IDEAS home Printed from https://ideas.repec.org/p/boc/bost10/10.html
   My bibliography  Save this paper

Hunting for Genes with Longitudinal Phenotype Data Using Stata

Author

Listed:
  • 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)

Abstract

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.

Suggested Citation

  • Chuck Huber & Michael Hallman & Ron Harrist & Victoria Friedel & Melissa Richard & Huandong Sun, 2010. "Hunting for Genes with Longitudinal Phenotype Data Using Stata," BOS10 Stata Conference 10, Stata Users Group.
  • Handle: RePEc:boc:bost10:10
    as

    Download full text from publisher

    File URL: http://repec.org/bost10/Huber2010.ppt
    Download Restriction: no

    More about this item

    NEP fields

    This paper has been announced in the following NEP Reports:

    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: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). General contact details of provider: http://edirc.repec.org/data/stataea.html .

    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.