Hunting for Genes with Longitudinal Phenotype Data Using Stata

Chuck Huber (), Michael Hallman, Ron Harrist, Victoria Friedel, Melissa Richard and Huandong Sun
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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

BOS10 Stata Conference from Stata Users Group

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.

Date: 2010-07-20
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