PMCC PMCC

Search tips
Search criteria

Advanced
Results 1-25 (1557339)

Clipboard (0)
None

Related Articles

1.  An algorithm for learning maximum entropy probability models of disease risk that efficiently searches and sparingly encodes multilocus genomic interactions 
Bioinformatics  2009;25(19):2478-2485.
Motivation: In both genome-wide association studies (GWAS) and pathway analysis, the modest sample size relative to the number of genetic markers presents formidable computational, statistical and methodological challenges for accurately identifying markers/interactions and for building phenotype-predictive models.
Results: We address these objectives via maximum entropy conditional probability modeling (MECPM), coupled with a novel model structure search. Unlike neural networks and support vector machines (SVMs), MECPM makes explicit and is determined by the interactions that confer phenotype-predictive power. Our method identifies both a marker subset and the multiple k-way interactions between these markers. Additional key aspects are: (i) evaluation of a select subset of up to five-way interactions while retaining relatively low complexity; (ii) flexible single nucleotide polymorphism (SNP) coding (dominant, recessive) within each interaction; (iii) no mathematical interaction form assumed; (iv) model structure and order selection based on the Bayesian Information Criterion, which fairly compares interactions at different orders and automatically sets the experiment-wide significance level; (v) MECPM directly yields a phenotype-predictive model. MECPM was compared with a panel of methods on datasets with up to 1000 SNPs and up to eight embedded penetrance function (i.e. ground-truth) interactions, including a five-way, involving less than 20 SNPs. MECPM achieved improved sensitivity and specificity for detecting both ground-truth markers and interactions, compared with previous methods.
Availability: http://www.cbil.ece.vt.edu/ResearchOngoingSNP.htm
Contact: djmiller@engr.psu.edu
Supplementary information:Supplementary data are available at Bioinformatics online.
doi:10.1093/bioinformatics/btp435
PMCID: PMC3140808  PMID: 19608708
2.  A Novel Statistic for Genome-Wide Interaction Analysis 
PLoS Genetics  2010;6(9):e1001131.
Although great progress in genome-wide association studies (GWAS) has been made, the significant SNP associations identified by GWAS account for only a few percent of the genetic variance, leading many to question where and how we can find the missing heritability. There is increasing interest in genome-wide interaction analysis as a possible source of finding heritability unexplained by current GWAS. However, the existing statistics for testing interaction have low power for genome-wide interaction analysis. To meet challenges raised by genome-wide interactional analysis, we have developed a novel statistic for testing interaction between two loci (either linked or unlinked). The null distribution and the type I error rates of the new statistic for testing interaction are validated using simulations. Extensive power studies show that the developed statistic has much higher power to detect interaction than classical logistic regression. The results identified 44 and 211 pairs of SNPs showing significant evidence of interactions with FDR<0.001 and 0.001
Author Summary
It is expected that genome-wide interaction analysis can be a possible source of finding heritability unexplained by current GWAS. However, the existing statistics for testing interaction have low power for genome-wide interaction analysis. To meet challenges raised by genome-wide interactional analysis, we develop a novel statistic for testing interaction between two loci (either linked or unlinked) and validate the null distribution and the type I error rates of the new statistic through simulations. By extensive power studies we show that the developed novel statistic has much higher power to detect interaction than the classical logistic regression. To provide evidence of gene–gene interactions as a possible source of the missing heritability unexplained by the current GWAS, we performed the genome-wide interaction analysis of psoriasis in two independent studies. The preliminary results identified 44 and 211 pairs of SNPs showing significant evidence of interactions with FDR<0.001 and 0.001
doi:10.1371/journal.pgen.1001131
PMCID: PMC2944798  PMID: 20885795
PLoS Genetics  2008;4(7):e1000130.
Testing one SNP at a time does not fully realise the potential of genome-wide association studies to identify multiple causal variants, which is a plausible scenario for many complex diseases. We show that simultaneous analysis of the entire set of SNPs from a genome-wide study to identify the subset that best predicts disease outcome is now feasible, thanks to developments in stochastic search methods. We used a Bayesian-inspired penalised maximum likelihood approach in which every SNP can be considered for additive, dominant, and recessive contributions to disease risk. Posterior mode estimates were obtained for regression coefficients that were each assigned a prior with a sharp mode at zero. A non-zero coefficient estimate was interpreted as corresponding to a significant SNP. We investigated two prior distributions and show that the normal-exponential-gamma prior leads to improved SNP selection in comparison with single-SNP tests. We also derived an explicit approximation for type-I error that avoids the need to use permutation procedures. As well as genome-wide analyses, our method is well-suited to fine mapping with very dense SNP sets obtained from re-sequencing and/or imputation. It can accommodate quantitative as well as case-control phenotypes, covariate adjustment, and can be extended to search for interactions. Here, we demonstrate the power and empirical type-I error of our approach using simulated case-control data sets of up to 500 K SNPs, a real genome-wide data set of 300 K SNPs, and a sequence-based dataset, each of which can be analysed in a few hours on a desktop workstation.
Author Summary
Tests of association with disease status are normally conducted one SNP at a time, ignoring the effects of all other genotyped SNPs. We developed a computationally efficient method to simultaneously analyse all SNPs, either in a genome-wide association (GWA) study, or a fine-mapping study based on re-sequencing and/or imputation. The method selects a subset of SNPs that best predicts disease status, while controlling the type-I error of the selected SNPs. This brings many advantages over standard single-SNP approaches, because the signal from a particular SNP can be more clearly assessed when other SNPs associated with disease status are already included in the model. Thus, in comparison with single-SNP analyses, power is increased and the false positive rate is reduced because of reduced residual variation. Localisation is also greatly improved. We demonstrate these advantages over the widely used single-SNP Armitage Trend Test using GWA simulation studies, a real GWA dataset, and a sequence-based fine-mapping simulation study.
doi:10.1371/journal.pgen.1000130
PMCID: PMC2464715  PMID: 18654633
PLoS Genetics  2012;8(4):e1002625.
Recently, Wu and colleagues [1] proposed two novel statistics for genome-wide interaction analysis using case/control or case-only data. In computer simulations, their proposed case/control statistic outperformed competing approaches, including the fast-epistasis option in PLINK and logistic regression analysis under the correct model; however, reasons for its superior performance were not fully explored. Here we investigate the theoretical properties and performance of Wu et al.'s proposed statistics and explain why, in some circumstances, they outperform competing approaches. Unfortunately, we find minor errors in the formulae for their statistics, resulting in tests that have higher than nominal type 1 error. We also find minor errors in PLINK's fast-epistasis and case-only statistics, although theory and simulations suggest that these errors have only negligible effect on type 1 error. We propose adjusted versions of all four statistics that, both theoretically and in computer simulations, maintain correct type 1 error rates under the null hypothesis. We also investigate statistics based on correlation coefficients that maintain similar control of type 1 error. Although designed to test specifically for interaction, we show that some of these previously-proposed statistics can, in fact, be sensitive to main effects at one or both loci, particularly in the presence of linkage disequilibrium. We propose two new “joint effects” statistics that, provided the disease is rare, are sensitive only to genuine interaction effects. In computer simulations we find, in most situations considered, that highest power is achieved by analysis under the correct genetic model. Such an analysis is unachievable in practice, as we do not know this model. However, generally high power over a wide range of scenarios is exhibited by our joint effects and adjusted Wu statistics. We recommend use of these alternative or adjusted statistics and urge caution when using Wu et al.'s originally-proposed statistics, on account of the inflated error rate that can result.
Author Summary
Gene–gene interactions are a topic of great interest to geneticists carrying out studies of how genetic factors influence the development of common, complex diseases. Genes that interact may not only make important biological contributions to underlying disease processes, but also be more difficult to detect when using standard statistical methods in which we examine the effects of genetic factors one at a time. Recently a method was proposed by Wu and colleagues [1] for detecting pairwise interactions when carrying out genome-wide association studies (in which a large number of genetic variants across the genome are examined). Wu and colleagues carried out theoretical work and computer simulations that suggested their method outperformed other previously proposed approaches for detecting interactions. Here we show that, in fact, the method proposed by Wu and colleagues can result in an over-preponderence of false postive findings. We propose an adjusted version of their method that reduces the false positive rate while maintaining high power. We also propose a new method for detecting pairs of genetic effects that shows similarly high power but has some conceptual advantages over both Wu's method and also other previously proposed approaches.
doi:10.1371/journal.pgen.1002625
PMCID: PMC3320596  PMID: 22496670
BMC Medical Genetics  2009;10:127.
Background
There is a growing awareness that interaction between multiple genes play an important role in the risk of common, complex multi-factorial diseases. Many common diseases are affected by certain genotype combinations (associated with some genes and their interactions). The identification and characterization of these susceptibility genes and gene-gene interaction have been limited by small sample size and large number of potential interactions between genes. Several methods have been proposed to detect gene-gene interaction in a case control study. The penalized logistic regression (PLR), a variant of logistic regression with L2 regularization, is a parametric approach to detect gene-gene interaction. On the other hand, the Multifactor Dimensionality Reduction (MDR) is a nonparametric and genetic model-free approach to detect genotype combinations associated with disease risk.
Methods
We compared the power of MDR and PLR for detecting two-way and three-way interactions in a case-control study through extensive simulations. We generated several interaction models with different magnitudes of interaction effect. For each model, we simulated 100 datasets, each with 200 cases and 200 controls and 20 SNPs. We considered a wide variety of models such as models with just main effects, models with only interaction effects or models with both main and interaction effects. We also compared the performance of MDR and PLR to detect gene-gene interaction associated with acute rejection(AR) in kidney transplant patients.
Results
In this paper, we have studied the power of MDR and PLR for detecting gene-gene interaction in a case-control study through extensive simulation. We have compared their performances for different two-way and three-way interaction models. We have studied the effect of different allele frequencies on these methods. We have also implemented their performance on a real dataset. As expected, none of these methods were consistently better for all data scenarios, but, generally MDR outperformed PLR for more complex models. The ROC analysis on the real dataset suggests that MDR outperforms PLR in detecting gene-gene interaction on the real dataset.
Conclusion
As one might expect, the relative success of each method is context dependent. This study demonstrates the strengths and weaknesses of the methods to detect gene-gene interaction.
doi:10.1186/1471-2350-10-127
PMCID: PMC2800840  PMID: 19961594
Biostatistics (Oxford, England)  2010;12(2):211-222.
Genetic mutations may interact to increase the risk of human complex diseases. Mapping of multiple interacting disease loci in the human genome has recently shown promise in detecting genes with little main effects. The power of interaction association mapping, however, can be greatly influenced by the set of single nucleotide polymorphism (SNP) genotyped in a case–control study. Previous imputation methods only focus on imputation of individual SNPs without considering their joint distribution of possible interactions. We present a new method that simultaneously detects multilocus interaction associations and imputes missing SNPs from a full Bayesian model. Our method treats both the case–control sample and the reference data as random observations. The output of our method is the posterior probabilities of SNPs for their marginal and interacting associations with the disease. Using simulations, we show that the method produces accurate and robust imputation with little overfitting problems. We further show that, with the type I error rate maintained at a common level, SNP imputation can consistently and sometimes substantially improve the power of detecting disease interaction associations. We use a data set of inflammatory bowel disease to demonstrate the application of our method.
doi:10.1093/biostatistics/kxq063
PMCID: PMC3062153  PMID: 20923970
Bayesian analysis; Case–control studies; Missing data
PLoS Genetics  2009;5(7):e1000582.
Genome-wide association studies (GWAS) aim to identify genetic variants related to diseases by examining the associations between phenotypes and hundreds of thousands of genotyped markers. Because many genes are potentially involved in common diseases and a large number of markers are analyzed, it is crucial to devise an effective strategy to identify truly associated variants that have individual and/or interactive effects, while controlling false positives at the desired level. Although a number of model selection methods have been proposed in the literature, including marginal search, exhaustive search, and forward search, their relative performance has only been evaluated through limited simulations due to the lack of an analytical approach to calculating the power of these methods. This article develops a novel statistical approach for power calculation, derives accurate formulas for the power of different model selection strategies, and then uses the formulas to evaluate and compare these strategies in genetic model spaces. In contrast to previous studies, our theoretical framework allows for random genotypes, correlations among test statistics, and a false-positive control based on GWAS practice. After the accuracy of our analytical results is validated through simulations, they are utilized to systematically evaluate and compare the performance of these strategies in a wide class of genetic models. For a specific genetic model, our results clearly reveal how different factors, such as effect size, allele frequency, and interaction, jointly affect the statistical power of each strategy. An example is provided for the application of our approach to empirical research. The statistical approach used in our derivations is general and can be employed to address the model selection problems in other random predictor settings. We have developed an R package markerSearchPower to implement our formulas, which can be downloaded from the Comprehensive R Archive Network (CRAN) or http://bioinformatics.med.yale.edu/group/.
Author Summary
Almost all published genome-wide association studies are based on single-marker analysis. Intuitively, joint consideration of multiple markers should be more informative when multiple genes and their interactions are involved in disease etiology. For example, an exhaustive search among models involving multiple markers and their interactions can identify certain gene–gene interactions that will be missed by single-marker analysis. However, an exhaustive search is difficult, or even impossible, to perform because of the computational requirements. Moreover, searching more models does not necessarily increase statistical power, because there may be an increased chance of finding false positive results when more models are explored. For power comparisons of different model selection methods, the published studies have relied on limited simulations due to the highly computationally intensive nature of such simulation studies. To enable researchers to compare different model search strategies without resorting to extensive simulations, we develop a novel analytical approach to evaluating the statistical power of these methods. Our results offer insights into how different parameters in a genetic model affect the statistical power of a given model selection strategy. We developed an R package to implement our results. This package can be used by researchers to compare and select an effective approach to detecting SNPs.
doi:10.1371/journal.pgen.1000582
PMCID: PMC2712761  PMID: 19649321
BMC Bioinformatics  2012;13:239.
Background
Performing high throughput sequencing on samples pooled from different individuals is a strategy to characterize genetic variability at a small fraction of the cost required for individual sequencing. In certain circumstances some variability estimators have even lower variance than those obtained with individual sequencing. SNP calling and estimating the frequency of the minor allele from pooled samples, though, is a subtle exercise for at least three reasons. First, sequencing errors may have a much larger relevance than in individual SNP calling: while their impact in individual sequencing can be reduced by setting a restriction on a minimum number of reads per allele, this would have a strong and undesired effect in pools because it is unlikely that alleles at low frequency in the pool will be read many times. Second, the prior allele frequency for heterozygous sites in individuals is usually 0.5 (assuming one is not analyzing sequences coming from, e.g. cancer tissues), but this is not true in pools: in fact, under the standard neutral model, singletons (i.e. alleles of minimum frequency) are the most common class of variants because P(f) ∝ 1/f and they occur more often as the sample size increases. Third, an allele appearing only once in the reads from a pool does not necessarily correspond to a singleton in the set of individuals making up the pool, and vice versa, there can be more than one read – or, more likely, none – from a true singleton.
Results
To improve upon existing theory and software packages, we have developed a Bayesian approach for minor allele frequency (MAF) computation and SNP calling in pools (and implemented it in a program called snape): the approach takes into account sequencing errors and allows users to choose different priors. We also set up a pipeline which can simulate the coalescence process giving rise to the SNPs, the pooling procedure and the sequencing. We used it to compare the performance of snape to that of other packages.
Conclusions
We present a software which helps in calling SNPs in pooled samples: it has good power while retaining a low false discovery rate (FDR). The method also provides the posterior probability that a SNP is segregating and the full posterior distribution of f for every SNP. In order to test the behaviour of our software, we generated (through simulated coalescence) artificial genomes and computed the effect of a pooled sequencing protocol, followed by SNP calling. In this setting, snape has better power and False Discovery Rate (FDR) than the comparable packages samtools, PoPoolation, Varscan : for N = 50 chromosomes, snape has power ≈ 35%and FDR ≈ 2.5%. snape is available at http://code.google.com/p/snape-pooled/ (source code and precompiled binaries).
doi:10.1186/1471-2105-13-239
PMCID: PMC3475117  PMID: 22992255
Human Heredity  2009;69(1):14-27.
In case-control studies identifying disease susceptibility loci, it has been shown that the interaction caused by multiple single nucleotide polymorphisms (SNPs) within a gene as well as by SNPs at unlinked genes plays an important role in influencing risk of a disease. A novel statistical approach is proposed to detect gene-gene interactions at the allelic level contributing to a disease trait. With a new allelic score inferred from the observed genotypes at two or more unlinked SNPs, we derive a score test from logistic regression and test for association of the allelic scores with a disease trait. Furthermore, F and likelihood ratio tests are derived from Cochran-Armitage regression. By testing for the association, the interaction can be assessed both in cases where the SNP association can be detected and cannot be detected as a main effect in single SNP approach. The analytical power and type I error rates over 6 two-way interaction models are investigated based on the non-centrality parameter approximation of the score test. Simulation studies demonstrate that (1) the power of the score test is asymptotically equivalent to that of the test statistics by the Cochran-Armitage method and (2) the allelic based method provides higher power than two genotypic based methods.
doi:10.1159/000243150
PMCID: PMC2880732  PMID: 19797905
Allelic test; Interaction effect; Score test; Cochran-Armitage method; Epistasis
PLoS Genetics  2009;5(5):e1000477.
Genome-wide association studies are revolutionizing the search for the genes underlying human complex diseases. The main decisions to be made at the design stage of these studies are the choice of the commercial genotyping chip to be used and the numbers of case and control samples to be genotyped. The most common method of comparing different chips is using a measure of coverage, but this fails to properly account for the effects of sample size, the genetic model of the disease, and linkage disequilibrium between SNPs. In this paper, we argue that the statistical power to detect a causative variant should be the major criterion in study design. Because of the complicated pattern of linkage disequilibrium (LD) in the human genome, power cannot be calculated analytically and must instead be assessed by simulation. We describe in detail a method of simulating case-control samples at a set of linked SNPs that replicates the patterns of LD in human populations, and we used it to assess power for a comprehensive set of available genotyping chips. Our results allow us to compare the performance of the chips to detect variants with different effect sizes and allele frequencies, look at how power changes with sample size in different populations or when using multi-marker tags and genotype imputation approaches, and how performance compares to a hypothetical chip that contains every SNP in HapMap. A main conclusion of this study is that marked differences in genome coverage may not translate into appreciable differences in power and that, when taking budgetary considerations into account, the most powerful design may not always correspond to the chip with the highest coverage. We also show that genotype imputation can be used to boost the power of many chips up to the level obtained from a hypothetical “complete” chip containing all the SNPs in HapMap. Our results have been encapsulated into an R software package that allows users to design future association studies and our methods provide a framework with which new chip sets can be evaluated.
Author Summary
Genome-wide association studies are a powerful and now widely-used method for finding genetic variants that increase the risk of developing particular diseases. These studies are complex and must be planned carefully in order to maximize the probability of finding novel associations. The main design choices to be made relate to sample sizes and choice of commercially available genotyping chip and are often constrained by cost, which can currently be as much as several million dollars. No comprehensive comparisons of chips based on their power for different sample sizes or for fixed study cost are currently available. We describe in detail a method for simulating large genome-wide association samples that accounts for the complex correlations between SNPs due to LD, and we used this method to assess the power of current genotyping chips. Our results highlight the differences between the chips under a range of plausible scenarios, and we demonstrate how our results can be used to design a study with a budget constraint. We also show how genotype imputation can be used to boost the power of each chip and that this method decreases the differences between the chips. Our simulation method and software for comparing power are being made available so that future association studies can be designed in a principled fashion.
doi:10.1371/journal.pgen.1000477
PMCID: PMC2688469  PMID: 19492015
BMC Bioinformatics  2011;12:331.
Background
SNP genotyping arrays have been developed to characterize single-nucleotide polymorphisms (SNPs) and DNA copy number variations (CNVs). Nonparametric and model-based statistical algorithms have been developed to detect CNVs from SNP data using the marker intensities. However, these algorithms lack specificity to detect small CNVs owing to the high false positive rate when calling CNVs based on the intensity values. Therefore, the resulting association tests lack power even if the CNVs affecting disease risk are common. An alternative procedure called PennCNV uses information from both the marker intensities as well as the genotypes and therefore has increased sensitivity.
Results
By using the hidden Markov model (HMM) implemented in PennCNV to derive the probabilities of different copy number states which we subsequently used in a logistic regression model, we developed a new genome-wide algorithm to detect CNV associations with diseases. We compared this new method with association test applied to the most probable copy number state for each individual that is provided by PennCNV after it performs an initial HMM analysis followed by application of the Viterbi algorithm, which removes information about copy number probabilities. In one of our simulation studies, we showed that for large CNVs (number of SNPs ≥ 10), the association tests based on PennCNV calls gave more significant results, but the new algorithm retained high power. For small CNVs (number of SNPs <10), the logistic algorithm provided smaller average p-values (e.g., p = 7.54e - 17 when relative risk RR = 3.0) in all the scenarios and could capture signals that PennCNV did not (e.g., p = 0.020 when RR = 3.0). From a second set of simulations, we showed that the new algorithm is more powerful in detecting disease associations with small CNVs (number of SNPs ranging from 3 to 5) under different penetrance models (e.g., when RR = 3.0, for relatively weak signals, power = 0.8030 comparing to 0.2879 obtained from the association tests based on PennCNV calls). The new method was implemented in software GWCNV. It is freely available at http://gwcnv.sourceforge.net, distributed under a GPL license.
Conclusions
We conclude that the new algorithm is more sensitive and can be more powerful in detecting CNV associations with diseases than the existing HMM algorithm, especially when the CNV association signal is weak and a limited number of SNPs are located in the CNV.
doi:10.1186/1471-2105-12-331
PMCID: PMC3173460  PMID: 21827692
Gene–gene interactions have an important role in complex human diseases. Detection of gene–gene interactions has long been a challenge due to their complexity. The standard method aiming at detecting SNP–SNP interactions may be inadequate as it does not model linkage disequilibrium (LD) among SNPs in each gene and may lose power due to a large number of comparisons. To improve power, we propose a principal component (PC)-based framework for gene-based interaction analysis. We analytically derive the optimal weight for both quantitative and binary traits based on pairwise LD information. We then use PCs to summarize the information in each gene and test for interactions between the PCs. We further extend this gene-based interaction analysis procedure to allow the use of imputation dosage scores obtained from a popular imputation software package, MACH, which incorporates multilocus LD information. To evaluate the performance of the gene-based interaction tests, we conducted extensive simulations under various settings. We demonstrate that gene-based interaction tests are more powerful than SNP-based tests when more than two variants interact with each other; moreover, tests that incorporate external LD information are generally more powerful than those that use genotyped markers only. We also apply the proposed gene-based interaction tests to a candidate gene study on high-density lipoprotein. As our method operates at the gene level, it can be applied to a genome-wide association setting and used as a screening tool to detect gene–gene interactions.
doi:10.1038/ejhg.2010.164
PMCID: PMC3025792  PMID: 20924406
gene–gene interaction; linkage disequilibrium; imputation
BMC Genomics  2013;14(Suppl 3):S10.
Background
It has been hypothesized that multivariate analysis and systematic detection of epistatic interactions between explanatory genotyping variables may help resolve the problem of "missing heritability" currently observed in genome-wide association studies (GWAS). However, even the simplest bivariate analysis is still held back by significant statistical and computational challenges that are often addressed by reducing the set of analysed markers. Theoretically, it has been shown that combinations of loci may exist that show weak or no effects individually, but show significant (even complete) explanatory power over phenotype when combined. Reducing the set of analysed SNPs before bivariate analysis could easily omit such critical loci.
Results
We have developed an exhaustive bivariate GWAS analysis methodology that yields a manageable subset of candidate marker pairs for subsequent analysis using other, often more computationally expensive techniques. Our model-free filtering approach is based on classification using ROC curve analysis, an alternative to much slower regression-based modelling techniques. Exhaustive analysis of studies containing approximately 450,000 SNPs and 5,000 samples requires only 2 hours using a desktop CPU or 13 minutes using a GPU (Graphics Processing Unit). We validate our methodology with analysis of simulated datasets as well as the seven Wellcome Trust Case-Control Consortium datasets that represent a wide range of real life GWAS challenges. We have identified SNP pairs that have considerably stronger association with disease than their individual component SNPs that often show negligible effect univariately. When compared against previously reported results in the literature, our methods re-detect most significant SNP-pairs and additionally detect many pairs absent from the literature that show strong association with disease. The high overlap suggests that our fast analysis could substitute for some slower alternatives.
Conclusions
We demonstrate that the proposed methodology is robust, fast and capable of exhaustive search for epistatic interactions using a standard desktop computer. First, our implementation is significantly faster than timings for comparable algorithms reported in the literature, especially as our method allows simultaneous use of multiple statistical filters with low computing time overhead. Second, for some diseases, we have identified hundreds of SNP pairs that pass formal multiple test (Bonferroni) correction and could form a rich source of hypotheses for follow-up analysis.
Availability
A web-based version of the software used for this analysis is available at http://bioinformatics.research.nicta.com.au/gwis.
doi:10.1186/1471-2164-14-S3-S10
PMCID: PMC3665501  PMID: 23819779
PLoS ONE  2013;8(7):e69321.
Gene-gene interactions may play an important role in the genetics of a complex disease. Detection and characterization of gene-gene interactions is a challenging issue that has stimulated the development of various statistical methods to address it. In this study, we introduce a method to measure gene interactions using entropy-based statistics from a contingency table of trait and genotype combinations. We also developed an exploration procedure by using graphs. We propose a standardized relative information gain (RIG) measure to evaluate the interactions between single nucleotide polymorphism (SNP) combinations. To identify the kth order interactions, contingency tables of trait and genotype combinations of k SNPs are constructed, with which RIGs are calculated. The RIGs are standardized using the mean and standard deviation from the permuted datasets. SNP combinations yielding high standardized RIG are chosen for gene-gene interactions. Detection of high-order interactions and comparison of interaction strengths between different orders are made possible by using standardized RIG. We have applied the proposed standardized entropy-based method to two types of data sets from a simulation study and a real genetic association study. We have compared our method and the multifactor dimensionality reduction (MDR) method through power analysis of eight different genetic models with varying penetrance rates, number of SNPs, and sample sizes. Our method shows successful identification of genetic associations and gene-gene interactions both in simulation and real genetic data. Simulation results suggest that the proposed entropy-based method is better able to detect high-order interactions and is superior to the MDR method in most cases. The proposed method is well suited for detecting interactions without main effects as well as for models including main effects.
doi:10.1371/journal.pone.0069321
PMCID: PMC3715501  PMID: 23874943
BMC Genetics  2014;15:3.
Background
Association mapping studies offer great promise to identify polymorphisms associated with phenotypes and for understanding the genetic basis of quantitative trait variation. To date, almost all association mapping studies based on structured plant populations examined the main effects of genetic factors on the trait but did not deal with interactions between genetic factors and environment. In this paper, we propose a methodological prospect of mixed linear models to analyze genotype by environment interaction effects using association mapping designs. First, we simulated datasets to assess the power of linear mixed models to detect interaction effects. This simulation was based on two association panels composed of 90 inbreds (pearl millet) and 277 inbreds (maize).
Results
Based on the simulation approach, we reported the impact of effect size, environmental variation, allele frequency, trait heritability, and sample size on the power to detect the main effects of genetic loci and diverse effect of interactions implying these loci. Interaction effects specified in the model included SNP by environment interaction, ancestry by environment interaction, SNP by ancestry interaction and three way interactions. The method was finally used on real datasets from field experiments conducted on the two considered panels. We showed two types of interactions effects contributing to genotype by environment interactions in maize: SNP by environment interaction and ancestry by environment interaction. This last interaction suggests differential response at the population level in function of the environment.
Conclusions
Our results suggested the suitability of mixed models for the detection of diverse interaction effects. The need of samples larger than that commonly used in current plant association studies is strongly emphasized to ensure rigorous model selection and powerful interaction assessment. The use of ancestry interaction component brought valuable information complementary to other available approaches.
doi:10.1186/1471-2156-15-3
PMCID: PMC3901036  PMID: 24393630
Association study; G × E; Power simulation; Model selection; REML; PHYC; Vgt1
PLoS ONE  2012;7(1):e29594.
Identifying gene-gene interactions or gene-environment interactions in studies of human complex diseases remains a big challenge in genetic epidemiology. An additional challenge, often forgotten, is to account for important lower-order genetic effects. These may hamper the identification of genuine epistasis. If lower-order genetic effects contribute to the genetic variance of a trait, identified statistical interactions may simply be due to a signal boost of these effects. In this study, we restrict attention to quantitative traits and bi-allelic SNPs as genetic markers. Moreover, our interaction study focuses on 2-way SNP-SNP interactions. Via simulations, we assess the performance of different corrective measures for lower-order genetic effects in Model-Based Multifactor Dimensionality Reduction epistasis detection, using additive and co-dominant coding schemes. Performance is evaluated in terms of power and familywise error rate. Our simulations indicate that empirical power estimates are reduced with correction of lower-order effects, likewise familywise error rates. Easy-to-use automatic SNP selection procedures, SNP selection based on “top” findings, or SNP selection based on p-value criterion for interesting main effects result in reduced power but also almost zero false positive rates. Always accounting for main effects in the SNP-SNP pair under investigation during Model-Based Multifactor Dimensionality Reduction analysis adequately controls false positive epistasis findings. This is particularly true when adopting a co-dominant corrective coding scheme. In conclusion, automatic search procedures to identify lower-order effects to correct for during epistasis screening should be avoided. The same is true for procedures that adjust for lower-order effects prior to Model-Based Multifactor Dimensionality Reduction and involve using residuals as the new trait. We advocate using “on-the-fly” lower-order effects adjusting when screening for SNP-SNP interactions using Model-Based Multifactor Dimensionality Reduction analysis.
doi:10.1371/journal.pone.0029594
PMCID: PMC3252336  PMID: 22242176
Association study (especially the genome-wide association study) now has a key function in identification and characterization of disease-predisposing genetic variant(s), which customarily involve multiple single nucleotide polymorphisms (SNPs) in a candidate region or across the genome. Case–control association design remains the most popular and a challenging issue in the statistical analysis is the optimal use of all information contained in these SNPs. Previous approaches often treated gene–gene interaction as deviation from additive genetic effects or replaced it with SNP–SNP interaction. However, these approaches are limited for their failure of consideration of gene–gene interaction or gene–gene co-association at gene level. Although the co-association of the SNPs within a candidate gene can be detected by principal component analysis-based logistic regression model, the detection of co-association between genes in genome remains uncertain. Here, we proposed a canonical correlation-based U statistic (CCU) for detecting gene-based gene–gene co-association in the case–control design. We explored its type I error rates and power through simulation and analyzed two real data sets. By treating gene as a functional unit in analysis, we found that CCU was a strong alternative to previous approaches. We discussed the performance of CCU as a gene-based gene–gene co-association statistic and the prospect of further improvement.
doi:10.1038/ejhg.2009.223
PMCID: PMC2987308  PMID: 20029457
gene-based; gene–gene co-association; canonical correlation
BMC Genetics  2004;5:32.
Background
Genome-wide association studies for complex diseases will produce genotypes on hundreds of thousands of single nucleotide polymorphisms (SNPs). A logical first approach to dealing with massive numbers of SNPs is to use some test to screen the SNPs, retaining only those that meet some criterion for futher study. For example, SNPs can be ranked by p-value, and those with the lowest p-values retained. When SNPs have large interaction effects but small marginal effects in a population, they are unlikely to be retained when univariate tests are used for screening. However, model-based screens that pre-specify interactions are impractical for data sets with thousands of SNPs. Random forest analysis is an alternative method that produces a single measure of importance for each predictor variable that takes into account interactions among variables without requiring model specification. Interactions increase the importance for the individual interacting variables, making them more likely to be given high importance relative to other variables. We test the performance of random forests as a screening procedure to identify small numbers of risk-associated SNPs from among large numbers of unassociated SNPs using complex disease models with up to 32 loci, incorporating both genetic heterogeneity and multi-locus interaction.
Results
Keeping other factors constant, if risk SNPs interact, the random forest importance measure significantly outperforms the Fisher Exact test as a screening tool. As the number of interacting SNPs increases, the improvement in performance of random forest analysis relative to Fisher Exact test for screening also increases. Random forests perform similarly to the univariate Fisher Exact test as a screening tool when SNPs in the analysis do not interact.
Conclusions
In the context of large-scale genetic association studies where unknown interactions exist among true risk-associated SNPs or SNPs and environmental covariates, screening SNPs using random forest analyses can significantly reduce the number of SNPs that need to be retained for further study compared to standard univariate screening methods.
doi:10.1186/1471-2156-5-32
PMCID: PMC545646  PMID: 15588316
PLoS Genetics  2008;4(9):e1000197.
For genome-wide association studies in family-based designs, we propose a powerful two-stage testing strategy that can be applied in situations in which parent-offspring trio data are available and all offspring are affected with the trait or disease under study. In the first step of the testing strategy, we construct estimators of genetic effect size in the completely ascertained sample of affected offspring and their parents that are statistically independent of the family-based association/transmission disequilibrium tests (FBATs/TDTs) that are calculated in the second step of the testing strategy. For each marker, the genetic effect is estimated (without requiring an estimate of the SNP allele frequency) and the conditional power of the corresponding FBAT/TDT is computed. Based on the power estimates, a weighted Bonferroni procedure assigns an individually adjusted significance level to each SNP. In the second stage, the SNPs are tested with the FBAT/TDT statistic at the individually adjusted significance levels. Using simulation studies for scenarios with up to 1,000,000 SNPs, varying allele frequencies and genetic effect sizes, the power of the strategy is compared with standard methodology (e.g., FBATs/TDTs with Bonferroni correction). In all considered situations, the proposed testing strategy demonstrates substantial power increases over the standard approach, even when the true genetic model is unknown and must be selected based on the conditional power estimates. The practical relevance of our methodology is illustrated by an application to a genome-wide association study for childhood asthma, in which we detect two markers meeting genome-wide significance that would not have been detected using standard methodology.
Author Summary
The current state of genotyping technology has enabled researchers to conduct genome-wide association studies of up to 1,000,000 SNPs, allowing for systematic scanning of the genome for variants that might influence the development and progression of complex diseases. One of the largest obstacles to the successful detection of such variants is the multiple comparisons/testing problem in the genetic association analysis. For family-based designs in which all offspring are affected with the disease/trait under study, we developed a methodology that addresses this problem by partitioning the family-based data into two statistically independent components. The first component is used to screen the data and determine the most promising SNPs. The second component is used to test the SNPs for association, where information from the screening is used to weight the SNPs during testing. This methodology is more powerful than standard procedures for multiple comparisons adjustment (i.e., Bonferroni correction). Additionally, as only one data set is required for screening and testing, our testing strategy is less susceptible to study heterogeneity. Finally, as many family-based studies collect data only from affected offspring, this method addresses a major limitation of previous methodologies for multiple comparisons in family-based designs, which require variation in the disease/trait among offspring.
doi:10.1371/journal.pgen.1000197
PMCID: PMC2529406  PMID: 18802462
PLoS Genetics  2008;4(6):e1000109.
To facilitate whole-genome association studies (WGAS), several high-density SNP genotyping arrays have been developed. Genetic coverage and statistical power are the primary benchmark metrics in evaluating the performance of SNP arrays. Ideally, such evaluations would be done on a SNP set and a cohort of individuals that are both independently sampled from the original SNPs and individuals used in developing the arrays. Without utilization of an independent test set, previous estimates of genetic coverage and statistical power may be subject to an overfitting bias. Additionally, the SNP arrays' statistical power in WGAS has not been systematically assessed on real traits. One robust setting for doing so is to evaluate statistical power on thousands of traits measured from a single set of individuals. In this study, 359 newly sampled Americans of European descent were genotyped using both Affymetrix 500K (Affx500K) and Illumina 650Y (Ilmn650K) SNP arrays. From these data, we were able to obtain estimates of genetic coverage, which are robust to overfitting, by constructing an independent test set from among these genotypes and individuals. Furthermore, we collected liver tissue RNA from the participants and profiled these samples on a comprehensive gene expression microarray. The RNA levels were used as a large-scale set of quantitative traits to calibrate the relative statistical power of the commercial arrays. Our genetic coverage estimates are lower than previous reports, providing evidence that previous estimates may be inflated due to overfitting. The Ilmn650K platform showed reasonable power (50% or greater) to detect SNPs associated with quantitative traits when the signal-to-noise ratio (SNR) is greater than or equal to 0.5 and the causal SNP's minor allele frequency (MAF) is greater than or equal to 20% (N = 359). In testing each of the more than 40,000 gene expression traits for association to each of the SNPs on the Ilmn650K and Affx500K arrays, we found that the Ilmn650K yielded 15% times more discoveries than the Affx500K at the same false discovery rate (FDR) level.
Author Summary
Advances in SNP genotyping array technologies have made whole-genome association studies (WGAS) a readily available approach. Genetic coverage and the statistical power are two key properties to evaluate on the arrays. In this study, 359 newly sampled individuals were genotyped using Affymetrix 500K and Illumina 650Y SNP arrays. From these data, we obtained new estimates of genetic coverage by constructing a test set from among these genotypes and individuals that is independent from the SNPs and individuals used to construct the arrays. These estimates are notably smaller than previous ones, which we argue is due to an overfitting bias in previous studies. We also collected liver tissue RNA from the participants and profiled these samples on a comprehensive gene expression microarray. The RNA levels were used as a large-scale set of quantitative traits to calibrate the relative statistical power of the commercial arrays. Through this dataset and simulations, we find that the SNP arrays provide adequate power to detect quantitative trait loci when the causal SNP's minor allele frequency is greater than 20%, but low power is less than 10%. Importantly, we provide evidence that sample size has a greater impact on the power of WGAS than SNP density or genetic coverage.
doi:10.1371/journal.pgen.1000109
PMCID: PMC2432039  PMID: 18584036
BMC Bioinformatics  2014;15:102.
Backgroud
Taking the advan tage of high-throughput single nucleotide polymorphism (SNP) genotyping technology, large genome-wide association studies (GWASs) have been considered to hold promise for unravelling complex relationships between genotype and phenotype. At present, traditional single-locus-based methods are insufficient to detect interactions consisting of multiple-locus, which are broadly existing in complex traits. In addition, statistic tests for high order epistatic interactions with more than 2 SNPs propose computational and analytical challenges because the computation increases exponentially as the cardinality of SNPs combinations gets larger.
Results
In this paper, we provide a simple, fast and powerful method using dynamic clustering and cloud computing to detect genome-wide multi-locus epistatic interactions. We have constructed systematic experiments to compare powers performance against some recently proposed algorithms, including TEAM, SNPRuler, EDCF and BOOST. Furthermore, we have applied our method on two real GWAS datasets, Age-related macular degeneration (AMD) and Rheumatoid arthritis (RA) datasets, where we find some novel potential disease-related genetic factors which are not shown up in detections of 2-loci epistatic interactions.
Conclusions
Experimental results on simulated data demonstrate that our method is more powerful than some recently proposed methods on both two- and three-locus disease models. Our method has discovered many novel high-order associations that are significantly enriched in cases from two real GWAS datasets. Moreover, the running time of the cloud implementation for our method on AMD dataset and RA dataset are roughly 2 hours and 50 hours on a cluster with forty small virtual machines for detecting two-locus interactions, respectively. Therefore, we believe that our method is suitable and effective for the full-scale analysis of multiple-locus epistatic interactions in GWAS.
doi:10.1186/1471-2105-15-102
PMCID: PMC4021249  PMID: 24717145
Cloud computing; Genome-wide association studies; Dynamic clustering
Biostatistics (Oxford, England)  2013;14(4):667-681.
We consider in this paper testing for interactions between a genetic marker set and an environmental variable. A common practice in studying gene–environment (GE) interactions is to analyze one single-nucleotide polymorphism (SNP) at a time. It is of significant interest to analyze SNPs in a biologically defined set simultaneously, e.g. gene or pathway. In this paper, we first show that if the main effects of multiple SNPs in a set are associated with a disease/trait, the classical single SNP–GE interaction analysis can be biased. We derive the asymptotic bias and study the conditions under which the classical single SNP–GE interaction analysis is unbiased. We further show that, the simple minimum p-value-based SNP-set GE analysis, can be biased and have an inflated Type 1 error rate. To overcome these difficulties, we propose a computationally efficient and powerful gene–environment set association test (GESAT) in generalized linear models. Our method tests for SNP-set by environment interactions using a variance component test, and estimates the main SNP effects under the null hypothesis using ridge regression. We evaluate the performance of GESAT using simulation studies, and apply GESAT to data from the Harvard lung cancer genetic study to investigate GE interactions between the SNPs in the 15q24–25.1 region and smoking on lung cancer risk.
doi:10.1093/biostatistics/kxt006
PMCID: PMC3769996  PMID: 23462021
Asymptotic bias analysis; Gene–environment interactions; Genome-wide association studies; Score statistic; Single-nucleotide polymorphism; Variance component test
BMC Proceedings  2009;3(Suppl 7):S77.
Knowledge of simulated genetic effects facilitates interpretation of methodological studies. Genetic interactions for common disorders are likely numerous and weak. Using the 200 replicates of the Genetic Analysis Workshop 16 (GAW16) Problem 3 simulated data, we compared the statistical power to detect weak gene-gene interactions using a haplotype-based test in the UNPHASED software with genotypic mixed model (GMM) and additive mixed model (AMM) mixed linear regression model in SAS. We assumed a candidate-gene approach where a single-nucleotide polymorphism (SNP) in one gene is fixed and multiple SNPs are at the second gene. We analyzed the quantitative low-density lipoprotein trait (heritability 0.7%), modulated by simulated interaction of rs4648068 from 4q24 and another gene on 8p22, where we analyzed seven SNPs. We generally observed low power calculated per SNP (≤ 37% at the 0.05 level), with the haplotype-based test being inferior. Over all tests, the haplotype-based test performed within chance, while GMM and AMM had low power (~10%). The haplotype-based and mixed models detected signals at different SNPs. The haplotype-based test detected a signal in 50 unique replicates; GMM and AMM featured both shared and distinct SNPs and replicates (65 replicates shared, 41 GMM, 27 AMM). Overall, the statistical signal for the weak gene-gene interaction appears sensitive to the sample structure of the replicates. We conclude that using more than one statistical approach may increase power to detect such signals in studies with limited number of loci such as replications. There were no results significant at the conservative 10-7 genome-wide level.
PMCID: PMC2795979  PMID: 20018072
Genetic epidemiology  2009;33(4):332-343.
Recent studies have shown that quantitative phenotypes may be influenced not only by multiple single nucleotide polymorphisms (SNPs) within a gene but also by the interaction between SNPs at unlinked genes. We propose a new statistical approach that can detect gene-gene interactions at the allelic level which contribute to the phenotypic variation in a quantitative trait. By testing for the association of allelic combinations at multiple unlinked loci with a quantitative trait, we can detect the SNP allelic interaction whether or not it can be detected as a main effect. Our proposed method assigns a score to unrelated subjects according to their allelic combination inferred from observed genotypes at two or more unlinked SNPs, and then tests for the association of the allelic score with a quantitative trait. To investigate the statistical properties of the proposed method, we performed a simulation study to estimate type I error rates and power and demonstrated that this allelic approach achieves greater power than the more commonly used genotypic approach to test for gene-gene interaction. As an example, the proposed method was applied to data obtained as part of a candidate gene study of sodium retention by the kidney. We found that this method detects an interaction between the calcium-sensing receptor gene (CaSR), the chloride channel gene (CLCNKB) and the Na, K, 2Cl cotransporter gene (CLC12A1) that contributes to variation in diastolic blood pressure.
doi:10.1002/gepi.20385
PMCID: PMC2825760  PMID: 19058262
quantitative trait loci; allelic test; interaction effect; blood pressure
Frontiers in Genetics  2012;3:176.
Genome-wide association studies (GWAS) have identified numerous associations between genetic loci and individual phenotypes; however, relatively few GWAS have attempted to detect pleiotropic associations, in which loci are simultaneously associated with multiple distinct phenotypes. We show that pleiotropic associations can be directly modeled via the construction of simple Bayesian networks, and that these models can be applied to produce single or ensembles of Bayesian classifiers that leverage pleiotropy to improve genetic risk prediction. The proposed method includes two phases: (1) Bayesian model comparison, to identify Single-Nucleotide Polymorphisms (SNPs) associated with one or more traits; and (2) cross-validation feature selection, in which a final set of SNPs is selected to optimize prediction. To demonstrate the capabilities and limitations of the method, a total of 1600 case-control GWAS datasets with two dichotomous phenotypes were simulated under 16 scenarios, varying the association strengths of causal SNPs, the size of the discovery sets, the balance between cases and controls, and the number of pleiotropic causal SNPs. Across the 16 scenarios, prediction accuracy varied from 90 to 50%. In the 14 scenarios that included pleiotropically associated SNPs, the pleiotropic model search and prediction methods consistently outperformed the naive model search and prediction. In the two scenarios in which there were no true pleiotropic SNPs, the differences between the pleiotropic and naive model searches were minimal. To further evaluate the method on real data, a discovery set of 1071 sickle cell disease (SCD) patients was used to search for pleiotropic associations between cerebral vascular accidents and fetal hemoglobin level. Classification was performed on a smaller validation set of 352 SCD patients, and showed that the inclusion of pleiotropic SNPs may slightly improve prediction, although the difference was not statistically significant. The proposed method is robust, computationally efficient, and provides a powerful new approach for detecting and modeling pleiotropic disease loci.
doi:10.3389/fgene.2012.00176
PMCID: PMC3438684  PMID: 22973300
pleiotropy; SNP; GWAS; prediction; Bayesian

Results 1-25 (1557339)