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Polygenic Risk Score (PRS) Calculations

Hello,

Is there a way to calculate polygenic risk scores using RapidMiner Studio? My advisor instructed me to calculate polygenic risk scores (from a list of genes and their associated genetic variations (SNPs)). I have tried the website “Impute.me” and tried looking to use other programs in RStudio, however I am unsure what to do and maybe RapidMiner can do it all.

Would you be able to provide any help on polygenic risk score calculations? I would have a large genomic data set with SNPs and genotype information that I can upload to RapidMiner and a score will be given associated to each variation.

Thank you very much.
-Rie

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Caperez

Hi @Rie,

Yes, you can construct a machine learning based polygenic Risk Score model.

Please check these two interesting links.

Identification of a novel gene signature for the prediction of recurrence in HCC patients by machine learning of genome-wide databases | Scientific Reports

https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=&cad=rja&uact=8&ved=2ahUKEwjBoaXiyNzvAhVxmVwKHURGCRkQFjADegQIBBAD&url=https://revistas.usal.es/index.php/2255-2863/article/download/22376/24560/&usg=AOvVaw1_drTqORXPIu5FBYwOQJza
regards