polygenic risk scores

Chating about polygenic risk scores

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.

Ancestry Matters: why do polygenic risk scores remain limited to a few?

Polygenic scores for height in admixed populations

Polygenic risk scores (PRS) use the results of genome-wide association studies (GWAS) to predict quantitative phenotypes or disease risk at an individual level. This provides a potential route to the use of genetic data in personalized medical care. …

Theoretical and empirical quantification of the accuracy of polygenic scores in ancestry divergent populations

This week in Journal Club at the Mathieson Lab we discussed the recently published paper by Wang et. al (2020) on the theoretical aspects of the transferability of polygenic risk scores across ancestries.

What drives the reduced prediction accuracy of polygenic scores in non-European individuals?

Investigations on different methods for PRS calculation, the effects of different modelling and pruning approeches, and transferability of PRS across ancestries

LDpred2: Better, Faster, Stronger

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.

Abstract: Polygenic risk scores (PRS) summarise the genetic information spread across several genetic variants into one single number. This number can be used to predict an individual’s phenotype or - more realistically - to place an individual in risk groups according to their PRS.

Loss of predictive power of polygenic risk scores in admixed populations

Here is a link for the poster in pdf format plus an audio guide presented at the TAGC 2020 Conferece.

Low transferability of height polygenic risk scores in admixed ancestry populations

Polygenic risk scores (PRS) summarize the results of GWAS into a single number that can predict quantitative phenotype or disease risk. One barrier to the use of PRS in clinical practice is that the majority of GWAS come from cohorts of European …

Polygenic risk scores perform poorly across populations

The vast majority of genome-wide association studies (GWAS) are performed in cohorts of European ancestry. Systematic differences in polygenic risk scores (PRS) between European and non-European ancestry populations are believed to be largely …