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- Journal List
- Genetics
- v.171(2); Oct 2005
- PMC1456787

# Quantitative Trait Loci Analysis Using the False Discovery Rate

^{1}

*Corresponding author:*Department of Statistics and Operations Research, The Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel 69978. E-mail: li.ca.uat.tsop@leitukey

## Abstract

False discovery rate control has become an essential tool in any study that has a very large multiplicity problem. False discovery rate-controlling procedures have also been found to be very effective in QTL analysis, ensuring reproducible results with few falsely discovered linkages and offering increased power to discover QTL, although their acceptance has been slower than in microarray analysis, for example. The reason is partly because the methodological aspects of applying the false discovery rate to QTL mapping are not well developed. Our aim in this work is to lay a solid foundation for the use of the false discovery rate in QTL mapping. We review the false discovery rate criterion, the appropriate interpretation of the FDR, and alternative formulations of the FDR that appeared in the statistical and genetics literature. We discuss important features of the FDR approach, some stemming from new developments in FDR theory and methodology, which deem it especially useful in linkage analysis. We review false discovery rate-controlling procedures—the BH, the resampling procedure, and the adaptive two-stage procedure—and discuss the validity of these procedures in single- and multiple-trait QTL mapping. Finally we argue that the control of the false discovery rate has an important role in suggesting, indicating the significance of, and confirming QTL and present guidelines for its use.

OVERLOOKING the multiplicity aspects in QTL studies with numerous markers and several quantitative traits can lead to many false discoveries of linkages. Lander and Kruglyak (1995, p. 241) were among the first to address the multiplicity problem in QTL mapping, arguing that “Adopting too lax a standard guarantees a burgeoning literature of false positive … Scientific disciplines erode their credibility when a substantial proportion of claims cannot be replicated.” The procedure they offered was designed to control the probability of making even one type I error—of making even one false discovery—in a QTL study with a single quantitative trait. This probability is termed the family-wise error rate (FWE) or in this case the genome-wise error rate (GWER).

Concerned that controlling the FWE at conventional levels results in very little power to discover QTL, Lander and Kruglyak (1995) set the following widely used terminology: *suggestive linkage*, statistical evidence that would be expected to occur one time at random in a genome scan; *significant linkage*, statistical evidence that would be expected to occur at random with probability 0.05; and *confirmed linkage*, significant linkage confirmed by a further sample with a nominal *P*-value <0.01.

The FWE-controlling procedures employed are designed to control the probability of making one or more false discoveries for a single trait. In studies with multiple traits FWE-controlling procedures have to be suitably adjusted by further raising the threshold for significant linkage according to the number of traits in the study. Consider, for example, a study with 12 quantitative traits. For a linkage to be suggestive, it should pass a threshold that is equivalent to controlling the FWE at level 0.6 (using the Poisson approximation when the average is 1). Findings that would have been reported as significant linkages (FWE = 0.05) in a single-trait study should now be reported only as suggestive linkages (if a simple Bonferroni correction was used the single-trait threshold should be divided by the number of traits). Such a solution may be acceptable in QTL studies with only a few traits. In studies with many traits the control of the FWE leaves very little power to make discoveries. The problem becomes serious even well before reaching current large problems that combine microarrays with QTL analysis, as in Williams *et al.* (2002) with 12,422 quantitative traits.

The conflict between the strict control of type I error, as a protection against false discoveries, and the need for increased power led Benjamini and Hochberg (1995) to suggest a new criterion for type I error in multiple testing: let **Q** be the proportion of false linkage claims in a genome scan, setting it at zero if no discoveries are made; then the false discovery rate (FDR) is the expected value of **Q**. It thus seems as if Benjamini and Hochberg have taken literally the warning of Lander and Kruglyak about the danger in allowing a substantial proportion of false claims and cast this danger into a well-defined statistical criterion.

Benjamini and Hochberg (1995) also introduced a FDR-controlling procedure [sometimes called linear step-up or the Benjamini-Hochberg (BH) procedure] and proved that it controls the FDR for independent test statistics. Benjamini and Yekutieli (2001) proved that the same holds for some types of positive dependence.

Weller *et al.* (1998) were the first to apply the FDR approach for QTL mapping. They explained the use of the BH procedure for single-marker analysis and demonstrated the increase in power. While commenting on this work, Zaykin *et al.* (2000) pointed out that the conditional interpretation of the FDR criterion, *i.e.*, that controlling the FDR at 0.05 means that 95% of the discoveries are true, does not always hold. Although Weller (2000) eased their concern, the issue is still alive and has resurfaced in discussions of alternative formulations of the FDR criterion: positive FDR (Storey *et al.* 2004), adjusted FDR (Mosig *et al*. 2001), and the proportion of false positives (PFP) (Fernando *et al*. 2004).

While the BH procedure received much attention in microarray analysis, the developments were slower in the context of QTL analysis. Sabatti *et al*. (2003) verified that the BH procedure controls the FDR for single-trait linkage (see also Yekutieli 2001) and association genome screens. Lee *et al.* (2002) addressed interval mapping, discussed the use of the FDR in multiple quantitative traits, and recommended the application of the BH procedure separately for each trait. Sabatti *et al*. (2003) further suggested substituting the BH procedure with a resampling-based FDR procedure capable of capturing the dependency structure of the data to achieve additional power.

What is common to the above researchers, and to the few other users of FDR ideas in QTL analysis, is their enthusiasm about the important role that these ideas can play in QTL analysis. Since we share this enthusiasm, it seems important to us to lay a solid foundation for the use of FDR in this area, as well as to expand our working methodologies. We present the FDR in precise terms, in conjunction with related formulations of the proportion of false discoveries. We make a clear distinction between the FDR criterion and the BH procedure that controls it under independence. We explain the role that adaptive FDR-controlling procedures can have in increasing power while controlling the FDR. We clarify what is known about the performance of FDR-controlling procedures under dependency in the context of QTL analysis and offer more progress on this question. We analyze the performance of the resampling procedure of Yekutieli and Benjamini (1999) in QTL analysis, and we address the important issue of multiple traits. In all of the above, we also make an effort to point at remaining gaps in our knowledge. Finally, we analyze FDR control in independently repeated experiments and make use of the results to offer a set of FDR guidelines for the significance of findings in QTL studies.

This article is structured as follows: with a slight danger of repetition, we review the FDR in the next section. We present the various types of FDR-controlling procedures. We discuss what “FDR control” means, its relations to conditional FDR control and the suggestive linkage criterion, and the control of FDR in multitrait studies. And we present a new framework, based on the BH procedure, for FDR-confirmed QTL mapping with an independent study and compare our new approach to Lander and Kruglyak's *confirmed linkage*. The subsequent section is dedicated to simulation studies. We compare the performance of the BH procedure to the performance of the FDR-resampling and FWE-resampling procedures. We examine the FDR control of the BH procedure in cases for which no analytical results are available. The final section summarizes our FDR guidelines for assessing the significance of the results of QTL experiments. Thus we hope to be able with this article to remove some of the hurdles placed before the use of FDR in QTL analysis and help with its wider and faster acceptance.

## THE FALSE DISCOVERY RATE

The FDR was defined in Benjamini and Hochberg (1995) as the expected proportion of false discoveries. Formally, if **R** is the total number of discoveries, and **V** of them are false discoveries, the proportion of false discoveries is **Q** = **V**/**R** if **R** > 0 and **Q** = 0 if **R** = 0. Although the value of **Q** is usually not known in a particular experiment, we can discuss and even control *its expectation*, FDR = *E*(**Q**).

Benjamini and Hochberg (1995) considered several alternative formulations for the FDR. Two such alternative formulations, passed over by Benjamini and Hochberg, reappeared in the statistical and genetic literature: *E*(**Q** | **R** > 0), the positive FDR (pFDR) in Storey (2002), and *E*(**V**)/*E*(**R**), the PFP in Fernando *et al.* (2004). The pFDR and PFP have very desirable properties; however, they are not appropriate criteria for multiple testing: a statistical procedure offering pFDR or PFP control for all configurations of true and false null hypotheses cannot be constructed. Let us articulate this point, if all tested hypotheses are true, say studying a totally nonhereditary trait, any discovery made is a false discovery—no matter what statistical method is being used. The proportion of false discoveries among these discoveries is identically 1. With the exception of the useless “never-reject-anything” rule, the pFDR and the PFP of all procedures are by definition 1. Thus even the procedure suggested in Storey (2002), designed to address the pFDR, is not a pFDR-controlling testing procedure. It is capable only of estimating the pFDR once a fixed rejection threshold is being used (see *The fixed rejection region approach*) and includes an estimate of *m*_{0}/*m* (see *Two-stage adaptive procedures*).

In contrast, if all tested hypotheses are true, the FDR equals the traditional FWE. Therefore it also makes sense to use the conventional levels such as 0.05 or 0.01 for FDR control, although in some applications higher values may be justifiable. In particular, for QTL analysis Mosig *et al.* (2001) recommend using 0.1, and Weller *et al.* (1998) use 0.25.

### FDR-controlling procedures:

#### The BH procedure:

Benjamini and Hochberg (1995) provided a simple stepwise procedure to control the FDR at a desired level *q*. The procedure makes use of the *P*-values only, so the statistical test itself may be tailored to the problem at hand, be it a LOD score or a nonparametric test. The procedure runs as follows. The individual *P*-values are sorted from smallest to largest: *P*_{(1)} ≤ *P*_{(2)} ≤ *P*_{(m)}. Starting from the largest *P*-value *P*_{(m)}, compare *P*_{(i)} with *q* · *i*/*m*. Continue as long as *P*_{(i)} > *q* · *i*/*m*. Let *k* be the first time *P*_{(i)} ≤ *q* · *i*/*m* and then declare the hypotheses corresponding to the smallest *k P*-values as significant.

An intuitive explanation of the connection between the BH procedure and FDR control was offered by Benjamini and Hochberg (1995) and later recited by Weller *et al.* (1998) and Mosig *et al.* (2001): if we reject the *k* hypotheses with *P*-values less than *p*_{(k)} and treat this *p*_{(k)} as if it is fixed, then regardless of the joint distribution of the *P*-values the average number of false discoveries is *p*_{(k)} · *m*_{0}, where *m*_{0} is the (unknown) number of true null hypotheses. As an upper bound for the FDR we take *p*_{(k)} · *m*/*k*. For this to be less than *q*, *p*_{(k)} has to be less than *q* · *k*/*m*. This argument by itself is inappropriate as a proof, mixing expectations with values in the experiment and ignoring the case when no discovery is made. Hence it cannot be used to imply that the BH procedure always controls the FDR regardless of the test statistic distribution, and in fact in some rare settings the FDR of the BH procedure may get as high as . The correct statement, proven precisely in Benjamini and Yekutieli (2001), is as follows:

Theorem 1. *If the test statistics are positively regression dependent on each hypothesis from the subset corresponding to true null hypotheses, the BH procedure controls the FDR at level q · m*_{0}/*m.*

The definition of the positive regression dependent on a subset (PRDS) condition and a review of important examples where it is satisfied can be found in Benjamini and Yekutieli (2001). The PRDS condition and FDR control of the BH procedure in single-trait QTL analysis are discussed in Sabatti *et al.* (2003). In *FDR control in multitrait studies* we discuss FDR control of the BH procedure in multiple-trait QTL analysis.

#### The fixed rejection region approach:

Weller *et al.* (1998) denote *q* = *P*_{(i)} · *m*/*i* as the false discovery rate when rejecting at *P*_{(i)}. They note the erratic behavior of this *q* as a function of *i* and demonstrate in simulations that the mean value of the above expression—for a fixed *i*—is greater than the mean of the number of tests with *P*-values ≤ *P*_{(i)} not linked to a simulated QTL divided by *i*.

Such an attempt does not verify the FDR control of the BH procedure. Instead, it shows that if one decides beforehand to reject the *i* hypotheses with the smallest *P*-values, the corresponding *P*_{(i)} · *m*/*i* is a conservative estimator of the FDR committed. A more natural choice in this direction is to use the fixed rejection region approach. For example, reject any hypothesis with LOD > *c* and study the FDR properties of such a rejection rule as *c* varies. A detailed discussion of this topic, in general settings, can be found in Yekutieli and Benjamini (1999) and Storey (2002).

In the BH procedure *q* is specified while the LOD threshold and the number of hypotheses rejected vary. If, for each *P*_{(i)}, instead of comparing *P*_{(i)} · *m*/*i* to *q* we take the minimum of such terms over all *P*-values larger than or equal to *P*_{(i)}, we get the BH FDR-adjusted *P*-values: (Westfall 1997; Yekutieli and Benjamini 1999). Obviously, rejecting all hypotheses whose BH FDR-adjusted *P*-values are smaller than *q* is equivalent to applying the BH procedure at level *q*. Thus reporting the FDR-adjusted *P*-values , or plotting them as a function of *i*, is convenient. Compared to plots of *q* = *P*_{(i)} · *m*/*i vs. i* (or *vs. P*_{(i)} as in Lee *et al.* 2002), they are monotonic and exhibit less erratic behavior. Plotting the FDR-adjusted *P*-values *vs.* their location on the chromosome is another informative way of displaying results.

#### Two-stage adaptive procedures:

When some QTL exist, implying that the number of markers unlinked to QTL *m*_{0} is less than *m*, the BH procedure controls the FDR at too strict a level by a factor of *m*_{0}/*m*. If this factor were known, using the BH procedure at level *q** = *q* · *m*/*m*_{0} instead of *q* would be more powerful and still achieve FDR control at level *q*. Since *m*_{0} is hardly ever known, it seems attractive to first estimate *m*_{0} and then use *q** as defined above, with the estimated *m*/*m*_{0} instead of the true quantity. Theorem 1 by itself does not guarantee that two-stage procedures control the FDR at the desired level, and their properties need separate attention (see Benjamini *et al.* 2003).

Two-stage adaptive FDR-controlling procedures were introduced by Benjamini and Hochberg (2000). The study and development of adaptive FDR-controlling procedures is a very active area of research: Storey (2002), Storey *et al.* (2004), and Black (2004), to name just a few. In the context of QTL analysis, Mosig *et al.* (2001) discussed the role of the estimated *m*_{0} in the control of FDR, their offering being an adaptive procedure aimed at controlling the FDR (rather than a new criterion). Important modifications to the procedure were offered in Fernando *et al.* (2004).

Benjamini *et al.* (2003) introduced a two-stage procedure in which *m*_{0} is estimated by the number of hypotheses *not* rejected by the BH procedure at level *q*, *m* − **R**, further multiplied by 1 + *q*. At the second stage the BH is used again with the modified *q**. They analytically prove FDR control of their new procedure for an independent test statistic. Benjamini *et al.* (2003) further show that with the exception of their procedure, all other two-stage procedures (including the two-stage procedure of Mosig *et al.* 2001) fail to control the FDR for some positively regression-dependent tests. This does not mean yet that all other procedures are not appropriate for the particular dependency structure encountered in QTL mapping, but it raises doubt as to their appropriateness in their current form.

#### Resampling procedures:

Resampling procedures, reshuffling, and randomization, being close variants, overcome the problem of specifying the marginal distributions of the test statistic at each marker under the null hypothesis of no linkage and even more importantly incorporate the dependency between the markers to increase the power of the analysis. It is done by imitating the way the data were generated by sampling, with or without replacement, under the assumption of no linkage. In QTL analysis resampled data can be generated by randomly drawing a with-replacement sample of the phenotype data and then correlating it with the original genotype data.

Yekutieli and Benjamini (1999) introduced a general FDR-controlling resampling procedure designed to control the FDR: for *i* = 1, 2, … ;, *m* compute the resampling-based FDR-adjusted *P*-value ; reject the null hypotheses corresponding to . This procedure controls the FDR if the sets of test statistics corresponding to true and false hypotheses are independent. This condition is satisfied in single-trait QTL analysis (see *FDR control in multitrait studies*). For multiple traits we bring support for FDR control in the simulation study.

### Control of the FDR:

Level *q* FDR means that the expected value of **Q** is less than or equal to *q*. The actual value of **Q** can theoretically vary from 0 to 1; thus FDR control does not generally imply that 95% of the discoveries are true discoveries. Genovese and Wasserman (2004) show that in very large problems with independently distributed test statistics if the data contain a proportion of true discoveries then applying the BH procedure does ensure that ~95% of the discoveries are true ones, and as **Q** hardly varies, FDR = pFDR = PFP = 0.05 · *m*_{0}/*m*. Note that while these assumptions might be reasonable for microarray data, they do not necessarily apply to QTL mapping.

#### Conditional control of the FDR:

Zaykin *et al.* (2000) argue against control of the FDR as it does not control the expected proportion of false discoveries if interest is restricted to experiments in which some discoveries were made (which is the pFDR) and recommend adhering to control of the FWE. Storey (2002) has been advancing the pFDR as the criterion of interest. Mathematically, pFDR = *E*(**Q** | **R** > 0) = FDR/*P*(**R** > 0) > FDR; thus control of the FDR does not imply pFDR control. We agree with Zaykin *et al.* (2000) that control of FWE offers more protection than FDR at the same level. However, as we argued before, FWE is not suitable for QTL analysis because at low levels such as 0.05, it leaves too little power to make discoveries of multiple QTL, and at higher levels, as allowed by suggestive linkage, it does not offer sufficient type I error control (details in *Replacing the suggestive linkage criterion with FDR control*). Moreover, in spite of its conservativeness, controlling the FWE still does not control the pFDR.

Actually, the control of the FDR strikes a balance between the usually too conservative control of the FWE and the sometimes impossible control of the pFDR, depending on the data at hand. Studying a totally nonhereditary trait with FDR = *q* is the same as with FWE = *q* (both being smaller than the pFDR). On the other hand, when QTL are present, as true discoveries are more likely than false ones, Pr(**R** > 0) > FWE. In particular, studies in which many hypotheses are rejected reflect configurations where Pr(**R** > 0) ≈ 1. Thus FDR ≈ pFDR, and controlling the FDR in such cases is reasonably close to controlling the pFDR (both being smaller than the FWE) (Weller 2000).

#### Replacing the suggestive linkage criterion with FDR control:

Let us carry the above discussion into the case of suggestive linkage. The threshold is chosen so that there will be one false linkage per genome scan on the average. Using the Poisson approximation, such a threshold is equivalent to controlling the FWE at 0.6. Now when Zaykin *et al.* (2000, p. 1918) claim that the control of FWE is better than the FDR, they argue: “ … using an FWER controlling method, one may claim that all significances obtained in the study are real, gambling upon the occurrence that the given study was not one of the 25% (or whatever FWE level that is used) that will produce a false positive.” Consider the above argument applied to the criterion for suggestive linkages: gambling that the given study is not one of the 12 out of 20 that will produce a false positive, is difficult to justify. It is therefore our view that controlling the FWE at 0.6 cannot by itself be trusted to indicate suggestive results. If one reads carefully Lander and Kruglyak (1995) similar skepticism can be sensed, as, for example, they do not see a way to confirm suggestive linkages in a second study. We therefore suggest that this criterion be abandoned and be replaced by FDR control at lower level. A good choice is *q* = 0.1, as done by Lee *et al.* (2002). We certainly do not recommend going higher than *q* = 0.2 in published reports.

Controlling the FDR at an even lower level, say *q* = 0.05, yields credible results while adapting to the number of traits, their complexity, and their degree of heritability. In studies with a few weak QTL, such FDR-significant linkage is as conservative as the usual (FWE) significant linkage. In studies with highly heritable complex traits FDR = 0.05 control offers much more power than FWE = 0.05 control. Thus false discoveries are likely to occur among the FDR-significant linkages, but the false discoveries are expected to be a small proportion of the discoveries made.

#### FDR control in multitrait studies:

Studying multiple traits, a question arises whether there is need to consider all traits jointly when controlling the FDR at level *q* or whether each trait can be considered separately. An intuitive reason for the second approach is that having a fixed proportion of errors in each trait implies the same fixed proportion of errors in the combined study. Lee *et al.* (2002) considered both options and recommended the latter. However, when each trait is considered separately the actual FDR over the entire study is determined by the type of data analyzed. For example, in a study with *k* independent nonheritable traits, the FDR for all traits combined equals 1 − (1 − *q*)* ^{k}*. On the other hand, in a study in which all traits are highly heritable, the combined FDR is approximately

*q*.

Fernando *et al.* (2004) show that if for each trait the PFP is controlled at level *q* then the PFP of the entire study is less than or equal to *q*. Our ongoing work (Benjamini and Yekutieli 2002) indicates that controlling the FDR at each trait separately is legitimate as long as the number of markers discovered this way across all traits greatly exceeds the number of traits in the study (*e.g.*, if the number of markers discovered is more than twice the number of traits the combined FDR is <2 · *q*). The connection between the two results is that in large studies with many discoveries PFP ≈ FDR. To be on the safe side, we recommend that the test statistics of all the traits in the study have to be tested simultaneously in a FDR-controlling procedure. Unlike in FWE-controlling approaches, the resulting decrease in power need not be large (see simulations in *Use of resampling-based procedures in QTL analysis*).

Yekutieli (2001) addressed the problem of controlling the FDR when simultaneously testing all test statistics in a multiple-trait study. For each trait locus and each quantitative trait the null hypothesis is that the allelic composition at the locus is unassociated with the quantitative trait. The alternative hypothesis depends on the design of the study and can be one sided, but for the most part is two sided: a nonzero additive effect for the back-cross design or nonzero additive or dominance effects for an intercross design. For each trait separately, Yekutieli (2001) proves the following:

- PRDS dependency between the test statistics in a backcross experiment corresponding to the true null hypotheses. Due to genetic linkage, for each trait all the hypotheses on a chromosome are either true or false depending on the presence of a QTL on the chromosome.Since test statistics on separate chromosomes are independent:
- Independence between the set of test statistics corresponding to false null hypotheses and those corresponding to true ones.Property b is a sufficient condition for the validity of the resampling-based FDR-controlling procedure. Properties a and b jointly imply the PRDS condition. Property b does not hold for multiple traits—a chromosome might contain QTL for only a subset of the traits in the study. Traits having negatively correlated environmental components rule out property a.

### Confirming QTL mapping with an independent study:

According to the guidelines suggested by Lander and Kruglyak (1995) the most credible linkage is a “confirmed linkage”—a significant linkage from one study found significant at the nominal 0.01 level in an independent study, preferably conducted by other investigators. They argue that each significant linkage can be tested by itself at the 0.05 level, since it was chosen in advance. Since typically one further considers a 20-cM neighborhood of markers around the significant linkage, their nominal threshold is lowered to 0.01.

The above approach has two limitations: (1) using the FWE at level 0.05 to test the significance of the results in the initial study may leave little power to make any discoveries, and (2) if a number of linkages are discovered in the first stage, neglecting to control for multiplicity in the confirmatory stage compromises the strength of the evidence. The latter is especially serious when we consider multiple complex traits, with their many potential QTL.

We therefore suggest a new FDR-controlling testing strategy in which the BH procedure is used in both the initial and the confirmatory studies. (Similarly, if FWE is controlled at the second stage then so does the two-stage procedure.)

Definition 2. A FDR procedure for confirming QTL mapping in an independent study is as follows:

- Test the
*m*null hypotheses in study 1 using the BH procedure at level*q*_{1}. - Test the
*r*_{1}hypotheses rejected in study 1 using the BH procedure at level*q*_{2}.

Proposition 3. *Under the conditions of Theorem* 1*, and for q*_{1} *and q*_{2} *fixed in advance, the FDR of procedure* 2 *is* ≤*q*_{1} · *q*_{2} · *m*_{0}*/m.*

The proof of Proposition 3 is deferred to the appendix.

If we wish to adhere to the Lander and Kruglyak (1995) choice of the “double 0.05” level, *FDR-confirmed linkages* are significant linkages from the first study that were tested at the FDR level of 0.05 in the confirmation study and remained significant. Thus FDR-confirmed linkages enjoy an FDR level of 0.0025. This way we address the two limitations of the Lander and Kruglyak approach to confirming linkages.

Otherwise, Proposition 3 can be used in the design of the experiment: determining the optimal significance level and sample sizes to be used in each study, with the possible goal of decreasing the number of sampling units (sample size times number of hypotheses), while the combined study still controls the FDR at level 0.05.

## SIMULATION STUDY

### Use of resampling-based procedures in QTL analysis:

Sabatti *et al.* (2003) suggest using resampling-based procedures in QTL analysis. To test their suggestion we compared the power of the BH procedure to the power of the resampling FDR procedure and the Churchill and Doerge (1994) FWE-controlling resampling procedure.

#### Single-trait power comparison:

This simulated experiment consisted of 550 backcross progeny. The genome of each individual consisted of 20 100-cM chromosomes. Markers were situated at 1-cM intervals—the dense marker map is meant to work in favor of the resampling-based procedures. Quantitative trait values were computed by summing the allelic effect at QTL and noise. Six QTL with effect sizes of 0.3, 0.2, 0.4, 0.1, 0.4, and 0.3 were planted on 4 chromosomes. Each simulation consisted of 500 repetitions. For each outcome variable and marker, the absolute valued *Z*-score and *P*-values were computed, and the two FDR procedures and the FWE procedure were applied at level 0.05. In all the simulations, the rejection of the null hypothesis of no association between a marker and a quantitative trait was considered a true discovery for markers on chromosomes with a QTL for the quantitative trait and a false discovery for markers on chromosomes with no QTL for the quantitative trait. To conduct the two resampling-based methods the data were resampled 3000 times under the complete null hypothesis of no QTL.

A summary of the results of this study is presented in Table 1. The two FDR-controlling procedures yield very similar results. Their FDR levels are 0.038 ± 0.004 and 0.039 ± 0.004, significantly (the expected FDR level for independently distributed test statistics). The two FDR procedures enjoy similar power and are superior to the FWE-controlling procedure. The FDR procedures have lower mean rejection thresholds (expressed in terms of *Z*-scores) and more true discoveries (>200 for the FDR procedures; 91 for the FWE procedure). The price for the increased power is a few more erroneous linkages and FWE levels of 0.63 and 0.64.

#### Multitrait power comparison:

In this set of simulations we altered the simulation of the phenotypes. We simulated one, two, four, and eight traits. QTL were placed at random. The number of chromosomes having QTL was sampled from a Poisson distribution with mean 3. The number of QTL per chromosome was either one or two. Effect sizes were sampled from *U*[−0.25, 0.4]. In this set of simulations an independent random error term was added to each trait.

In Table 2 we present the average threshold for rejecting null hypotheses for the three procedures at level 0.05 (expressed in terms of *Z*-scores and *P*-values). The two FDR procedures retain, and even increase, their power as the number of traits increases. This property is characteristic of FDR procedures when QTL are present. On the other hand, if no QTL are present FDR procedures control the FWE and the FDR threshold increases as the number of hypotheses increases. This type of behavior is evident in the performance of the FWE-controlling procedure. As the number of traits increases twofold the critical *P*-value is multiplied by 0.5.

### FDR control of the BH procedure:

According to the simulation results in *Use of resampling-based procedures in QTL analysis* the BH and the FDR resampling procedures are practically identical. In this set of simulations we verify whether the BH procedure controls the FDR in situations for which no analytical results are available.

#### FDR control in an intercross experiment:

The setting is as in the single-trait power comparison, but we altered the design of the experiment from a backcross to an intercross. We therefore added the following six dominance effects to the six QTL: 0.15, −0.15, 0.3, −0.06, −0.01, and −0.25. The simulation included 1000 replications. The simulated FDR of the BH procedure was 0.0396 ± 0.001, indicating that it also controls the FDR at level *q* · *m*_{0}/*m* in single-trait intercross experiments.

#### FDR control for negatively correlated multiple traits:

The setting is as in the multitrait power comparison with the number of traits set to eight, only this time correlated (rather than independent) errors are added to the traits. This set of simulations consisted of two runs of 1000 replications.

In the first simulation the random error terms added to the phenotypes were a sample from a multivariate normal distribution with 0 mean, unit variance, and 0.36 correlation. The FDR value for the BH procedure was 0.042 ± 0.001.

In the second simulation the eight traits were divided into two blocks of four traits (traits 1–4 and traits 5–8). The correlation of the error terms within each block remained 0.36, and the correlation of the error terms between traits belonging to different blocks was changed to −0.36. The FDR value was now 0.044 ± 0.001.

While the number of true null hypotheses varied, the expected value of *q* · *m*_{0}/*m* was 0.0425. This reveals that the introduction of negatively correlated error terms may result in FDR exceeding *q* · *m*_{0}/*m*. But the striking feature, evident in all the simulations conducted, is that the FDR level of the BH procedure is practically unaffected by correlation: in all simulations the FDR varied from *q* · *m*_{0}/*m* by <0.002.

## SUMMARY

The two advantages of the FDR approach, which make it particularly suitable for QTL analysis, are its adaptivity to the amount of information in the data and its scalability—controlling the FDR for multiple traits may come with no loss of power. By comparison, the thresholds set by Lander and Kruglyak (1995) are valid only for a single trait. If these thresholds are further modified to achieve FWE control when many traits are studied, the required size of the experiment that is needed to achieve significance may not be feasible.

We establish, via simulations, that the BH procedures can effectively be used to control the FDR in multiple-trait studies. Controlling the FDR at the 0.10 level can take the place of the suggestive linkage criterion of Lander and Kruglyak. At the 0.05 level it can assume the role of identifying significant QTL. Such FDR significant linkages can further be confirmed in an independent study by controlling the FDR again at the 0.05 level, thereby giving rise to FDR-confirmed linkages.

## Acknowledgments

We are especially thankful to two reviewers whose suggestions contributed much to the presentation of this article. This research was supported by a Focal Initiatives for Research in Science and Technology grant of the Israeli Academy of Sciences and Humanities. Yoav Benjamini was also partly supported by a National Institutes of Health grant.

## APPENDIX: PROOF OF PROPOSITION 3

Let **R**_{1}, **V**_{1}, **R**_{2}, and **V**_{2} denote the number of discoveries and false discoveries in the initial and confirmatory studies when applying procedure 2. Let

therefore, the FDR of procedure 2 is *E*(**Q**_{2}).

Conditioning on the number of discoveries and the number of false discoveries at the initial study, **R**_{1} = *r*_{1} and **V**_{1} = *v*_{1}, and using Theorem 1 with *v*_{1} and *r*_{1} taking the role of *m*_{0} and *m*, we get for *r*_{1} > 0 and **Q**_{2} 0 if *r*_{1} = 0. To complete the proof we use the independence of the two studies and express the FDR of procedure 2,

where the last inequality holds since the BH procedure is also used in the initial stage of procedure 2.

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