PRSice-2

Polygenic Risk Scores analysis

- Homepage : https://choishingwan.github.io/PRS-Tutorial/

- Basic : http://www.prsice.info/quick_start/

- Paper

  : https://academic.oup.com/gigascience/article/8/7/giz082/5532407

  : https://doi.org/10.1038/s41596-020-0353-1

- Author : https://choishingwan.github.io/

- Github : https://github.com/choishingwan/PRSice

 

Requirement

- Base data (GWAS QCed summary statistics)

- Target data (GWAS QCed bed, bim, fam prefix)

- Phenotype (Case / Control)

 

Heritability

- LD score regression

  : https://github.com/bulik/ldsc

  : https://alkesgroup.broadinstitute.org/LDSCORE/

 

QC guidance

- A tutorial on conducting genome-wide association studies: Quality control and statistical analysis

  : https://onlinelibrary.wiley.com/doi/full/10.1002/mpr.1608

 

Run

#!/bin/bash

tname=$1

plink2 --bfile ${tname} --glm allow-no-covars -ci 0.95 --out ${tname}

echo -e "SNP\tCHR\tBP\tA1\tA2\tOR\tSE\tP" |cat - <(awk 'NR>1 {print $3"\t"$1"\t"$2"\t"$5"\t"$4"\t"$10"\t"$11"\t"$15}' ${tname}.PHENO1.glm.logistic.hybrid) > ${tname}.assoc

Rscript PRSice.R \
	--dir . \
	--prsice ./PRSice \
	--base ${tname}.assoc \
	--target ${tname} \
	--binary-target T

Base data

$ bname='base_data'
$ plink2 --bfile ${bname} --glm allow-no-covars -ci 0.95 --out ${bname}
$ echo -e "SNP\tCHR\tBP\tA1\tA2\tOR\tSE\tP" |cat - <(awk 'NR>1 {print $3"\t"$1"\t"$2"\t"$5"\t"$4"\t"$10"\t"$11"\t"$15}' ${bname}.PHENO1.glm.logistic.hybrid) > ${bname}.assoc

or

--base ${bname}.PHENO1.glm.logistic.hybrid
--a1 ALT
--a2 REF
--chr #CHROM
--bp POS
--snp ID
--stat OR

 

Full options

./PRSice \
    --a1 A1 \
    --a2 A2 \
    --bar-levels 0.001,0.05,0.1,0.2,0.3,0.4,0.5,1 \
    --base TOY_BASE_GWAS.assoc \
    --binary-target T \
    --bp BP \
    --chr CHR \
    --clump-kb 250kb \
    --clump-p 1.000000 \
    --clump-r2 0.100000 \
    --interval 5e-05 \
    --lower 5e-08 \
    --num-auto 22 \
    --or  \
    --out PRSice \
    --pvalue P \
    --seed 1132945803 \
    --snp SNP \
    --stat OR \
    --target TOY_TARGET_DATA \
    --thread 1 \
    --upper 0.5