PSYC 5112
STATISTICAL GENETICS FOR COMPLEX TRAITS
FINAL PROJECT
The goal of any gene-mapping project is to identify chromosomal regions and/or causal variants that might
be related to the disease under study. Toward that end, the final project for PSYC5112 is geared towards
identifying genetic variants underlying Alcoholism on chromosome 7. First, a linkage analysis will be run
using phenotypes provided to you. Once linkage regions are identified, we can then employ more refined
and powerful association analysis methodology to guide our search for the disease susceptibility loci.
LINKAGE
Each student will receive one linkage dataset for the analysis, and the data will be provided in the MERLIN
linkage format, resulting in three separate files: pedigree, map and dat files. Alcoholism is defined through
the affection status variable in the datasets. There is one chromosome under investigation: Chromosome 7.
No two datasets are identical, as the clinical definition of Alcoholism varies from dataset to dataset. Each
person will analyze only one definition of Alcoholism for linkage. I will reveal the different clinical
definitions of Alcoholism when the results are presented.
ASSOCIATION
Each student will receive one association dataset for the analysis, and the data will be provided in
FBAT/PBAT format as well as QTDT format. Various definitions of alcoholism will be provided. Each
student will have identical files. There will be 7 phenotype variables that may be of interest:
ALDX1
ALDX2
ALDX3
ALDX4
EEG
AGE
GENDER
- DSM-III classified “affected”
- DSM-III classified “affected” or “unaffected with some symptoms”
- DSM-IV classified “affected”
- DSM-III or DSM-IV classified “affected”
- Electrophysiological data (“Eyes Closed Resting EEG”)
- Age at EEG measurement
- 1 = male, 2 = female
The population prevalence of alcoholism varies, but for the purposes of the project, we can assume anywhere
from a 10% to 15% prevalence. The EEG measurement is approximately normally distributed and has a
mean of 14.5.
Since Alcoholism is exceedingly complex and there lacks a compelling parametric model, I ask that you
perform one (or more) of the non-parametric linkage analyses discussed in class. For association, you are
welcome to carry any approach you feel appropriate. Each student will present their findings during the final
scheduled class period. Content will vary, however I would like to see the following information presented:
1)
2)
3)
4)
Descriptive Information (briefly)
Analytic Strategy
Results
Overall Conclusions