Computer Practical Exercise on family-based association for quantitative traits using the QTDT program

Purpose

In this exercise you will be carrying out family-based association analysis of a quantitative trait.

Methodology

We will use the QTDT program written by Goncalo Abecasis:

http://www.sph.umich.edu/csg/abecasis/QTDT/index.html

Data overview

We will be using two data sets: 1. A small set of simulated trios typed for a single SNP marker and two quantitative traits. 2. A set of four child families (sibships) typed for three SNP markers. The data include a single trait and covariate, and parental genotypes are not available.

Appropriate data

QTDT can be used to analyse nuclear families or extended pedigrees, phenotyped with some quantitative trait of interest.

Instructions

Data files

trios.ped
trios.dat

sibs.ped
sibs.dat
sibs.ibd
sibs.map

You should save these to an appropriate directory on your machine.

Step-by-step instructions

We will use the tutorial from the QTDT website

http://www.sph.umich.edu/csg/abecasis/QTDT/tour/

If you have any questions, please ask an instructor.

References

Abecasis GR, Cardon LR, Cookson WO (2000) A General Test of Association for Quantitative Traits in Nuclear Families. Am J Hum Genet 66:279-292.

Abecasis GR, Cookson WO and Cardon LR (2000) Pedigree tests of transmission disequilibrium. Eur J Hum Genet 8:545-551.