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PubMed2005

A new family-based association test via a least-squares method.

To test the association between a dichotomous phenotype and genetic marker based on family data, we propose a least-squares method using the vector of phenotypes and their cross products within each family. This new approach allows covariate adjustment and is numerically much simpler to implement compared to likelihood- based methods. The new approach is asymptotically equivalent to the generalized estimating equation approach with a diagonal working covariance matrix, thus avoiding some difficulties with the working covariance matrix reported previously in the literature. When applied to the data from Collaborative Study on the Genetics of Alcoholism, this new method shows a significant association between the marker rs1037475 and alcoholism.

Family↗
PubMed2006

The impact of missing and erroneous genotypes on tagging SNP selection and power of subsequent association tests.

OBJECTIVE: Single nucleotide polymorphisms (SNPs) serve as effective markers for localizing disease susceptibility genes, but current genotyping technologies are inadequate for genotyping all available SNP markers in a typical linkage/association study. Much attention has recently been paid to methods for selecting the minimal informative subset of SNPs in identifying haplotypes, but there has been little investigation of the effect of missing or erroneous genotypes on the performance of these SNP selection algorithms and subsequent association tests using the selected tagging SNPs. The purpose of this study is to explore the effect of missing genotype or genotyping error on tagging SNP selection and subsequent single marker and haplotype association tests using the selected tagging SNPs. METHODS: Through two sets of simulations, we evaluated the performance of three tagging SNP selection programs in the presence of missing or erroneous genotypes: Clayton's diversity based program htstep, Carlson's linkage disequilibrium (LD) based program ldSelect, and Stram's coefficient of determination based program tagsnp.exe. RESULTS: When randomly selected known loci were relabeled as 'missing', we found that the average number of tagging SNPs selected by all three algorithms changed very little and the power of subsequent single marker and haplotype association tests using the selected tagging SNPs remained close to the power of these tests in the absence of missing genotype. When random genotyping errors were introduced, we found that the average number of tagging SNPs selected by all three algorithms increased. In data sets simulated according to the haplotype frequecies in the CYP19 region, Stram's program had larger increase than Carlson's and Clayton's programs. In data sets simulated under the coalescent model, Carlson's program had the largest increase and Clayton's program had the smallest increase. In both sets of simulations, with the presence of genotyping errors, the power of the haplotype tests from all three programs decreased quickly, but there was not much reduction in power of the single marker tests. CONCLUSIONS: Missing genotypes do not seem to have much impact on tagging SNP selection and subsequent single marker and haplotype association tests. In contrast, genotyping errors could have severe impact on tagging SNP selection and haplotype tests, but not on single marker tests.

Algorithms↗
PubMed2003

Power of association test for detecting minor histocompatibility gene causing graft-versus-host disease following bone marrow transplantation [correction].

Incompatibility of minor histocompatibility antigen (mHa) is a major cause of acute graft-versus-host disease (GVHD) following bone marrow transplantation in human leukocyte antigen (HLA)-matched donor-recipient pairs. To avoid acute GVHD, as many mHa genes as possible need to be identified. In this study, we introduce a comparison of two proportions as an association test for detecting mHa genes in HLA-matched pairs with and without GVHD. Assuming multiple mHa loci, each with two alleles, we evaluated the effects of (1). minor allele frequency of the mHa locus of interest (denoted by p), and (2). probability of GVHD developing in a donor-recipient pair being incompatible at an mHa locus (denoted by r) on the powers of association tests for unrelated pairs and for sib pairs. Our results showed that based on a candidate gene approach, an mHa gene with high p and r values can be detected by the association test with a small sample size. Application of the present method to the Japanese population revealed that the association test for unrelated pairs is more suitable for detecting an mHa gene with a high r value than that for sib pairs. The present method will be helpful to researchers who evaluate the power of association study in advance.

Bone Marrow Transplantation↗
PubMed2006

Olfactory-tactile compatibility effects demonstrated using a variation of the Implicit Association Test.

We investigated whether the crossmodal associations between olfaction and touch reported previously in studies involving subjective report measures could also be demonstrated using an indirect measure of crossmodal association. To this end, we used a modified version of the Implicit Association Test. The participants had to make speeded discrimination responses to a series of unimodally presented olfactory (lemon vs. animal odour) or tactile stimuli (soft vs. rough fabric) using two response keys. In compatible blocks of trials, the olfactory and tactile stimuli that were mapped onto the same response key were considered to share a stronger association (e.g., the lemon odour and the soft fabric) than those that were combined onto the same response key in the incompatible blocks of trials (e.g., the animal odour and the soft fabric). The results showed that the participants responded significantly more rapidly in the compatible response mapping blocks than in the incompatible blocks, thus confirming the existence of associations between the stimuli that were considered to be compatible. These results provide the first empirical evidence that olfactory-tactile crossmodal associations are stable enough to influence performance even when not directly relevant to a participant's task.

Adult↗
PubMed2001

Family-based association tests for qualitative and quantitative traits using single-nucleotide polymorphism and microsatellite data.

Using the Genetic Analysis Workshop 12 simulated data, we contrasted results for association tests in nuclear families and extended pedigrees using single-nucleotide polymorphism (SNP) data, and we compared results for different trait definitions, for outbred and isolate populations, and for SNP and microsatellite data. SNPs in major genes 1 and 6 were analyzed using transmission disequilibrium testing (TDT) [Spielman et al., Am J Hum Genet 52:506-16, 1993], sibship disequilibrium testing (SDT) [Horvath and Laird, Am J Hum Genet 63:1886-97, 1998], family-based association testing (FBAT) [Horvath et al., Eur J Hum Genet 9:301-6, 2001], and a chi-square analysis of founders. TDT and SDT were applied in a sample of independent nuclear families, while FBAT was applied in extended pedigrees. SNPs and microsatellites were analyzed with dichotomous and quantitative trait definitions using FBAT in the isolate and outbred populations. The results of the TDT, SDT, and FBAT analyses are comparable using SNP data to identify the disease gene. However, these tests of association were not helpful in discriminating between functional and non-functional SNPs in disequilibrium. SNP data were able to identify association with affection status in a gene that influences the liability directly (MG6), but did not perform as well when assessing association with affection status in a gene that influences the outcome only through a quantitative trait (MG1). Association with MG1 was observed using the SNP data when the outcome was defined quantitatively. Microsatellite data were relatively unsuccessful in identifying association with the markers in the region of a major gene. The magnitude of the associations between SNPs and the dichotomous or quantitative trait definitions were similar in the outbred and isolated populations.

Adult↗
PubMed2005

The implicit association test as a general measure of similarity.

The Implicit Association Test (IAT) is widely used as a measure of semantic similarity (i.e., associations in semantic memory). The results of previous research and of a new study show that IAT effects can, however, also be based on other types of similarity between stimuli. We therefore put forward the hypothesis that the IAT provides a general measure of similarity. Given that similarity is highly dynamic and context-dependent, our view that the IAT measures similarity is compatible with existing evidence showing that IAT effects are highly malleable. We provide further evidence for this in a new study in which the outcome of an IAT depended on whether the perceptual or functional characteristics of the stimuli were made salient.

Analysis of Variance↗
PubMed1985

Construction of matched verbal and design continuous paired associate tests.

We developed verbal and figural continuous paired associate tests (CPAT) that are matched on internal consistency and on the distributional properties of mean item difficulty, variance, and skewness. The Verbal CPAT is composed of high frequency nouns, verbs, and adjectives. Selection of the designs was guided by literature on the effects of right-hemisphere damage on memory for designs. One hundred subjects were given 80 items from the verbal CPAT and 80 items from the designs CPAT. Twenty subjects at these five ranges of Wechsler Memory Quotient were evaluated: less than or equal to 79, 80-89, 90-99, 100-109, greater than or equal to 109. The final 40-item version of the Verbal CPAT had a mean of 26.72, a SD of 7.03, and an alpha of .859. The Designs CPAT had a mean of 26.42, a SD of 7.75, and an alpha of .886. Neither test was significantly skewed. These matched tests should be useful in making inferences about differences between verbal and figural memory that are not confounded with the problem of differential test sensitivity.

Adolescent↗
PubMed2004

Reducing the influence of extrapersonal associations on the Implicit Association Test: personalizing the IAT.

The authors argue that the Implicit Association Test (IAT; A.G. Greenwald, D.E. McGhee, & J.L.K. Schwartz, 1998) can be contaminated by associations that do not contribute to one's evaluation of an attitude object and thus do not become activated when one encounters the object but that are nevertheless available in memory. The authors propose a variant of the IAT that reduces the contamination of these "extrapersonal associations." Consistent with the notion that the traditional version of the IAT is affected by society's negative portrayal of minority groups, the "personalized" IAT revealed relatively less racial prejudice among Whites in Experiments 1 and 2. In Experiments 3 and 4, the personalized IAT correlated more strongly with explicit measures of attitudes and behavioral intentions than did the traditional IAT. The feasibility of disentangling personal and extrapersonal associations is discussed.

Adult↗
PubMed2001

Attitudes and the Implicit Association Test.

Three studies examined the relationship between the Implicit Association Test (IAT) and explicit attitudes. In the 1st and all subsequent studies, the lack of any correlation between the IAT and explicitly measured attitudes supports the view that the IAT is independent from explicit attitudes. Study 2 examined the relationships among the IAT, explicit attitudes, and behavior and found that the explicit attitudes predicted behavior but the IAT did not. Finally, in Study 3 it was found that the IAT was affected by exposing participants to new associations between attitude objects, whereas the explicit attitudes remained unchanged. Taken together, these results support an environmental association interpretation of the IAT in which IAT scores reflect the associations a person has been exposed to in his or her environment rather than the extent to which the person endorses those evaluative associations.

Attitude↗
PubMed2004

Family-based association tests for survival and times-to-onset analysis.

In this paper, we discuss family-based association test (FBATs) relating genetic data to survival and time-to-onset data. We show how the standard logrank and Wilcoxon statistics can be used with family data to develop tests of association. We prove that the FBAT-logrank approach can be identical to the proportional hazard approach discussed in Mokliatchouk et al. (2000). Further, using simulation studies, we compare the power of the logrank, Wilcoxon and an approach developed for censored exponential data (Euro J Hum Gen 2001; 9:301-306). Based on the results of the simulation study, we suggest rules of thumb about which statistics to use in a given situation. An application of all three tests to an Alzheimer study illustrates the practical relevance of our discussion.

Age of Onset↗
PubMed2003

Understanding and using the implicit association test: I. An improved scoring algorithm.

In reporting Implicit Association Test (IAT) results, researchers have most often used scoring conventions described in the first publication of the IAT (A.G. Greenwald, D.E. McGhee, & J.L.K. Schwartz, 1998). Demonstration IATs available on the Internet have produced large data sets that were used in the current article to evaluate alternative scoring procedures. Candidate new algorithms were examined in terms of their (a) correlations with parallel self-report measures, (b) resistance to an artifact associated with speed of responding, (c) internal consistency, (d) sensitivity to known influences on IAT measures, and (e) resistance to known procedural influences. The best-performing measure incorporates data from the IAT's practice trials, uses a metric that is calibrated by each respondent's latency variability, and includes a latency penalty for errors. This new algorithm strongly outperforms the earlier (conventional) procedure.

Adult↗
PubMed2006

Improving the power of association tests for quantitative traits in family studies.

Association mapping based on family studies can identify genes that influence complex human traits while providing protection against population stratification. Because no gene is likely to have a very large effect on a complex trait, most family studies have limited power. Among the commonly used family-based tests of association for quantitative traits, the quantitative transmission-disequilibrium tests (QTDT) based on the variance-components model is the most flexible and most powerful. This method assumes that the trait values are normally distributed. Departures from normality can inflate the type I error and reduce the power. Although the family-based association tests (FBAT) and pedigree disequilibrium tests (PDT) do not require normal traits, nonnormality can also result in loss of power. In many cases, approximate normality can be achieved by transforming the trait values. However, the true transformation is unknown, and incorrect transformations may compromise the type I error and power. We propose a novel class of association tests for arbitrarily distributed quantitative traits by allowing the true transformation function to be completely unspecified and empirically estimated from the data. Extensive simulation studies showed that the new methods provide accurate control of the type I error and can be substantially more powerful than the existing methods. We applied the new methods to the Collaborative Study on the Genetics of Alcoholism and discovered significant association of single nucleotide polymorphisms (SNP) tsc0022400 on chromosome 7 with the quantitative electrophysiological phenotype TTTH1, which was not detected by any existing methods. We have implemented the new methods in a freely available computer program.

Alcoholism↗
PubMed1999

Normative comparisons for the controlled oral word association test following acute traumatic brain injury.

The Controlled Oral Word Association Test (COWAT) is widely used in clinical neuropsychology as a measure of verbal fluency. It is important for psychologists to realize that using the recently published normative data will result in different clinical conclusions because the updated normative sample performed better than the original normative sample. The purpose of this study was to compare the original and updated norms in a large sample of patients with acute traumatic brain injuries (N=669). The percentages of patients who scored below the 5th centile in each system varied as a function of brain injury severity. Moreover, a substantially larger number of patients scored in the impaired range according to the updated normative data.

Acute Disease↗
PubMed2005

Understanding and using the Implicit Association Test: II. Method variables and construct validity.

The Implicit Association Test (IAT) assesses relative strengths of four associations involving two pairs of contrasted concepts (e.g., male-female and family-career). In four studies, analyses of data from 11 Web IATs, averaging 12,000 respondents per data set, supported the following conclusions: (a) sorting IAT trials into subsets does not yield conceptually distinct measures; (b) valid IAT measures can be produced using as few as two items to represent each concept; (c) there are conditions for which the administration order of IAT and self-report measures does not alter psychometric properties of either measure; and (d) a known extraneous effect of IAT task block order was sharply reduced by using extra practice trials. Together, these analyses provide additional construct validation for the IAT and suggest practical guidelines to users of the IAT.

Adult↗
PubMed2005

Does the compatibility effect in the race Implicit Association Test reflect familiarity or affect?

In the Implicit Association Test (IAT; Greenwald, McGhee, & Schwartz, 1998) involving race classification (white vs. black), an apparent compatibility effect is found between the "pleasant" attribute and the "white" category. This race IAT effect has been interpreted in terms of "implicit prejudice"--that is, more positive evaluation of whites than of blacks that is not open to consciousness. We suggested instead that the race IAT effect is better interpreted in terms of the salience asymmetry account proposed by Rothermund and Wentura (2004), whereby greater familiarity with the white category makes it more salient. Evidence that has been presented against the familiarity interpretation is considered, and alternative interpretations of findings related to the race IAT effect are discussed.

Affect↗
PubMed2001

Health of the Implicit Association Test at age 3.

Since its first publication in 1998, the Implicit Association Test (IAT) has been used repeatedly to measure implicit attitudes and other automatic associations. Although there have also been a few studies critical of the IAT, there now exists substantial evidence for the IAT's convergent and discriminant validity, including new evidence reported in several of the articles in this special issue. IAT attitude measures have often correlated only weakly with explicit (self-report) measures of the same associations. It therefore seems appropriate to conclude that the IAT assesses constructs that are often (but not always) distinct from the corresponding constructs measured by self-report.

Association↗
PubMed2002

Antisocial alcoholism and serotonin-related polymorphisms: association tests.

Central serotonin dysfunction appears to be related to a subtype of alcoholism with antisocial impulsive features (type II; antisocial alcoholism). The serotonergic deficit may be associated with greater impulsivity, which in turn facilitates both alcohol dependence and antisocial behavior. The present study tested association of antisocial impulsive alcoholism with candidate genes related to serotonergic neurotransmission, using families. Eight markers were assayed using polymerase chain reaction: tryptophan hydroxylase (intron 7), the serotonin transporter SLC6A4 (VNTR 9/12), HTTLPR, the three serotonin receptor types HTR1B (G861C), HTR2A (T102C) and HTR2C (Cys23Ser), monoamine oxidase A (T1460C), and (CA)(n). Eligible probands had early age of onset of alcoholism, child conduct disorder, and two or more symptoms of adult Antisocial Personality Disorder. This sample included 35 probands, their parents, and some siblings (n = 116). Association tests were conducted using the Haplotype Relative Risk method for antisocial alcoholism diagnosis and the George-Elston regression method (the S.A.G.E. program ASSOC) for quantitative antisocial alcoholism severity. Haplotype Relative Risk analyses were not significant at the 0.05 level for any of the markers. Trends suggestive for future research occurred for tryptophan hydroxylase and HTR2A. Quantitative ASSOC analyses showed significant marker effects (P < 0.05) for both monoamine oxidase A markers, which were in linkage disequilibrium. Antisocial alcoholism symptom severity was higher with monoamine oxidase A C homozygotes or hemizygotes, indicating that low monoamine oxidase activity may be important. Future studies are needed to examine joint and interactive effects of serotonin-related markers.

Adult↗