Polygenic risk scores (PRS) rely on the genome-wide association studies (GWAS) to predict the phenotype based on the genotype. However, the prediction accuracy suffers when GWAS from one population are used to calculate PRS within a different population, which is a problem because the majority of the GWAS are done on cohorts of European ancestry.
Tl; dr, I love to tell a good story. If you don’t wanna read that, no worries. Just skip ahead or get straight to business!
Now, to the story.
I have been working on a project where I was using population allelic frequencies for about 6,000 SNPs (single nucleotide polymorphisms) for CEU (North Americans from UTAH with European ancestry) individuals from the 1000 Genomes Project.
Today we discussed the new version of LDpred: LDpred2 (preprint here).
The preprint is short and technical and does not go through the trouble of explaining the models implemented in LDpred1 and LDpred2, since that has been described in great detail in the original publication.