Figure 1
From: Summarizing polygenic risks for complex diseases in a clinical whole-genome report
Comparison of polygenic score calculation methods. Using the risk alleles and allele frequencies reported in the GWAS catalog, we calculated polygenic scores for 379 individuals of the 1000 Genomes Project European cohort. We counted the number of risk alleles in an individual—counting method—and compared with the multiplicative polygenic risk score (MPRS) and multiple single-nucleotide polymorphism (SNP) population attribution risk (PAR) using odd ratios (ORs) and ORs with risk allele frequency, respectively. Red circles represent the individuals in the same decile according to MPRS and PAR. The resulting decile of the counting method was different from those from MPRS and PAR, although they were significantly correlated (c and g). The results for coronary heart disease (60 risk alleles, a–c) and type 2 diabetes (70 risk alleles, e–g) showed the same trend. Venn diagrams show the agreement between polygenic scoring methods for the individuals in the 10th deciles by three methods (d and h). GWAS, genome-wide association study.
