Risk score modeling of multiple gene to gene interactions using aggregated-multifactor dimensionality reduction

Human diseases usually have complex inheritance patterns, and single nucleotide polymorphisms (SNPs) has been utilized to explain the variation in susceptibility to many common complex diseases as well as the response to drug therapy. The advancement of genotyping technology has made genotypic data readily accessible to investigators at low cost. However, many challenges remain with regard to identifying genes that render people susceptible to non-Mendelian disorders and in understanding the associations and functional relationships among genes. More and more, researchers have been advocating for advanced statistical analysis to quantify complex and interactive biological and genetic relationships[1, 2].

Multifactor Dimensionality Reduction (MDR) is a statistical paradigm for characterizing and detecting nonlinear complex gene-to-gene interactions (epistasis) possibly associated with susceptibility to disease[3]. When numerous genes are involved in a complex canonical pathway or network, traditional approaches for data analysis, such as a Chi-square test or Fisher’s exact test, might not detect the associations between risk factors and outcomes since these approaches assess only marginal main effects of the identified risk factors. Although one can employ logistic regression or other standard multivariate categorical data analysis approaches to explore interactions among SNPs, there are an enormous number of possible interactions in a model with both linear and nonlinear effects. Consequently, standard multivariate categorical data analysis approaches might detect very few interactions, and even then the cost in terms of sample size might be immense. MDR addresses these difficulties by converting high-dimensional genotypic data into a single predictive variable. Genotypic combinations are used to define high risk and low risk strata for the one-dimensional predisposing risk factor. MDR can reveal non-linear epistasis at a moderate sample size with no requirements on the underlying distributions of genotypes or outcomes[4].

The most commonly used MDR approach is described in detail by Ritchie et al.[3]. To distinguish this method from its various extensions, we will refer to it as the original MDR method. Related statistical software has been developed by Hahn et al.[4], Bush et al.[5], Winham and Motsinger-Reif[6], and Moore and colleagues (http://www.epistasis.org). In general, the MDR process can also be combined with a filter preprocess step by first applying global testing and filtration techniques to select the optimal number of SNPs for MDR analysis by searching for a subset of genes likely to interact with other genes using the ReliefF filtering process[7, 8].

Details of the MDR[3] are briefly described here. MDR performs an exhaustive search of all variables and variable combinations to identify univariate or multivariate disease risk models. For each locus or multi-locus combination, attribute construction is performed to make a single variable with two categories: high risk and low-risk. A genotype or combination of genotypes is assigned high risk status if the ratio of affected subjects to unaffected subjects exceeds a pre-determined threshold, and low-risk otherwise. This step consolidates the high-dimensional risk space into a one-dimensional predictive variable. Typically, a 5-fold or 10- fold cross-validation procedure is employed, beginning with the random division of the original data set into five or ten subsets of approximately equal sizes[9]. For 10-fold cross-validation, a model is fit using nine of the ten subsets (collectively referred to as training data), and then the model is applied to classify observations in both the training data and the tenth subset not used to fit the model (referred to as validation data). This entire process is repeated ten times, with one of the ten subsets acting as the validation data[10]. The model’s training accuracy and testing accuracy are defined as the percentage of correct classifications in the corresponding data sets. The optimal one-locus, two-locus, and three-locus MDR models with the highest testing accuracy are identified. A one-locus model estimates the main effect of each SNP, while multi-locus models investigate the interactions among relevant SNPs. The cross validation consistency (CVC) is the number of times in a 10-fold cross validation that a particular multifactorial combination is identified as an optimal model for the training data. Finally, statistical significance of the optimal models is assessed by 1000- or 10000-count permutation testing[11].

MDR has been applied to identify gene-gene interactions conferring susceptibility to common diseases, including hypertension[12], bladder cancer[13], Type 2 diabetes[14], and rheumatoid arthritis[15, 16]. Several extensions of the MDR method have been proposed. These methods entail the use of odds ratios[17], log-linear methods[18], generalized linear models[19], methods for data highly imbalanced with the disease outcome[20], model-based methods[21], contingency table measures of classification accuracy[22] and familial data[23, 24].

In the present work, we propose an Aggregated-Multifactor Dimensionality Reduction (A-MDR) method that exhaustively searches for statistically significant gene-gene (GxG) interactions to generate a gene interaction network. In particular, an epistasis enriched risk score replaces the traditional dichotomous predisposing risk factor in quantifying the degree of susceptibility to a disease. We also introduce and compare new GxG interaction measures (pOR, pRR and pChi). An adjustment for multiple comparisons is implemented to limit false positive discoveries. In the current study we introduce the new approach, evaluate its performance in a range of simulations, and apply it to a real dataset from Juvenile Idiopathic Arthritis patients treated with methotrexate (MTX).

To assess the power of the A-MDR method, we randomly generated 100 sets of data in the above described scenarios and performed the MDR and A-MDR tests for each random sample. The power is the percentage of rejection of null hypothesis for the loci with a GxG interaction. Type I error is the percentage of rejection of null hypothesis when the simulated loci have no GxG interaction.

Standard logistic regression analysis did not identify significant main effects from SNPs or GxG interactions. This could primarily due to the complex and non-linear interactions among SNPs. For the rest article, the A-MDR and original MDR methods were applied to the MTX data to search for genetic predictors of response to MTX. Redundant SNPs and SNPs with no prediction of the phenotype were removed by the ReliefF algorithm[7]. A complete set of 34 SNPs and 7 filtered SNPs were analyzed respectively.

The original MDR analysis method was applied to obtain the one-locus, two-locus, and three-locus models with the highest validation accuracy in the original MDR. Two-locus interactions between genes ATIC and MTHFD2 were significant in testing accuracy but not in CVC. The prediction accuracy from the optimal MDR model was 75%.

Another goal of our A-MDR analysis was to integrate numerous significant GxG interactions into a continuous epistasis enriched risk score for the prediction of which patients would have active arthritis despite MTX treatment. A higher epistasis enriched risk score would indicate that a patient carried more high-risk genotypic combinations in loci with significant GxG interactions, and vice versa. To compare prediction accuracies based on the number of candidate SNPs as well as the presence or absence of adjustment for multiple comparisons, we generated epistasis enriched risk scores from 82 significant GxG interactions from 34 SNPs (Figure2B).

Subjects with persistent active arthritis had significantly higher mean and median epistasis enriched risk scores compared to subjects without active arthritis (p < 0.0001). When 82 GxG interactions from 34 SNPs with unadjusted p-values < 0.0167 were used to generate epistasis enriched risk scores (Figure2B boxplot inset), these scores ranged from 0 to 44. A higher risk score suggests that a subject is less likely to respond favorably to MTX treatment. The ROC curve assessing the overall ability of the epistasis enriched risk score to distinguish between subjects with active joints and subjects without active joints had 85% area under the curve (p < 0.0001). (The 0.0167 cutoff for unadjusted p-values was chosen to maximize this area.) We correctly classify 82% of the subjects if we predict that those with epistasis enriched risk scores above 11.5 have active joints and that those with epistasis enriched risk scores below 11.5 do not have persistent joint involvement.

Examination of the five genes in the 15-interaction model presented in Figure2A reveals a testable hypothesis for future studies. All genes fall within a pathway leading to purine biosynthesis and adenosine formation: SLC25A32 transports folates from the cytoplasm to mitochondria; MTHFD2 is a component of the mitochondrial folate pathway that produces one-carbon donors in the form of formate (10-formyl-tetrahydrofolate) exclusively to support de novo purine biosynthesis; and ITPA, ATIC, and GART are involved in purine biosynthesis. Thus, all genes map to a core pathway associated with adenosine accumulation, which is considered to be a mechanism of action of MTX that contributes to response in JIA and Rheumatoid Arthritis.

In this work, we have proposed an Aggregated Multifactor Dimensionality Reduction (A-MDR) model to elucidate complex and non-linear genetic associations contributing to disease risk and variability in response to treatment. The proposed method is innovative in three important ways: 1) a continuous GxG enriched risk score is generated to replace the dichotomous risk factor in prediction of susceptibility to disorders; 2) new measures of gene-gene interaction using pOR, pRR, and pChi along with p-values and confidence intervals are proposed to detect and characterize multiple gene-gene interactions; and, 3) a radial network is generated to depict patterns of epistasis. This approach allows for prediction on not just a single interactive model, which is important given the growing appreciation in human genetics for the accumulative impact of a large number of variants with low effect size[28]. By pooling moderate and inter-related genetic contributors together, the A-MDR model becomes robust and predictive of complex traits. In addition to GxG interactions, the A-MDR can also be applied to model gene-environment interactions where environmental risk factors such as smoking, alcohol consumption, exercise, and diet can be incorporated into multi-factorial models.

The original MDR model selects an optimal multi-factorial (SNP) combination for each two-way, three-way or higher order interaction. When multiple genes function together in a pathway, the original MDR is prone to overlook genes with weaker signals and lose power for selecting one optimal GxG interaction in cross-validation. For the MTX data, the optimal two-locus interaction detected by the original MDR among 7 candidate SNPs was ATIC (rs4673990) + MTHFD2 (rs12196) with testing accuracy of 0.73 (p=0.0005). However, there exist other pairs of interactions with comparable accuracy. As a result, CVC, which measures the percentage of times that an optimal GxG interaction is selected when splitting the training and validation sets randomly, was not significant (CVC=8/10, p=0.2700). Our A-MDR analysis in Table5 identified 15 pairs of two-locus interactions. When multiple GxG interactions with bio-equivalent effects are involved in epistasis, the original MDR will select an optimal model, by chance and lose some of the real pathway-based signals. The recent extended MDR methods, including OR-MDR[17], LM-MDR[18] and G-MDR[19], adopt the same strategy of selecting one optimal GxG interaction as does the original MDR, which means they have the same limitations.

A continuous GxG enriched risk score is another major distinction between A-MDR and all the majority of existing MDR models, in which a binary risk factor is utilized to predict the outcome variable. For M-way interactions, the existing MDR models classify ~3 ^M genotypic combinations as either high-risk or low-risk. A-MDR evolves from the traditional MDR outputs to the predisposing risk scores and epistasis based network as shown in Figure2.

Another important result of the simulation experiments is the potential of A-MDR to detect models that include genetic heterogeneity. Previous work with the original MDR has shown that heterogeneity is disastrous when using MDR to detect interactions[26][29]. Because of the use of the continuous enrichment score, A-MDR is less impacted by heterogeneity in the enclosed simulations. Further evaluation of this initial result with expanded simulations and real data applications will be an important next step.

We explore a radial network (Figure2A) to depict patterns of epistasis. From the systems biology perspective, genetic variants might jointly impact the disease susceptibility and response to treatment. The gene-gene interaction network reveals intriguing information when interpreted in the context of what we know about the folate pathway and the effect that MTX has upon the disruption of this pathway as it relates to arthritis. ATIC and MTHFD2 were the two genes with the strongest interaction, and it is of interest to note that the genes included in the model (Figure2A) include a transporter involved in folate uptake into mitochondria, SLC25A32, and the bifunctional methylenetetrahydrofolate dehydrogenase-cyclohydrolase MTHFD2, a key constituent of the mitochondrial folate pathway. The mitochondrial folate pathway is responsible for the generation of formate (in the form of 10-formylTHF) specifically to support purine biosynthesis, represented by ATIC, GART, and ITPA. The anti-inflammatory effect of low-dose MTX used to treat JIA and RA is thought to be due the anti-inflammatory effects of adenosine, formed as a consequence of the inhibitory effects of MTX on amino-imidazole carboxamide ribonucleotide (AICAR) transformylase (gene name, ATIC), which promotes the accumulation of AICAR ribotide, inhibiting adenosine deaminase and leading to a build up of adenosine, a potent anti-inflammatory agent[30]. A disruption of this process may result in a decreased anti-inflammatory effect of the drug. Therefore, the combined effect of SNPs in ATIC and MTHFD2 may indeed yield a more clinically apparent result by altering the anti-inflammatory effects of methotrexate. There is a potential to apply the proposed method to GWAS study by dissecting SNPs into pathways in order to detect GxG interactions in GWAS pathways. The major computational challenges from the proposed A-MDR and other approach in MDR framework are in the generation of p-values for MDR. MDR permutation computing time is largely dependent on the dimension of data sets. In other words, the computing time increases as the number of SNPs and/or the number of subjects increases. Several works have been devoted to improve the efficiency and shorten the computing time in MDR analysis in high-throughput data[5, 31, 32]. We will defer interested readers to the corresponding citations for computing issues in high-throughput MDR analysis. These computational limitations make our strategy appropriate in large scale candidate gene studies, but may be limited in application to genome-wide association studies until further improvements in computing speed are realized or very large-scale computing resources are available.

In summary, bioinformatics challenges remain in detecting and modeling epistasis in complex biological traits. We have developed a new A-MDR framework to interpret complex genetic variation and have proposed predicting an outcome using a continuous risk factor. Several other extensions and modifications of the original MDR have been proposed in the literature. Incorporation of valuable features from other MDR extension models into the A-MDR framework is worth further investigation. Prospective studies and validation in independent samples are needed to assess reliability of the A-MDR model’s predictive ability. Tools for statistical inference, including asymptotic distributions of the proposed test statistics, need to be developed to save computing time and improve reliability.

Appendix I. Justification, 95% confidence intervals and permutation tests of pOR, pRR and pChi.

Since the predisposing risk factor (Table1) is conditioned on the naïve Bayes classifier, standard inference procedures based on normal or chi-square asymptotic distributions with 1 degree of freedom do not apply to the numerators in (1)-(3), which are the unadjusted odds ratio (OR), relative risk (RR) and Chi-square statistics (Chi). As a result, 95% confidence intervals of OR and RR are often greater than 1 under H₀. To address this issue, we propose pOR, pRR and pChi by taking the null distribution of unadjusted statistics into account. Let x=pOR,pRR, or pChi, F(x) be the cumulative distribution function of the corresponding statistic under the alterative hypothesis (GxG interaction present) F ₀(x),be the cumulative distribution function of the corresponding statistic under the null hypothesis (GxG interaction absent) and F ₀ ^{− 1}(x) be the inverse function of F ₀(x). The corrected pOR, pRR and pChi are then defined by$\frac{x}{F_0^{-1}\left(F\left(x\right)\right)}$. Under H ₀, F(x)=F ₀(x), so pOR, pRR and pChi should equal$\frac{x}{F_0^{-1}\left(F\left(x\right)\right)}=\frac{x}{F_0^{-1}\left(F_0\left(x\right)\right)}=1$. This adjustment will ensure the insignificant GxG interactions to have 95% confidence interactions cross 1 under Under H ₀. In this work, we evaluated pOR, pRR and pChi using a full data set while these methods can also be evaluated under the cross validation scheme typically used in MDR.

The functions F(x) and F ₀(x) can be estimated by the corresponding empirical distribution function. Permutation is applied to estimate F ₀(x) by reshuffling the relationship between SNPs and a phenotype, where SNPs for each individual in a system are maintained as a vector to preserve their correlation structure. For each permutation, we generated odds ratio (OR), relative risk (RR) and chi-square test statistic (Chi). Jackknife re-sampling was applied to estimate F(x) by generating random subsets of data, where 80% to 90% of subjects were randomly selected. SNPs and the phenotype from each subject are maintained as a vector to preserve the association between SNPs and the phenotype. Denote the OR, RR and Chi statistic from permutation or re-sampling as x ₁,x ₂,…x _B where B is the number of permutation or resampling. The null distribution function F ₀(x) and F(x) can be estimated by$B^{-1}{\displaystyle {\sum }_{i=1}^B{I}_{\left\{x_i\le x\right\}}}$. The 95% confidence interval pOR, pRR and pChi can be obtained by resampling. Denote the pOR, pRR and pChi statistics from resampling or permutation as z ₁,z ₂…,z _B then the 95% confidence interval pOR, pRR and pChi is the interval from 2.5 to 97.5 percentile of z ₁,z ₂…,z _B from resampling. The p-value for pOR, pRR and pChi for the i ^th GxG interaction, denoted by Pvalue _i , will be calculated by the permutation testing, i.e.$\mathit{\text{Pvalu}}{e}_i=B^{-1}{\displaystyle {\sum }_{i=1}^B{I}_{\left\{z<z_i\right\}}}$ where z ₁,z ₂…,z _B are calculated from permutation samples and z is the pOR, pRR and pChi statistic calculated from the current data.