Polygenic risk scores (PRS)

This page has been last updated for R11.

Sandbox directory

Polygenic risk scores (PRS) are available in the following Sandbox directory:

/finngen/library-red/finngen_R[RELEASE]/prs_1.0

Data files

The PRS data files are available for specific studies in the /data subdirectory.

The following types of files are available:

• Score files

• Weight files

• Correlation files

Please refer to the readme file in the sandbox directory for full details of the available data.

Score files

• finngen_R[RELEASE]_[STUDY].sscore: Individual scores for the specific study

• finngen_R[RELEASE]_[STUDY].no_regions.sscore: Individual scores with regions removed

Score files are produced using the plink -score option and contain the following tab-separated columns:

Column	Description
#FID	Family ID
IID	Sample ID
NMISS_ALLELE_C	Non-missing allele count
NAMED_ALLELE_DOSAGE_SUM	Sum of named allele dosages
SCORE1_AVG	Score

Weight files

• finngen_R[RELEASE]_[STUDY].weights.txt: SNP weights produced by PRS-CS

Weight files are produced by PRScs. They contain the following tab-separated columns without column headers:

Column	Description
1	CHROM
2	SNP
3	POS
4	REF
5	ALT
6	WEIGHT

Correlation files

• finngen_R[RELEASE]_prs_pheno_corr.tsv: GLM ross correlation between all PRS studies and all other phenotypes, sorted by p-value and filtered for p < 0.0001

Correlation files contain the following tab-separated columns:

Column	Description
PHENO	Phenotype
beta	Type II error prob. (beta statistic)
pval	p-value
p_R2	p R-squared value
pval_F	P-value of F-statistics
study	Study name

Further information

See also the Using polygenic risk scores and how to run PRS sections.