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PubMed1996

Polygenic inheritance of Tourette syndrome, stuttering, attention deficit hyperactivity, conduct, and oppositional defiant disorder: the additive and subtractive effect of the three dopaminergic genes--DRD2, D beta H, and DAT1.

Polymorphisms of three different dopaminergic genes, dopamine D2 receptor (DRD2), dopamine beta-hydroxylase (D beta H), and dopamine transporter (DAT1), were examined in Tourette syndrome (TS) probands, their relatives, and controls. Each gene individually showed a significant correlation with various behavioral variables in these subjects. The additive and substractive effects of the three genes were examined by genotyping all three genes in the same set of subjects. For 9 of 20 TS associated comorbid behaviors there was a significant linear association between the degree of loading for markers of three genes and the mean behavior scores. The behavior variables showing the significant associations were, in order attention deficit hyperactivity disorder (ADHD), stuttering oppositional defiant, tics, conduct, obsessive-compulsive, mania, alcohol abuse and general anxiety-behaviors that constitute the most overt clinical aspects of TS. For 16 of the 20 behavior scores there was a linear progressive decrease in the mean score with progressively lesser loading for the three gene markers. These results suggest that TS, ADHD, stuttering oppositional defiant and conduct disorder, and other behaviors associated with TS, are polygenic, due in part to these three dopaminergic genes, and that the genetics of other polygenic psychiatric disorders may be deciphered using this technique.

Adolescent↗

PubMed1999

Polygenic expression of somatostatin in rainbow trout, Oncorhynchus mykiss: evidence of a preprosomatostatin encoding somatostatin-14.

Previously we reported the existence of two distinct cDNAs in rainbow trout that encode for separate preprosomatostatins (PPSS), each containing [Tyr7, Gly10]-somatostatin-14. In the present study, we used rainbow trout to further characterize the polygenic origin of somatostatins (SSs), a peptide hormone important in the regulation of growth, development, and metabolism of vertebrates. A two-phase rapid amplification of cDNA ends (RACE)-PCR was used for the isolation of selected cDNAs. We amplified and sequenced a ca. 350-bp 3' RACE-PCR fragment. Based upon this sequence we designed a second gene-specific primer for 5' RACE-PCR which yielded a 452-bp fragment. Sequence analysis revealed a 745-bp cDNA containing the complete 5'-untranslated region, a single initiation site 118 bases from the most 5' end, and a single putative polyadenylation site 17 bases from the most 3' end that was terminated with a polyadenylated tail. The deduced protein is a 114-amino acid PPSS molecule that contains a number of putative processing sites, potentially yielding a 26-amino acid peptide that could be processed further to a 14-amino acid peptide identical in structure to mammalian SS-14. Northern analysis revealed that PPSS-I was expressed in the pancreas, stomach, intestine, and brain of rainbow trout. These results suggest a polygenic origin of SS, possibly resulting from gene duplication events prior to the divergence of teleosts.

Amino Acid Sequence↗

PubMed1991

Moments, cumulants, and polygenic dynamics.

A new approach for describing the evolution of polygenic traits subject to selection and mutation is presented. Differential equations for the change of cumulants of the allelic frequency distribution at a particular locus and for the cumulants of the distributions of genotypic and phenotypic values are derived. The derivation is based on the assumptions of random mating, no sex differences, absence of random drift, additive gene action, linkage equilibrium, and Hardy-Weinberg proportions. Cumulants are a set of parameters that, like moments, describe the shape of a probability density. Compared with moments, however, they have properties that make them a much more convenient tool for investigating polygenic traits. Applications to directional and stabilizing selection are given.

Alleles↗

PubMed1991

Low density lipoprotein receptor levels and the response to dietary and pharmacological intervention in polygenic hypercholesterolemia.

To assess its hypolipidemic predictive value, maximally induced low density lipoprotein receptor activity was measured in vitro in peripheral blood lymphocytes from 20 polygenic hypercholesterolemic patients prior to their recruitment into a rigorous dietary and pharmacological treatment program. The patients in the diet program demonstrated significant beneficial changes in plasma, LDL and HDL cholesterol concentrations. After 12 weeks, those patients who had not had reductions in LDL cholesterol to within the reference range, had cholestyramine and/or bezafibrate supplements to the diet for a further six weeks. The beneficial trends continued. The LDL receptor values correlated well with pre-treatment LDL cholesterol and plasma apoprotein B concentrations (r = -0.472, P less than 0.01 and r = -0.526, P less than 0.01, respectively) and with the percentage change induced by diet (r = 0.510, P less than 0.01 and r = 0.480, P less than 0.01, respectively) and by diet supplemented with bezafibrate and cholestyramine (r = 0.634, P less than 0.05 and r = 0.629, P less than 0.05, respectively). In polygenic hypercholesterolemic patients in whom LDL receptor activity is high, treatment with diet alone may be sufficient whereas those with low receptor activity would require specific pharmacological intervention.

Adult↗

PubMed2005

Improved prediction of early-onset coronary artery disease using APOE epsilon4, BChE-K, PPARgamma2 Pro12 and ENOS T-786C in a polygenic model.

OBJECTIVES: Coronary artery disease (CAD) is often polygenic due to multiple mutations that contribute small effects to susceptibility. Since most prior studies only evaluated the contribution of single candidate genes, we therefore looked at a combination of genes in predicting early-onset CAD [apolipoprotein E (APOE) epsilon4, butyrylcholinesterase (BChE) K, peroxisome proliferator-activated receptor gamma2 (PPARgamma2) Pro12Ala and endothelial nitric oxide synthase (ENOS) T-786C]. DESIGN AND METHODS: We examined the frequencies, individually and in combination, of all four alleles among patients with early-onset CAD (n = 150; <50 years), late-onset CAD (n = 150; >65 years) and healthy controls (n = 150, age range 47-93 years). Differences in the proportion of subjects in each group with the given gene combination were assessed and likelihood ratios (LR) were calculated using logistic regression to combine the results of multiple genes. RESULTS: Early-onset CAD patients had increased, but non-significant, frequencies of PPARgamma2 Pro12/Pro12 (P = 0.39) and ENOS T-786C (P = 0.72), while BChE-K was only significantly higher in early-onset CAD patients compared to controls (P = 0.03). There were significantly more APOE epsilon4 alleles alone (P = 0.02) or in combination with BChE-K (P = 0.02) among early-onset CAD patients compared to late-onset CAD ones or controls. When combined, there was a higher prevalence of all four alleles in early-onset CAD (early-onset CAD patients: 10.7%, late-onset CAD patients: 3.3% and controls: 2.7%, P = 0.01). LR for early-onset CAD for a single allele was relatively small (1.08 for PPARgamma2 to 1.70 for APOE epsilon4). This increased to 2.78 (1.44-5.37) when combining all four alleles, therefore increasing the pre-test probability of CAD from 5% to a post-test probability of 12.7%. CONCLUSIONS: While any single mutation causes only a mildly increased LR (none > 1.7), in combination, the likelihood of early-onset CAD increased to 2.78 with four mutations. The genetics of early-onset CAD appear to be multifactorial, requiring polygenic models to elucidate risk.

Age of Onset↗

PubMed2004

The elicitor-induced oxidative processes in leaves of Solanum species with differential polygenic resistance to Phytophthora infestans.

Previous studies have shown that suspension-cultured cells of Solanum genotypes with various polygenic resistances to Phytophthora infestans differed in activities of early oxidative processes in response to culture filtrate (CF) from this pathogen. These studies have now been extended by analysing production of reactive oxygen species (ROS), lipid peroxidation and Lipoxygenase (LOX, E.C.1.13.11.12) activity induced by CF in detached leaves of S. tuberosum cv Bzura and clone H-8105, polygenically resistant and susceptible, respectively, as well as S. nigrum, nonhost, completely resistant. The relative increase in the ROS production was higher in the susceptible clone H-8105 than in both resistant genotypes. Lipid peroxidation increased only in the nonhost S. nigrum. An increase in lipid peroxidation in S. nigrum leaves coincided with enhanced LOX activity. In both S. tuberosum genotypes, significant increases in LOX activity were delayed and unaccompanied by changes in the level of lipid peroxidation. LOX activity attained a higher level in both of the resistant genotypes than in the susceptible one. The present results suggest that the involvement of both ROS production and LOX activity in the defense strategy in Solanum species/P. infestans interactions.

Immunity, Innate↗

PubMed2004

Contributions of dysregulated energy metabolism to type 2 diabetes development in NZO/H1Lt mice with polygenic obesity.

New Zealand Obese (NZO) male mice develop a polygenic juvenile-onset obesity and maturity-onset hyperinsulinemia and hyperglycemia (diabesity). Here we report on metabolic and molecular changes associated with the antidiabesity action of CL316,243 (CL), a beta(3)-adrenergic receptor agonist. Dietary CL treatment initiated at weaning reduced the peripubertal rise in body weight and adiposity while promoting growth without suppressing hyperphagia. The changes in adiposity, in turn, suppressed development of hyperinsulinemia, hyperleptinemia, hyperlipidemia, and hyperglycemia. These CL-induced alterations were reflected by decreased adipose tissue mass, increased expression of transcripts for uncoupling protein-1 (UCP-1), peroxisome proliferator-activated receptor alpha (PPARalpha), peroxisome proliferater-activated receptor coactivator-1 (PGC-1), and robust development of brown adipocyte function in white fat. Increased drug-mediated energy dissipation elicited a 1.5 degrees C increase in whole body temperature under conditions of increased food intake but with no change in physical activity. Indirect calorimetry of mice treated with CL showed both increased energy expenditure and a restoration of a prominent diurnal pattern in the respiratory exchange ratio suggesting improved nutrient sensing. Our data suggest that CL promotes increased energy dissipation in white and brown fat depots by augmenting thermogenesis and by metabolic re-partitioning of energy in a diabesity-protective fashion. This is the first report demonstrating the effects of dietary beta(3)-agonist in preventing the onset of diabesity in a polygenic rodent model of type 2 diabetes.

Adipose Tissue↗

PubMed2004

Polygene DNA vaccine induces a high level of protective effect against HIV-vaccinia virus challenge in mice.

Single HIV-1 subtype DNA vaccine is unlikely to provide reactive protection across a wide range of HIV strains since the HIV virus changes the antigenic sites, particularly, in env gene. To overcome these issues, we constructed a multivalent poly-epitope DNA vaccine. A polygenic DNA vaccine encoding 20 antigenic epitopes from the HIV-1 Env, Gag, and Pol proteins of several clades was constructed using humanized and optimized codons and it was named here hDNA vaccine. In mice, this hDNA vaccine stimulated the following strong (1) antigen-specific serum antibody (Ab) responses, (2) delayed-type hypersensitivity, (3) the activation of IFN-gamma secretion cells targeting gp120 and synthetic antigenic peptides, in addition (4) a significant level of several peptide specific cytotoxic T lymphocytes (CTL) responses. Challenged with modified vaccinia viruses vPE16 and vP1206 expressing HIV-1 env and gag.pol genes, respectively, demonstrated the viral titers in the ovary of the mice vaccinated with hDNA significantly less compared to the unvaccinated mice. Thus, the use of polygene DNA vaccine appears to induce a high level of HIV-specific immune responses and is very effective against challenge with recombinant HIV-vaccinia viruses.

AIDS Vaccines↗

PubMedDate not supplied

Self-administration of ethanol: towards the location of predisposing polygenes in quasi-congenic animal models.

Alcohol consumption by C57BL/6By background and BALB/cJ donor strains, and by two recently developed quasi-congenic QTL-introgression strains, which share about 96% of their genes with the background strain, was studied in a limited access paradigm. Alcohol and water were offered for 60 min per day using modified pipettes on a drinking cage. Increasing concentration of alcohol solutions, 3, 6, and 12%, were given for days 1-7, 8-14, and 15-22, respectively. Consumption of the 12% alcohol solution was highest in C57BL/6By (0.72 g/kg/h), lowest in BALB/cJ (0.14 g/kg/h). The B6.Cb4i5 beta 13 quasi-congenic strain, in spite of its genetic similarity to the C57BL/6By background strain, consumed significantly less alcohol (0.41 g/kg/h) than the background strain. The results suggest that polygenes that reduce alcohol consumption were introgressed from the BALB/cJ donor strain into the C57BL/6By background strain, and that the b4i5 series of the B6.C quasi-congenic QTL-introgression strains may be useful in mapping genes that influence alcohol-related behaviors. Locations of the introgressed candidate polygenes were tentatively identified by analyzing microsatellite maps of two of the quasi-congenic strains.

Animals↗

PubMed1998

Why different rules are required for polygenic inheritance: lessons from studies of the DRD2 gene.

In 1990 Blum, Noble and coworkers reported a significant association between the 1 allele of the Tarq1A polymorphism of the D2 dopamine receptor gene (DRD2) and severe alcoholism. Subsequently, some reports using both linkage and association techniques supported this finding whereas others either did not, or seemed not to support this association. Although some of the controversy is due to true variability in the frequency of the D2A1 allele in different groups of alcoholics and controls, some is also due to the frequent attempt to apply the rules of single-gene disorders to what is in all likelihood a multifactorial, polygenic disorder. When the rules that are appropriate to polygenic inheritance are used a significant portion of the controversy is resolved. Those rules, and their application to the role of the DRD2 gene in addictive, impulsive behaviors, are reviewed.

Alcoholism↗

PubMed2000

Power of quantitative trait locus mapping for polygenic binary traits using generalized and regression interval mapping in multi-family half-sib designs.

A generalized interval mapping (GIM) method to map quantitative trait loci (QTL) for binary polygenic traits in a multi-family half-sib design is developed based on threshold theory and implemented using a Newton-Raphson algorithm. Statistical power and bias of QTL mapping for binary traits by GIM is compared with linear regression interval mapping (RIM) using simulation. Data on 20 paternal half-sib families were simulated with two genetic markers that bracketed an additive QTL. Data simulated and analysed were: (1) data on the underlying normally distributed liability (NDL) scale, (2) binary data created by truncating NDL data based on three thresholds yielding data sets with three different incidences, and (3) NDL data with polygenic and QTL effects reduced by a proportion equal to the ratio of the heritabilities on the binary versus NDL scale (reduced-NDL). Binary data were simulated with and without systematic environmental (herd) effects in an unbalanced design. GIM and RIM gave similar power to detect the QTL and similar estimates of QTL location, effects and variances. Presence of fixed effects caused differences in bias between RIM and GIM, where GIM showed smaller bias which was affected less by incidence. The original NDL data had higher power and lower bias in QTL parameter estimates than binary and reduced-NDL data. RIM for reduced-NDL and binary data gave similar power and estimates of QTL parameters, indicating that the impact of the binary nature of data on QTL analysis is equivalent to its impact on heritability.

Algorithms↗

PubMed1997

Genetic dissection of obesity in polygenic animal models.

In contrast to diseases caused by single-gene defects, many of the most common human maladies such as obesity, atherosclerosis, diabetes, and hypertension exhibit continuous phenotypic variation and a predominantly multifactorial and polygenic basis. Genes with roles in energy balance, nutrient partitioning, lipid and insulin metabolism, and a variety of behavioral traits are likely interacting with environmental stimuli to regulate obesity phenotypes. With the current proliferation of highly polymorphic genetic markers and the refinement of experimental approaches, it is now possible to screen thoroughly the genomes of model organisms for the individual genes or quantitative trait loci (QTL) that control measurable polygenic traits such as obesity. With the growing wealth of comparative mapping, it will be possible to predict the location of a homologous locus in the human after first mapping it in the mouse. Many experiments have been conducted in mice, rats, and pigs to estimate the number, location, and effect of QTL controlling obesity and related traits. This review describes the design and strategies of such studies and summarizes the results and their implications toward understanding the complex nature of obesity in humans.

Animals↗

PubMed2000

Incomplete penetrance of MHC susceptibility genes: prospective analysis of polygenic MHC-determined traits.

We propose an approach to understanding incomplete penetrance of disease susceptibility genes as a method of studying the underlying mechanisms of polygenic diseases. Incomplete penetrance is the failure of genetically susceptible individuals to exhibit a trait. We define as baseline penetrance that which occurs in genetically identical (monozygotic) twins of an index subject with a major histocompatibility complex (MHC)-associated disease or trait. We consider two mechanisms for incomplete baseline penetrance: an extrinsic (environmental) trigger and an intrinsic stochastic, gene-associated process. The latter can be detected for dominant expression because susceptibility genes in homozygotes (with their two intrinsic triggers) will be up to twice as frequently penetrant as those in heterozygotes. The extent of MHC and non-MHC gene contribution determines differences between baseline penetrance and apparent penetrance in MHC-identical sib pairs, sib pairs in general and MHC-identical unrelated individuals. Inheritance patterns in families do not reveal modes of inheritance of incompletely penetrant polygenic MHC-determined traits. A method is proposed to study such traits prospectively in persons presumed to be homozygous, heterozygous or non-carrying for susceptibility genes by determining trait expression in homozygotes, heterozygotes or non-carriers of trait-associated conserved extended MHC haplotypes. The method provides direct estimates of apparent penetrance rates, modes of genetic determination, and, if the trait is dominant, the origin of penetrance. When applied to dominant MHC susceptibility gene-determined immunoglobulin deficiencies in two populations, the ratios of affected haplotype homozygotes to heterozygotes near 2.0 were consistent with an intrinsic mechanism for baseline penetrance acting on the MHC susceptibility genes.

Environment↗

PubMed1992

Location of X-linked polygenic effects causing sterility in male hybrids of Drosophila simulans and D. mauritiana.

There is general agreement that hybrid male sterility in Drosophila is caused by changes at several (perhaps many) factors, most of them located on the X chromosome. These factors have been generally considered as major genes, each one of them able to bring about sterility by itself. However, the evidence on this last point is not conclusive. In principle, the possibility that they correspond to located polygenic effects instead of genes with a large effect cannot be excluded. This paper shows that some of the factors that cause male sterility in D. simulans/D. mauritiana hybrids, located by recombination on the X chromosome, are indeed 'effective factors', or located polygenic effects. Some of the consequences of this finding are explored.

Animals↗

PubMed1996

A polygenic basis of hybrid sterility may give rise to spurious localizations of major sterility factors.

A simple model is presented to illustrate how an underlying generalized polygenic basis of hybrid sterility is expected to lead to spurious localizations of factors with major effects, when a conventional experiment of recombination mapping is carried out. The model shows that a major gene will be detected at roughly the same distance from each of the chromosome markers used in the experiment. These expectations are contrasted with the results from several experiments on hybrid male sterility in Drosophila, which claimed to have mapped single sterility factors. It is concluded that, except for one report, all the evidence presented so far on the genetic basis of hybrid male sterility in Drosophila is in fact compatible with the generalized polygenic model.

Alleles↗

PubMed2025

Polygenic and developmental profiles of autism differ by age at diagnosis.

Although autism has historically been conceptualized as a condition that emerges in early childhood1,2, many autistic people are diagnosed later in life3-5. It is unknown whether earlier- and later-diagnosed autism have different developmental trajectories and genetic profiles. Using longitudinal data from four independent birth cohorts, we demonstrate that two different socioemotional and behavioural trajectories are associated with age at diagnosis. In independent cohorts of autistic individuals, common genetic variants account for approximately 11% of the variance in age at autism diagnosis, similar to the contribution of individual sociodemographic and clinical factors, which typically explain less than 15% of this variance. We further demonstrate that the polygenic architecture of autism can be broken down into two modestly genetically correlated (rg = 0.38, s.e. = 0.07) autism polygenic factors. One of these factors is associated with earlier autism diagnosis and lower social and communication abilities in early childhood, but is only moderately genetically correlated with attention deficit-hyperactivity disorder (ADHD) and mental-health conditions. Conversely, the second factor is associated with later autism diagnosis and increased socioemotional and behavioural difficulties in adolescence, and has moderate to high positive genetic correlations with ADHD and mental-health conditions. These findings indicate that earlier- and later-diagnosed autism have different developmental trajectories and genetic profiles. Our findings have important implications for how we conceptualize autism and provide a model to explain some of the diversity found in autism.

Humans↗

PubMed2026

Rare variant effect estimation and polygenic risk prediction.

Due to their low frequency, estimating the effects of rare variants is challenging. Here we propose RareEffect, a method that first estimates gene-based or region-based heritability and then each variant effect size using an empirical Bayes approach. Our method uses a variance component model, which is popular in rare variant tests, and is designed to provide two levels of effect sizes-gene/region level and variant level-that can provide better interpretation. To adjust for the case-control imbalance in phenotypes, our approach uses a fast implementation of the Firth bias correction. We demonstrate the accuracy and computational efficiency of our method through extensive simulations and analysis of UK Biobank whole-exome sequencing data for 100 traits. Additionally, we show that the effect sizes obtained from our model can be leveraged to improve polygenic score performance, thereby outperforming recently developed methods for rare variant polygenic scoring.

Humans↗

PubMed2026

All of Us diversity and scale yield context-dependent improvements in polygenic prediction.

Polygenic risk scores (PRSs) trained on multiancestry data can improve prediction in under-represented groups, but large linked genetic and health datasets capturing broad human diversity remain limited. Using 245,388 whole-genome sequences from the All of Us research program (AoU) together with UK Biobank data, we developed multiancestry PRSs for 32 traits and diseases. We evaluated how ancestry, methodology and genetic architecture influenced PRS performance across ancestrally diverse AoU participants. Increased diversity in the AoU improved PRS accuracy for several traits, especially in under-represented populations. However, maximizing sample size by meta-analyzing AoU and UK Biobank was not universally optimal: for less polygenic traits, AoU-only training performed best in African ancestry participants, consistent with ancestry-enriched effects. Individual PRS accuracy declined linearly with increasing ancestry divergence from the discovery GWAS, but this decay was attenuated using multiancestry training data. These findings underscore the value of more representative biobanks for equitable PRS performance.

Journal Article↗