Dataset Information

Fitting ACE structural equation models to case-control family data.

ABSTRACT: Investigators interested in whether a disease aggregates in families often collect case-control family data, which consist of disease status and covariate information for members of families selected via case or control probands. Here, we focus on the use of case-control family data to investigate the relative contributions to the disease of additive genetic effects (A), shared family environment (C), and unique environment (E). We describe an ACE model for binary family data; this structural equation model, which has been described previously, combines a general-family extension of the classic ACE twin model with a (possibly covariate-specific) liability-threshold model for binary outcomes. We then introduce our contribution, a likelihood-based approach to fitting the model to singly ascertained case-control family data. The approach, which involves conditioning on the proband's disease status and also setting prevalence equal to a prespecified value that can be estimated from the data, makes it possible to obtain valid estimates of the A, C, and E variance components from case-control (rather than only from population-based) family data. In fact, simulation experiments suggest that our approach to fitting yields approximately unbiased estimates of the A, C, and E variance components, provided that certain commonly made assumptions hold. Further, when our approach is used to fit the ACE model to Austrian case-control family data on depression, the resulting estimate of heritability is very similar to those from previous analyses of twin data.

SUBMITTER: Javaras KN

PROVIDER: S-EPMC2922975 | biostudies-literature | 2010 Apr

REPOSITORIES: biostudies-literature

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Fitting ACE structural equation models to case-control family data.

Javaras K N KN Hudson J I JI Laird N M NM

Genetic epidemiology 20100401 3

Investigators interested in whether a disease aggregates in families often collect case-control family data, which consist of disease status and covariate information for members of families selected via case or control probands. Here, we focus on the use of case-control family data to investigate the relative contributions to the disease of additive genetic effects (A), shared family environment (C), and unique environment (E). We describe an ACE model for binary family data; this structural eq ...[more]

PMID: 19918760

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Project description:BackgroundIt is currently accepted that the perturbation of complex intracellular networks, rather than the dysregulation of a single gene, is the basis for phenotypical diversity. High-throughput gene expression data allow to investigate changes in gene expression profiles among different conditions. Recently, many efforts have been made to individuate which biological pathways are perturbed, given a list of differentially expressed genes (DEGs). In order to understand these mechanisms, it is necessary to unveil the variation of genes in relation to each other, considering the different phenotypes. In this paper, we illustrate a pipeline, based on Structural Equation Modeling (SEM) that allowed to investigate pathway modules, considering not only deregulated genes but also the connections between the perturbed ones.ResultsThe procedure was tested on microarray experiments relative to two neurological diseases: frontotemporal lobar degeneration with ubiquitinated inclusions (FTLD-U) and multiple sclerosis (MS). Starting from DEGs and dysregulated biological pathways, a model for each pathway was generated using databases information biological databases, in order to design how DEGs were connected in a causal structure. Successively, SEM analysis proved if pathways differ globally, between groups, and for specific path relationships. The results confirmed the importance of certain genes in the analyzed diseases, and unveiled which connections are modified among them.ConclusionsWe propose a framework to perform differential gene expression analysis on microarray data based on SEM, which is able to: 1) find relevant genes and perturbed biological pathways, investigating putative sub-pathway models based on the concept of disease module; 2) test and improve the generated models; 3) detect a differential expression level of one gene, and differential connection between two genes. This could shed light, not only on the mechanisms affecting variations in gene expression, but also on the causes of gene-gene relationship modifications in diseased phenotypes.

Project description:Background: The ordering of molecules or particles in the vicinity of a confining surface leads to the formation of an interfacial region with layers of decreasing order normal to the confining surfaces. The overlap of two interfacial regions gives rise to the well-known phenomenon of oscillatory structural forces. These forces are commonly fitted with an exponentially decaying harmonic oscillation as introduced by Israelachvili (Israelachvili, J. N. Intermolecular & surface forces; Academic Press: San Diego, CA, USA, 1985). From the fit three important parameters are obtained, namely wavelength, amplitude and decay length, which are related to the period, the strength and the correlation length of the oscillatory structural forces, respectively. The paper addresses structural forces between a silica microsphere and a silicon wafer across silica nanoparticle suspensions measured with a colloidal probe AFM. Using the simple fitting procedure with three parameters often leads to underestimation of actually measured forces. The deviation of the fit from the experimental data is especially pronounced at small distances of the confining surfaces and at high concentrations of silica nanoparticles. As a consequence, the parameters of the common fit equation vary with the starting point of the fit. Although the wavelength is least affected and seems to be quite robust against the starting point of the fit, all three parameters show distinct oscillations, with a period similar to the wavelength of the oscillatory structural forces themselves. The oscillations of amplitude and decay length, which are of much higher magnitude, show a phase shift of 180° implying not only a dependence on the starting point of the fit but also on each other. The range affected by this systematic deviation of the fit parameters is much larger than the optically perceived mismatch between fit and experimental data, giving a false impression of robustness of the fit. Results: By introducing an additional term of exponentially decaying nature the data can be fitted accurately down to very small separations and even for high silica nanoparticle concentrations (10 wt %). Furthermore wavelength, amplitude and decay length become independent of the starting point of the fit and in case of the latter two of each other. The larger forces at small separations indicate a more pronounced ordering behavior of the particles in the final two layers before the wall. This behavior is described by the proposed extension of the common fit equation. Conclusion: Thus, the extension increases the accessible data range in terms of separation and concentration and strongly increases the accuracy for all fitting parameters in the system studied here.

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Fitting ACE structural equation models to case-control family data.

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Fitting ACE structural equation models to case-control family data.

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