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Am J Hum Genet. Nov 2007; 81(5): 927–938.
Published online Oct 3, 2007. doi:  10.1086/521558
PMCID: PMC2265651

Haplotype-Based Association Analysis via Variance-Components Score Test


Haplotypes provide a more informative format of polymorphisms for genetic association analysis than do individual single-nucleotide polymorphisms. However, the practical efficacy of haplotype-based association analysis is challenged by a trade-off between the benefits of modeling abundant variation and the cost of the extra degrees of freedom. To reduce the degrees of freedom, several strategies have been considered in the literature. They include (1) clustering evolutionarily close haplotypes, (2) modeling the level of haplotype sharing, and (3) smoothing haplotype effects by introducing a correlation structure for haplotype effects and studying the variance components (VC) for association. Although the first two strategies enjoy a fair extent of power gain, empirical evidence showed that VC methods may exhibit only similar or less power than the standard haplotype regression method, even in cases of many haplotypes. In this study, we report possible reasons that cause the underpowered phenomenon and show how the power of the VC strategy can be improved. We construct a score test based on the restricted maximum likelihood or the marginal likelihood function of the VC and identify its nontypical limiting distribution. Through simulation, we demonstrate the validity of the test and investigate the power performance of the VC approach and that of the standard haplotype regression approach. With suitable choices for the correlation structure, the proposed method can be directly applied to unphased genotypic data. Our method is applicable to a wide-ranging class of models and is computationally efficient and easy to implement. The broad coverage and the fast and easy implementation of this method make the VC strategy an effective tool for haplotype analysis, even in modern genomewide association studies.

Haplotypes of multiple SNPs are considered a more informative format of polymorphisms for genetic association analysis than single SNPs.1 Haplotypes are more informative because they preserve the joint linkage disequilibrium (LD) structure among multiple adjacent markers.2 Even when only tag SNPs are used, haplotypes serve as a proxy for unobserved SNPs and increase the predictive power for the genomic variation.3,4 However, in terms of practical efficacy, the power of haplotype-based association analysis is challenged by a trade-off between the benefits of modeling abundant variation and the cost of the extra degrees of freedom for modeling the multimarker variations. To avoid the curse of dimensionality encountered in haplotype association analysis, various strategies have been proposed in the literature. They include (1) clustering evolutionarily close haplotypes,58 (2) modeling the level of haplotype sharing instead of the haplotypes themselves,911 and (3) smoothing haplotype effects by introducing a correlation structure for the effects of similar haplotypes.1214 Although these strategies appear to be different, the fundamental principle is to use the evolutionary history of haplotypes to reduce the parameter space from individual haplotypes to haplotypes with similar ancestry. However, although the approaches of haplotype clustering and haplotype sharing enjoy a fair amount of power gain, empirical studies found that the smoothing approach may exhibit only similar or less power than the standard methods that regress trait values on haplotypes and impose no assumptions on haplotypes, even when there are many haplotypes.14

In haplotype smoothing, a dependence structure is introduced to the effects of different haplotypes, according to the similarity between haplotypes, under a Bayesian hierarchical model or a mixed-model framework, and the overall gene-trait association can be studied via the variance components (VC).1214 The idea of correlating haplotype effect is based on the assumption that the present mutation-bearing haplotypes have descended from a small number of ancestral haplotypes, and, as a result, the disease haplotypes tend to be correlated because of this shared ancestry. Without losing generality, in this work, we refer to these methods as “VC” approaches and discuss them under a mixed-model framework. We also refer to the standard haplotype regression method as a “fixed-effect” approach. Schaid14 first noted the underpowered phenomenon of the VC method, using the likelihood-ratio test (LRT), and explored potential reasons based on the noncentrality (NC) parameter of the distribution of the LRT statistics. The NC parameter reflects the distance between the alternative distribution and the null distribution of the test statistics, and the larger the null-to-alternative distance is, the higher the power a test possesses. By expressing the NC parameter as a function of heritability (h2), it can be seen that, although the NC parameter of a fixed-effect model is proportional to equation M1, the NC parameter of a VC model is much smaller (proportional to h4). As a result, the power gain brought by the low degrees of freedom can be compromised with the small NC parameter in a VC-LRT approach.

Here, we report other key factors that contribute to this underpowered phenomenon. In brief, unlike the usual VC model in which the VC represents the potential variability from a source that is independently distributed in the population (e.g., the family effect in the study of linkage or familial aggregation), in the population-based haplotype analysis, the source of variability is not independent. That is, the design matrix of the random haplotype effect does not have a diagonal or block-diagonal structure. Furthermore, the dimension of the random haplotype effect is fixed. Therefore, the data under the alternative hypothesis cannot be represented as a collection of independent data vectors. As a result, the distribution of the LRT statistic does not converge to the conventional 50:50 mixture of χ20 and χ21 (i.e., the limiting distribution predicted by the usual asymptotic theory15). Instead, empirical evidence indicates that the distribution of VC-LRT statistics has higher weighting of χ20. Hence, the threshold value obtained from the 50:50 χ2 mixture is overstringent and causes a too-conservative testing result. Such overconservative findings of the LRT was obtained also by Crainiceanu and Ruppert16 in certain linear mixed models.

To overcome the problem of a lack of independence and also to generalize the VC approach to all types of trait values, we propose a score test under the generalized linear mixed-model (GLMM) framework. Specifically, we construct a score statistic based on the restricted maximum likelihood (REML) or the marginal likelihood function of the VC and identify its nontypical asymptotic distribution. The proposed test is easy to implement and computationally efficient yet is general enough to accommodate a broad class of phenotypes and correlation structures. It allows for covariate information and can be used for phase-unknown genotypic data. Through simulation, we demonstrate the validity of the test and investigate the power performance of the VC approach and the fixed-effect approach under general scenarios. We also apply the proposed method to a case-control data set from a genomewide association study of amyotrophic lateral sclerosis (ALS) conducted by Schymick et al.17 In the analysis, we test for gene-trait association on chromosome 10 with the 275 ALS cases and 271 controls and examine statistical significance at the genomewide level. We verify the findings from the proposed method by comparing them with the results reported by Schymick et al.17

Material and Methods

VC Method for Association Analysis

We denote the data with the following notations. For individual i (i=1,2,…,n), we have trait value Yi, environmental covariates Xi (a K×1 vector including the intercept term), and haplotype Hi (an L×1 vector, where L is the number of distinct haplotypes observed in the population). Vector Hi records individual i’s haplotype pair via a certain scoring rule, such as by setting its hth element as the number of haplotype h that individual i carries. Throughout this article, we treat explanatory variables (e.g., Xi and Hi) as constants and will omit them in the lists of the conditional variables. This means that, for example, we will use Var(Yi) instead of Var(Yi[mid ]Xi,Hi).

Assume that the trait value Yi follows some distribution with conditional mean E(Yi[mid ]β)=μi and conditional variance equation M2, where mi is a known prior weight (e.g., binomial denominator), [var phi] is the dispersion parameter (e.g., measurement-error variance for a normal quantitative trait), and equation M3 is the variance function. Then, the VC model can be expressed under the framework of GLMM as

equation image

where g(·) is a link function that connects the conditional mean μi and the explanatory variables, γK×1 represents the fixed effect of environmental covariates, and βL×1 is the random effect of haplotypes. The haplotype effect is assumed to have a multivariate normal (MN) prior. With model (1), the marginal phenotypic variance, Var(Yi), can be partitioned into genetic components and environment components, and the association between haplotypes and traits can be detected by testing for zero genetic VC (i.e., τ=0). Intuitively, τ=0 implies that all βh share the same value, and this is essentially the null hypothesis of the standard fixed-effect approaches.

The correlation structure of βh is specified through the L×L matrix Rβ. Here, we consider a general formulation for Rβ by letting its (h,k) element, denoted by rhk, depend on the similarity level between haplotypes h and k, which is quantified by a certain similarity metric, s(h,k). One simple choice of the correlation structure is to let Rβ=I, where I is the identity matrix. This independence structure imposes no correlation among distinct haplotypes and reflects the “unstructured” variation among haplotypes. The independence prior may be reasonable if haplotype variants were created mainly by recombinations instead of mutations. In contrast, one can introduce local-dependence structures to account for the role of mutation and to reflect the conjecture that evolutionarily close haplotypes tend to have similar effects on traits. One convenient choice of such Rβ is the conditional autoregressive (CAR) structure. The CAR structure assumes that all βh are correlated but that the correlation diminishes as the haplotype similarity decays. With our representation, a CAR structure is to let Rβ=C, where C-1 has diagonal elements equal to 1 and off-diagonal elements equal to -s(h,k).18 Alternatively, to avoid choosing between an independence prior and a sole CAR prior, an intermediate option, in practice, is the convolution model that combines the two: τRβ1I2C.12,13 In this work, we focus on the model that was considered by Schaid14 and set equation M4, with 0[less-than-or-eq, slant]s(h,k)[less-than-or-eq, slant]1. This model uses the haplotype similarity to reflect the correlation directly. It is more extreme but uses a simpler concept than the convolution model, by compromising between the dependence and the independence priors. It allows for correlation induced from partially similar haplotypes but assumes independence among haplotypes that share zero similarity.

VC-Score Test for Haplotype-Phenotype Association

To motivate our VC-score test for haplotype-phenotype association, we illustrate the method, assuming a normally distributed trait (perhaps after some transformation, such as the logarithm transformation) with a known dispersion parameter, [var phi]. We then present the VC-score test for general scenarios of unknown [var phi] and trait values with an arbitrary distribution. We provide the derivation of the generalization in appendixes A and B.

Quantitative traits with known dispersion parameter [var phi]

For quantitative traits that follow a normal distribution directly or after appropriate transformations, model (1) reduces to a linear mixed-model in matrix notation:

equation image

where X is the design matrix for γ, whose ith row is XTi; H is the design matrix for β, whose ith row is HTi; β~MN(0,τRβ) is the same as described in model (1); and ε~N(0,[var phi]I) represents the uncertainty in measuring traits Y. Since our primary interest is to test H0:τ=0, we consider the REML log-likelihood function of VC (τ,[var phi]). It is well known that the REML estimating equation for (τ,[var phi]) is unbiased and will produce less biased estimates compared with the maximum-likelihood approach.19

Denote by [ell]REML(τ,[var phi];Y) the REML log-likelihood function of τ and [var phi], which is given by

equation image

where VHRβHT+[var phi]I[equivalent]τS+[var phi]I is the marginal variance of Y and where P=V-1-V-1X(XTV-1X)-1XTV-1 is the projection matrix for the linear mixed model (2). The REML log-likelihood function (3) can also be viewed as the marginal log-likelihood of (τ,[var phi]) from the Bayesian perspective obtained by specifying a flat prior for γ and integrating out γ from f(Y;γ,τ,[var phi]).

Simple algebra20 shows that the score statistic of τ evaluated under H0 on the basis of the REML function (3) is equal to

equation image

where P0=[var phi]-1{I-X(XTX)-1XT}=[var phi]-1Q is the projection matrix P evaluated under H0:τ=0 and where Q=I-X(XTX)-1XT. It is immediately seen from equation (4) that E(Uτ)=0 under H0:τ=0, and, when τ>0, E(Uτ)=τ·tr(QSQS)/(2[var phi]2), which is a strictly increasing function of τ unless QS=0. Therefore, larger values of Uτ provide stronger evidence against H0. This suggests that the testing procedure for H0:τ=0 using Uτ should be one sided.

In a situation where the VC τ represents the potential variability due to a source that is independently distributed in the population such as the subject-specific effects in a longitudinal study, the score statistic Uτ given in equation (4) under H0:τ=0 has an asymptotic normal distribution with zero mean and some variance when the number of independent clusters goes to infinity.21 However, this condition does not satisfy in our case. In model (1), the design matrix H for the random effects β is not block diagonal and the dimension of β is fixed. Hence, the Lin’s21 asymptotic result does not directly apply to Uτ.

Since [var phi] is known, the second term in Uτ is a constant. Therefore using the score statistic Uτ is equivalent to using the first term of Uτ (denoted by Tτ):

equation image

We show in appendix A that Tτ has the same distribution as the weighted χ2 random variables equation M5, where χ21,i’s are independent χ2 random variables with 1 df, and λi is the ordered non-zero eigenvalues of the semipositive definite matrix equation M6 with λ1[gt-or-equal, slanted]λ2[gt-or-equal, slanted][center dot][center dot][center dot][gt-or-equal, slanted]λc>0 (c[less-than-or-eq, slant]L). If the (1-α)th quantile of this weighted χ2 distribution is denoted by T(α), then a level α score test will reject H0 if Tτ[gt-or-equal, slanted]T(α).

General traits with unknown dispersion parameter [var phi]

Here, we present the VC-score test for the general case in which the traits may not be normally distributed and the dispersion parameter [var phi] may or may not be known. As indicated by the derivation given in appendix B, our test statistic can be defined as

equation image

where μ=g-1(Xγ), Δ=diag{gi)}, equation M7 is the maximum-likelihood estimate of γ under H0, and equation M8 is the REML type of estimate (such as the one that uses Pearson residuals) of [var phi] under H0. Matrix W=diag{wi}, with equation M9. These quantities are readily available by fitting a standard generalized linear model, g(μ)=Xγ. We derive in appendix B that Tτ also follows approximately the weighted χ2 distribution equation M10, where λ1[gt-or-equal, slanted]λ2[gt-or-equal, slanted][center dot][center dot][center dot][gt-or-equal, slanted]λc>0 (c[less-than-or-eq, slant]L) is the nonzero eigenvalues of matrix W-1/2P0SP0W-1/2/2. We note that the conclusions given in the previous section are a special case of the results given here. For normally distributed traits, Δ=I, and W=V-1, which equals [var phi]-1I under H0. Hence, equation (6) reduces to equation (5), and the matrix W-1/2P0SP0W-1/2/2 reduces to equation M11

Gamma approximation of the distribution of test statistic Tτ

Given the fact that Tτ follows a weighted χ2 distribution, one can obtain the significance threshold equation M12 at level α from simulation. However, such a task may not be trivial when α is small. As an alternative, we introduce a Gamma approximation of the distribution of Tτ. Empirical evidence indicates that the eigenvalues λ12,[center dot][center dot][center dot]c of the matrix W-1/2P0SP0W-1/2/2 are dominated by the first few ones and decay rapidly to 0 (fig. 1). Following the work of Zhang and Lin,22 we use the Satterthwaite method to approximate the null distribution of Tτ by a Gamma distribution with parameters (a,b). Let x2130 and V denote the mean and variance of Tτ, respectively. We match the mean and the variance of the Gamma distribution and those of the test statistic by setting ab=x2130 and ab2=V, and we get a=x21302/V and b=V/x2130. We can then obtain equation M13 or calculate the P value of the test statistic from the distribution of Gamma (a,b). The mean, x2130, and variance, V, of Tτ can be calculated (appendixes A and B) by

equation image


equation image


equation image


equation image
Figure  1.
The 10 largest eigenvalues of matrix W-1/2P0SP0W-1/2. The eigenvalues are dominated by the first few and decrease rapidly to 0. The eigenvalues are averages across the 1,000 replications in the simulation scenario of high haplotype diversity ...

Phased haplotype data versus unphased genotype data

Although we have described our test, assuming that the haplotype information H is observed, the phase information can be not crucial. From equations (5) and (6), we see that the haplotype information appears in Tτ only through S=HRβHT, whose (i,j) element, denoted by Sij, can be rewritten as

equation image

The right-hand side of the equation states that Sij is simply the similarity score between the haplotype pair of person i and that of person j measured by metric equation M14. As a result, by choosing those metrics that do not require phase information, we can calculate S without resorting to the phased data. One choice is to set s(h,k) as the proportion of matching alleles between two haplotypes, h and k. As demonstrated by Tzeng et al.11 and Schaid,14 such Sij is equivalent to the proportion of matching alleles between the genotypes of individual i and individual j and hence can be calculated directly from genotypes with unknown phase.

Simulation Studies

We conduct simulation studies to examine the performance of the proposed score test. In the simulation, we generated covariates Xi, haplotypes Hi, and trait values Yi, given Xi and Hi, for each individual. The covariate Xi is drawn from a standard normal distribution, and the haplotype Hi is generated using a technique similar to those reported by Roeder et al.23 and Tzeng et al.8 Specifically, we simulated 100 haplotypes under the coalescent model,24 with an effective population size of 104, a scaled mutation rate of 5.6×10-4 per bp, and a scaled recombination rate of ~6×10-3 per bp for the cold spots and a rate 45 times greater for the hotspots. These parameters are chosen to roughly match the genes observed in the SeattleSNP database. We discarded SNPs with minor-allele frequencies <0.05. The hypothetical disease locus is selected on the basis of a predetermined minor-allele frequency, q, and the diversity of haplotypes flanking the SNP. In the simulation, we considered q=0.1, 0.3, and 0.5 and haplotype-diversity levels of high (11–16 distinct haplotypes), moderate (9–11 distinct haplotypes), and low (6–9 distinct haplotypes). We set a haplotype region to be a segment of five adjacent SNPs, including the two SNPs on the left and the three SNPs on the right of the disease locus. Given that the disease SNP is excluded, we also considered whether the disease SNP is “tagged” or “not tagged” by the surrounding five SNPs under each scenario. We defined that the disease SNP is “tagged” if there is at least one SNP whose R2 with the disease SNP is >0.7, and it is “not tagged” otherwise. We then randomly sampled with replacement of 2 haplotypes from the 100 haplotypes to form an individual. The simulated haplotype data were then converted into unphased genotype data.

We next generated the trait values Yi on the basis of Xi and the genotypes at the disease locus. We determined the trait value of individual i according to Xi and the number of disease alleles (Gi), using an additive-effect model. In the simulation study, we considered both quantitative traits and binary traits and adopted the same trait-generating scheme as did Lake et al.25 and Tzeng et al.8 For quantitative traits, we used a random-sampling scheme and generated 200 trait values from the normal conditional distribution of Yi with mean γ01×Xi+(Gi-1) and variance equation M15. We set the heritability (h2) at 0.1 and γ01=1. For binary traits, we used a case-control sampling scheme and generated trait values of 0 or 1, using the penetrance function logitP(Y=1[mid ]Gi,Xi)=γ01×Xi+θ×Gi. We set the odds ratio (OR) (eθ) at 2.0 and set the disease prevalence at 0.01 by letting γ0=-4.5 and γ1=0. We repeated the process until we collected 100 cases and 100 controls.

We analyzed these simulated data to evaluate the power performance of the VC-score method. To compare, we also conducted haplotype analyses, using the fixed-effect method and, in addition, the VC method via regular LRT (VC-LRT) under some scenarios. These analyses were performed assuming unknown phases. For fixed-effect analysis, we used the haplotype-score test of Schaid et al.,26 as implemented in the R function ”haplo.score,” and determined the P values by using the asymptotic χ2 distribution. The P values of our VC-score method were obtained from the approximated Gamma distribution, and the P values of the VC-LRT method were obtained from 50:50 mixtures of χ20 and χ21.

Data Application

We considered the data set from the genetic association study of ALS conducted by Schymick et al.17 The ALS data set consists of 276 patients with sporadic ALS and 271 neurologically normal control subjects27 and contains their genotypes at the 550K SNPs across the genome in the Illumina chip assays. The original genotyping was performed in the laboratory of Drs. Singleton and Hardy at National Institute of Aging. The genotype data have been made publicly available in the SNP Database at the National Institute of Neurological Disorders and Stroke (NINDS) Human Genetics DNA and Cell Line Repository. Schymick et al.17 performed a genomewide association analysis and reported 34 SNPs that have P values <.0001 on the basis of the single-SNP genotypic test with 2 df. They used the Bonferroni correction to adjust for multiple testing, and the threshold of significance at the nominal level of 0.05 is 9.1×10-8. Although none of the 34 SNPs was significant after the Bonferroni correction, the most significant SNP (rs4363506) lay in close proximity to one of the actin cytoskeleton genes (the dedicator of cytokinesis 1 gene [DOCK1 {MIM 601403}]) that are increasingly recognized as playing an important role in motorneuron disease. To assess the performance of our method, we applied the proposed VC-score method to part of this data set. We focused our analysis on chromosome 10, where the most significant SNP is located. We used the results reported by Schymick et al.17 as a benchmark to evaluate our findings.


Simulation Studies

In the comparison of our VC-score method with the fixed-effect method, we reported the results for quantitative traits and binary traits under 18 scenarios (3 values of allele frequency × 3 levels of haplotype diversity × 2 different tagging statuses of the disease SNP). Type I error rates were calculated on the basis of 2,000 replications, and power was calculated on the basis of 1,000 replications.

We listed the results of type I error rates of the VC-score test in table 1 for quantitative traits and in table 2 for binary traits. The values are around the nominal levels of α=0.05 and α=0.01, indicating that the Gamma distribution approximates the null distribution of Tτ adequately. To ensure this conclusion, we also examined the null distribution of the test statistics; the results are displayed in figure 2. The left panels of figure 2 show the two quantile plots (hereafter, “QQ-plots”) that compared the quantiles of the standardized Tτ from the null distribution with the quantiles of the standard normal distribution. The upper panels are for quantitative traits, and the lower panels are for binary traits. In both cases, it is apparent that standardized Tτ does not have a standard normal distribution, following Lin’s21 asymptotic result. We then draw the QQ-plots of Tτ against the Gamma distribution (fig. 2, right panels). In the simulation, each replication i generated a Tτ,i that follows approximately a Gamma distribution with a unique shape parameter, ai, and a unique scale parameter, bi. To create a QQ-plot against these nonidentical Gamma variables, we first created a scaled Tτ,i=Tτ,i/bi that follows Gamma (ai,1). Then, we used a single shape parameter of equation M16 to obtain the theoretical quantiles. Although use of a single shape parameter can cause some deviation in the QQ-plot (such as what can be observed in the right section of the graph), overall we see that the data points agree with the 45° line, indicating that the Gamma approximation works reasonably well.

Figure  2.
QQ-plots of the test statistic Tτ. We defined the standardized Tτ as equation M42 and the scaled Tτ,i as Tτ,i/bi, where bi is the scale parameter of the Gamma approximation. The left panels show the standardized Tτ ...
Table 1.
Type I Error Rates of the VC-Score Test for Quantitative Traits[Note]
Table 2.
Type I Error Rates of the VC-Score Test for Binary Traits[Note]

The results of power comparison are displayed in tables tables33 and and44 for quantitative traits and in tables tables55 and and66 for binary traits. We highlighted those cases in which the power gain is significant at a 0.05 level by use of McNemar’s test. We found that the correlation between the disease SNP and its nearby SNPs plays a key role in predicting the performance of the VC-score test compared with the fixed-effect test. When the disease SNP was tagged by at least one of surrounding SNPs, we observed a systemic power improvement of the VC-score method over the fixed-effect method. This is consistent for both trait types across all scenarios (tables (tables33 and and5).5). If none of the adjacent SNPs was highly correlated (i.e., R2>0.7) with the unobserved disease SNP, we saw a power drop compared with that seen for the tagged SNPs. In these cases, the fixed-effect method tends to retain a higher power than that of the VC-score method, although the pattern is not universal (tables (tables44 and and66).

Table 3.
Power for Quantitative Traits When the Disease SNP Is Tagged[Note]
Table 4.
Power for Quantitative Traits When the Disease SNP Is Not Tagged[Note]
Table 5.
Power for Binary Traits When the Disease SNP Is Tagged[Note]
Table 6.
Power for Binary Traits When the Disease SNP Is Not Tagged[Note]

We also examined the performance of the VC-score test by varying the strength of genetic effects. We set the heritability h2 at 0.00, 0.05, and 0.10 for quantitative traits and set the OR at 1.0, 2.0, and 2.5 for binary traits. This simulation considered the scenario of high haplotype diversity, a tagged disease SNP, and an allele frequency of 0.1 and used a sample size of 200 individuals generated from random sampling for both trait types. The power is calculated on the basis of 500 replications, and the type I error rate (i.e., for h2=0 and OR=1) is calculated on the basis of 1,000 replications. As a quick verification, we see from table 7 that the power of the VC-score method increases as the genetic effect becomes stronger.

Table 7.
Comparison of the Fixed-Effect Test, VC-Score Test, and VC-LRT[Note]

As a comparison, we also conducted the fixed-effect analysis and the VC analysis with the regular LRT. We were unable to obtain the result of the VC-LRT for binary traits because of computational limitations, since one has to calculate a c-dimensional (c = the number of the nonzero eigenvalues) numerical integration to obtain the LRT statistics. Table 7 shows that, as expected, the VC-LRT produces the lowest power among the three methods. The analysis of type I error rate helps to explain the low power of the VC-LRT; the size determined from the regular 50:50 mixture of χ20 and χ21 is extremely small, and the overconservative threshold obtained from the χ2 mixture leads to a loss of power. When compared with the fixed-effect method, we noticed that the power loss of the VC-LRT method in our simulation is more substantial than seen in the results of Schaid.14 We think this is probably because Schaid simulated data from a VC model, which would favor the performance of a VC approach.

Analysis of the ALS Data Set

Using unphased genotype data from the ALS study, we replicated the single-SNP genotypic test of Schymick et al.17 and performed two haplotype association analyses, one with the fixed-effect method and the other with the proposed VC-score method. There are a total of 28,818 SNPs genotyped on chromosome 10, and we removed the 26,258th SNP because of its ambiguous marker information. Following the same haplotype definition as that in the work of Schymick et al.,17 we also defined haplotypes by using a sliding window of three SNPs in the haplotype analyses.

The results from the VC-score method showed that the most significant association signal, with a P value of 1.2×10-7, is near rs4363506. The P values are presented in figure 3, with the location of rs4363506 indicated by the arrows. The two adjacent windows around the most significant signal also have similar P values: 1.3×10-7 and 2.7×10-7. These locations agree with the findings of Schymick et al.,17 who reported that rs4363506 has a P value of 6.8×10-7 for the genotypic test and a P value of 4.8×10-6 for the three-marker haplotype test. Although our P values appeared smaller, they were not significantly different from the results of the single-SNP analyses and were not significant after Bonferroni correction with the threshold of 9.1×10-8. We also compared the VC-score results with those of the fixed-effect method (fig. 3B). The fixed-effect method also indicated a peak signal around rs4363506, with the peak P value (4.9×10-6) slightly larger than those of the VC-score test and the single-SNP test. In general, we observed that analyses at the haplotype level reduced the noisy association signals of single SNPs. Although the clearer association pattern of haplotypic analyses came with the cost of extra degrees of freedom used in multimarker variations, we see that the VC-score haplotype test achieved a level of significance that is comparable to that of single-SNP analyses.

Figure  3.
P values from the ALS data analysis around the most promising SNP reported by Schymick et al.17 (i.e., SNP rs4363506, with location indicated by the arrows). The P values are presented on the scale of negative logarithm of base 10. A, P values of the ...

To ensure that the results are not sensitive to the definition of the haplotypes, we repeated our analysis with window sizes of three, four, and five SNPs. The P values for a window size of four SNPs for fixed-effect and VC-score methods are shown in figure 3C, in which the P value curves retain a similar pattern to the P value curves in the three-SNP analysis (fig. 3B). Indeed, the P value curves of various window sizes for the same method are similar (data not shown), except that larger window sizes led to a more smoothing effect on the P values across SNPs. With window sizes of four and five SNPs, the P values at the windows containing rs4363506 are 8.3×10-8 and 7.7×10-8, respectively; both are significant at the threshold determined by the Bonferroni correction. Judging by the criteria of locating the signal around rs4363506 and producing reasonable P values, we think that the VC-score method performed competitively with the standard analyses of these data.


The VC approaches have been considered as one common strategy to reduce the degrees of freedom required in haplotype association analyses. However, it is noticed that direct application of the VC-LRT to haplotype association often fails to increase power. In this article, we reported possible reasons that contribute to this phenomenon, which include that (a) the LRT statistic has a nontypical limiting distribution in a haplotype random-effect model and (b) none of the surrounding SNPs is highly correlated with the unobserved disease SNP. Although the latter reason naturally limits the performance of the type of VC approaches discussed in this article, the former can be overcome. In essence, our work tackles this limiting-distribution problem; we introduced a VC-score test based on the REML or the marginal likelihood function of the VC under the GLMM. We showed that the test statistic follows a weighted χ2 distribution and provided a Gamma approximation. We demonstrated the validity of the proposed method through simulation. Constructed under the GLMM framework, our VC method can be applied to a broad class of data, allowing for traits of various types, different choices of correlation structure, and a flexible range of model assumptions. Finally, by choosing suitable similarity metrics, the proposed method can be directly applied to unphased genotypic data.

We note that the LRT statistic in the VC haplotype model does not converge to the distribution derived from the typical asymptotic theory that assumes independent clusters. As a result, use of the conventional limiting distribution could lead to an overconservative testing result. Crainiceanu and Ruppert16 reported similar findings and provided a practical procedure to find the distribution of the LRT statistic for continuous Y variables. However, we still recommend the score test over the LRT, for several reasons. First, the correct LRT procedure of Crainiceanu and Ruppert16 is applicable only to continuous traits. Second, the LRT is generally a more difficult test to implement under the GLMM framework. For example, with binary traits, it is almost impractical to obtain the exact maximum-likelihood estimates of the VC and, hence, the LRT statistic. On the contrary, our score test is applicable to a wide-ranging class of models, and it requires only the estimates under H0 that can be easily obtained from standard statistical software. The broad coverage and the fast and easy implementation of the score test makes the VC strategy an effective tool for haplotype analysis, even in modern genomewide association studies. We have implemented the VC-score test in R and have distributed the R code at our Authors’ Web site.

An additional factor that would influence the power performance is the LD pattern between the observed SNPs and the unobserved disease SNP. Our power analysis showed that, if at least one marker is in high LD with the disease SNP (i.e., R2>0.7), the VC-score method performs better than the fixed-effect method. If all markers are in low LD with the disease SNP, both methods suffer from power loss. This is understandable because low correlation indicates lack of information from neighboring SNPs to make the correct inference. However, we noticed that the VC-score test appears to have a larger drop in power. The VC method is developed from an evolutionary point of view, which implicitly assumes high correlation among adjacent SNPs with the disease locus and uses the correlation to reduce the degrees of freedom. On the other hand, the fixed-effect approach does not rely on this assumption. We conjecture that this is the explanation for the observation of different degrees of power loss under the “untagged” scenarios, as well as for the observation of the power gain of the VC method under the “tagged” scenarios. We plan to continue exploring this aspect of the problem.

In this work, we suggested the use of similarity metrics that do not require phase information. For example, a candidate is the metric that counts the number of matching alleles between two haplotypes. Theoretically, metrics that make use of the phase information should be more powerful. A corresponding metric to our candidate that incorporates phase information is one that counts the number of longest consecutive matching alleles. Metrics of this type are more likely to capture the identity-by-descent sharing and to better reflect the results of the decay of haplotype sharing. However, these metrics are not robust to genotyping errors and recent market mutations, which often limit their power in practice. Our previous work found that phase-dependent and phase-independent metrics have similar performance.11 In addition, the use of phase-independent metrics bypasses the need to infer the phase information, which is often achieved under unrealistic assumptions. For example, the expectation-maximization algorithm is typically used to impute haplotype phases, and it assumes that the population has common haplotype frequencies and is in Hardy-Weinberg equilibrium (HWE). These assumptions tend to not hold with the existence of population substructure; the haplotype frequencies could vary across subpopulations, and the HWE may hold only within the subpopulations but not for the entire population. Consequently, the phases are not inferred accurately—hence, the subsequent association inference. Use of phase-independent measures does not rely on imputing the haplotype information and, therefore, avoids these issues naturally.

Although we have introduced a Gamma approximation of the distribution of the score test for the sake of simplicity, we note that there exists alternative approaches to estimate the distribution. One approach is to use a three-moment approximation,28,29 as opposed to the two-moment matching method described in this article. The three-moment method uses the information of the nonzero eigenvalues λ1,…,λc of the matrix W-1/2P0SP0W-1/2/2 and approximates the α-level significance threshold equation M17 as equation M18, where equation M19, h=k32/k23, and χα is the αth quantile of χ2h (i.e., a χ2 distribution with h df). The P value of the test statistic Tτ is then the right-tail portion of equation M20 of the χ2h distribution. Another approach is to obtain directly the empirical distribution of Tτ through simulation based on the fact that equation M21. To do so, find eigenvalues λ1,…,λc, and generate c sets of random values from the χ21 distribution, each set with a certain sample size—say, 500,000. Then, the weighted sums of these random values form the empirical distribution of the VC-score statistics. The simplicity of the simulation carries over to genomewide association studies, in which case, the sample size of the simulated χ21 values has to be reasonably large with respect to the stringent genomewide significance level. Fortunately, these simulated χ21 random values can be used repeatedly in every haplotype region, and all that needs to be recalculated is the nonzero eigenvalues of matrix W-1/2P0SP0W-1/2/2 obtained in each region.

The VC-score method introduced here focuses on detecting the haplotype main effect, but the framework can be extended to consider interactions. For example, one can incorporate terms for gene-environment and gene-gene interactions in the model and can examine their significance by testing the corresponding VC. We are exploring these ideas in an ongoing work. We also note that the VC-score method has a direct connection to the strategy of reducing the degrees of freedom in haplotype association tests through haplotype sharing. The haplotype information appears in the formula of the score statistic Tτ as S=HRβHT, and the elements of S record the level of haplotype similarity between two subjects by a certain haplotype metric, s(h,k). On the one hand, in the VC methods, the selection of Rβ (and hence the similarity metric) largely emphasizes the evolutionary relationship of haplotypes in history. On the other hand, in the haplotype-sharing approaches, we choose the similarity metric to quantify the similarity level in the current population. We believe that taking advantage of the implicit relationship between the two methods can offer more insights into both strategies. We plan to further investigate this issue.


We are grateful to the NINDS Human Genetics DNA and Cell Line Repository at Coriell and the laboratory, for supplying the data of the ALS study used in this work. We also thank the reviewers, for their constructive feedback, and Dr. Andrew Allen, Dr. Silviu-Alin Bacanu, and Dr. Patrick Sullivan, for their helpful discussion and suggestions. J.-Y.T. was supported by National Science Foundation grant DMS-0504726 and National Institutes of Health (NIH) grant R01 MH074027. D.Z. was supported by NIH grant R01 CA85848-04.

Appendix A: Distribution and Moments of the VC-Score Statistic for Normal Traits

From equation (5), we have equation M22 for normal traits. Define vector equation M23, which follows a standard multivariate normal distribution. We then can rewrite Tτ as

equation image

where Z2i21 distribution. Equation (A1) holds as μTQ=0 by the fact of Q, a projection matrix.

When [var phi] is unknown, we replace [var phi] in our test statistic Tτ with its REML estimate under H0, which yields the regular mean squared error for the linear regression model Y=Xγ+ε:

equation image

Since, under H0:τ=0, traits Y reduce to independent data, the variance of equation M24 will be negligible when the total sample size, n, is large. Therefore, the exact distribution of Tτ with [var phi] replaced by equation M25 can be approximated by the distribution of equation M26, where equation M27 are the eigenvalues of equation M28, if such ”exact” distribution is critically needed.

We can approximate the distribution of Tτ by a Gamma distribution by matching the first two moments. Following the work of Harville,20 the mean, x2130, and variance, V, of Tτ are

equation image


equation image

To take into account the fact that [var phi] is estimated, we obtained the following result by Taylor expansion:

equation image

where Iτ[var phi]=E([partial differential]Tτ/[partial differential][var phi]), I[var phi][var phi]=E[[partial differential]2[ell]REML(τ,[var phi])/[partial differential][var phi]2], and U[var phi]=[partial differential][ell]REML(τ,[var phi])/[partial differential][var phi]. Hence, we can estimate the mean of Tτ by

equation image

and can estimate the variance of Tτ by

equation image


equation image


equation image

Appendix B: Derivation of the VC-Score Test for General Traits

Motivated by the nice properties of the REML or the marginal log-likelihood function of the VC for a normal trait, presented in equation (3), and the success of the score test for testing a polynomial covariate effect in semiparametric additive mixed models by use of mixed-model representation,22 we take a similar approach for a nonnormal trait, Y, such as a binary disease trait. Under model specification (1), the marginal log-likelihood function [ell]M(τ,[var phi];Y) of τ and the possible dispersion parameter [var phi] are given by

equation image

The marginal log-likelihood in (B1) usually involves a high-dimensional and mathematically intractable integration. To overcome this problem, Zhang and Lin22 used Laplace approximation to derive an approximate score statistic for testing H0:τ=0 on the basis of a similar marginal log-likelihood function. For our model, their score statistic (eq. [16] in the work of Zhang and Lin22) reduces to

equation image

where μ=g-1(Xγ) is the mean of Y under H0:τ=0; Δ=diag{gi)}; W=diag{wi}, with w-1i=[var phi]m-1ivi){gi)}2; P0=W-WX(XTWX)-1XTW; equation M29 is the maximum-likelihood estimate of γ under H0; and equation M30 is the REML type of estimate of [var phi] under H0.

Under H0:τ=0, equation M31 and equation M32 are consistent estimates of γ and [var phi], respectively. Hence, there is not much variability in the second term (relative to the first term) of Uτ when sample size n is large. Therefore, we can again use the first term for testing H0:τ=0:

equation image

To derive the distribution of Tτ, first we show, through Taylor expansion, that, under H0:τ=0,

equation image


equation image

Then, we have

equation image

As a result,

equation image

where the ith element of equation M33 is defined by equation M34 and where μi and Var(Yi) are the true mean and variance, respectively, of Yi under H0. The result indicates that Tτ has approximately the same distribution as

equation image

Again, denote by λ1[gt-or-equal, slanted]λ2[gt-or-equal, slanted][center dot][center dot][center dot][gt-or-equal, slanted]λc>0 (c[less-than-or-eq, slant]L) the eigenvalues of W-1/2P0SP0W-1/2/2, and denote by u1,u2,…,uc the corresponding orthonormal eigenvectors. Then, under H0, Tτ will have approximately the same distribution as equation M35, where equation M36. Under the condition that each uj is not dominated by a few elements, Z1,Z2,[center dot][center dot][center dot],Zc will be approximately independent standard normal random variables. So, Tτ has approximately the same distribution as that of equation M37, which is similar to the case of normal traits.

We can approximate the distribution of Tτ by a Gamma distribution by matching the first two moments, as was done in appendix A. The approximate mean of Tτ is given by x2130=tr(P0S)/2, and the approximate variance by equation M38, where equation M39, equation M40, and equation M41.

Web Resources

The URLs for data presented herein are as follows:

Authors’ Web site, http://www4.stat.ncsu.edu/~tzeng/Softwares/Hap-VC/R/ (for R code for implementing the VC-score test)
NINDS Human Genetics DNA and Cell Line Repository, http://ccr.coriell.org/ninds/ (for the ALS study by Schymick et al.)
Online Mendelian Inheritance in Man (OMIM), http://www.ncbi.nlm.nih.gov/Omim/ (for DOCK1)


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