IDEAS home Printed from https://ideas.repec.org/a/bpj/sagmbi/v4y2005i1n15.html
   My bibliography  Save this article

Extension of the SIMLA Package for Generating Pedigrees with Complex Inheritance Patterns: Environmental Covariates, Gene-Gene and Gene-Environment Interaction

Author

Listed:
  • Schmidt Mike

    (Center for Human Genetics, Duke University Medical Center)

  • Hauser Elizabeth R

    (Center for Human Genetics, Duke University Medical Center)

  • Martin Eden R.

    (Center for Human Genetics, Duke University Medical Center)

  • Schmidt Silke

    (Center for Human Genetics, Duke University Medical Center)

Abstract

We have previously distributed a software package, SIMLA (SIMulation of Linkage and Association), which can be used to generate disease phenotype and marker genotype data in three-generational pedigrees of user-specified structure. To our knowledge, SIMLA is the only publicly available program that can simulate variable levels of both linkage (recombination) and linkage disequilibrium (LD) between marker and disease loci in general pedigrees. While the previous SIMLA version provided flexibility in choosing many parameters relevant for linkage and association mapping of complex human diseases, it did not allow for the segregation of more than one disease locus in a given pedigree and did not incorporate environmental covariates possibly interacting with disease susceptibility genes.Here, we present an extension of the simulation algorithm characterized by a much more general penetrance function, which allows for the joint action of up to two genes and up to two environmental covariates in the simulated pedigrees, with all possible multiplicative interaction effects between them. This makes the program even more useful for comparing the performance of different linkage and association analysis methods applied to complex human phenotypes. SIMLA can assist investigators in planning and designing a variety of linkage and association studies, and can help interpret results of real data analyses by comparing them to results obtained under a user-controlled data generation mechanism.A free download of the SIMLA package is available at http://wwwchg.duhs.duke.edu/software.

Suggested Citation

  • Schmidt Mike & Hauser Elizabeth R & Martin Eden R. & Schmidt Silke, 2005. "Extension of the SIMLA Package for Generating Pedigrees with Complex Inheritance Patterns: Environmental Covariates, Gene-Gene and Gene-Environment Interaction," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 4(1), pages 1-22, June.
    • Handle: RePEc:bpj:sagmbi:v:4:y:2005:i:1:n:15
    DOI: 10.2202/1544-6115.1133
    as

    Download full text from publisher

    File URL: https://doi.org/10.2202/1544-6115.1133
    Download Restriction: For access to full text, subscription to the journal or payment for the individual article is required.
    File URL: https://libkey.io/10.2202/1544-6115.1133?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    As the access to this document is restricted, you may want to search for a different version of it.

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Arafat Tayeb & Aurélie Labbe & Alexandre Bureau & Chantal Mérette, 2011. "Solving genetic heterogeneity in extended families by identifying sub-types of complex diseases," Computational Statistics, Springer, vol. 26(3), pages 539-560, September.
    2. Labbe Aurelie & Bureau Alexandre & Merette Chantal, 2009. "Integration of Genetic Familial Dependence Structure in Latent Class Models," The International Journal of Biostatistics, De Gruyter, vol. 5(1), pages 1-30, January.
    3. Crosslin David R. & Qin Xuejun & Hauser Elizabeth R., 2010. "Assessment of LD Matrix Measures for the Analysis of Biological Pathway Association," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 9(1), pages 1-46, October.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:bpj:sagmbi:v:4:y:2005:i:1:n:15. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    We have no bibliographic references for this item. You can help adding them by using this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Peter Golla (email available below). General contact details of provider: https://www.degruyter.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.