Calculating PRS in UK Biobank · Biostar

This is a test version of Biostars. For the public version, visit https://www.biostars.org.

Calculating PRS in UK Biobank

Hi, I want to calculate PRS in UK Biobank with PRSice2. However, the GWAS used a lot of UK biobank participants as control and proxy case. They then ran a PRS on a cohort where the meta-analysis of the summary stats excluding the cohort and replicating it in another cohort. The PRS was comprised of 1800 variants. Of course, it is much less computation to only use 1800 variants than calculating it from scratch on UK Biobank. I was wondering what might be the best approach? Request a version of the summary stats without UK Biobank and calculating from scratch?

snp

• 2,059 views • link

updated 4.8 years ago by Jenish •

• written 6.5 years ago by ericyubet •

Did you find any solution/work around for this?

• 0 views • link

written 4.8 years ago by Jenish •

0 answers

No answers yet.

Log in to answer this question.

More posts like this

PRS result interpretation
written 1.2 years ago by trkfs •

I have the genotype info of an individual in a vcf file. From that, I extracted relevant info like the REF, ALT and GT columns. …
Proxy Variant SNP for PRS
written 1.9 years ago by curious_butterfly •

Hi, I'm relatively new to calculating PRS and I have a quick question regarding proxy variants. If SNPs that are in the GWAS are not …
What is the best GWAS tool to use for a very large cohort data (UK Biobank data)?
written 2.5 years ago by lsy9 •

I'm considering conducting a GWAS analysis using the UK Biobank data, which involves a very large cohort of 500,000 participants. In our lab, we've previously …
additive genetic variance
written 2.7 years ago by unepanthere056 •

Q. Which tool(s), other than GCTA, can provide for the "additive genetic variance". Bonus if it can do it from a summary GWAS result. GCTA …
Free access European cohort study
written 3.5 years ago by nyanovsky •

I'm wondering if there's a free access cohort type study (of European ancestry) out there, like the UK BioBank. I tried accessing several ones mentioned …
Running a validated polygenic risk score (PRS) on a new dataset using VCF/PGEN files (in the 100K g…
written 3.9 years ago by tacrolimus

I have downloaded a PRS from the PRS catalogue that has been published and validated in a cohort from the UK Biobank. I would like …
PRS from a dataset on which the GWAS is based on
written 4.9 years ago by Jenish •

I am using the PRSice tool to calculate PRS scores for a dataset (d1) using a set of weights from the PGS catalog. Although the …
PRS using PGS Catalog
written 5.4 years ago by Humza •

When using PRSice for PRS calculation of target data using a file of variants from the PGS catalog, does the variant file from the PGS …
Deviance in allele frequencies between arrays and WGS
written 5.6 years ago by German.M.Demidov

Dear community members, I am trying to adapt a PRS score from arrays ([famous 313 markers breast cancer PRS][2]) to thousands of WGS data. There …
Effect Allele Frequency in base summary statistics for PRSs calculation
written 6.5 years ago by bigfoot •

I want to use summary statistics containing only the Effect Allele Frequency (EAF) and not the Minor Allele Frequency (MAF) as base dataset for PRS …