Genetic Polymorphism for Human Platelet Thermostable Phenol Sulfotransferase (Ts Pst) Activity

Platelet TS PST basal activity and thermal stability were measured in blood samples from 237 individuals in 50 nuclear families. Significant correlations were found among first degree relatives, confirming the previously reported familial aggregation of TS PST basal activity and thermal stability. Commingling analysis of basal TS PST activity provided evidence for multiple component distributions, and after transformation to remove skewness, segregation analysis supported a major gene hypothesis. For TS PST thermal stability, commingling analysis also provided evidence for multiple component distributions. However, segregation analyses were equivocal with regard to the presence of a major gene for thermal stability, since support for a major gene model depended on skewness. Bivariate commingling analysis, which examined thermal stability by simultaneously considering basal activity and activity after heating, suggested that genotypes, as defined by the inferred component distributions for TS PST activity, differ in thermal stability. A three-allele model is proposed as one hypothesis that may account for the combined results of basal activity and thermal stability. The results of this study indicate that a major gene polymorphism in conjunction with polygenic inheritance plays an important role in the regulation of both level of activity and thermal stability of this important drug-metabolizing enzyme in humans.     

Inferring a major gene for quantitative traits by using segregation analysis with tests on transmission probabilities: how often do we miss?

In an effort to safeguard against false inference of a major gene in segregation analysis, it has become common practice to require nonrejection of the Mendelian-transmission hypothesis (Mendelian tau's) and rejection of the no-transmission hypothesis (equal tau's). However, it is not known how often one would actually infer a major gene, when one exists, by using these criteria. A simulation study was undertaken to investigate this issue. Segregation of a Mendelian gene under a variety of models was simulated in families with both parents and three children. The data were analyzed by using POINTER; the assumptions under the generating and analysis models were identical. By design, the power to reject the no-major-effect hypothesis (q = 0) was > 60% for all models considered; tests on the transmission probabilities were carried out only when q = 0 was rejected, using alpha = 0.05 for all tests. The rates of Mendelian inference were mostly in the range of 22%-50% under recessive inheritance, versus 60%-99% under dominant inheritance. Notably, it was not possible to resolve the transmission (from among Mendelian tau's, equal tau's, and general unconstrained tau's) in approximately 20%-70% of the cases under recessive models, versus 3%-15% under dominant models. Therefore, while tests on transmission probabilities can serve to reduce rates of false inference of a major gene, it is also possible to fail to infer a major gene when one indeed exists, especially under recessive inheritance.     

Platelet monoamine oxidase (MAO) activity: evidence for a single major locus.

Monoamine oxidase (MAO), a mitochondrial enzyme involved in the degradation of biogenic amines, has been associated with psychiatric morbidity. Although twin and family studies have indicated that MAO activity is familial, the exact mode of transmission is unclear. We performed segregation analysis on 154 nuclear families containing 419 individuals using the mixed model, which allows for a single major locus with a polygenic background. We were able to reject a dominant and additive locus with or without a heritable background and a recessive locus without background. The acceptable models were: (1) a codominant model without background where the mean of the heterozygote distribution was 30% of the distance from the low to the high homozygote distributions, and (2) a recessive locus with heritable background. In both cases, the gene frequency for the high-MAO allele is approximately .25--at odds with suggestions that low-MAO represents a genetic marker for a disorder such as schizophrenia with a lifetime risk of only 0.85%. To ensure that results were not artifacts from a familial, skewed distribution, the data were also analyzed after power transformation. In addition, hypotheses were tested using both the joint and conditional likelihoods to examine for possible misspecification of the model with respect to intergenerational differences. Finally, we allowed for non-Mendelian transmission probabilities to provide another class of alternatives against which to test the hypothesis of a major locus. All these approaches provided additional confirmation for the presence of a major locus segregating within these families.     

Complex segregation analysis of non-myoclonic idiopathic generalized epilepsy in families ascertained from probands affected with idiopathic epilepsy with tonic-clonic seizures in Antioquia,Colombia

In an attempt to identify the possible role of major genes, multifactorial inheritance, and cohort effects in the susceptibility to idiopathic epilepsy with generalized tonic-clonic seizures of the awakening type (GTCS), complex segregation analysis was performed in 196 nuclear families ascertained through affected probands with idiopathic epilepsy with GTCS belonging to the Paisa community of Antioquia (Colombia). Models postulating no transmission, single major locus (dominant and recessive) only, and multifactorial component only, were rejected. Since the codominant single major locus model could not be rejected and models that assign no major locus to transmission, no polygenic component to transmission, and no transmission of the major effect were rejected, complex segregation analysis suggested that a major autosomal codominant allele together with a multifactorial component (mixed model) best explained clustering of idiopathic epilepsy with GTCS in families of the Paisa community. The deficit of transmission of heterozygotes (0.17) is compatible with the existence of epistasis acting on a major gene whose frequency was estimated to be 0.0211. Its transmission variance accounts for 81% of the susceptibility to idiopathic epilepsy with GTCS. The complementary variance (19%) is due to the polygenic component. Received: 19 January 1996 / Revised: 11 March 1996     

The role of major gene in clubfoot.

The roles of major gene and multifactorial inheritance in the etiology of clubfoot (talipes equinovarus) were studied using Caucasian clubfoot families ascertained in Indiana. The method of analysis used was complex segregation analysis under the mixed model, in which five genetic parameters were examined to test hypotheses on major gene by displacement (t), degree of dominance (d), gene frequency (q), transmission probability (tau2), and multifactorial inheritance by heritability (H). The analysis showed that the segregation pattern of clubfoot in these families is best explained by assuming the action of a major gene with additional contribution of multifactorial inheritance. The estimates of the parameters under the best-fitting model were d = .82, t = 4.69, q = .030, tau2 = .50, and H = .17.     

Genetic regulation of plasma and red blood cell magnesium concentration in man. II. Segregation analysis.

A previous paper in this series reported that genetic factors play a major role in the familial transmission of plasma (P) and red blood cell (RBC) magnesium (Mg) concentrations. We report here the results of commingling analysis based on a random sample of unrelated individuals, and complex segregation analysis of a random sample of nuclear families. For RBC Mg, there is evidence for a mixture of two distributions, but not for three. For P Mg, there is no evidence for commingling. Complex segregation analysis under a mixed model yielded significant support for a major gene effect on RBC Mg, but not on P Mg. Parameter estimates indicated that the data are compatible with a rather common major gene (q = .23) for elevated RBC Mg, roughly 5% of the population being homozygotes for this gene, that the nonfamilial factors account for a small fraction of the total variance, and that the overlap of distributions of homozygotes is not large.     

Inheritance of acute appendicitis: familial aggregation and evidence of polygenic transmission.

We explored familiality as well as the heritability and possible mode(s) of inheritance of acute appendicitis in childhood and early adolescence. Our case-control study showed that a positive family history for reported appendectomy was significantly more frequent in families of 80 consecutive patients eventually proved to have histopathologic acute appendicitis than in families of surgical controls matched for sex, age, and number of siblings. The relative risk was 10.0 (95% confidence limits 4.7-21.4). The pattern of familial aggregation was further supported by the fact that the age-standardized morbidity ratio was four times greater among family members of cases than among controls. We then applied the unified mixed model of segregation analysis, as implemented in the computer program POINTER, to a new set of 100 multigenerational pedigrees of children with histopathologically confirmed acute appendicitis that were broken down into 674 nuclear families. Age-specific morbidity risk and lifetime incidence of acute appendicitis were estimated from relatives of controls matched for age and sex to probands. Complex segregation analysis supported a polygenic or multifactorial model with a total heritability of 56%. There was no evidence to support a major gene, although a rare gene could not be ruled out as the cause of a small proportion of cases. Specific studies to address genetic and environmental factors in this serious disease seem worthwhile; but, for now, a positive family history of appendicitis might join other evidence leading to improved clinical recognition of acute appendicitis.     

Segregation analysis of non-insulin-dependent diabetes mellitus in Pima Indians: evidence for a major-gene effect.

Non-insulin-dependent diabetes mellitus (NIDDM) has a high prevalence in Pima Indians. The disorder is familial, but the extent to which genetic factors are involved in its etiology is largely unknown. Segregation analysis was used to determine whether familial aggregation of NIDDM in this population could reflect the action of a single major gene. The analysis included 2,697 subjects from 653 nuclear families in which both parents and at least one offspring had been examined in the course of a longitudinal epidemiological study. The REGTL program of the SAGE package was used to fit models in which age at onset of NIDDM is transmitted from parent to offspring under the unified model for segregation analysis. Likelihood-ratio tests were used to test hypotheses related to genetic transmission. The hypothesis of no major effect was strongly rejected (P < .01), as was that of no transmission of the major effect (P < .01). Mendelian transmission was not rejected (P = .91). Similar results were obtained when covariates for obesity and birth cohort were added to the models and when a power transformation of age at onset was estimated. A strong effect of birth cohort with earlier age at onset in the later born cohorts was observed (P < .01). The findings are consistent with the hypothesis that a major gene influences the risk for NIDDM in Pima Indians by affecting age at onset. The expression of this gene may depend on environmental factors that have become more prevalent in recent-birth cohorts.     

Segregation analysis of low levels of high-density lipoprotein cholesterol in the collaborative Lipid Research Clinics Program Family Study.

Complex segregation analysis with the unified mixed model in white families from nine lipid research clinics was carried out to delineate the mode of familial transmission of plasma high-density-lipoprotein cholesterol (HDL-C). Three groups of families from the collaborative Lipid Research Clinics Program Family Study were assessed: 1,146 selected at random, 483 obtained through hypercholesterolemic probands, and 177 selected from the random sample because a number had low HDL-C, the sample sizes being 4,279, 1,807 and 735, respectively. The data were first transformed and adjusted for effects of covariates. Analyses were performed within clinic and selection strata and also pooled across clinics within strata. The results were consistent across strata and identified two major HDL-C clusters with means separated by approximately 3 SD. There was significant evidence of transmission of a major factor for low HDL-C, but transmission did not conform to Mendelian segregation expectations. There was also evidence of significant multifactorial transmission. Since low HDL-C levels are a major independent risk factor for coronary heart disease, the association of a major factor with familial aggregation of low HDL-C emphasizes the importance of detailed within-family sampling for low HDL-C after identifying a proband whose predominant dyslipoproteinemia is low HDL-C.     

Complex segregation analysis of plasma lipid and lipoprotein variables in a Jerusalem sample of nuclear families

Plasma lipid and lipoprotein concentrations from 3,074 nuclear families in the multiethnic Jerusalem Lipid Research Clinic study population were analyzed for possible involvement of major genes in determination of high levels of these traits. Complex segregation analysis under a mixed model including major gene and multifactorial transmissible components was performed on transformed-plasma lipids and lipoproteins after covariance adjustment for age, sex and environmental measures. Likelihood analysis provided evidence for recessive major genes influencing plasma triglyceride, and low-density lipoprotein cholesterol (LDL-C). The estimated gene frequencies for triglyceride and for hyperbetalipoproteinemia in our study population were about 0.1. Our positive results for total cholesterol and high-density lipoprotein cholesterol (HDL-C) were nonconclusive and the major effects could result from causes other than major genes. The mixed-model parameters were homogeneous across origin groups for LDL-C and HDL-C and heterogeneous for total plasma cholesterol and triglyceride. The multifactorial-transmission heritability index was similar in all origin groups for all the traits. The origin heterogeneity in the major gene parameters appeared to be mainly due to the North African group which favored a multifactorial transmission for all traits except for LDL-C.     

Errors of inference in the detection of major gene effects on psychological test scores.

Computer simulation methods were employed to generate abilities of 10 sets of 250 nuclear families, each comprising a pair of randomly mated parents and two children. It was assumed that the distribution of abilities in the population was normal and caused entirely by additive polygenic effects. A simulated psychological test was administered to each sample to generate test scores for each subject. A different test, consisting of 40 items of varying difficulty and discriminating power, was used in each sample. The "mixed model," specifying a single major gene with polygenic and environmental background variation, was tested for each data set. Likelihood ratios were computed to test for the contribution of a major locus and its conformity to Mendelian segregation. Only one out of 10 samples was consistent with pure multifactorial inheritance. Of the remaining nine samples, four showed non-Mendelian segregation and five were consistent with current statistical criteria for establishing the contribution of a major gene to variation in psychological test scores. This high frequency of false conclusions suggests that the naïve application of such methods to behavioral data is often likely to be misleading. Raw test scores alone are not sufficient to test the mixed model. The development of tractable models for behavioral traits requires the responses of subjects to individual items.     

A major gene for primary hypoalphalipoproteinemia.

Sixteen kindreds were ascertained through probands clinically determined to have primary hypoalphalipoproteinemia, characterized by bottom decile high-density lipoprotein cholesterol (HDL-c), but otherwise normolipidemic. Age- and sex-adjusted, standardized HDL-c levels on 64 individuals in 14 nuclear families in which the proband was a parent were analyzed using the unified mixed model of segregation analysis as implemented in the computer program POINTER. The analysis proceeded by using the likelihood of offspring conditional on the parental phenotypes (conditional likelihood), which appears to overcome the limitation of possible heterogeneity in the selection criteria and provides an appropriate correction for the ascertainment. In these families, the multifactorial contribution to the phenotype appears to be small and significant only in the offspring generation. Although it was not possible to resolve the dominance pattern at the major locus since none of a recessive, additive, or dominant hypothesis could be firmly rejected, these families provided clear evidence for a major gene. Genetic heterogeneity is still a possibility, even within "primary" hypoalphalipoproteinemia.     

Conclusions of segregation analysis for family data generated under two-locus models.

Susceptibility to a disease may involve the interactive effect of two genes. What conclusions will be drawn by segregation analysis in such a case? To answer this question, we considered a set of two-locus models and the corresponding exact distribution for 300 families. We investigated the conclusions and parameter estimations obtained for this sample, by comparing the likelihood expectations of the unified model and of more restricted models. In many cases, segregation analysis leads to the conclusion of a major gene effect, with or without a polygenic component--usually without a polygenic component in multiplicative models (i.e., where two genes have a multiplicative effect) and with such a component in nonmultiplicative models. For all the models considered, existence of a major gene effect is supported by transmission probability tests; there is evidence for transmission and agreement with the hypothesis of Mendelian transmission. Accordingly, there is no means of detecting that the effect of a major gene, with or without a polygenic component, does not correspond to the correct model. In addition, the parameter estimates for the major gene do not correspond to the characteristics of either of the two genes of the true model. This may substantially affect further linkage analysis.     

Segregation analysis of schizophrenia and related disorders

Segregation analysis was applied to 79 nuclear families ascertained through chronic schizophrenic probands. Analysis was performed on the diagnosis of schizophrenia alone and on schizophrenia and schizotypal personality disorder (milder phenotype) combined. The models used were the transmission probability model and the mixed model. Because the disease is associated with reduced fertility, all likelihoods were calculated conditional on parental phenotypes. However, compatibility of the mating-type distribution predicted by each model with the observed was also examined. In all analyses, results suggested consistency with genetic transmission. In the analysis of schizophrenia alone, discrimination among models was difficult. In the analysis including the milder phenotypes, all single-locus models without polygenic background were excluded, while pure polygenic inheritance could not be eliminated. The polygenic model also gave good agreement with supplementary observations (lifetime disease incidences, mating-type distribution, and monozygotic twin concordance). The estimated components of variance for the polygenic model were: polygenes (H) 81.9%; common sib environment (B) 6.9%; random environment (R) 11.2%. Although the polygenic model was parsimonious, segregation analysis and the supplementary observations were also consistent with a mixed model, with a single major locus making a large contribution to genetic liability. Such a locus is more likely to be recessive than dominant, with a high gene frequency and low penetrance. The most likely recessive mixed model gave the following partition of liability variance: major locus, 62.9%; polygenes, 19.5%; common sib environment, 6.6%; and random environment, 11.0%.     

An indication of major genes affecting hip and elbow dysplasia in four Finnish dog populations

The aim of the study was to assess the possible existence of major genes influencing hip and elbow dysplasia in four dog populations. A Bayesian segregation analysis was performed separately on each population. In total, 34 140 dogs were included in the data set. Data were analysed with both a polygenic and a mixed inheritance model. Polygenic models included fixed and random environmental effects and additive genetic effects. To apply mixed inheritance models, the effect of a major gene was added to the polygenic models. The major gene was modelled as an autosomal biallelic locus with Mendelian transmission probabilities. Gibbs sampling and a Monte Carlo Markov Chain algorithm were used. The goodness-of-fit of the different models were compared using the residual sum-of-squares. The existence of a major gene was considered likely for hip dysplasia in all the breeds and for elbow dysplasia in one breed. Several procedures were followed to exclude the possible false detection of major genes based on non-normality of data: permuted datasets were analysed, data-transformations were applied, and residuals were judged for normality. Allelic effects at the major gene locus showed nearly to complete dominance, with a recessive, unfavourable allele in both traits. Relatively high estimates of the frequencies of unfavourable alleles in each breed suggest that considerable genetic progress would be possible by selection against major genes. However, the major genes that are possibly affecting hip and elbow dysplasia in these populations will require further study.     

Complex segregation analysis of dilated cardiomyopathy (DCM) in Irish wolfhounds

The objective of the present study was to analyse the mode of inheritance for dilated cardiomyopathy (DCM) in Irish wolfhounds using regressive logistic models by testing for mechanisms of genetic transmission. Insights from this spontaneous animal model should aid importantly in understanding basic pathogenic mechanisms with regard to genetics and molecular biology of DCM in humans. Moreover, a procedure for the simultaneous prediction of breeding values and the estimation of genotype probabilities for DCM is expected to markedly improve breeding programmes. Results of cardiovascular examinations of 1018 dogs carried out between 1987 and 2003 by one veterinarian were analysed. Data of 878 dogs from 531 litters in 147 different kennels were used for complex segregation analyses. Pedigree information was available for more than 15 generations. Male dogs were affected significantly more often by DCM than female dogs. The segregation analysis showed that among all other tested models a mixed monogenic-polygenic model including a sex-dependent allele effect best explained the segregation of affected animals in the pedigrees. A pure monogenic inheritance of DCM could be significantly rejected in favour of the major gene and most general model. The gene action of the major gene was significantly different between female and male dogs.     

Simulation of Mendelism revisited: the recessive gene for attending medical school.

Much of the recent confusion concerning studies of complex phenotypes such as neuropsychiatric disorders may derive from the inappropriate assumption of simple Mendelian transmission. This has sometimes led to unrealistic expectations regarding the potential benefits of linkage studies. To investigate how Mendelism may be simulated, we collected data on a common familial behavioral trait, attendance at medical school, among the relatives of 249 preclinical medical students. The "risk" of first-degree relatives going to medical school was approximately 61 times that of the general population. Complex segregation analysis carried out under a unified model provided strong evidence of vertical transmission. The results were compatible with transmission of a major effect, and a recessive model provided as satisfactory a fit as a general single-locus model. Moreover, a commonly applied test, allowing the transmission probability parameter (tau 2) to deviate from its Mendelian value, did not give a significant improvement of fit. Only a more general model where all three transmission probabilities (tau 1, tau 2, and tau 3) were unrestricted resulted in a significantly better fit than did the recessive model.     

Multifactorial genetic models for quantitative traits in humans.

Quantitative traits measured in human families can be analyzed to partition the total population variance into genetic and environmental components, or to elucidate the genetic mechanism involved. We review the estimation of variance components directly from human pedigree data, or in the form of path coefficients from correlations between pairs of relatives. To elucidate genetic mechanisms, a mixed model that allows for segregation at a major locus, a polygenic effect and a sibling environmental correlation is described for nuclear families. In each case appropriate likelihoods are derived as a basis, using numerical maximum likelihood methods, for parameter estimation and hypothesis testing. A general model is then described that allows for several familial sources of environmental variation, assortative mating, and both major gene and polygenic effects; and an algorithm for calculating the likelihood of a pedigree under this model is indicated. Finally, some of the remaining problems in this area of biometric analysis are pointed out.     

Evidence for major gene inheritance of Alzheimer disease in families of patients with and without apolipoprotein E epsilon 4.

Apolipoprotein E (APOE) genotype is the single most important determinant to the common form of Alzheimer disease (AD) yet identified. Several studies show that family history of AD is not entirely accounted for by APOE genotype. Also, there is evidence for an interaction between APOE genotype and gender. We carried out a complex segregation analysis in 636 nuclear families of consecutively ascertained and rigorously diagnosed probands in the Multi-Institutional Research in Alzheimer Genetic Epidemiology study in order to derive models of disease transmission which account for the influences of APOE genotype of the proband and gender. In the total group of families, models postulating sporadic occurrence, no major gene effect, random environmental transmission, and Mendelian inheritance were rejected. Transmission of AD in families of probands with at least one epsilon 4 allele best fit a dominant model. Moreover, single gene inheritance best explained clustering of the disorder in families of probands lacking epsilon 4, but a more complex genetic model or multiple genetic models may ultimately account for risk in this group of families. Our results also suggest that susceptibility to AD differs between men and women regardless of the proband's APOE status. Assuming a dominant model, AD appears to be completely penetrant in women, whereas only 62%-65% of men with predisposing genotypes develop AD. However, parameter estimates from the arbitrary major gene model suggests that AD is expressed dominantly in women and additively in men. These observations, taken together with epidemiologic data, are consistent with the hypothesis of an interaction between genes and other biological factors affecting disease susceptibility.     

Segregation analysis detects a major gene controlling blood infection levels in human malaria.

The profound influence that the genetic makeup of the host has on resistance to malaria infection has been established in numerous animal studies. This genetic heterogeneity is one of the main causes of the difficulties in developing an effective malaria vaccine. Segregation analysis is the first step in identifying the nature of genetic factors involved in the expression of human complex diseases, as infectious diseases. To assess the role of host genes in human malaria, we performed segregation analysis of blood parasite densities in 42 Cameroonian families by using both the unified mixed model and the class D regressive model of analysis. The results provide clear evidence for the presence of a recessive major gene controlling the degree of infection in human malaria. Parameter estimates show a frequency of .44-.48 for the deleterious allele, indicating that about 21% of the population is predisposed to high levels of infection.