Hi

I am doing pedigree analysis (linear linkage analysis ) for polygenic diseases such as obesity, hypertension in parent-children. I have seen the tutorial video and manual, but I am not sure how to input the parent's phenotype.
My research data does not contain genetic information, only the phenotype.

I'm wondering if there is a way to put the parent's phenotype (categorical variables like with disease vs. without disease) in the pheno file.

Thank you.

Hi,
I am not sure that linkage analyses can be performed w/o access to the genotypes. At this point you are limited to heritability and genetic correlation analyses. You can use parents' DX status as a binary trait to correlate heritability in the offspring.

Thank you for your reply.

You can use parents' DX status as a binary trait to correlate heritability in the offspring.
--> Could you please tell me how to prepare the phenotype file?

On the tutorial video, I could not find how to add parent's trait and IDs.

for example, if I want to study the heritability of hypertension between parent-child relationship, where should I put the parental hypertension status?

Thank you

You simply treat it as any other phenotype. You can simply say that having a parent with a dx carries one unit of genetic+phenotype risk. Thus a subject with one parent with DX has a genetic risk score as 1, a subject with both parents affected has a genetic risk score of 2. You can also expand this to more distant relatives e.g. assign a genetic risk score of 0.5 to each of the grandparents affected with the illness and so on. Then you can run heritability on this trait. It will explain the proportion of additive genetic variance in the total risk score.