Question: Quantitative Trait Analysis Using Twins
1
gravatar for geetha.r.v
5.9 years ago by
geetha.r.v30
geetha.r.v30 wrote:

Hi,

I am using Plink to conduct a eQTL analysis for twins dataset. QFAM family based test can be used here. I came across a paper by Loukola et al. where they have explained :

"The QFAM family-based test of association was used for quantitative and categorical traits. QFAM performs a simple linear regression of phenotype on genotype. Adaptive permutation (up to 1x109 permutations) was used to correct for family structures. As the QFAM model allows no covariates, the original quantitative trait values were adjusted for gender (age-related traits) as well as testing age (all other traits), fitted to a linear model in R 2.12.0 2, and the resulting standardized residuals were used as analysis phenotypes". Also, "In all analyses, the DZ twin pairs were treated as regular siblings, whereas one individual from each MZ pair was included".

We have phenotype and genotype data for all individuals of DZ pair but for MZ, we have genotype data for 1 individual and phenotype data for both individuals. So, I am wondering how to include MZ twins in this analysis. Should I use phenotypes from both individuals of MZ pair or only one individual for which we have genotype data? Also how would QFAM consider the zygosity, should we include this information in the analysis?

Any help would be highly appreciated.

Thank you,

Pinki

eqtl plink • 1.9k views
ADD COMMENTlink modified 4.8 years ago by Biostar ♦♦ 20 • written 5.9 years ago by geetha.r.v30
0
gravatar for fridhackery
5.9 years ago by
fridhackery140
fridhackery140 wrote:

MZ twins have identical genotype by definition, except for somatic mutations.

They are likely included in your experimental design to establish normal phenotypic variability that is due to the environment etc rather than due to genotype.

So put the same genotype data in for MZ twins.

ADD COMMENTlink modified 5.9 years ago • written 5.9 years ago by fridhackery140

Thank you for your reply. I am wondering which tool would be appropriate for this analysis. Do you have any suggestions?

ADD REPLYlink written 5.9 years ago by geetha.r.v30
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