessing genetic background diversity. These strategies typically focus on genotype data collected on the individuals in the study, based on a panel of DNA markers. However, many of these strategies are either rooted in cluster analysis techniques, and hence suffer from problems inherent to the assignment of the biological and statistical meaning to resulting clusters, or have formulations that do not permit easy and intuitive extensions. We describe a very general approach to the problem of assessing genetic background diversity that extends the analysis of molecular variance (AMOVA) strategy introduced by Excoffier and colleagues some time ago. As in the original AMOVA strategy, the proposed approach, termed generalized AMOVA (GAMOVA), requires a genetic similarity matrix constructed from the allelic profiles of individuals under study and/or allele frequency summaries of the populations from which the individuals have been sampled. The proposed strategy can be used to either estimate the fraction of genetic variation explained by grouping factors such as country of origin, race, or ethnicity, or to quantify the strength of the relationship of the observed genetic background variation to quantitative measures collected on the subjects, such as blood pressure levels or anthropometric measures. Since the formulation of our test statistic is rooted in multivariate linear models, sets of variables can be related to genetic background in multiple regression-like contexts. GAMOVA can also be used to complement graphical representations of genetic diversity such as tree diagrams (dendrograms) or heatmaps. We examine features, advantages, and power of the proposed procedure and showcase its flexibility by using it to analyze a wide variety of published data sets, including data from the Human Genome Diversity Project, classical anthropometry data collected by Howells, and the International HapMap Project.
Author Summary
Humans exhibit great genetic diversity. Understanding the factors that contribute to and sustain this diversity is an important research area. Not only can such understanding shed light on human origins, but it can also assist in the discovery of genes and genetic factors that contribute to debilitating diseases. Statistical analysis methods that can facilitate the identification of factors contributing to or associated with human genetic diversity are growing in number as new high-throughput molecular genetic assays and technologies are developed. We consider the use of an analysis method termed generalized analysis of molecular variance (GAMOVA), which builds off of previously proposed analysis methods for testing hypotheses about the factors associated with genetic background diversity. We apply the method in a wide variety of settings and show that it is both flexible and powerful. GAMOVA has great potential to assist in population-based human genetic studies, as it can be used to address questions such as: Is a sample of affected cases and unaffected controls from a homogeneous population, or is there evidence of heterogeneity that could affect the results of an association study? Is there reason to believe that the ancestry of a set of individuals influences the traits that they have?
PMCID: PMC1847693  PMID: 17411342
11.  Multivariate Phenotype Association Analysis by Marker-Set Kernel Machine Regression 
Genetic epidemiology  2012;36(7):686-695.
Genetic studies of complex diseases often collect multiple phenotypes relevant to the disorders. As these phenotypes can be correlated and share common genetic mechanisms, jointly analyzing these traits may bring more power to detect genes influencing individual or multiple phenotypes. Given the advancement brought by the multivariate phenotype approaches and the multimarker kernel machine regression, we construct a multivariate regression based on kernel machine to facilitate the joint evaluation of multimarker effects on multiple phenotypes. The kernel machine serves as a powerful dimension-reduction tool to capture complex effects among markers. The multivariate framework incorporates the potentially correlated multi-dimensional phenotypic information and accommodates common or different environmental covariates for each trait. We derive the multivariate kernel machine test based on a score-like statistic, and conduct simulations to evaluate the validity and efficacy of the method. We also study the performance of the commonly adapted strategies for kernel machine analysis on multiple phenotypes, including the multiple univariate kernel machine tests with original phenotypes or with their principal components. Our results suggest that none of these approaches has the uniformly best power, and the optimal test depends on the magnitude of the phenotype correlation and the effect patterns. However, the multivariate test retains to be a reasonable approach when the multiple phenotypes have none or mild correlations, and gives the best power once the correlation becomes stronger or when there exist genes that affect more than one phenotype. We illustrate the utility of the multivariate kernel machine method through the CATIE antibody study.
PMCID: PMC3703860  PMID: 22899176
Kernel machine regression; Multivariate regression; multivariate phenotypes; Score based test
12.  Leveraging input and output structures for joint mapping of epistatic and marginal eQTLs 
Bioinformatics  2012;28(12):i137-i146.
Motivation: As many complex disease and expression phenotypes are the outcome of intricate perturbation of molecular networks underlying gene regulation resulted from interdependent genome variations, association mapping of causal QTLs or expression quantitative trait loci must consider both additive and epistatic effects of multiple candidate genotypes. This problem poses a significant challenge to contemporary genome-wide-association (GWA) mapping technologies because of its computational complexity. Fortunately, a plethora of recent developments in biological network community, especially the availability of genetic interaction networks, make it possible to construct informative priors of complex interactions between genotypes, which can substantially reduce the complexity and increase the statistical power of GWA inference.
Results: In this article, we consider the problem of learning a multitask regression model while taking advantage of the prior information on structures on both the inputs (genetic variations) and outputs (expression levels). We propose a novel regularization scheme over multitask regression called jointly structured input–output lasso based on an ℓ1/ℓ2 norm, which allows shared sparsity patterns for related inputs and outputs to be optimally estimated. Such patterns capture multiple related single nucleotide polymorphisms (SNPs) that jointly influence multiple-related expression traits. In addition, we generalize this new multitask regression to structurally regularized polynomial regression to detect epistatic interactions with manageable complexity by exploiting the prior knowledge on candidate SNPs for epistatic effects from biological experiments. We demonstrate our method on simulated and yeast eQTL datasets.
Availability: Software is available at
PMCID: PMC3371859  PMID: 22689753
13.  Meta-Analysis Identifies Gene-by-Environment Interactions as Demonstrated in a Study of 4,965 Mice 
PLoS Genetics  2014;10(1):e1004022.
Identifying environmentally-specific genetic effects is a key challenge in understanding the structure of complex traits. Model organisms play a crucial role in the identification of such gene-by-environment interactions, as a result of the unique ability to observe genetically similar individuals across multiple distinct environments. Many model organism studies examine the same traits but under varying environmental conditions. For example, knock-out or diet-controlled studies are often used to examine cholesterol in mice. These studies, when examined in aggregate, provide an opportunity to identify genomic loci exhibiting environmentally-dependent effects. However, the straightforward application of traditional methodologies to aggregate separate studies suffers from several problems. First, environmental conditions are often variable and do not fit the standard univariate model for interactions. Additionally, applying a multivariate model results in increased degrees of freedom and low statistical power. In this paper, we jointly analyze multiple studies with varying environmental conditions using a meta-analytic approach based on a random effects model to identify loci involved in gene-by-environment interactions. Our approach is motivated by the observation that methods for discovering gene-by-environment interactions are closely related to random effects models for meta-analysis. We show that interactions can be interpreted as heterogeneity and can be detected without utilizing the traditional uni- or multi-variate approaches for discovery of gene-by-environment interactions. We apply our new method to combine 17 mouse studies containing in aggregate 4,965 distinct animals. We identify 26 significant loci involved in High-density lipoprotein (HDL) cholesterol, many of which are consistent with previous findings. Several of these loci show significant evidence of involvement in gene-by-environment interactions. An additional advantage of our meta-analysis approach is that our combined study has significantly higher power and improved resolution compared to any single study thus explaining the large number of loci discovered in the combined study.
Author Summary
Identifying gene-by-environment interactions is important for understand the architecture of a complex trait. Discovering gene-by-environment interaction requires the observation of the same phenotype in individuals under different environments. Model organism studies are often conducted under different environments. These studies provide an unprecedented opportunity for researchers to identify the gene-by-environment interactions. A difference in the effect size of a genetic variant between two studies conducted in different environments may suggest the presence of a gene-by-environment interaction. In this paper, we propose to employ a random-effect-based meta-analysis approach to identify gene-by-environment interaction, which assumes different or heterogeneous effect sizes between studies. Our approach is motivated by the observation that methods for discovering gene-by-environment interactions are closely related to random effects models for meta-analysis. We show that interactions can be interpreted as heterogeneity and can be detected without utilizing the traditional approaches for discovery of gene-by-environment interactions, which treats the gene-by-environment interactions as covariates in the analysis. We provide a intuitive way to visualize the results of the meta-analysis at a locus which allows us to obtain the biological insights of gene-by-environment interactions. We demonstrate our method by searching for gene-by-environment interactions by combining 17 mouse genetic studies totaling 4,965 distinct animals.
PMCID: PMC3886926  PMID: 24415945
14.  Combining Genome-Wide Association Mapping and Transcriptional Networks to Identify Novel Genes Controlling Glucosinolates in Arabidopsis thaliana 
PLoS Biology  2011;9(8):e1001125.
Genome-wide association mapping is highly sensitive to environmental changes, but network analysis allows rapid causal gene identification.
Genome-wide association (GWA) is gaining popularity as a means to study the architecture of complex quantitative traits, partially due to the improvement of high-throughput low-cost genotyping and phenotyping technologies. Glucosinolate (GSL) secondary metabolites within Arabidopsis spp. can serve as a model system to understand the genomic architecture of adaptive quantitative traits. GSL are key anti-herbivory defenses that impart adaptive advantages within field trials. While little is known about how variation in the external or internal environment of an organism may influence the efficiency of GWA, GSL variation is known to be highly dependent upon the external stresses and developmental processes of the plant lending it to be an excellent model for studying conditional GWA.
Methodology/Principal Findings
To understand how development and environment can influence GWA, we conducted a study using 96 Arabidopsis thaliana accessions, >40 GSL phenotypes across three conditions (one developmental comparison and one environmental comparison) and ∼230,000 SNPs. Developmental stage had dramatic effects on the outcome of GWA, with each stage identifying different loci associated with GSL traits. Further, while the molecular bases of numerous quantitative trait loci (QTL) controlling GSL traits have been identified, there is currently no estimate of how many additional genes may control natural variation in these traits. We developed a novel co-expression network approach to prioritize the thousands of GWA candidates and successfully validated a large number of these genes as influencing GSL accumulation within A. thaliana using single gene isogenic lines.
Together, these results suggest that complex traits imparting environmentally contingent adaptive advantages are likely influenced by up to thousands of loci that are sensitive to fluctuations in the environment or developmental state of the organism. Additionally, while GWA is highly conditional upon genetics, the use of additional genomic information can rapidly identify causal loci en masse.
Author Summary
Understanding how genetic variation can control phenotypic variation is a fundamental goal of modern biology. A major push has been made using genome-wide association mapping in all organisms to attempt and rapidly identify the genes contributing to phenotypes such as disease and nutritional disorders. But a number of fundamental questions have not been answered about the use of genome-wide association: for example, how does the internal or external environment influence the genes found? Furthermore, the simple question of how many genes may influence a trait is unknown. Finally, a number of studies have identified significant false-positive and -negative issues within genome-wide association studies that are not solvable by direct statistical approaches. We have used genome-wide association mapping in the plant Arabidopsis thaliana to begin exploring these questions. We show that both external and internal environments significantly alter the identified genes, such that using different tissues can lead to the identification of nearly completely different gene sets. Given the large number of potential false-positives, we developed an orthogonal approach to filtering the possible genes, by identifying co-functioning networks using the nominal candidate gene list derived from genome-wide association studies. This allowed us to rapidly identify and validate a large number of novel and unexpected genes that affect Arabidopsis thaliana defense metabolism within phenotypic ranges that have been shown to be selectable within the field. These genes and the associated networks suggest that Arabidopsis thaliana defense metabolism is more readily similar to the infinite gene hypothesis, according to which there is a vast number of causative genes controlling natural variation in this phenotype. It remains to be seen how frequently this is true for other organisms and other phenotypes.
PMCID: PMC3156686  PMID: 21857804
15.  Genome-Wide Pleiotropy of Osteoporosis-Related Phenotypes: The Framingham Study 
Journal of Bone and Mineral Research  2010;25(7):1555-1563.
Genome-wide association studies offer an unbiased approach to identify new candidate genes for osteoporosis. We examined the Affymetrix 500K + 50K SNP GeneChip marker sets for associations with multiple osteoporosis-related traits at various skeletal sites, including bone mineral density (BMD, hip and spine), heel ultrasound, and hip geometric indices in the Framingham Osteoporosis Study. We evaluated 433,510 single-nucleotide polymorphisms (SNPs) in 2073 women (mean age 65 years), members of two-generational families. Variance components analysis was performed to estimate phenotypic, genetic, and environmental correlations (ρP, ρG, and ρE) among bone traits. Linear mixed-effects models were used to test associations between SNPs and multivariable-adjusted trait values. We evaluated the proportion of SNPs associated with pairs of the traits at a nominal significance threshold α = 0.01. We found substantial correlation between the proportion of associated SNPs and the ρP and ρG (r = 0.91 and 0.84, respectively) but much lower with ρE (r = 0.38). Thus, for example, hip and spine BMD had 6.8% associated SNPs in common, corresponding to ρP = 0.55 and ρG = 0.66 between them. Fewer SNPs were associated with both BMD and any of the hip geometric traits (eg, femoral neck and shaft width, section moduli, neck shaft angle, and neck length); ρG between BMD and geometric traits ranged from −0.24 to +0.40. In conclusion, we examined relationships between osteoporosis-related traits based on genome-wide associations. Most of the similarity between the quantitative bone phenotypes may be attributed to pleiotropic effects of genes. This knowledge may prove helpful in defining the best phenotypes to be used in genetic studies of osteoporosis. © 2010 American Society for Bone and Mineral Research.
PMCID: PMC3153998  PMID: 20200953
bone mineral density; quantitative ultrasound; femoral geometry; genome-wide association; single-nucleotide polymorphisms; genetic correlations; pleiotropy
16.  Genetic correlates of longevity and selected age-related phenotypes: a genome-wide association study in the Framingham Study 
BMC Medical Genetics  2007;8(Suppl 1):S13.
Family studies and heritability estimates provide evidence for a genetic contribution to variation in the human life span.
We conducted a genome wide association study (Affymetrix 100K SNP GeneChip) for longevity-related traits in a community-based sample. We report on 5 longevity and aging traits in up to 1345 Framingham Study participants from 330 families. Multivariable-adjusted residuals were computed using appropriate models (Cox proportional hazards, logistic, or linear regression) and the residuals from these models were used to test for association with qualifying SNPs (70, 987 autosomal SNPs with genotypic call rate ≥80%, minor allele frequency ≥10%, Hardy-Weinberg test p ≥ 0.001).
In family-based association test (FBAT) models, 8 SNPs in two regions approximately 500 kb apart on chromosome 1 (physical positions 73,091,610 and 73, 527,652) were associated with age at death (p-value < 10-5). The two sets of SNPs were in high linkage disequilibrium (minimum r2 = 0.58). The top 30 SNPs for generalized estimating equation (GEE) tests of association with age at death included rs10507486 (p = 0.0001) and rs4943794 (p = 0.0002), SNPs intronic to FOXO1A, a gene implicated in lifespan extension in animal models. FBAT models identified 7 SNPs and GEE models identified 9 SNPs associated with both age at death and morbidity-free survival at age 65 including rs2374983 near PON1. In the analysis of selected candidate genes, SNP associations (FBAT or GEE p-value < 0.01) were identified for age at death in or near the following genes: FOXO1A, GAPDH, KL, LEPR, PON1, PSEN1, SOD2, and WRN. Top ranked SNP associations in the GEE model for age at natural menopause included rs6910534 (p = 0.00003) near FOXO3a and rs3751591 (p = 0.00006) in CYP19A1. Results of all longevity phenotype-genotype associations for all autosomal SNPs are web posted at .
Longevity and aging traits are associated with SNPs on the Affymetrix 100K GeneChip. None of the associations achieved genome-wide significance. These data generate hypotheses and serve as a resource for replication as more genes and biologic pathways are proposed as contributing to longevity and healthy aging.
PMCID: PMC1995604  PMID: 17903295
17.  Pathways-Driven Sparse Regression Identifies Pathways and Genes Associated with High-Density Lipoprotein Cholesterol in Two Asian Cohorts 
PLoS Genetics  2013;9(11):e1003939.
Standard approaches to data analysis in genome-wide association studies (GWAS) ignore any potential functional relationships between gene variants. In contrast gene pathways analysis uses prior information on functional structure within the genome to identify pathways associated with a trait of interest. In a second step, important single nucleotide polymorphisms (SNPs) or genes may be identified within associated pathways. The pathways approach is motivated by the fact that genes do not act alone, but instead have effects that are likely to be mediated through their interaction in gene pathways. Where this is the case, pathways approaches may reveal aspects of a trait's genetic architecture that would otherwise be missed when considering SNPs in isolation. Most pathways methods begin by testing SNPs one at a time, and so fail to capitalise on the potential advantages inherent in a multi-SNP, joint modelling approach. Here, we describe a dual-level, sparse regression model for the simultaneous identification of pathways and genes associated with a quantitative trait. Our method takes account of various factors specific to the joint modelling of pathways with genome-wide data, including widespread correlation between genetic predictors, and the fact that variants may overlap multiple pathways. We use a resampling strategy that exploits finite sample variability to provide robust rankings for pathways and genes. We test our method through simulation, and use it to perform pathways-driven gene selection in a search for pathways and genes associated with variation in serum high-density lipoprotein cholesterol levels in two separate GWAS cohorts of Asian adults. By comparing results from both cohorts we identify a number of candidate pathways including those associated with cardiomyopathy, and T cell receptor and PPAR signalling. Highlighted genes include those associated with the L-type calcium channel, adenylate cyclase, integrin, laminin, MAPK signalling and immune function.
Author Summary
Genes do not act in isolation, but interact in complex networks or pathways. By accounting for such interactions, pathways analysis methods hope to identify aspects of a disease or trait's genetic architecture that might be missed using more conventional approaches. Most existing pathways methods take a univariate approach, in which each variant within a pathway is separately tested for association with the phenotype of interest. These statistics are then combined to assess pathway significance. As a second step, further analysis can reveal important genetic variants within significant pathways. We have previously shown that a joint-modelling approach using a sparse regression model can increase the power to detect pathways influencing a quantitative trait. Here we extend this approach, and describe a method that is able to simultaneously identify pathways and genes that may be driving pathway selection. We test our method using simulations, and apply it to a study searching for pathways and genes associated with high-density lipoprotein cholesterol in two separate East Asian cohorts.
PMCID: PMC3836716  PMID: 24278029
18.  A Bayesian method and its variational approximation for prediction of genomic breeding values in multiple traits 
BMC Bioinformatics  2013;14:34.
Genomic selection is an effective tool for animal and plant breeding, allowing effective individual selection without phenotypic records through the prediction of genomic breeding value (GBV). To date, genomic selection has focused on a single trait. However, actual breeding often targets multiple correlated traits, and, therefore, joint analysis taking into consideration the correlation between traits, which might result in more accurate GBV prediction than analyzing each trait separately, is suitable for multi-trait genomic selection. This would require an extension of the prediction model for single-trait GBV to multi-trait case. As the computational burden of multi-trait analysis is even higher than that of single-trait analysis, an effective computational method for constructing a multi-trait prediction model is also needed.
We described a Bayesian regression model incorporating variable selection for jointly predicting GBVs of multiple traits and devised both an MCMC iteration and variational approximation for Bayesian estimation of parameters in this multi-trait model. The proposed Bayesian procedures with MCMC iteration and variational approximation were referred to as MCBayes and varBayes, respectively. Using simulated datasets of SNP genotypes and phenotypes for three traits with high and low heritabilities, we compared the accuracy in predicting GBVs between multi-trait and single-trait analyses as well as between MCBayes and varBayes. The results showed that, compared to single-trait analysis, multi-trait analysis enabled much more accurate GBV prediction for low-heritability traits correlated with high-heritability traits, by utilizing the correlation structure between traits, while the prediction accuracy for uncorrelated low-heritability traits was comparable or less with multi-trait analysis in comparison with single-trait analysis depending on the setting for prior probability that a SNP has zero effect. Although the prediction accuracy with varBayes was generally lower than with MCBayes, the loss in accuracy was slight. The computational time was greatly reduced with varBayes.
In genomic selection for multiple correlated traits, multi-trait analysis was more beneficial than single-trait analysis and varBayes was much advantageous over MCBayes in computational time, which would outweigh the loss of prediction accuracy caused by the approximation procedure, and is thus considered a practical method of choice.
PMCID: PMC3574034  PMID: 23363272
Genomic selection; Multiple traits; Bayesian regression; MCMC iteration; Variational approximation
19.  A Unified Method for Detecting Secondary Trait Associations with Rare Variants: Application to Sequence Data 
PLoS Genetics  2012;8(11):e1003075.
Next-generation sequencing has made possible the detection of rare variant (RV) associations with quantitative traits (QT). Due to high sequencing cost, many studies can only sequence a modest number of selected samples with extreme QT. Therefore association testing in individual studies can be underpowered. Besides the primary trait, many clinically important secondary traits are often measured. It is highly beneficial if multiple studies can be jointly analyzed for detecting associations with commonly measured traits. However, analyzing secondary traits in selected samples can be biased if sample ascertainment is not properly modeled. Some methods exist for analyzing secondary traits in selected samples, where some burden tests can be implemented. However p-values can only be evaluated analytically via asymptotic approximations, which may not be accurate. Additionally, potentially more powerful sequence kernel association tests, variable selection-based methods, and burden tests that require permutations cannot be incorporated. To overcome these limitations, we developed a unified method for analyzing secondary trait associations with RVs (STAR) in selected samples, incorporating all RV tests. Statistical significance can be evaluated either through permutations or analytically. STAR makes it possible to apply more powerful RV tests to analyze secondary trait associations. It also enables jointly analyzing multiple cohorts ascertained under different study designs, which greatly boosts power. The performance of STAR and commonly used RV association tests were comprehensively evaluated using simulation studies. STAR was also implemented to analyze a dataset from the SardiNIA project where samples with extreme low-density lipoprotein levels were sequenced. A significant association between LDLR and systolic blood pressure was identified, which is supported by pharmacogenetic studies. In summary, for sequencing studies, STAR is an important tool for detecting secondary-trait RV associations.
Author Summary
Next-generation sequencing has greatly expanded our ability to identify missing heritability due to rare variants. In order to increase the power to detect associations, one desirable study design is to combine samples from multiple cohorts for mapping commonly measured traits. However, many current studies sequence selected samples (e.g. samples with extreme QT), which can bias the analysis of secondary traits, unless the sampling ascertainment mechanisms are properly adjusted. We developed a unified method for detecting secondary trait associations with rare variants (STAR) in selected and random samples, which can flexibly incorporate all rare variant association tests and allow joint analysis of multiple cohorts ascertained under different study designs. We demonstrate via simulations that STAR greatly boosts the power for detecting secondary trait associations. As an application of STAR, a dataset from the SardiNIA project was analyzed, where DNA samples from well-phenotyped individuals with extreme low-density lipoprotein levels were sequenced. LDLR was identified to be significantly associated with systolic blood pressure, which is supported by a previous pharmacogenetics study. In conclusion, STAR is an important tool for sequence-based association studies.
PMCID: PMC3499373  PMID: 23166519
20.  Why Do We Test Multiple Traits in Genetic Association Studies? 
In studies of complex disorders such as nicotine dependence, it is common that researchers assess multiple variables related to a disorder as well as other disorders that are potentially correlated with the primary disorder of interest. In this work, we refer to those variables and disorders broadly as multiple traits. The multiple traits may or may not have a common causal genetic variant. Intuitively, it may be more powerful to accommodate multiple traits in genetic traits, but the analysis of multiple traits is generally more complicated than the analysis of a single trait. Furthermore, it is not well documented as to how much power we may potentially gain by considering multiple traits. Our aim is to enhance our understanding on this important and practical issue. We considered a variety of correlation structures between traits and the disease locus. To focus on the effect of accommodating multiple traits, we examined genetic models that are relatively simple so that we can pinpoint the factors affecting the power. We conducted simulation studies to explore the performance of testing multiple traits simultaneously and the performance of testing a single trait at a time in family-based association studies. Our simulation results demonstrated that the performance of testing multiple traits simultaneously is better than that of testing each trait individually for almost models considered. We also found that the power of association tests varies among the underlying models. The advantage of conducting a multiple traits test is minimized when some traits are influenced by the gene only through other traits; and it is maximized when there are causal relations between the traits and the gene, and among the traits themselves or when there are extraneous traits.
PMCID: PMC2719985  PMID: 19655045
Directed acyclic graphs; Family-based association studies; Linear structural equation model; Multiple traits
21.  A Multi-Trait, Meta-analysis for Detecting Pleiotropic Polymorphisms for Stature, Fatness and Reproduction in Beef Cattle 
PLoS Genetics  2014;10(3):e1004198.
Polymorphisms that affect complex traits or quantitative trait loci (QTL) often affect multiple traits. We describe two novel methods (1) for finding single nucleotide polymorphisms (SNPs) significantly associated with one or more traits using a multi-trait, meta-analysis, and (2) for distinguishing between a single pleiotropic QTL and multiple linked QTL. The meta-analysis uses the effect of each SNP on each of n traits, estimated in single trait genome wide association studies (GWAS). These effects are expressed as a vector of signed t-values (t) and the error covariance matrix of these t values is approximated by the correlation matrix of t-values among the traits calculated across the SNP (V). Consequently, t'V−1t is approximately distributed as a chi-squared with n degrees of freedom. An attractive feature of the meta-analysis is that it uses estimated effects of SNPs from single trait GWAS, so it can be applied to published data where individual records are not available. We demonstrate that the multi-trait method can be used to increase the power (numbers of SNPs validated in an independent population) of GWAS in a beef cattle data set including 10,191 animals genotyped for 729,068 SNPs with 32 traits recorded, including growth and reproduction traits. We can distinguish between a single pleiotropic QTL and multiple linked QTL because multiple SNPs tagging the same QTL show the same pattern of effects across traits. We confirm this finding by demonstrating that when one SNP is included in the statistical model the other SNPs have a non-significant effect. In the beef cattle data set, cluster analysis yielded four groups of QTL with similar patterns of effects across traits within a group. A linear index was used to validate SNPs having effects on multiple traits and to identify additional SNPs belonging to these four groups.
Author Summary
We describe novel methods for finding significant associations between a genome wide panel of SNPs and multiple complex traits, and further for distinguishing between genes with effects on multiple traits and multiple linked genes affecting different traits. The method uses a meta-analysis based on estimates of SNP effects from independent single trait genome wide association studies (GWAS). The method could therefore be widely used to combine already published GWAS results. The method was applied to 32 traits that describe growth, body composition, feed intake and reproduction in 10,191 beef cattle genotyped for approximately 700,000 SNP. The genes found to be associated with these traits can be arranged into 4 groups that differ in their pattern of effects and hence presumably in their physiological mechanism of action. For instance, one group of genes affects weight and fatness in the opposite direction and can be described as a group of genes affecting mature size, while another group affects weight and fatness in the same direction.
PMCID: PMC3967938  PMID: 24675618
22.  A Testable Prognostic Model of Nicotine Dependence 
Journal of neurogenetics  2009;23(3):283-292.
Individuals’ dependence on nicotine, primarily through cigarette smoking, is a major source of morbidity and mortality worldwide. Many smokers attempt but fail to quit smoking, motivating researchers to identify the origins of this dependence. Because of the known heritability of nicotine-dependence phenotypes, considerable interest has been focused on discovering the genetic factors underpinning the trait. This goal, however, is not easily attained: no single factor is likely to explain any great proportion of dependence because nicotine dependence is thought to be a complex trait (i.e., the result of many interacting factors). Genomewide association studies are powerful tools in the search for the genomic bases of complex traits, and in this context, novel candidate genes have been identified through single nucleotide polymorphism (SNP) association analyses. Beyond association, however, genetic data can be used to generate predictive models of nicotine dependence. As expected in the context of a complex trait, individual SNPs fail to accurately predict nicotine dependence, demanding the use of multivariate models. Standard approaches, such as logistic regression, are unable to consider large numbers of SNPs given existing sample sizes. However, using Bayesian networks, one can overcome these limitations to generate a multivariate predictive model, which has markedly enhanced predictive accuracy on fitted values relative to that of individual SNPs. This approach, combined with the data being generated by genomewide association studies, promises to shed new light on the common, complex trait nicotine dependence.
PMCID: PMC2722684  PMID: 19184766
addiction; nicotine; genetics; prediction
23.  Gene-Based Tests of Association 
PLoS Genetics  2011;7(7):e1002177.
Genome-wide association studies (GWAS) are now used routinely to identify SNPs associated with complex human phenotypes. In several cases, multiple variants within a gene contribute independently to disease risk. Here we introduce a novel Gene-Wide Significance (GWiS) test that uses greedy Bayesian model selection to identify the independent effects within a gene, which are combined to generate a stronger statistical signal. Permutation tests provide p-values that correct for the number of independent tests genome-wide and within each genetic locus. When applied to a dataset comprising 2.5 million SNPs in up to 8,000 individuals measured for various electrocardiography (ECG) parameters, this method identifies more validated associations than conventional GWAS approaches. The method also provides, for the first time, systematic assessments of the number of independent effects within a gene and the fraction of disease-associated genes housing multiple independent effects, observed at 35%–50% of loci in our study. This method can be generalized to other study designs, retains power for low-frequency alleles, and provides gene-based p-values that are directly compatible for pathway-based meta-analysis.
Author Summary
Genome-wide association studies (GWAS) have successfully identified genetic variants associated with complex human phenotypes. Despite a proliferation of analysis methods, most studies rely on simple, robust SNP–by–SNP univariate tests with ever-larger population sizes. Here we introduce a new test motivated by the biological hypothesis that a single gene may contain multiple variants that contribute independently to a trait. Applied to simulated phenotypes with real genotypes, our new method, Gene-Wide Significance (GWiS), has better power to identify true associations than traditional univariate methods, previous Bayesian methods, popular L1 regularized (LASSO) multivariate regression, and other approaches. GWiS retains power for low-frequency alleles that are increasingly important for personal genetics, and it is the only method tested that accurately estimates the number of independent effects within a gene. When applied to human data for multiple ECG traits, GWiS identifies more genome-wide significant loci (verified by meta-analyses of much larger populations) than any other method. We estimate that 35%–50% of ECG trait loci are likely to have multiple independent effects, suggesting that our method will reveal previously unidentified associations when applied to existing data and will improve power for future association studies.
PMCID: PMC3145613  PMID: 21829371
24.  MultiPhen: Joint Model of Multiple Phenotypes Can Increase Discovery in GWAS 
PLoS ONE  2012;7(5):e34861.
The genome-wide association study (GWAS) approach has discovered hundreds of genetic variants associated with diseases and quantitative traits. However, despite clinical overlap and statistical correlation between many phenotypes, GWAS are generally performed one-phenotype-at-a-time. Here we compare the performance of modelling multiple phenotypes jointly with that of the standard univariate approach. We introduce a new method and software, MultiPhen, that models multiple phenotypes simultaneously in a fast and interpretable way. By performing ordinal regression, MultiPhen tests the linear combination of phenotypes most associated with the genotypes at each SNP, and thus potentially captures effects hidden to single phenotype GWAS. We demonstrate via simulation that this approach provides a dramatic increase in power in many scenarios. There is a boost in power for variants that affect multiple phenotypes and for those that affect only one phenotype. While other multivariate methods have similar power gains, we describe several benefits of MultiPhen over these. In particular, we demonstrate that other multivariate methods that assume the genotypes are normally distributed, such as canonical correlation analysis (CCA) and MANOVA, can have highly inflated type-1 error rates when testing case-control or non-normal continuous phenotypes, while MultiPhen produces no such inflation. To test the performance of MultiPhen on real data we applied it to lipid traits in the Northern Finland Birth Cohort 1966 (NFBC1966). In these data MultiPhen discovers 21% more independent SNPs with known associations than the standard univariate GWAS approach, while applying MultiPhen in addition to the standard approach provides 37% increased discovery. The most associated linear combinations of the lipids estimated by MultiPhen at the leading SNPs accurately reflect the Friedewald Formula, suggesting that MultiPhen could be used to refine the definition of existing phenotypes or uncover novel heritable phenotypes.
PMCID: PMC3342314  PMID: 22567092
25.  Genome Wide Association Studies Using a New Nonparametric Model Reveal the Genetic Architecture of 17 Agronomic Traits in an Enlarged Maize Association Panel 
PLoS Genetics  2014;10(9):e1004573.
Association mapping is a powerful approach for dissecting the genetic architecture of complex quantitative traits using high-density SNP markers in maize. Here, we expanded our association panel size from 368 to 513 inbred lines with 0.5 million high quality SNPs using a two-step data-imputation method which combines identity by descent (IBD) based projection and k-nearest neighbor (KNN) algorithm. Genome-wide association studies (GWAS) were carried out for 17 agronomic traits with a panel of 513 inbred lines applying both mixed linear model (MLM) and a new method, the Anderson-Darling (A-D) test. Ten loci for five traits were identified using the MLM method at the Bonferroni-corrected threshold −log10 (P) >5.74 (α = 1). Many loci ranging from one to 34 loci (107 loci for plant height) were identified for 17 traits using the A-D test at the Bonferroni-corrected threshold −log10 (P) >7.05 (α = 0.05) using 556809 SNPs. Many known loci and new candidate loci were only observed by the A-D test, a few of which were also detected in independent linkage analysis. This study indicates that combining IBD based projection and KNN algorithm is an efficient imputation method for inferring large missing genotype segments. In addition, we showed that the A-D test is a useful complement for GWAS analysis of complex quantitative traits. Especially for traits with abnormal phenotype distribution, controlled by moderate effect loci or rare variations, the A-D test balances false positives and statistical power. The candidate SNPs and associated genes also provide a rich resource for maize genetics and breeding.
Author Summary
Genotype imputation has been used widely in the analysis of genome-wide association studies (GWAS) to boost power and fine-map associations. We developed a two-step data imputation method to meet the challenge of large proportion missing genotypes. GWAS have uncovered an extensive genetic architecture of complex quantitative traits using high-density SNP markers in maize in the past few years. Here, GWAS were carried out for 17 agronomic traits with a panel of 513 inbred lines applying both mixed linear model and a new method, the Anderson-Darling (A-D) test. We intend to show that the A-D test is a complement to current GWAS methods, especially for complex quantitative traits controlled by moderate effect loci or rare variations and with abnormal phenotype distribution. In addition, the traits associated QTL identified here provide a rich resource for maize genetics and breeding.
PMCID: PMC4161304  PMID: 25211220

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