IDEAS home Printed from
MyIDEAS: Log in (now much improved!) to save this paper

Hunting for Genes with Longitudinal Phenotype Data Using Stata

Listed author(s):
  • Chuck Huber


    (Texas A&M Health Science Center School of Rural Public Health)

  • Michael Hallman

    (University of Texas School of Public Health)

  • Ron Harrist

    (University of Texas School of Public Health)

  • Victoria Friedel

    (University of Texas School of Public Health)

  • Melissa Richard

    (University of Texas School of Public Health)

  • Huandong Sun

    (University of Texas School of Public Health)

Registered author(s):

    Project Heartbeat! was a longitudinal study of metabolic and morphological changes in adolescents aged 8-18 years and was conducted in the 1990s. A study is currently being conducted to consider the relationship between a collection of phenotypes including BMI, blood pressure and blood lipids and a panel of 1500 candidate SNPs (single nucleotide polymorphisms). Traditional genetics software such as PLINK and HelixTree lacks the ability to model longitudinal phenotype data. This talk will describe the use of Stata for a longitudinal genetic association study from the early stages of data checking (allele frequencies and Hardy-Weinberg Equilibrium), modeling of individual SNPs, the use of False Discovery Rates to control for the large number of comparisons, exporting and importing the data through PHASE for haplotype reconstruction, selection of tagSNPs in Stata, and the analysis of haplotypes. We will also discuss strategies for scaling up to an Illumina 100k SNP chip using Stata. All SNP and gene names will be de-identified as this is a work in progress.

    If you experience problems downloading a file, check if you have the proper application to view it first. In case of further problems read the IDEAS help page. Note that these files are not on the IDEAS site. Please be patient as the files may be large.

    File URL:
    Download Restriction: no

    Paper provided by Stata Users Group in its series BOS10 Stata Conference with number 10.

    in new window

    Date of creation: 20 Jul 2010
    Handle: RePEc:boc:bost10:10
    Contact details of provider: Web page:

    More information through EDIRC

    No references listed on IDEAS
    You can help add them by filling out this form.

    This item is not listed on Wikipedia, on a reading list or among the top items on IDEAS.

    When requesting a correction, please mention this item's handle: RePEc:boc:bost10:10. 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: (Christopher F Baum)

    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.

    If references are entirely missing, you can add them using this form.

    If the full references list an item that is present in RePEc, but the system did not link to it, you can help with 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 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.

    This information is provided to you by IDEAS at the Research Division of the Federal Reserve Bank of St. Louis using RePEc data.