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PubMed1998

Linkage and association.

Methods of both linkage analysis and association analysis may be model-based or model-free. The former are useful for initial exploratory analysis, the latter for more detailed multivariate genometric analysis. Linkage leads to an association, but that association may be solely intrafamilial. Allelic association may be due to pleiotropy, linkage disequilibrium, meiotic drive, selection, or population stratification. Using non-transmitted parental alleles as controls for alleles transmitted to cases, in conjunction with a McNemar-type test, does not detect association in the absence of linkage. Model-based analyses should use models that approximate the complexity of the disease being studied in order to be both robust and powerful.

Case-Control Studies↗
PubMed1999

Likelihoods and TDT for the case-parents design.

Association studies using diseased cases and their parents avoid biases due to population stratification, and the transmission/disequilibrium test (TDT) is a popular method of analysis. Sample size and power calculations for the TDT method have been reported, but often for the special situation of multiplicative effects of alleles on the genotype relative risks. Furthermore, some of the proposed calculations ignore the dependence of transmitted alleles from a pair of heterozygous parents when the effects are not multiplicative, which can lead to erroneous sample size calculations. We demonstrate how to calculate sample size and power for the TDT method for general genotype relative risks. As an alternative to the TDT method, we present likelihood methods for a variety of genotype relative risk models. Exact likelihood methods are presented to allow for accurate small-sample analyses. We demonstrate by numerical comparisons: (1) that the TDT method is inefficient for recessive patterns of relative risks, (2) for alleles that are not rare, falsely assuming a multiplicative model can lead to gross underestimation of the required sample size for the TDT statistic, and (3) for common alleles, if the true genotype relative risks have an approximately dominant pattern, then the TDT method can be grossly inefficient compared to likelihood methods. An alternative likelihood ratio statistic, based on two degrees of freedom, tends to be robust for a wide range of genotype relative risk models. Finally, we discuss how to use standard software for conditional logistic regression to accurately assess effects of alleles as well as genotype-environment interaction.

Genome, Human↗
PubMed2000

ApoE polymorphism accounts for only part of the genetic variation in quantitative ApoE levels.

ApoE levels and chromosome 19 ApoE polymorphisms were measured in a sample of 156 Dutch families. Each pedigree consisted of parents aged 35-65 years and their twin offspring aged 14-21 years. A significant effect of the chromosome 19 apoE locus on quantitative plasma levels of apolipoprotein E was observed. The ApoE polymorphism explained 16% of the variance in ApoE levels. Tests of association of ApoE levels with the apoC1 locus, which is in complete linkage disequilibrium with the ApoE locus, also showed a significant effect, although the variance explained by ApoC1 was only 1%. Examination of the covariance between twins classified according to allele sharing indicates that the association is not due to population stratification, but to a genuine effect of the ApoE locus on levels. However, the ApoE locus accounts for only one-fourth of the genetic variation in ApoE levels.

Adolescent↗
PubMed2000

Association study of the tryptophan hydroxylase gene and bipolar affective disorder using family-based internal controls.

The tryptophan hydroxylase (TPH) gene encodes for the rate-limiting enzyme of the serotonin metabolism and, therefore, has to be considered a major candidate for association studies in affective disorders. Recently, an association between this gene and bipolar affective disorder has been reported in a French population. We sought to replicate this finding in a German sample. Allele frequencies of a biallelic polymorphism (A218C) of the TPH gene were determined in 95 bipolar I patients and their parents. Preferential transmission of alleles from heterozygous parents to bipolar offspring was tested with the "transmission disequilibrium test" (TDT), which eliminates the contribution of population stratification to an association finding. Our sample yielded a power >90% to detect the originally reported effect. Neither allele 218A nor allele 218C were preferentially transmitted from heterozygous parents to bipolar offspring. Our results, therefore, do not support the hypothesis that the TPH gene is involved in the etiology of bipolar disorder.

Adult↗
PubMed2000

Genetic polymorphism at the CLOCK gene locus and major depression.

Genetic analysis in both mouse and Drosophila has indicated that the product of the CLOCK gene is an essential component of a circadian rhythm timing system. A single nucleotide polymorphism (SNP), T3111C, in the 3' flanking region of the human CLOCK gene has been identified. Homozygotes or heterozygotes for the 3111C allele have been reported to have higher mean scores on a measure of evening preference for activity (vs. morning preference) than subjects homozygous for the 3111T allele. Since major depression is hypothesized to be closely linked to circadian rhythms, we explored whether this polymorphism might be related to susceptibility to major depression. We also ascertained allele frequency in an African-American control population, to begin to evaluate population variation at this locus. CLOCK T3111C allele frequencies were determined in 280 European American (EA) subjects, 143 with a history of major depression and 137 screened controls, and in 58 African American (AA) screened control subjects, using a polymerase chain reaction (PCR) - restriction fragment length polymorphism (RFLP) method. There was no significant difference between EA depressed and control subjects in allele frequency. There was a significant difference in allele frequency between EA and AA subjects, demonstrating a potential for population stratification. In none of these groups were significant deviations from Hardy-Weinberg equilibrium found. The present data do not support an association between CLOCK gene alleles at the T3111C locus and major depression.

Alleles↗
PubMed2000

Robust transmission regression models for linkage and association.

We present a general regression model that accounts for both linkage and linkage disequilibrium (LD) when analyzing nuclear family data. The method does not require LD to exist in order to evaluate linkage, but if LD does exist, the power to detect linkage can increase due to improved information on linkage phase. The proposed method is general, allowing for a variety of traits (e.g., binary affection status, categorical and quantitative phenotypes), affecteds only analyses, and covariates. Covariates can be useful to assess heterogeneity of linkage and LD, as well as gene-environment interactions. Other advantages of our methods are that: LD parameters are not defined without linkage, so that population stratification cannot bias the analyses; a combined test for linkage and LD can be used to test for linkage; given the existence of linkage, an adjusted LD test useful for fine-mapping can be constructed; covariate effects can be flexibly modeled; and families containing a single child and families containing multiple offspring can be combined for a single analysis (capitalizing on the LD information provided by single-child families and the combined linkage and LD information provided by multiple offspring). The basic features of the regression model are presented, as well as discussions of potential applications and critical statistical issues.

Adult↗
PubMed2001

Efficient use of siblings in testing for linkage and association.

Tests of linkage and association between a disease and either a candidate gene or marker allele can be based on sibships with at least one affected and one unaffected sibling. However, specialized techniques are required to account for within-sibship correlation if some sibships contain more than one affected or more than one unaffected sib. In this paper, we propose Within Sibship Paired Resampling (WSPR), a technique that is designed to test the null hypothesis of no linkage or no association, even when sibships contain variable numbers of sibs. One repeatedly generates data subsets based on randomly sampling one affected and one unaffected sibling from each sibship, and each subset is analyzed individually. Then, evidence is combined by averaging results across these resampled data sets, applying a variance expression that implicitly accounts for the correlation among siblings. While the general WSPR procedure allows for numerous testing strategies, we describe two in detail. Simulation results for scenarios with varying degrees of population stratification demonstrate good power for the WSPR testing methods compared to the sib TDT (S-TDT) and the sibship disequilibrium test (SDT).

Computer Simulation↗
PubMed1998

Transmission disequilibrium as a test of linkage and association between HLA alleles and pauciarticular-onset juvenile rheumatoid arthritis.

OBJECTIVE: To determine if HLA class I and II alleles previously found to be associated with (or protective against) pauciarticular-onset juvenile rheumatoid arthritis (pauci-onset JRA) in population-association studies are transmitted from heterozygous parents to an extent different from the expected 50%. METHODS: One hundred one Caucasian North American families that had a child with pauci-onset JRA and at least 1 parent who was heterozygous for the allele of interest were available for analysis. Both biologic parents and all children (affected and unaffected) were typed for HLA class I and II alleles. The transmission disequilibrium test (TDT) was used to determine if affected offspring received the disease-associated (or protective) allele more (or less) frequently than its alternate allele. In families in which an unaffected sibling was available, the unmatched chi-square test was used to determine if a meiotic segregation distortion bias existed. RESULTS: HLA class I alleles A2, B27, and B35 showed a significantly higher than expected frequency of transmission to affected offspring, as did class II alleles DR5 and DR8. HLA-DR4 was found to be transmitted significantly less frequently than expected to affected, but not unaffected, offspring. All alleles that showed an excess transmission to affected offspring were transmitted to unaffected offspring at expected rates. When the data were stratified by age and sex, the likelihood of transmission of some of the alleles was strongly influenced by these variables. For example, excess transmission of HLA-DR5 was found exclusively in female patients who were younger at the time of disease onset. CONCLUSION: Results from these family-based studies rule out the possibility that HLA disease associations found in earlier studies were a result of population stratification and establish linkage and association between the major histocompatibility complex and pauci-onset JRA.

Adolescent↗
PubMed2002

Dopamine transporter polymorphism associated with externalizing behavior problems in children.

Early childhood externalizing behavior is a stable and heritable pattern of aggressive and delinquent behavior that often leads to the development of serious psychiatric disorders such as conduct disorder and attention deficit hyperactivity disorder. We examined the relationship between parent reported externalizing behavior (assessed at ages 4, 7, and 9 years) and the VNTR polymorphism of the 3' untranslated region of SLC6A3 (DAT1) in a community sample of 790 children ascertained as part of our longitudinal twin and adoption studies. We applied the sibling-based methodology developed by Fulker et al. [1999: Am J Hum Genet 64:259-267] for estimating allelic association with quantitative traits, while controlling for population stratification. An extension of these methods allowed for the inclusion of monozygotic twins, dizygotic twins, siblings, and singletons. We have demonstrated that the 9-repeat variant of the DAT1 is a significant risk allele for externalizing behavior at ages 4 (P=0.001) and 7 years (P=0.02). Although the effect size was negligible at age 9 (P=0.92), a formal test of the developmental decrease in effect across the three ages was non-significant (P=0.70).

Adolescent↗
PubMed2002

Candidate genes involved in cardiovascular risk factors by a family-based association study on the island of Kosrae, Federated States of Micronesia.

Altered plasma levels of lipids and lipoproteins, obesity, hypertension, and diabetes are major risk factors for atherosclerotic cardiovascular disease. To identify genes that affect these traits and disorders, we looked for association between markers in candidate genes (apolipoprotein AII (apo AII), apolipoprotein AI-CIII-AIV gene cluster (apo AI-CIII-AIV), apolipoprotein E (apo E), cholesteryl ester transfer protein (CETP), cholesterol 7alpha-hydroxylase (CYP7a), hepatic lipase (HL), and microsomal triglyceride transfer protein (MTP)) and known risk factors (triglycerides (Tg), total cholesterol (TC), apolipoprotein AI (apo AI), apolipoprotein AII (apo AII), apolipoprotein B (apo B), body mass index (BMI), blood pressure (BP), leptin, and fasting blood sugar (FBS) levels.) A total of 1,102 individuals from the Pacific island of Kosrae were genotyped for the following markers: Apo AII/MspI, Apo CIII/SstI, Apo AI/XmnI, Apo E/HhaI, CETP/TaqIB, CYP7a/BsaI, HL/DraI, and MTP/HhpI. After testing for population stratification, family-based association analysis was carried out. Novel associations found were: 1) the apo AII/MspI with apo AI and BP levels, 2) the CYP7a/BsaI with apo AI and BMI levels. We also confirmed the following associations: 1) the apo AII/MspI with Tg level; 2) the apo CIII/SstI with Tg, TC, and apo B levels; 3) the Apo E/HhaI E2, E3, and E4 alleles with TC, apo AI, and apo B levels; and 4) the CETP/TaqIB with apo AI level. We further confirmed the connection between the apo AII gene and Tg level by a nonparametric linkage analysis. We therefore conclude that many of these candidate genes may play a significant role in susceptibility to heart disease.

Adult↗
PubMed1995

Association and linkage studies of the TAQI A1 allele at the dopamine D2 receptor gene in samples of female and male alcoholics.

To address the controversy surrounding DRD2 and alcoholism, we performed linkage and association studies utilizing alcoholic men from high-density families largely uncontaminated by other psychopathology and female alcoholics for whom secondary drug dependence (averaging 10 years later onset) was a prominent feature. The males and females were combined for a total of 52 alcoholics, and compared to 30 controls screened for the absence of alcoholism and other psychopathology, revealing a significant association between the frequency of the TaqI A1 allele and alcoholism. However, linkage and family-based association studies conducted on 20 families of male alcoholics found no evidence for association or linkage between Taq A and alcoholism. The results of our population-based association study, placed in the context of the literature, suggest that minimizing psychopathology in control groups is probably a more important explanation for divergent results than either sampling error or population stratification. When combined with the complete lack of within-family evidence, we concluded that the association, while not appearing to be artifactual, is not specific to the alcoholism phenotype, per se.

Alcoholism↗
PubMed2001

Caught in the trio trap? Potential selection bias inherent to association studies using parent-offspring trios.

During the last years, the validity of classic case control studies in psychiatric genetic research has been increasingly under question due to the risk of population stratification problems inherent to this type of association study. By consequence, the application of family-based association studies using parent-offspring trios has been strongly advocated. Recently, however, in a study comparing clinical characteristics between index patients from parent-offspring trios and singleton patients with bipolar affective disorder, the question was raised whether a systematic neglect of case control association studies could lead to a selection bias of susceptibility genes. In a similar approach, we compared demographic and clinical characteristics of 122 singleton bipolar patients with those of 54 bipolar patients derived from parent-offspring trios. The singleton patients did not only present with a higher age of onset, but also with a higher frequency of suicidal behavior and a higher familial loading for suicidality. These findings suggest that the genetic mechanism for disease might be different between trio-based and classic case control samples, where patients are examined whose parents are not available for genetic studies. Thus, giving up case control designs for the sake of family-based association studies could be at the risk of selecting against several genetically determined factors.

Adult↗
PubMed2001

Association of the tryptophan hydroxylase gene with smoking initiation but not progression to nicotine dependence.

We investigated the association between two markers in the seventh intron of the tryptophan hydroxylase gene (TPH C218A and C779A) in a population-based case control study of 780 genotyped subjects. As in prior studies, the two markers were in strong linkage disequilibrium. The phenotypes we studied were smoking initiation and progression to nicotine dependence. Allele, genotype, and estimated haplotype frequencies for each marker were highly significantly different for smoking initiation (P < 0.0004 for each comparison) and were nonsignificant for progression to nicotine dependence. An empirical test suggested that the positive results were unlikely to have resulted from population stratification. Our results are similar to those of Lerman et al. [2001: Am J Med Genet (Neuropsychiatr Genet) 105:000-000] in associating these TPH markers with a construct related to smoking initiation but dissimilar in the variable implicated. If these results replicate in other samples, the serotonergic system may be involved in the etiology of smoking initiation given the rate-limiting role of TPH in the biosynthesis of serotonin.

Alleles↗
PubMed2005

The 3111T/C polymorphism of hClock is associated with evening preference and delayed sleep timing in a Japanese population sample.

Sleep timing is influenced by the circadian system. Morningness-eveningness (ME) preference in humans is affected by the free-running period, which is determined by circadian clock-relevant genes. In this study, we investigated association between the 3111T/C polymorphism in the 3'-flanking region of hClock (Homo sapiens Clock homolog) and ME preference in 421 Japanese subjects. The Horne-Ostberg ME questionnaire (MEQ) scores showed normal distribution, with mean score of 51.2 +/- 1.4 (range, 25-73), and scores were positively correlated with sleep onset time (r = 0.541, P < 0.001) and wake time (r = 0.513, P < 0.001). MEQ scores were significantly lower in subjects with 3111C/C (n = 12) than in subjects with 3111T/C (n = 106, P < 0.001) or 3111T/T (n = 303, P < 0.001), suggesting a stronger eveningness preference in 3111C/C homozygotes. This group also showed significantly delayed sleep onset (P < 0.001), shorter sleep time (P < 0.001), and greater daytime sleepiness (P < 0.001) in comparison to parameters in the subjects with the 3111T allele. There was no significant difference in any of these parameters between the 3111C/T and 3111T/T genotypes. The influence of the 3111T/C polymorphism on ME preferences in Caucasian populations remains controversial. The present findings in a Japanese population sample, which should have a relatively low risk of population stratification effects, suggest the significance of the association of the 3111C/C allele of hClock with evening preference.

Adult↗
PubMed2007

Dopaminergic polymorphisms in Tourette syndrome: association with the DAT gene (SLC6A3).

Tourette syndrome (TS) is a chronic neuropsychiatric disorder characterized by involuntary motor and phonic tics. The pattern of inheritance and associated genetic abnormality has yet to be fully characterized. A dopaminergic abnormality in this disorder is supported by response to specific therapies, nuclear imaging, and postmortem studies. In this protocol, dopaminergic polymorphisms were examined for associations with TS and attention-deficit hyperactivity disorder (ADHD). Polymorphisms investigated included the dopamine transporter (DAT1 DdeI and DAT1 VNTR), dopamine receptor (D4 Upstream Repeat and D4 VNTR), dopamine converting enzyme (dopamine beta-hydroxylase), and the acid phosphatase locus 1 (ACP1) gene. DNA was obtained from 266 TS individuals +/- ADHD and 236 controls that were ethnicity-matched. A significant association, using a genotype-based association analysis, was identified for the TS-total and TS-only versus control groups for the DAT1 DdeI polymorphism (AG vs. AA, P = 0.004 and P = 0.01, respectively). Population structure, estimated by the genotyping of 27 informative SNP markers, identified 3 subgroups. A statistical re-evaluation of the DAT1 DdeI polymorphism following population stratification confirmed the association for the TS-total and TS-only groups, but the degree of significance was reduced (P = 0.017 and P = 0.016, respectively). This study has identified a significant association between the presence of TS and a DAT polymorphism. Since abnormalities of the dopamine transporter have been hypothesized in the pathophysiology of TS, it is possible that this could be a functional allele associated with clinical expression.

Adolescent↗
PubMed2003

Pedigree disequilibrium tests for multilocus haplotypes.

Association tests of multilocus haplotypes are of interest both in linkage disequilibrium mapping and in candidate gene studies. For case-parent trios, I discuss the extension of existing multilocus methods to include ambiguous haplotypes in tests of models which distinguish between the cis and trans phase. A likelihood-ratio test is proposed, using the expectation-maximization (E-M) algorithm to account for haplotype ambiguities. Assumptions about the population structure are required, but realistic situations, including population stratification, which violate the assumptions lead to conservative tests. I describe a permutation procedure for the null hypothesis of interest, which controls for violation of the assumptions. For general pedigrees, I describe extensions of the pedigree disequilibrium test to include uncertain haplotypes. The summary statistics are replaced by their expected values over prior distributions of haplotype frequencies. If prior distributions are not available, a valid test is possible by using the E-M algorithm to estimate the null distribution of haplotype frequencies. Similar methods are available for quantitative traits. Exact permutation tests are difficult to construct in small samples, but an approximate procedure is appropriate in large samples, and can be used to account for dependencies between tests of multiple haplotypes and loci.

Algorithms↗
PubMed2003

Candidate gene association analysis for a quantitative trait, using parent-offspring trios.

With the increasing availability of genetic data, many studies of quantitative traits focus on hypotheses related to candidate genes, and also gene-environment (G x E) and gene-gene (G x G) interactions. In a population-based sample, estimates and tests of candidate gene effects can be biased by ethnic confounding, also known as population stratification bias. This paper demonstrates that even a modest degree of ethnic confounding can lead to unacceptably high type I error rates for tests of genetic effects. The parent-offspring trio design is reviewed, and several forms of the quantitative transmission disequilibrium test (QTDT) are summarized. A variation of the QTDT (QTDTM) is described that is based on a linear regression model with multiple intercepts, one per parental mating type. This and other models are expanded to allow testing of G x E and G x G interactions. A method for computing required sample sizes using direct computations is described. Sample size requirements for tests of genetic main effects and G x E and G x G interactions are compared across various QTDT approaches to infer their efficiencies relative to one another. The QTDTM is found to meet or exceed the efficiency of other QTDT approaches. For example, the QTDTM is approximately 3% more efficient than the QTDT of Rabinowitz ([1997] Hum. Hered. 47:342-350) for testing a genetic main effect, but can be as much as twice as efficient for testing G x E interaction, and three times more efficient for testing G x G interaction.

Algorithms↗