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PubMed2025

Contributions of Common, Rare, and Somatic Genetic Variants to Incidence of Atrial Fibrillation.

IMPORTANCE: Atrial fibrillation (AF) has a complex genetic architecture involving common, rare, and somatic variants. The association between these components requires further investigation. OBJECTIVE: To examine the individual and combined contributions of polygenic, monogenic, and somatic genetic variants to AF incidence, and develop an integrated genomic model (IGM-AF) for improved risk prediction. DESIGN, SETTING, AND PARTICIPANTS: This cohort study used whole-genome sequence data from participants of the UK Biobank, with follow-up for AF events through hospital records, death registries, and self-report. The UK Biobank recruited participants aged 40 to 69 years in the UK between 2006 and 2010. Study data were analyzed from August 2022 to November 2024. EXPOSURES: IGM-AF comprising an AF polygenic risk score (PRS), a composite rare variant gene set (AFgeneset), and somatic variants associated with clonal hematopoiesis of indeterminate potential (CHIP). Clinical AF risk was estimated using the Cohorts for Heart and Aging Research in Genomic Epidemiology AF (CHARGE-AF) score. MAIN OUTCOMES AND MEASURES: The primary outcome was hazard ratios (HRs) for 5-year incident AF attributable to PRS, AFgeneset, CHIP, and their interactions. The predictive performance of IGM-AF and its components was quantified using HRs, C statistics, and reclassification indices. RESULTS: A total of 416 085 individuals (mean [SD] age, 56.6 [8.0] years; 224 642 female [54.0%]) with 30 797 AF cases were included. The PRS (HR per 1 SD, 1.65; 95% CI, 1.63-1.67; P < 1 × 10-8), AFgeneset (HR, 1.63; 95% CI, 1.52-1.75; P = 1.46 × 10-42), and CHIP (HR, 1.26; 95% CI, 1.15-1.38; P = 1.41 × 10-6) were associated with incident AF. The 5-year cumulative incidence of AF was at least 2-fold among individuals having all 3 genetic drivers (common, rare, and somatic drivers) compared with those with only 1 driver. Integration of IGM-AF with a clinical risk model (CHARGE-AF) showed higher predictive performance (C statistic, 0.80; 95% CI, 0.80-0.80) compared with IGM-AF and CHARGE-AF alone. The classification of the at-risk population for AF was improved when IGM-AF was added to CHARGE-AF (net reclassification index, 0.08; 95% CI, 0.07-0.09). CONCLUSIONS AND RELEVANCE: Results of this cohort study demonstrated the complementary value of common, rare, and somatic variants in shaping genomic AF risk. Leveraging comprehensive genetic information may enhance screening and preventive interventions for AF.

Humans↗

PubMed1999

A frailty approach for modelling diseases with variable age of onset in families: the NHLBI Family Heart Study.

We use frailty models to analyse the effect of latent genetic and environmental risk factors on hazard functions in nuclear families. The approach expresses latent risk factors (frailties) as functions of the effects of a single major gene and shared familial risk. The latter may result from shared polygenes and/or a common environment. Genetic frailties are modelled using a two-point distribution, and residual frailties (shared environment, polygenes) using a gamma distribution. The two-point distribution follows the laws of Mendelian transmission, under either dominant or recessive gene action. We describe a robust EM approach for the joint estimation of the magnitude of genetic, covariate, gene by covariate interaction effects while allowing residual familial correlation. We illustrate the method on coronary heart disease data from the National Heart, Lung, and Blood Institute Family Heart Study. In addition, a simulation study shows that ignoring possible residual correlation in disease status due to a shared familial environment leads to an overestimate of the relative risk associated with a latent genotype.

Age of Onset↗

PubMed1996

Influence of apolipoprotein E genotypes on plasma lipid and lipoprotein concentrations: results from a segregation analysis in pedigrees with molecularly defined familial hypercholesterolemia.

Familial hypercholesterolemia (FH) is a monogenic disorder caused by mutations in the low-density lipoprotein (LDL) receptor gene. Large variations in plasma lipids and lipoprotein levels have been observed in FH families. These may be caused by other environmental and genetic factors of which apolipoprotein E (apo E) is a candidate. The possible influence of apo E polymorphism on components of variation in plasma LDL-C, triglycerides, high-density lipoprotein cholesterol (HDL-C), and lipoprotein(a) (Lp(a)) levels was investigated in 235 members of 14 families with FH. Sex-and age-adjusted mean LDL-C was influenced significantly by the apo E genotype in non-FH subjects (P <or= .01), and a similar trend was observed in FH cases. Mean plasma levels of triglyceride, HDL-C, and Lp(a) were not significantly different across the apo E genotypes in FH and in non-FH family members. Complex segregation analysis was first applied to these sex- and age-adjusted data. In addition to the major gene involved in LDL-C levels (i.e., the LDL receptor gene), there was evidence for a non-transmitted environmental major factor in addition to polygenic effect that explained the mixture of distributions in TG and a major effect in addition to polygenic loci which influenced Lp(a) levels. There was no evidence for a single major factor controlling HDL-C levels in these pedigrees. When the segregation models allowed apo E regression coefficients to be ousiotype (class) specific, the results suggested that apo E genotypes have a significant effect on LDL-C, TG, and Lp(a) levels. In conclusion, the analysis presented here supports the concept that the apo E gene has an important role in the regulation of plasma lipid and lipoproteins in FH.

Adolescent↗

PubMed1998

Pedigree analysis package (PAP) vs. MORGAN: model selection and hypothesis testing on a large pedigree.

The MORGAN package of programs is compared to a commonly used package, PAP, with respect to model selection in segregation analysis of a quantitative trait. MORGAN uses Monte Carlo Markov chain (MCMC) methods to estimate the likelihood, whereas both versions of PAP used employ an approximation to the likelihood for the mixed model. Comparisons are done by using results obtained from simulated data. All simulations were done on the same 232-member pedigree using data generated under each of several variations of models, which included different combinations of environmental, polygenic, and major gene components. PAP, version 4.0, and MORGAN gave similar results with respect to model selection for the majority of situations, suggesting that MCMC methods provide a computationally tractable approach for analysis of more complex models that cannot be analyzed by more direct computational methods. PAP, version 3.0, gave somewhat more disparate results compared with either PAP version 4.0 or MORGAN. Both MORGAN and the two versions of PAP confirmed that the major gene component is much easier to detect in the presence of some dominance. All three packages frequently falsely accepted the polygenic model when there was high residual heritability.

Computer Simulation↗

PubMed1999

Methods to estimate genetic components of variance for quantitative traits in family studies.

The aim of this paper was to compare several methods of estimating the genetic components of a quantitative trait in familial data. The Expectation and Maximization (E-M) algorithm, the Newton-Raphson method, and the scoring method were compared for estimating polygenic and environmental effects on nuclear families. We also compared scoring and quasilikelihood (QL) methods when a linked genetic marker was available to estimate effects from a major gene. Generally, all procedures performed similarly in estimating polygenic and environmental variance components. The E-M algorithm yielded more precise estimators when heritability was low. The scoring method was much faster than the other methods and yielded slightly more precise estimates of mean effects but slightly less precise estimates of the variance components. Estimates of major gene effects were not affected by the number of alleles at the trait locus. For these relatively large sample sizes, QL and scoring had similar precision, but QL took 32 times longer than scoring. Finally, we compared the results of applying these methods to data from the Bogalusa Heart Study. Results showed larger imprecision when the QL method was applied, consistent with earlier studies that showed decreased precision of quasilikelihood compared with maximum likelihood in moderately small sample sizes.

Algorithms↗

PubMed1998

Familial autoimmunity in pedigrees of idiopathic inflammatory myopathy patients suggests common genetic risk factors for many autoimmune diseases.

OBJECTIVE: To test the hypothesis that many autoimmune diseases share common genetic risk factors and to define the frequency and distribution of autoimmune diseases in relatives of patients with very rare disorders, the idiopathic inflammatory myopathies (IIM). METHODS: We evaluated, in a prospective case-control study, consecutive patients with IIM who were referred to our center and ascertained without regard to family history or known risk factors for autoimmunity, and all available family members. We used a standardized assessment to determine the presence and type of autoimmune disease in each subject. A matched comparison group of control subjects without autoimmune disease who were referred to our center and their families were similarly assessed. RESULTS: Autoimmune diseases were significantly increased in prevalence (21.9%) in the 151 first-degree relatives of the 21 IIM probands compared with the prevalence (4.9%) in the 143 relatives of the 21 control probands (odds ratio [OR] by regression analysis 7.9, 95% confidence interval [95% CI] 2.9-21.9, P < 0.001). Women had more autoimmune disease than men (OR by regression analysis 4.6, 95% CI 2.3-9.0) and the odds ratio for autoimmune disease increased 0.02 per year of age. These disorders tended to follow the frequency distribution of autoimmune diseases in the general population. Genetic modeling studies showed that a non-Mendelian polygenic inheritance pattern for autoimmune disease was most consistent with these data. CONCLUSION: Autoimmune diseases are significantly increased in frequency in first-degree relatives of IIM patients, affect more women than men, increase with age, and are distributed in a pattern similar to that in the general population. Many autoimmune disorders share genes that together act as polygenic risk factors for autoimmunity.

Adolescent↗

PubMed1987

The molecular genetics of diabetes mellitus.

Diabetes mellitus is a clinically heterogeneous disorder which is characterized by hyperglycaemia due to an absolute or relative deficiency of insulin. Both genetic and non-genetic factors contribute to its development and, as such, it represents a multifactorial disorder. In addition, it may also be, in some instances, a polygenic disorder resulting from the cumulative effects of several genes with or without environmental factors. Serological and/or DNA markers for genes that confer susceptibility to the insulin-dependent form of the disorder (IDDM; type 1) have been identified in the HLA-D region of chromosome 6 and near the insulin gene on chromosome 11. Patients with non-insulin-dependent diabetes mellitus (NIDDM; type 2) make up a more heterogeneous group than those with IDDM and it is likely that in these patients similar clinical phenotypes may be produced by different genetic defects. The synthesis of either an abnormal insulin/proinsulin molecule or an abnormal insulin receptor can confer susceptibility to NIDDM. The genes encoding insulin and the insulin receptor are on chromosomes 11 and 19, respectively. In addition, studies of restriction fragment length polymorphism and disease associations suggest that two other genes may contribute to the development of NIDDM on chromosome 11, one near the insulin gene on the short arm of this chromosome and the other near the apolipoprotein A-I gene on the long arm. None of the susceptibility genes that have been identified to date causes diabetes in the absence of other genetic or non-genetic contributing factors, which is consistent with a multifactorial or polygenic origin for this disorder.

Alleles↗

PubMed1990

Prenatal diagnosis: current status and future trends.

Many of the major single-gene disorders in man can now be detected in utero using restriction fragment length polymorphisms (RFLPs). This approach is based on the knowledge of established linkage between RFLPs and mutations in an adjacent gene. The development of the polymerase chain reaction has altered the available approaches to this problem. This technique permits very rapid detection of the specific mutation from small amounts of starting material and may enable us to detect the genotype from fetal cells in maternal blood or from single cells in embryos before implantation. This may lead to the selection of embryos that lack a defect before they are implanted, avoiding the need for termination of pregnancy. Perhaps the greatest ethical challenge related to the application of these techniques will come with the understanding of the genetic basis for common polygenic disorders. The clarification of the multiple genetic factors responsible for a large part of susceptibility to diseases such as diabetes mellitus, rheumatoid arthritis or ischaemic heart disease will be greatly facilitated by a one-centimorgan genetic map. The strategy involved in establishing such a map, using the polymerase chain reaction, and then the identification of genetic loci responsible for susceptibility to a typical polygenic disease (insulin-dependent diabetes mellitus), is discussed. The ability to identify individuals at high risk of developing such diseases may present opportunities for early intervention.

Female↗

PubMed1983

Inheritance of immunoglobulin E: genetic model fitting.

Total serum immunoglobulin E (IgE) concentration was measured on 316 members of five pedigrees selected through breast cancer probands. Sex- and age-adjusted natural logarithm-transformed IgE level was not found to differ between individuals with breast cancer or with cancer of any site and other relatives. Likelihoods of the polygenic and of one-locus, two-allele major gene and mixed models were computed. The analysis provided evidence for the presence of a polygenic component in the determination of IgE; it did not show evidence of a major gene effect.

Alleles↗

PubMed1984

Genetic analysis of sodium-lithium countertransport in 10 hypertension-prone kindreds.

The rate of sodium-lithium countertransport (SLC flux) across red cell membranes has been reported to be elevated in hypertensive persons and their relatives as compared to normotensive individuals without family histories of hypertension. We have investigated the inheritance of this trait in 434 persons from 10 kindreds. Relatives show positive correlation of SLC flux values, but there is no spouse-spouse correlation. Pedigree analysis favors a model of polygenic inheritance over models of major-gene inheritance. Major-gene index statistics and offspring-between-parent statistics provide similar results. The proportion of total phenotypic variance that is attributable to polygenic differences between persons is estimated at 71%. The SLC flux values of hypertensive persons in this study population are lower than those reported from Boston, but are similar to those reported from Europe. We found a broad overlap of SLC flux values for hypertensive and normotensive persons. We conclude that SLC flux probably is not useful as a preclinical marker for essential hypertension.

Adolescent↗

PubMed1985

Segregation and linkage analysis of alpha-N-acetyl-D-glucosaminidase (NAG) levels in a black family.

Alpha-N-acetyl-D-glucosaminidase (NAG) activities were evaluated on serum samples from 67 persons in a large black family. These data were analyzed in conjunction with those from 126 previously tested unrelated blacks [Vance et al, 1980]. After loge transformation, admixture analysis indicated a significantly better fit (P less than .01) of a mixture of 2 normal distributions for NAG activity versus a single normal distribution. Segregation analysis using the transmission probability model of Elston and Stewart [1971] demonstrated that a genetic model fits the data better than the random "environmental" model. Thus, the existence of a major gene is suggested in the family, although the possibility of polygenic or other familial effects cannot be ruled out. These results confirm the existence of a polymorphism for NAG reported earlier in a series of White half-sib twin families [Vance et al, 1980]. However, the estimates of the means of the three genotypes (AA, AA', A'A') appear to differ in the two racial groups. Thus, the data suggest either a racial polygenic effect and/or different alleles segregating in the two populations. In fact, thermal stability data [Vance et al, 1981a] suggest that at least two alleles are structurally distinct. Linkage analysis of the pedigree with 20 marker loci gave no clear indication of linkage. A lod score of 1.44 was found at 0 recombination with orosomucoid (ORM).

Acetylglucosaminidase↗

PubMed1987

Preliminary evidence for genetic determination of intraerythrocytic sodium concentration in Utah pedigrees.

Intraerythrocytic sodium concentration has been reported to be increased in hypertensive individuals and some of their normotensive relatives. We investigated the "familiality" of this trait in 572 nonhypertensive subjects from 34 Utah kindreds. Most of these kindreds were selected because of a high incidence of hypertension, heart attack, or stroke. Intraerythrocytic sodium concentration was correlated with the sex of the subject and suprailiac skinfold thickness. Intraerythrocytic sodium concentration was adjusted by linear regression for these 2 factors. The residual values were positively correlated in parent-offspring pairs and among sibs, both those presumed to be living together and those presumed to be living apart. The spouse-spouse correlation was not significant. Pedigree analysis suggested a mixed major-gene/polygenic model of inheritance, but these data did not allow us to distinguish between dominant and recessive inheritance for the major gene component. Total heritability due to both major-gene and polygenic components was estimated to be 90-95%; the proportion of the total variance due to polygenes was estimated to be 60-75%. These results suggest that further study of the relationship between the inheritance of intraerythrocytic sodium and the pathophysiology of hypertension is warranted.

Epidemiologic Methods↗

PubMed1993

Combined pedigree and twin family study to determine the sources of variation in serum biotinidase activity: the usefulness of multiple study designs.

Biotinidase, the enzyme responsible for recycling the vitamin biotin, is deficient in most individuals with late-onset multiple carboxylase deficiency. Based on clinical criteria, biotinidase deficiency appears to be inherited as an autosomal recessive trait; however, the inheritance of biotinidase serum activity as a quantitative trait has not been studied previously. In this study, both segregation analysis of proband families and the analysis of twin family data were used to determine the relative contributions of a major gene, polygenes and environment to the variation in serum biotinidase activity. Segregation analysis of 24 families of biotinidase-deficient individuals indicated that serum biotinidase activity is determined by the segregation of a single codominant major gene with the variability about the mean of each major genotype attributable to environmental effects. Significant polygenic effects could not be detected by this analysis. Variance component analysis of 128 twin families, which included the twins, their spouses, and their offspring, indicated that 70% of total variance in biotinidase activity is attributable to additive genetic effects, 22% to individual environmental effects, and 8% to shared environmental effects. The model also included an age effect for females. A portion (27%) of the estimated additive variance may be attributed to the segregation of the major gene. This study emphasizes the usefulness of studying multiple data sets representing different types of family relationships.

Amidohydrolases↗

PubMed1995

Tel Aviv-Heidelberg three-generation offspring study: genetic determinants of apolipoprotein A1 and apolipoprotein B.

The contribution of major gene and multifactorial effects on variation of plasma apolipoproteins A1 and B has been tested in a large sample of population-based Israeli pedigrees. Our most parsimonious and best fitting model for both apolipoproteins is consistent with Mendelian transmissibility, with significant contribution of major genes (with 2 alleles recessive and dominant within each locus) and polygenes, but neglects effects of common sib environment as well as related intergeneration differences in polygenic effects. Total genetic effects explain 71 and 58% of phenotypic variance of APO-A1 and APO-B levels. The major genes account for about 44 and 32% of the variance in APO-A1 and APO-B, respectively, and the frequency of the recessive alleles determining the high level of apolipoproteins under the study in the Israeli population is in the vicinity of 40% at each locus.

Apolipoprotein A-I↗

PubMed1985

A family study of dermatoglyphic traits in India: resolution of genetic and uterine environmental effects for palmar pattern ridge counts.

The inheritance of palmar pattern ridge counts for individual palmar areas, combined distal areas, and all ten areas combined was investigated in families belonging to two strictly endogamous Brahmin castes of peninsular India. Ridge count phenotypes were obtained by the method proposed by Malhotra et al. (1981a), however, zero observations (indicating patterns not circumscribed by triradii) were excluded from analysis. Path analytic methods were applied in order to determine the relative influences of polygenes, intrauterine environment, and residual environment. The proportion of genetic variation was, in general, consistently greater in one population than the other, and significant intrauterine environmental effects were detected for the population with lower heritabilities. The results of this investigation suggest that a simple polygenic model may not be sufficient to explain the inheritance of ridge counts in the interdigital IV configurational area. Distal pattern ridge counts do not appear to be influenced by more or less uterine environmental effects than all areas considered together. The proportion of genetic variation for the total palmar pattern ridge count was 52% in both populations.

Consanguinity↗

PubMed2005

Familial aggregation of systemic lupus erythematosus, rheumatoid arthritis, and other autoimmune diseases in 1,177 lupus patients from the GLADEL cohort.

OBJECTIVE: To determine whether there is familial aggregation of systemic lupus erythematosus (SLE) and/or other autoimmune diseases in SLE patients and to identify clinical differences between patients with and those without familial autoimmunity. METHODS: We interviewed members of the Grupo Latinoamericano de Estudio del Lupus Eritematoso (GLADEL) inception cohort of 1,214 SLE patients to ascertain whether they had relatives with SLE and/or other autoimmune diseases. Identified relatives were studied. Familial aggregation was tested using reported highest and intermediate population prevalence data for SLE, rheumatoid arthritis (RA), or all autoimmune diseases, and studies were performed to identify the genetic model applicable for SLE. RESULTS: We identified 116 first-, second-, or third-degree relatives with SLE, 79 with RA, 23 with autoimmune thyroiditis, 3 with scleroderma, 1 with polymyositis, and 16 with other autoimmune diseases, related to 166 of the 1,177 SLE patients in the GLADEL cohort who agreed to participate. Forty-two SLE patients had 2 or more relatives with an autoimmune disease. We found a lambda(sibling) of 5.8 and 29.0 for SLE and of 3.2-5.3 for RA, when comparing with their reported high or intermediate population prevalence, respectively. We also found familial aggregation for autoimmune disease in general (lambda(sibling) = 1.5) and determined that for SLE, a polygenic additive genetic model, rather than a multiplicative one, is applicable. CONCLUSION: In SLE there is familial aggregation of SLE, RA, and autoimmune disease in general. A polygenic additive model applies for SLE. American Indian-white Mestizo SLE patients and those with higher socioeconomic level were more likely to have familial autoimmunity.

Arthritis, Rheumatoid↗

PubMed1981

Genetic control of the expression of immunoglobulin isotypes in the responses of mice to sheep red blood cells.

Studies have been carried out on the genetic control of the expression of individual Ig classes in the responses of A/J (A) and C57BL/6J (B6) mice to sheep red blood cells (SRBC). An isotopic anti-immunoglobulin test employing Ig class-specific reagents was used to measure levels of IgM, IgA, IgG1, IgG2a, IgG2b and IgG3 anti-SRBC antibodies in sera of hyperimmunized mice. Compared with B6 mice, A mice are low IgM and IgA responders but high responders with respect to all IgG subclasses. In (B6 X A)F1 mice low responsiveness was dominant for all Ig classes indicating that IgM and IgA responses are controlled by genes different from those which control IgG subclass responses. Analysis of the responses of [(B6 X A)F1 X A] and [(B10.A X A)F1 X A] backcross mice indicates multigenic control of IgG subclass responses. Expression of IgG2a and IgG3 responses appear to be regulated largely by single genes whose action is modified by genes at other loci; control of IgG1 and IgG2b is, clearly, polygenic with no evidence for major control by any single gene. The magnitude of all IgG subclass responses appears to be regulated by a gene(s) associated with or linked to the IgCH locus. Analysis of the responses of H-2-congenic mice shows that major histocompatibility genes do not have a strong influence on the patterns on IgM and IgG responses in A or B6 mice. The overall results indicate that while there is some common control of all IgG classes, there is also separate polygenic control of individual Ig classes.

Animals↗

PubMed1985

Studies on vitiligo. II. Familial aggregation and genetics.

Data on 298 pedigrees, each collected through an affected proband, have been analyzed to study familial aggregation and genetics of vitiligo. The extent of familial aggregation is statistically significant at the 5% level. The disease does not appear to be inherited in a simple dominant or recessive fashion. The heritability of liability to the disease is 46% +/- 4.82%. Neither common family environment nor a major locus with additional sources (environmental and/or polygenic) can be excluded as a cause of familial aggregation. Association of the disease with six polymorphic genetic marker loci have been studied. Significant associations with ACP1 and RH loci have been found. This and earlier studies indicate that the disease is associated with genetic loci on different chromosomes, which points to a polygenic nature of the disease.

Acid Phosphatase↗