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st: test for association btw genotype and continuous phenotype


From   Rachel Dvo <rlk208@yahoo.com>
To   statalist@hsphsun2.harvard.edu
Subject   st: test for association btw genotype and continuous phenotype
Date   Tue, 30 May 2006 14:53:02 -0700 (PDT)

Hello,

I have a dataset that includes continuous phenotype
data (such as time spent grooming) on a population of
monkeys. I also have genotype information on the
monkeys, such that each individual shows either state
1 or 2 (1: homozygous for a common allele or 2:
heterozygous). I want to test for a possible
association between genotype (state 1 or 2) and the
behavioral phenotype. However, some of the individuals
are related; the relatedness is mostly of the
half-sibling type because there are sets of
individuals with the same father, but the dataset
includes other sets of relatives as well. All pedigree
information is known (i.e. it is known how the
individuals are related to each other), but I do not
know of a way to account for the relatedness (as
genetic relatedness could be independently affecting
phenotype). 

I have had trouble finding examples of appropriate
tests/statistics because this dataset is different
from typical ones that can use association/pedigree
analysis methods such as the TDT test, as I do not
have matched pairs, case-controls, or a large number
of sib-pairs, and I am measuring a continuous
phenotype rather than affected vs. not affected, for
example.

Also, it has been suggested that because the average
identity by descent (IBD) for any two individuals
chosen randomly from the population is low (1.29%),
relatedness will not be a confounding factor in
association analysis using ANOVA. Does anyone know of
a cutoff for IBD in this regard?

Thank you very much, in advance, for your help!
RD


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