About Genetic Scores

What is a genetic score ?

A genetic score, also called a polygenic score (PGS), polygenic risk score (PRS), genetic risk score, or genome-wide score, is a number that summarises the estimated effect of many genetic variants (usually SNPs) on an individual’s phenotype, typically calculated as a weighted sum of trait-associated alleles (wikipedia).

What does a genetic score model look like in the Atlas?

A genetic score model file presents in the following format:

rsid chr pos effect_allele other_allele effect
rs116576188 6 31296369 C A 0.015
rs568630420 6 31315587 T G 0.02
         
rs78630340 6 31342334 A T 0.05

where:

rsid rsID
chr Chromosome code
pos Base-pair coordinate (GRCh37)
effect_allele Effect allele with regard to the dosage of a variant
other_allele The other allele
effect Effect size of the variant

How do we calculate genetic scores with the genetic score model of a trait?

An easy way to calculate genetic scores of a new cohort is to use PLINK2. Here is an example:

>plink2
--bfile ${bed_file}
--score ${model_file} 1 4 6 header list-variants cols=scoresums
--out  ${results}

where:

bed_file Plink bed file of genetic data in a new cohort
model_file Path for a genetic model file downloaded from the Atlas
results Result file path