Preparing to use PRSice

To install PRSice v.2.3.5 (Linux 64 bit)

wget https://github.com/choishingwan/PRSice/releases/download/2.3.5/PRSice_linux.zip
unzip PRSice_linux.zip

To get the required scoring files

The following scoring files were taken from PGS Catalog on the basis of the cohort distribution, year of compilation, and number of variants for the required phenotype. Each of these scoring files had 103 variants for colorectal cancer for white cohorts.

• PGS000074

• PGS000785

These scoring files were loaded using the following command on the Linux terminal:

wget https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000074/ScoringFiles/PGS000074.txt.gz
gunzip PGS000074.txt.gz

wget https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000785/ScoringFiles/PGS000785.txt.gz
gunzip PGS000785.txt.gz

Quality control of the scoring files

To remove metadata (in Linux terminal)

sed '1,14d' PGS000074.txt > PGS000074.txt

sed '1,14d' PGS000785.txt > PGS000785.txt

Since scoring files from the PGS Catalog do not include p-values, it was set to a default value of 0 (in R)

df1 <- read.table("PGS000074.txt", header=TRUE, sep="\t")
df1$P <- '0'
write.table(df1, "PGS000074.txt", quote=FALSE, row.names=FALSE)

df2 <- read.table("PGS000785.txt", header=TRUE, sep="\t")
df2$P <- '0'
write.table(df2, "PGS000785.txt", quote=FALSE, row.names=FALSE)