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Results for “Multifactorial Inheritance”

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PubMed2003

Association between Val108/158 Met polymorphism of the COMT gene and schizophrenia.

Schizophrenia is a complex disorder with a multifactorial polygenic inheritance with several genes conferring susceptibility at many genetic locations, each with a small effect. An attractive candidate gene for schizophrenia is the catechol-O-methyltransferase (COMT) gene, which is a modulator of dorsolateral prefrontal cortical function. A missense G to A mutation in this gene that results in a substitution of Methionine (Met) for Valine (Val) at codon 108/158 (Val(108/158) Met) has recently been identified in association to schizophrenia. We compared allele frequencies of the variant Val allele between 96 schizophrenia cases and 80 normal controls. We selected controls from a similar pool to cases in ethnicity and gender. The frequency of the Val allele was significantly higher in schizophrenia cases compared to controls (0.620 vs. 0.506; P = 0.043). Calculation of the population attributable risk suggests that the Val allele accounts for as much as 23% of schizophrenia in this population (range: 3-38%). These results provide support for a role of this variant in the etiopathophysiology of schizophrenia.

Adult↗

PubMed2006

Maternal age at the birth of the first child as an epistatic factor in polygenic disorders.

The identification of the genes for complex, polygenic disorders has proven difficult. This is due to the small effect size of each gene and genetic heterogeneity. An additional important factor could be the presence of unidentified epistatic factors. In the broad definition of epistasis, the effect of one unit is not predicable unless the value of another unit is known and one of the units may not be a gene. We have previously identified maternal age as an epistatic factor for the effect of the LEP gene on the age of onset of menarche. We report here the effect of maternal age and the age of the mother at the birth of her first child (maternal age 1st) as epistatic factors for the interaction of the dopamine D1 gene (DRD1) with obsessive-compulsive behaviors and with stuttering. The epistatic effects of maternal age 1st were stronger than maternal age. This type of epistatic factor may be generalizable to many other gene-trait interactions.

Adolescent↗

PubMed2001

Genetic and environmental correlations between various anthropometric and blood pressure traits among adult Samoans.

Shared polygenic effects (i.e., pleiotropy) are assumed to exist for such obesity-related phenotypes as blood pressure and adiposity. It is possible to identify these shared genetic effects through bivariate genetic analyses. This analysis of 1,342 adult Samoans, across 801 pedigrees, indicates that significant heritable components (P < 0.05) ranging from 29-58% exist for weight, height, systolic blood pressure, diastolic blood pressure, triceps skinfold, subscapular skinfold, body mass index, and sum of skinfolds. In general, the anthropometric measurements share additive genetic effects, as do the anthropometric measures, with blood pressure. Heritabilities for central fat distribution are not significant in this population, which could be due to a lack of power. On the other hand, heritabilities have been found in Hispanics; hence the genes responsible for central fat distribution may not be evenly distributed among populations.

Adult↗

PubMed2005

Why are rare traits unilaterally expressed?: trait frequency and unilateral expression for cranial nonmetric traits in humans.

Based on an analysis of nonmetric trait databases from several large skeletal series in Northern Europe and South America, representing 27 bilateral traits, we report a predictable relationship between the frequency of nonmetric traits and the probability that they are expressed bilaterally. In a wider sampling of traits and populations, this study thus confirms the findings of an earlier study by Ossenberg ([1981] Am. J. Phys. Anthropol. 54:471-479), which reported the same relationship for two mandibular traits. This trend was previously explained by extending the multifactorial threshold model for discontinuous traits to incorporate either separate thresholds for unilateral or bilateral expression, or by a fuzzy threshold in which the probability of bilateral expression increases away from the median threshold value. We show that the trend is produced under the standard multifactorial threshold model for discontinuous traits simply if the within-individual or developmental instability variance remains relatively constant across the range of liability. Under this assumption, the number of individuals in which one side but not the other is pushed over the threshold for trait formation will be a larger proportion of the number of individuals expressing the trait when the trait frequency is low. As trait frequency increases, the significance of within-individual variance as a determinant of trait formation decreases relative to the genetic and among-individual environmental variance. These results have implications for interpreting nonmetric trait data as well as for understanding the prevalence of unilateral vs. bilateral expression of a wide variety of discontinuous traits, including dysmorphologies in humans.

Anthropology, Physical↗

PubMed2026

Shared genetic architecture between DTI-ALPS traits and neurodegenerative diseases.

INTRODUCTION: Diffusion tensor image analysis along the perivascular space (DTI-ALPS) index is associated with neurodegenerative diseases (NDDs), but its shared genetic basis with NDDs remains unclear. METHODS: By integrating genome-wide association datasets for three DTI-ALPS traits and seven NDDs, we quantified polygenic overlap using MiXeR, identified shared loci using conditional and conjunctional false discovery rate analyses, and performed gene mapping, enrichment, temporal expression, and transcriptome-wide association analyses. RESULTS: DTI-ALPS traits showed widespread but heterogeneous polygenic overlap with NDDs. We identified 22 shared loci, including novel associations implicating GAK and SIAH3, with the strongest convergence at 17q21.31. Shared loci mapped to 183 protein-coding genes enriched in the endolysosomal system and microtubule cytoskeleton. These genes showed similar temporal expression patterns, and 45 were associated with both DTI-ALPS traits and NDDs. DISCUSSION: These findings reveal a shared genetic architecture between DTI-ALPS traits and NDDs, highlighting mechanisms that may contribute to their overlap.

Neurodegenerative Diseases↗

PubMed2002

Polygenic expression of somatostatin in the sturgeon Acipenser transmontanus: molecular cloning and distribution of the mRNAs encoding two somatostatin precursors.

The sequence of somatostatin-14 (SS1) has been strongly preserved throughout the evolution of vertebrates from agnathans to mammals. In Acipenseridae (sturgeons), two isoforms of somatostatin have been characterized to date: somatostatin-14 has been identified from the gastrointestinal tract of the pallid sturgeon Scaphirhynchus albus and [Pro(2)]somatostatin-14 has been identified from the pituitary of the Russian sturgeon Acipenser gueldenstaedti. In the present study, we report the cloning of two distinct somatostatin cDNAs from the brain of the sturgeon Acipenser transmontanus. One of the cDNAs encodes a 116-amino acid protein (PSS1) that contains the SS1 sequence at its C-terminal extremity and, thus, is clearly orthologous to other vertebrate PSS1. The other cDNA encodes a 111-amino acid protein that contains the somatostatin variant [Pro(2)]somatostatin-14 at its C-terminal extremity. This second precursor exhibits more than 67% identity with the recently characterized lungfish PSS2 and goldfish PSS2. Reverse transcriptase-polymerase chain reaction analysis revealed that PSS1 is expressed in the central nervous system, the pancreas and the gut, whereas PSS2 is found in the central nervous system but not in the digestive system. In situ hybridization histochemistry showed that the PSS1 and PSS2 genes are differently expressed in numerous regions of the sturgeon brain. Interestingly, PSS1 and PSS2 mRNAs are present in the hypothalamus suggesting that, in sturgeon, both SS1 and SS2 may play hypophysiotropic functions. The PSS2 mRNA but not the PSS1 mRNA was found in the intermediate lobe of the pituitary. The present data demonstrate that two somatostatin genes are expressed in the sturgeon brain: one precursor generates somatostatin-14 and the other one gives rise to a [Pro(2)]somatostatin-14 variant, which is orthologous to goldfish, lungfish, and frog SS2.

Amino Acid Sequence↗

PubMed2003

Robustness of inference on measured covariates to misspecification of genetic random effects in family studies.

Family studies to identify disease-related genes frequently collect only families with multiple cases. It is often desirable to determine if risk factors that are known to influence disease risk in the general population also play a role in the study families. If so, these factors should be incorporated into the genetic analysis to control for confounding. Pfeiffer et al. [2001 Biometrika 88: 933-948] proposed a variance components or random effects model to account for common familial effects and for different genetic correlations among family members. After adjusting for ascertainment, they found maximum likelihood estimates of the measured exposure effects. Although it is appealing that this model accounts for genetic correlations as well as for the ascertainment of families, in order to perform an analysis one needs to specify the distribution of random genetic effects. The current work investigates the robustness of the proposed model with respect to various misspecifications of genetic random effects in simulations. When the true underlying genetic mechanism is polygenic with a small dominant component, or Mendelian with low allele frequency and penetrance, the effects of misspecification on the estimation of fixed effects in the model are negligible. The model is applied to data from a family study on nasopharyngeal carcinoma in Taiwan.

Analysis of Variance↗

PubMed2003

Diagnostic tools in linkage analysis for quantitative traits.

Diagnostic methods are key components in any good statistical analysis. Because of the similarities between the variance components approach and regression analysis with respect to the normality assumption, when performing quantitative genetic linkage analysis using variance component methods, one must check the normality assumption of the quantitative trait and outliers. Thus, the main purposes of this paper are to describe methods for testing the normality assumption, to describe various diagnostic methods for identifying outliers, and to discuss the issues that may arise when outliers are present when using variance components models in quantitative trait linkage analysis. Data from the Rochester Family Heart Study are used to illustrate the various diagnostic methods and related issues.

Coronary Artery Disease↗

PubMed2004

Conditional multipoint linkage analysis using affected sib pairs: an alternative approach.

Recently, Liang et al. ([2001b] Genet. Epidemiol. 21:105-122) proposed a conditional approach to assess linkage evidence on the target region by incorporating linkage information from an unlinked (reference) region using allele shared IBD (identity-by-decent) from affected sib pairs. This is carried out by conditioning on the IBD sharing value at the estimated trait locus of the reference region. Since markers considered are typically non-fully informative, the IBD sharing at each marker needs to be estimated (or imputed). In this report, we propose an alternative approach to deal with the IBD sharing in the reference region. This new approach makes full use of the observed data without having to categorize the imputed IBD sharing as needed in Liang et al. ([2001b] Genet. Epidemiol. 21:105-122). We compare these two approaches by simulating data from a variety of two-locus models including heterogeneity, additive and multiplicative with either fully informative markers or non-fully informative markers. The performance of both approaches is quite comparable showing consistent estimates of the trait locus and key genetic parameters.

Alleles↗

PubMed1984

Genetic Analysis Workshop II: results of segregation analyses using POINTER and linkage analyses using LIPED.

Genetic Analysis Workshop II Problems 2 and 3 were analyzed using the segregation analysis program, POINTER and the linkage analysis program LIPED. Results of the segregation analyses were acceptable with respect to both parameter estimation and hypothesis testing. Results of the linkage analyses were also good. Although it was noted that the linkage and population association data were sometimes compatible with more than one hypothesis, the correct relationships among the trait and marker loci were generally among those found compatible with the data.

Alleles↗

PubMed1984

Genetic Analysis Workshop II: pedigree analysis of a binary trait without assuming an underlying liability.

A model for concordance in a binary measure that does not rely on the assumption of an underlying latent liability dichotomized about a threshold has been demonstrated for twin pairs [Hannah et al, 1983]. It is extended here to pedigrees of arbitrary structure by making an assumption that is, for small incidence rates, almost equivalent to postulating that relative risks are multiplicative. The model is applied to the workshop data to determine the extent to which the known structure of the simulated models can be recovered.

Alleles↗

PubMed1984

Genetic Analysis Workshop II: combined segregation, linkage, and association analysis.

A combined segregation, linkage, and association analysis using the program COMBIN was performed on the simulated pedigree data prepared for the Second Genetic Analysis Workshop. The model used in COMBIN is described and the presented results illustrate its effectiveness in the analysis of such data. Linkage analysis was performed and maps for each linkage group are presented.

Adult↗

PubMed1999

A normalized identity-by-state statistic for linkage analysis of sib pairs.

A sib-pair analysis was performed on a simulated data set for a fictitious disease, with a prevalence of approximately 3% to 6%. The disease could manifest itself in a severe or mild form and the analyses focused primarily on families with the mild form, barring any misdiagnoses. The numbers of shared genes identical by descent (IBD) and identical by state (IBS) were used to detect linkage between the marker loci and the disease. The results of the two methods were compared. We considered the distribution of the number of shared alleles IBS (for different parental allele combinations) and suggest a normalized IBS method. A large proportion of pedigrees in this data set had at least one homozygous parent or both parents sharing a common gene, thus generating the need for an adjustment of the IBS method. Our results indicate that the normalized IBS method gives results similar to those obtained by the traditional IBD approach. The adjusted score requires no assumptions be made with regard to the allele frequencies.

Alleles↗

PubMed1999

Covariates in linkage analysis.

We apply a novel technique to detect significant covariates in linkage analysis using a logistic regression approach. An overall test of linkage is first performed to determine whether there is significant perturbation from the expected 50% sharing under the hypothesis of no linkage; if the overall test is significant, the importance of the individual covariate is assessed. In addition, association analyses were performed. These methods were applied to simulated data from multiple populations, and detected correct marker linkages and associations. No population heterogeneity was detected. These methods have the advantages of using all sib pairs and of providing a formal test for heterogeneity across populations.

Genetic Linkage↗

PubMed1999

An evaluation of affected-sib-pair methods and transmission/disequilibrium tests for detecting genes underlying a complex trait.

For the analysis of complex traits, it is of interest to compare a few nonparametric methods such as affected-sib-pair (ASP) analyses and transmission/disequilibrium tests (TDT). The affected-sib-pair approaches we have examined here are ASP and ALL-SP which are implemented in SIBPAIR program. We also applied the BETA program which has not so far been extensively compared with other methods. The study indicates that the ASP program and the BETA program give concordant results although BETA tends to give higher lod scores. However, when all sibs were included in the analysis (ALL-SP), linkage signals became weaker, compared with ASP and BETA. The TDT detected 66 positive signals at a significance level of 0.05 and identified a true locus. Overall, our results suggest that affected-sib-pair analysis has reasonable power (p < 0.0001) to detect linkage given the disease model and the family structure specified in the GAW11 Problem 2 data set.

Genetic Testing↗

PubMed1999

A generalized estimating equations approach to linkage analysis in sibships in relation to multiple markers and exposure factors.

We describe a multiple regression approach to nonparametric linkage analysis in sibships incorporating multiple genetic loci, environmental covariates, and interactions. The covariance in trait residuals between sib pairs is treated as the dependent variable, regressed upon identical-by-descent sharing probabilities and interaction effects, using generalized estimating equations to allow for the correlations among multiple sib pairs within a sibship. Individual covariates can also be introduced in the model for the trait means. An application to the GAW11 simulated data revealed linkage with each of the four simulated loci, as well as gene x environment interactions of E1 with loci C and D and gene x gene interactions among the cluster of loci A, B, and D.

Environment↗

PubMed1999

Stratification techniques to explore genotype environment interactions.

Linkage analysis was performed on the GAW11 Problem 2 data set using stratification to explore the effects of the environmental risk factors and the differences between mild and severe phenotypes. Analysis of the four study populations stratified by the two risk factors identified regions on chromosomes 3 and 5 with significant evidence for linkage. Other loci were sought by removing families consistent with linkage to the chromosome 3 locus. Our studies identified a locus on chromosome 3 (markers 43-46) associated with the mild phenotype in the presence of risk factor 1 and with the severe phenotype independent of risk factor 1. This suggests that distinct allelic variants at the chromosome 3 locus may cause different forms of disease. The locus identified on chromosome 5 (markers 36-39) was linked to the severe phenotype, but exposure to factor 1 or 2 may have a protective effect. The regions on chromosomes 3 and 5 appeared to have independent roles in disease etiology. Evidence for two loci on chromosome 1 linked to the mild form was found. The methods successfully identified linkages and interaction consistent with the generating model.

Environment↗

PubMed1999

A method for meta-analysis of genome searches: application to simulated data.

Genome searches have been performed for many complex traits, and in some cases several searches have been performed in a single disease. Replication of significant results is rare, and a systematic method of reviewing results from a number of searches is needed. A method for meta-analysis is presented which provides a systematic descriptive overview of the separate analyses while dealing with some of the problems specific to meta-analysis of genome searches. The results of two separate meta-analyses correctly indicate the presence of susceptibility loci on chromosomes 1, 3, and 5 in the GAW11 Problem 2 data.

Genetic Linkage↗