NITRC Solar Eclipse Imaging Genetics tools Forum: help

RE: Phenotype of parents

Peter Kochunov — Wed, 20 Oct 2021 11:01:38 GMT

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.

RE: Phenotype of parents

yewan park — Wed, 20 Oct 2021 3:25:13 GMT

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

RE: Phenotype of parents

Peter Kochunov — Tue, 19 Oct 2021 13:15:11 GMT

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.

Phenotype of parents

yewan park — Tue, 19 Oct 2021 2:08:15 GMT

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.

RE: genotype-environment interaction analysis in solar

Peter Kochunov — Wed, 26 Feb 2020 0:17:05 GMT

Hi,
This is easy to explain. The two variances represent different pool.

Say a trait has a variance of 100%. In the first step you regress the variance explained by fixed factors e.g. age and sex. Some of this variance is genetic and some of it is environmental but together it explains 61% of the trait variance. The residual 39% of the variance goes into the additive genetic modeling.
Out of that variance 52% is being explained by the additive genetic factors. Therefore, the total variance explained by the additive genetics is .39*.52 or about 20% and remaining 19% are enviromental.

So together this will add:

61% fixed factor variance + 20% additive genetic + 19% enviromental factors =100

RE: genotype-environment interaction analysis in solar

zhc95522 — Thu, 20 Feb 2020 11:35:58 GMT

Thanks for your reply and I have contacted the author.
There is another question I encountered in heritability analysis. I have done a heritability estimation of height adjusting for sex, age, age square, and their interaction. The result was that the heritability estimation of height was 0.612 and the covariates explained 0.518 of the trait variance.
Theoretically, the sum of heritability and covariates' effect should be less or equal than 1. But here, 0.612+0.518=1.13>1.
The code is as below:

trait height
cov age^1,2#sex
polygenic

Do you have any idea about this?

RE: genotype-environment interaction analysis in solar

Peter Kochunov — Wed, 19 Feb 2020 15:54:48 GMT

Hi,
The genotype by environment interaction modeling was coded in solar-eclipse by the authors of that paper. I would urge you to contact the authors directly. We also would be happy to share these scripts in the standard solar distribution if they are willing to share it.

genotype-environment interaction analysis in solar

zhc95522 — Tue, 18 Feb 2020 12:44:25 GMT

Hi solar developers,
I am a student from Department of Epidemiology, Peking university. I am trying to run a genotype-environment interaction analysis with solar. I am inspired by a paper titled "The heritable basis of gene–environment interactions in cardiometabolic traits" and intended to conduct a similar analysis. But I have difficulties in the usage of SOLAR software. I have no idea about which command I should use and how to write the code.
Do you have any suggestion or support file?
I am very thankful if you can help me out. Looking forward to your reply.

Best

Welcome to Help

Christian Haselgrove — Fri, 30 Dec 2011 15:06:27 GMT

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