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PubMed2003

The role of Wnk4 in polygenic hypertension: a candidate gene analysis on rat chromosome 10.

Linkage analyses in experimental crosses of stroke-prone spontaneously hypertensive (SHRSP) and normotensive Wistar-Kyoto (WKY) rats have strongly suggested the presence of quantitative trait loci (QTL) influencing blood pressure and ACE levels on rat chromosome 10, which have been confirmed in multiple independent studies. Analysis of the orthologous region on human chromosome 17 also revealed significant linkage to blood pressure in several populations. Wnk4, a gene previously identified to cause pseudohypoaldosteronism type II, a rare mendelian form of arterial hypertension, is located on human chromosome 17. The hypothesis has been advanced that molecular variants of this gene might contribute to common polygenic forms of hypertension, since Wnk4 is located in a region of conserved synteny that demonstrates an overlap between quantitative trait loci for primary hypertension in humans and rats. In this report, we describe the confirmation of the blood pressure QTL on rat chromosome 10 by congenic approaches, spanning the Wnk4 locus. Comparative analysis of the complete coding sequence of Wnk4 in SHRSP and WKY strains revealed no mutation and demonstrated high conservation between rat and human proteins. Furthermore, comparison of mRNA levels in the kidney showed no differences between SHRSP and WKY. Additionally, we excluded a secondary effect of blood pressure on the transcriptional regulation of Wnk4. Our results fail to support a material contribution of Wnk4 to blood pressure regulation in this model of polygenic hypertension. Thus, Wnk4 is likely not to represent the underlying disease gene for the QTL captured in chromosome 10 congenic animals.

Amino Acid Sequence↗

PubMed1997

Role of the alpha-, beta-, and gamma-subunits of epithelial sodium channel in a model of polygenic hypertension.

The pathophysiological basis of Liddle's syndrome, a rare autosomal dominant form of arterial hypertension, has been found to rest on missense mutations or truncations of the beta- and gamma-subunits of the epithelial sodium channel. The hypothesis has been advanced that molecular variants of these genes might also contribute to the common polygenic forms of hypertension. We tested this hypothesis by performing a cosegregation study in a reciprocal cross between the stroke-prone spontaneously hypertensive rat (SHRSPHD) and a Wistar-Kyoto rat (WKY-1HD) reference strain. We carried out genetic mapping and chromosomal assignment of the alpha-, beta-, and gamma-subunits of the epithelial sodium channel using both linkage analysis and fluorescent in situ hybridization techniques. We demonstrate that in the rat, the beta- and gamma-subunits, as in humans, are in close linkage; they map to rat chromosome 1 and cosegregate with systolic pressure after dietary NaCl (logarithm of the odds [LOD] score, 3.7), although the peak LOD score of 5.0 for this quantitative trait locus was detected 4.4 cM away from the beta-/gamma-subunit locus. The alpha-subunit was mapped to chromosome 4 and exhibited no linkage to blood pressure phenotype. Comparative analysis of the complete coding sequences of all three subunits in the SHRSPHD and WKY-1HD strains revealed no biologically relevant mutations. Furthermore, Northern blot comparison of mRNA levels for all three subunits in the kidney showed no differences between SHRSPHD and WKY-1HD. Our results fail to support a material contribution of the epithelial sodium channel genes to blood pressure regulation in this model of polygenic hypertension.

Animals↗

PubMed2005

Support for polygenic influences on ocular refractive error.

PURPOSE: Refractive errors, myopia, and hyperopia are common conditions requiring corrective lenses. The familial clustering of myopia has been well established. Several chromosomal regions have been linked to high myopia (12q, 17q, and 18q), to quantitative refraction among twins (3q, 4q, 8p, and 11p), and to families with moderate myopia (22q). This study examined the familial aggregation and pattern of inheritance of ocular refraction in an adult population, by using data from the Beaver Dam Eye Study. METHODS: Familial correlations were examined and segregation analysis was performed on the average refractive error measurements in the right and left eyes after adjustment for age, sex, and education. Analyses were based on 2138 individuals in 620 extended pedigrees with complete data on age, sex, education, and spherical equivalent. RESULTS: Substantial positive correlation was found between siblings (0.33), parents and offspring (0.17), and cousins (0.10) and lower correlation among avuncular pairs (0.08) after adjustment for age, sex, and years of education. The results of this segregation analysis do not support the involvement of a single major locus throughout the entire range of refractive error. However, models allowing for familial correlation, attributable in part to polygenic effects, provided a better fit to the observed data than models without a polygenic component, suggesting that several genes of modest effect may influence refractive error, possibly in conjunction with environmental factors. CONCLUSIONS: These results support the involvement of genetic factors in the etiology of refractive error and are consistent with reports of linkage to multiple regions of the genome.

Family Health↗

PubMed2026

Variance Polygenic Scores (vPGS) as a Tool for Studying Gene-Environment Interactions Associated With Refractive Error.

PURPOSE: Conventional polygenic scores predict an individual's phenotype based on their genetics. By contrast, variance polygenic scores (vPGS) quantify genetic predisposition to phenotypic variance. We tested the hypothesis that a vPGS for refractive error can identify individuals with increased susceptibility to environmental risk factors for myopia. METHODS: Six vPGS construction strategies were evaluated in UK Biobank participants: three variance heterogeneity genome-wide association study (vGWAS) methods and two reweighting schemes. vPGS performance was assessed using two metrics: (i) "Diff"-difference in phenotypic variance in vPGS decile ten versus one; (ii) Spearman correlation of phenotypic variance versus vPGS decile. The optimal vPGS was used to test for vPGS × time spent reading or vPGS × time spent outdoors interactions in children aged 15 years (ALSPAC cohort; n = 3471). RESULTS: Of the vGWAS methods, conditional quantile regression outperformed SCAMPI and Levene's Test. Of the re-weighting schemes, LDpred2 outperformed pruning and thresholding. In an independent sample of UK Biobank participants (n = 19,470), the top-performing vPGS successfully stratified individuals into groups with increasing variance in refractive error, even after adjusting for a conventional PGS (Diff: 2.55, 95% confidence interval [CI], 1.64-3.47; Spearman correlation = 0.87; 95% CI, 0.43-0.93). However, in ALSPAC participants, there was minimal support for vPGS interactions with time reading (P = 0.80) or time outdoors (P = 0.89). CONCLUSIONS: A novel vPGS successfully stratified individuals into groups with relatively high or low genetic susceptibility to refractive error variance. However, the vPGS could not identify individuals at enhanced risk from lifestyle risk factors for myopia.

Humans↗

PubMed1997

Development of non-insulin-dependent diabetes mellitus in the double knockout mice with disruption of insulin receptor substrate-1 and beta cell glucokinase genes. Genetic reconstitution of diabetes as a polygenic disease.

Non-insulin-dependent diabetes mellitus (NIDDM) is considered a polygenic disorder in which insulin resistance and insulin secretory defect are the major etiologic factors. Homozygous mice with insulin receptor substrate-1 (IRS-1) gene knockout showed normal glucose tolerance associated with insulin resistance and compensatory hyperinsulinemia. Heterozygous mice with beta cell glucokinase (GK) gene knockout showed impaired glucose tolerance due to decreased insulin secretion to glucose. To elucidate the interplay between insulin resistance and insulin secretory defect for the development of NIDDM, we generated double knockout mice with disruption of IRS-1 and beta cell GK genes by crossing the mice with each of the single gene knockout. The double knockout mice developed overt diabetes. Blood glucose levels 120 min after intraperitoneal glucose load (1.5 mg/g body wt) were 108 +/- 24 (wild type), 95 +/- 26 (IRS-1 knockout), 159 +/- 68 (GK knockout), and 210 +/- 38 (double knockout) mg/dl (mean +/- SD) (double versus wild type, IRS-1, or GK; P < 0.01). The double knockout mice showed fasting hyperinsulinemia and selective hyperplasia of the beta cells as the IRS-1 knockout mice (fasting insulin levels: 0.38 +/- 0.30 [double knockout], 0.35 +/- 0.27 [IRS-1 knockout] versus 0.25 +/- 0.12 [wild type] ng/ml) (proportion of areas of insulin-positive cells to the pancreas: 1.18 +/- 0.68%; P < 0.01 [double knockout], 1.20 +/- 0.93%; P < 0.05 [IRS-1 knockout] versus 0.54 +/- 0.26% [wild type]), but impaired insulin secretion to glucose (the ratio of increment of insulin to that of glucose during the first 30 min after load: 31 [double knockout] versus 163 [wild type] or 183 [IRS-1 knockout] ng insulin/mg glucose x 10(3)). In conclusion, the genetic abnormalities, each of which is nondiabetogenic by itself, cause overt diabetes if they coexist. This report provides the first genetic reconstitution of NIDDM as a polygenic disorder in mice.

Animals↗

PubMed2003

Imputation methods for missing data for polygenic models.

Methods to handle missing data have been an area of statistical research for many years. Little has been done within the context of pedigree analysis. In this paper we present two methods for imputing missing data for polygenic models using family data. The imputation schemes take into account familial relationships and use the observed familial information for the imputation. A traditional multiple imputation approach and multiple imputation or data augmentation approach within a Gibbs sampler for the handling of missing data for a polygenic model are presented.We used both the Genetic Analysis Workshop 13 simulated missing phenotype and the complete phenotype data sets as the means to illustrate the two methods. We looked at the phenotypic trait systolic blood pressure and the covariate gender at time point 11 (1970) for Cohort 1 and time point 1 (1971) for Cohort 2. Comparing the results for three replicates of complete and missing data incorporating multiple imputation, we find that multiple imputation via a Gibbs sampler produces more accurate results. Thus, we recommend the Gibbs sampler for imputation purposes because of the ease with which it can be extended to more complicated models, the consistency of the results, and the accountability of the variation due to imputation.

Adult Children↗

PubMed2026

Enhancing detection of polygenic adaptation: a comparative study of machine learning and statistical approaches using simulated evolve-and-resequence data.

BACKGROUND: Detecting signals of polygenic adaptation remains a significant challenge in population genomics, as traditional methods often struggle to identify the associated subtle, multi-locus allele-frequency shifts. Here, we introduced and tested several novel approaches combining machine learning techniques with traditional statistical tests to detect polygenic adaptation patterns in time-series of allele frequency changes from whole genome data. We implemented a Naive Bayesian Classifier (NBC) and One-Class Support Vector Machines (OCSVM), and compared their performance against the classical Fisher's Exact Test (FET). Furthermore, we combined machine learning and statistical models (OCSVM-FET and NBC-FET), resulting in 5 competing approaches. The framework is mainly designed and validated for evolve-and-resequence (EaR) experimental designs, where defined selection pressures and temporal sampling are feasible, but might be applicable for certain natural experiments as well. RESULTS: Using a simulated dataset based on empirical C. riparius Pool-Seq data, we evaluated methods across evolutionary scenarios varying in generation, selection strength, and number of loci under selection. Our results demonstrate that the combined OCSVM-FET approach consistently outperformed competing methods, achieving the lowest false positive rate, highest area under the curve, and high accuracy. The performance peak aligned with what we term the 'late dynamic phase' of adaptation - the period after initial selection has occurred but before fixation - highlighting the method's sensitivity to ongoing selective processes. CONCLUSIONS: Furthermore, we emphasize the critical role of parameter tuning, balancing biological assumptions with methodological rigor. While broader applicability remains an important direction for future work, the present benchmarking is intentionally scoped to EaR experimental contexts.

Machine Learning↗

PubMed2026

Assessing the comorbidity between asthma and depression through polygenic risk scoring and time-to-event models.

BACKGROUND: Patients with asthma have an increased risk of developing depression, affecting their quality of life. To date, the processes contributing to this comorbidity remain unclear. METHODS: We integrated two large genome-wide association studies (88,486 patients with asthma and 447,859 controls; 412,024 patients with depression and 1,587,577 controls) with cross-sectional and longitudinal information available from the All of Us Research Program (N = 87,167) through polygenic risk scoring (PRS), Cox proportional-hazards models, one-sample Mendelian randomization (MR), and gene-set and drug-repurposing analyses. RESULTS: We observed that depression PRS was associated with increased asthma risk (hazard ratio, HR = 1.13, 95% CI = 1.09-1.17), also when accounting for comorbidity status (HR = 1.08, 95% CI = 1.04-1.12). Conversely, the effect of asthma PRS was null after accounting for comorbidity status. One-sample MR analysis showed an effect of depression genetic liability on asthma, ranging from beta = 0.36 ± 0.03 when considering a linear relationship to beta = 3.21 ± 0.31 when considering possible nonlinear relationships. Conversely, the effect of asthma genetic risk on depression was null after accounting for potential confounders. The gene-set analyses showed that asthma and depression polygenic risks share biological processes, molecular functions, and cellular components related to the immune system and the lung-brain axis. CONCLUSIONS: Genetic predisposition contributes to asthma-depression comorbidity through direct effects and shared pathogenic processes. These findings highlight the potential to develop targeted interventions to prevent and treat the co-occurrence of respiratory and neuropsychiatric disorders.

Comorbidity↗

PubMed2006

[The mixed major gene plus polygenes inheritance for female fertility in wheat (Triticum aestivum L.)].

Three sets of data for the P1, P2, F1, and F2 populations derived from three crosses between the normal fertility wheat (Triticum aestivum L.) cultivars with different ecotypes and the female sterile line (XND126) were used to investigate the inheritance of female fertility in wheat using mixed major gene plus polygenes inheritance model in 2005 and 2006. The results from the joint segregation analysis of the four generations showed that female fertility in wheat is controlled by two major genes plus polygenes, and the interaction between the two major genes is also detected.

Fertility↗

PubMed2002

Bioinformatics and approaches to identifying polygenic susceptibility traits.

The role of genetic factors in periodontal disease is now well recognized, although details for the genetic mechanisms of the disease and implications for therapy can be as obscure as they are for other human traits. This paper addresses the role that the analysis of genome-wide data might play in helping to understand the molecular determinants of periodontal risk. Very few human diseases are not polygenic, in that an individual's susceptibility depends on his or her constitution at many genetic loci, each of which may have a small effect. Not only do these loci interact, but also their actions and interactions depend on nongenetic factors. Much of the statistical machinery to handle this complexity was developed in the plant and animal breeding context, where crosses between inbred lines selected for trait differences could be conducted. Human polygenic studies began with studies on large pedigrees, but have expanded to include case-control analyses of random samples of individuals who differ in disease status, and studies of marker transmissions within nuclear families. In the area of characterizing the genetic architecture of complex traits, the relatively new field of bioinformatics is distinguished from the more mature fields of statistical genetics or genetic epidemiology by its focus on genome-wide data. The very dense sets of genetic markers now available, particularly those at single nucleotide positions (SNPs), have meant that it is possible to seek linkages or associations between chromosomal position and disease from the whole genome in a single study. Apart from the obvious problems of scale, there are real issues involved with multiple testing and recognizing interactions. Current thinking tends to focus on relatively conserved "haplotype blocks" instead of single genetic markers, although there is no consensus on the utility of this emphasis.

Dental Informatics↗

PubMed2003

Diversity in intrinsic strengths of the human complement system: serum C4 protein concentrations correlate with C4 gene size and polygenic variations, hemolytic activities, and body mass index.

Among the genes and proteins of the human immune system, complement component C4 is extraordinary in its frequent germline variation in the size and number of genes. Definitive genotypic and phenotypic analyses were performed on a central European population to determine the C4 polygenic and gene size variations and their relationships with serum C4A and C4B protein concentrations and hemolytic activities. In a study population of 128 healthy subjects, the number of C4 genes present in a diploid genome varied between two to five, and 77.4% of the C4 genes belonged to the long form that contains the endogenous retrovirus HERV-K(C4). Intriguingly, higher C4 serum protein levels and higher C4 hemolytic activities were often detected in subjects with short C4 genes than those with long genes only, suggesting a negative epistatic effect of HERV-K(C4) on the expression of C4 proteins. Also, the body mass index appeared to affect the C4 serum levels, particularly in the individuals with medium or high C4 gene dosages, a phenomenon that was dissimilar in several aspects from the established correlation between body mass index and serum C3. As expected, there were strong, positive correlations between total C4 gene dosage and serum C4 protein concentrations, and between serum C4 protein concentrations and C4 hemolytic activities. There were also good correlations between the number of long genes with serum levels of C4A, and the number of short genes with serum levels of C4B. Thus, the polygenic and gene size variations of C4A and C4B contribute to the quantitative traits of C4 with a wide range of serum protein levels and hemolytic activities, and consequently the power of the innate defense system.

Adult↗

PubMed2004

Selecting SNPs for association studies based on population frequencies: a novel interactive tool and its application to polygenic diseases.

Common complex polygenic diseases as autoimmune diseases have not been completely understood on a molecular level. While many genes are known to be involved in the pathways responsible for the phenotype, explicit causes for the susceptibility of the disease remain to be elucidated. The susceptibility to disease is thought to be the result of genetic epistatic interactions between common polymorphic genes. This polymorphism is mostly caused by single nucleotide polymorphisms (SNPs). Human subpopulations are known to differ in the susceptibility to the diseases and generally in the distribution of single nucleotide polymorphisms. The here presented approach retrieves SNPs with the most divergent frequencies for selected human subpopulations to help defining properties for the experimental verification of SNPs within defined regions. A web-accessible program implementing this approach was evaluated for multiple sclerosis (MS), a common human polygenic disease. A link to a summary of data from "The SNP Consortium" (TSC) with sex-dependencies of SNPs is available. Associations of SNPs to genes, genetic markers and chromosomal loci are retrieved from the Ensembl project. This tool is recommended to be used in conjunction with microarray analyses or marker association studies that link genes or chromosomal loci to particular diseases.

Gene Frequency↗

PubMed2005

Polygenic analysis of ammonia-oxidizing bacteria using 16S rDNA, amoA, and amoB genes.

Finding a unique molecular marker capable of quickly providing rigorous and useful phylogenetic information would facilitate assessing the diversity of ammonia-oxidizing bacteria in environmental samples. Since only one of several available markers can be used at a time in these kinds of studies, the 16S rDNA, amoA and amoB genes were evaluated individually and then compared in order to identify the one that best fits the information provided by the composite dataset. Distance-based neighbor-joining and maximum parsimony trees generated using the sequences of the three mentioned genes were analyzed with respect to the combined polygenic trees. Maximum parsimony trees were found to be more accurate than distance-based ones, and the polygenic topology was shown to best fit the information contained in the sequences. However, the taxonomic and phylogenetic information provided by the three markers separately was also valid. Therefore, either of the functional markers (amoA or amoB) can be used to trace ammonia oxidizers in environmental studies in which only one gene can be targeted.

Ammonia↗

PubMed2006

[Analysis on the major gene and polygene mixed inheritance of lycopene content in fresh consumptive tomato fruit].

Two cultivars significantly different in lycopene content were used for the study of inheritance pattern of lycopene content in fresh consumptive tomato fruit. Combination analysis of six generations proved that a major gene plus additive-dominance-epistasis polygenes dominate the inheritance of lycopene in fresh consumption tomato. The major gene heritability in B1, B2 and F2 was 6.85%, 34.78% and 58.33%, respectively, and the polygene heritability was 58.48%, 30.69% and 0, correspondingly.

Carotenoids↗

PubMed1990

[Changes in lipoproteins and hormones induced by diet and drugs in patients with polygenic hypercholesterolemia. Predictive value of the determination of low density lipoprotein receptor activity].

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 subjects 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 6 weeks. The beneficial trends continue. The initial LDL receptor values correlated well with pre-treatment LDL cholesterol and plasma cholesterol and apoprotein B concentrations, and with the percentage change induced by diet and by diet supplemented with bezafibrate and cholestyramine. During the trial the only significant variations in plasmatic hormones were observed in TSH and T3 concentrations, but always within the reference range. 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↗

PubMed1977

The influence of the mating system on the maintenance of genetic variability in polygenic characters.

The traditional models of the effect of assortative mating and inbreeding on the genetic variance of polygenic characters (FISHER 1918; WRIGHT 1921) presume that there is no natural selection or mutation. In a large population, the genetic variance determined by additive genes may then increase by up to a factor of two with local inbreeding, and even more with assortative mating. The classical models are still used to interpret data from natural populations. But contrary to their assumptions, most metrical characters in natural populations are usually thought to be under a type of selection which depletes polygenic variation. Mutation is then necessary to maintain genetic variation. The present models show that with the additional features of mutation and selection, in a large population, the mating system has no influence on the amount of genetic variability maintained by additive genes.

Animals↗

PubMed1994

[Genetic analysis of a polygenic system for a quantitative character after negative and positive selection. II. Chromosome contributions to the expression of the radial vein fragments].

Hybridological genetic analysis of a polygenic system of the character radius incompletus in Drosophila was conducted by intercrossing the contrasting selection lines riSN and riSP and crossing them with the tester line y bw st ri. Two vein segments were shown to have different polygenic systems which control penetrance and expressivity of the character. Determination of the proximal segment was additive with regard to the contribution of the haploid genomes in the hybrid zygote and to the contribution of different chromosomes. The contributions of individual chromosomes of the riSN line compared to those of the tester line were equal to -0.97 (1), -0.31 (2), and -0.14 (3). The contributions of the chromosomes of the riSP line were 0.26 (1), 0.095 (2), and 0.31 (3). Determination of the distal segment was nonadditive in all respects. Specifically, in the hybrid zygotes of riSN and the tester line, the absence of the distal segment was completely dominant over its presence; for that, only one riSN chromosome was necessary. Both intergenomic and interchromosome contributions were nonadditive. The results are discussed with regard to penetrance, expressivity and morphological mechanisms of the longitudinal wing vein formation in Drosophila.

Animals↗

PubMed1997

Application of polygenic threshold models in the etiology of affective disorders.

Multiple studies show that familial transmission of affective disorders does not conform to the classical principles of Mendelian inheritance. With the purpose of testing polygenic threshold models of inheritance of affective disorders, a study was carried out on 1184 probands with affective disorders with secondary cases in their families (siblings and offspring). Nonparametric analysis (Chi square test) indicates that there is no statistically significant difference between the observed and expected frequencies of secondary cases, when the probands are divided into two subgroups--unipolar and bipolar. It is proved that the two forms have common etiologic factors and the clinical differences between them can be attributed to the threshold gene effects. The hypothesis that bipolar and unipolar disorders are respectively severe and mild forms of the same disorder and that the two-threshold multifactorial polygenic model most adequately predicts the familial transmission of affective disorders is accepted.

Bipolar Disorder↗