Questions tagged [polygenic-risk-score]

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Problem with Calculating Polygenic Risk Score (PRS) in Plink

I've been struggling with constructing a PRS score. In the pics you can see how my summary stats and my target data look like. Target Data Summary Stats I've tried the following code which should be ...
John Johnson's user avatar
2 votes
1 answer

Does using a microarray chip that matches the chip used in training lead to higher explained variance of a polygenic score?

I'm trying to replicate an existing polygenic score (i.e. test the accuracy in a new sample), and want to know if matching the original study's microarray chip will improve the accuracy (that is, ...
BigMistake's user avatar
5 votes
2 answers

Converting VCF format to text for use with PLINK and understanding column mapping

I successfully completed Nature PRS tutorial, which is based on PLINK. Turning to my real data, I downloaded ukb-d-20544_1.vcf.gz. Now I'm facing the problem that I seem to be unable to use it in ...
jay.sf's user avatar
  • 173
2 votes
1 answer

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
0 votes
1 answer

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
2 votes
2 answers

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