Question: SNP genotyping and analysis of association with phenotype
gravatar for orzech_mag
4.5 years ago by
orzech_mag220 wrote:

Dear colleges,

I would like to analyse the association of few SNPs with phenotypes and summarize if those SNPs may cause increased risk or normal risk for assumed phenotypes. In brief, I would like to genotype SNPs, obtain the list of SNPs identified in specimens and analyse the meaning of those SNPs. I read a lot of articles about it as well as familiarized with GWAS, however I still do not know how to perform the last part of the study - association of the SNP with phenotype. In some source I found the method described (they performed something like I'd like to), however it is unclear for me how to reproduce those steps. And here I'd like to ask for your help.

They wrote "The outcomes for each phenotype are calculated based on cut off reporting thresholds, which are set based on the negative log of p-value for the strongest SNP GWAS-associations (high) and the weakest SNP associations (low). Then, combined SNP weight for each phenotype is calculated based on aggregation of all individual SNP weights, which are statistically significant from published GWAS studies and SNPs ranking on aggregated public databases (Phenotype-Genotype Integrator@NCBI)".

My questions are: 1. Is there any software, which performs such analysis and is just not mentioned above? 2. If not, how to set thresholds and find the strongest and the weakest SNP associations based on my data? 3. How to aggregate properly weights of all SNPs? 4. How to obtain the aggregation of SNP weights fro mentioned public databases? 5. Is the mentioned above method in general correct for analysing the association of SNPs with phenotype?

I would very appreciate if you help me with that as I am not so familiar with such methods.

Best regards.

genotyping phenotype snp gwas • 2.8k views
ADD COMMENTlink modified 4.4 years ago by Biostar ♦♦ 20 • written 4.5 years ago by orzech_mag220

What is the nature of the phenotype? Is it a continuous variable, categorical, or binary? Are there any covariates that you need to control for? Are you comfortable with a command-line solution?

ADD REPLYlink written 4.5 years ago by Sean Davis26k

Command line is not a problem at all. Phenotypes present i.e. high risk for vitamin A deficiency. In general example, I want to genotype (i.e.) my SNPs and predict some risks associated with presence of those SNPs. Additionally, genotyped SNPs are limited by the list of SNPs associated with known phenotypes like susceptibility to syndrome X, etc.

ADD REPLYlink written 4.5 years ago by orzech_mag220

Which diseases are you interested in? Have you looked at the Open Targets Platform? This application was developed by the Core Bioinformatics and Computational Pipelines team in Open Targets. You can search for a disease and get the genes associated with it. The association between genes and disease can be made through several fronts, including Genetic association (from GWAS, EVA, UniProt, Gene2Phenotype), Somatic mutations, etc. We also give you the strength of the association based on those pieces of evidence (e.g. Somatic mutations, Genetic Associations, Text mining, etc). These are the genes associated with asthma using SNPs as evidence. Click on the cells of the table to explore each gene separately.

ADD REPLYlink modified 4.0 years ago • written 4.5 years ago by Denise CS5.1k

I have a list of many disorders and SNPs among genes, which are associated with listed phenotypes. I looked at the platform, however I am not sure if this is something what I am interested in. After genotyping assay I will get raw data, which I need to "translate" into meaning - the phenotype based on SNPs found. The method mentioned in first post is something what I am looking for, however I do not know how to perform all of steps.

ADD REPLYlink written 4.5 years ago by orzech_mag220

Why don't you ask the authors?

ADD REPLYlink written 4.4 years ago by H.Hasani970
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