Questions tagged [polygenic-risk-score]

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Can the PGS Calculator give the contribution of each variant to the overall PGS?

I am using the PGS Calculator ( to compute the polygenic scores of individuals based on a scoring file. PGS Calculator works wonderfully and outputs the ...
Cristian Riccio's user avatar
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How to associate point mutations to quantitative protein levels

My experiment is based on a quantitative continuous variable levels (B12 vitamin) in a sample of patients retrospectively selected based on values that can take (under our criteria): normal low ...
Javier Hernando's user avatar
2 votes
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Input for --score in PLINK 1.9 when generationg PRS using GWAS summary statistics

I'm conducting a simulation and I need to obtain polygenic risk scores (PRS) using genome wide association studies (GWAS) summary statistics. It is known that the GWAS will give BETA and OR for ...
Dovini Jayasinghe's user avatar
3 votes
1 answer

Polygenic Risk score calculation using vcf files

I have about 750 vcf files and I am looking to generate a Polygenic Risk Score for each individual. I am planning to use either PLINK or LDPhred to generate a Risk Score. I have phenotype information ...
user15921's user avatar
1 vote
1 answer

Summary statistics version problem

I am learning GWAS study and PRS for predicting disease. I was aligning my sequencing data with GRCH38 reference panel. However, in the PRS analysis step, I found that most of the summary statistics ...
Shafayet Rahat's user avatar
0 votes
1 answer

Polygenic Risk Scores

I have run a GWAS and used PRSice ( to calculate polygenic risk scores on the data collected from the GWAS. I need to check whether alcohol dependence can predict gambling ...
Shelby Labuschagne's user avatar
2 votes
2 answers

Loss of predictive power of polygenic risk score when dataset contains missing variants

I am trying to calculate polygenic risk scores (PRS) scores for a new dataset. This dataset does not have all the variants that the PRS score needs. The PRS score I am interested in has 40 variants, ...
hpatronage's user avatar