Entering edit mode
11 days ago
Arun
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0
hello everyone, I am trying to calculate Polygenic risk score from the Genotype results of two person, i want to calculate PRS for some disease like Cardiovascular and Pancreatic cancer.
I don't have any phenotype data, but i have Rs ID, Chr name and position, Genotype of each SNPs. I have many doubts as my sample size is two small, i dont have any other value such as Beta, Effect allele and Eaf value. how to utilize the GWAS summary of other studies of same disease. Thank you in advance
How many samples do you have? for both case and control?
However, you need to calculate sample amount before conducting the PRS. PRS is just a method, but it depends on your sample size.
Hope it helps!
Thank you so much for replying,
Actually i have only genotype results of two samples, along with SNP name, Rs ID, Chr number and genomic position. The actual task given to me was to calculate Polygenic risk score and to check whether the people are susceptible to the particular disease or not based on PRS.
I don't have any Phenotype data which was required by PLINK, So using other GWAS studies for getting effect allele and Beta value is a right way? Please let me know that am I going in any wrong direction in this.
If your task is only to determine whether people are susceptible to a particular disease based on SNPs, the odds ratio (OR) has already given you an answer. OR interpretation is easier than PRS, I think, particularly for preliminary study.
Yes, you may use other studies to obtain desired SNPs, but I am not sure if you can use a similar beta value. You are not going in the wrong direction, but you need to ensure your current method is in accordance with your design experiment.
Hope it helps!