IDEAS home Printed from https://ideas.repec.org/a/eee/csdana/v55y2011i3p1236-1249.html
   My bibliography  Save this article

Allowing for missing genotypes in any members of the nuclear families in transmission disequilibrium test

Author

Listed:
  • Alpargu, Gülhan

Abstract

The Transmission Disequilibrium Test (TDT) detects linkage between a marker and a disease-susceptibility locus in the presence of linkage disequilibrium. The TDT requires data on the genotypes of affected offspring and their parents, which might not always be available. For example, for late onset diseases it might be difficult to find parents still alive, or genotypes of offspring might not be available. Genotyping unaffected siblings, combining different genotype data sets, or assuming a model mechanism for missing parents have all been proposed to deal with missing genotypes in parents but not in offspring. In this paper, we propose a Mendel Inheritance-Transmission Disequilibrium Test (MI-TDT) to impute missing genotypes in any members of a family with two affected offspring. Our method does not require any of the remedies mentioned above but simply utilizes the fundamental property of Mendel Inheritance on the transmission of alleles from parents to offspring. Most importantly, the MI-TDT reassures researchers about the declared significant genes when incomplete data is ignored. We illustrate the MI-TDT by identifying significant genes in type 1 diabetes from the Warren families in the United Kingdom.

Suggested Citation

  • Alpargu, Gülhan, 2011. "Allowing for missing genotypes in any members of the nuclear families in transmission disequilibrium test," Computational Statistics & Data Analysis, Elsevier, vol. 55(3), pages 1236-1249, March.
  • Handle: RePEc:eee:csdana:v:55:y:2011:i:3:p:1236-1249
    as

    Download full text from publisher

    File URL: http://www.sciencedirect.com/science/article/pii/S0167-9473(10)00347-6
    Download Restriction: Full text for ScienceDirect subscribers only.

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

    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:eee:csdana:v:55:y:2011:i:3:p:1236-1249. See general information about how to correct material in RePEc.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: (Dana Niculescu). General contact details of provider: http://www.elsevier.com/locate/csda .

    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 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.

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

    IDEAS is a RePEc service hosted by the Research Division of the Federal Reserve Bank of St. Louis . RePEc uses bibliographic data supplied by the respective publishers.