Extended Data Figure 6 |. Testing the accuracy of the rare variant polygenic score.

As described in Figure 3 and Methods, for each of the nine rare variant polygenic scores (three variant weighting schemes for each of three gene set definitions; Extended Data Figure 5), we calculated Fisher’s odds ratios and 95% confidence intervals for the fraction of true T2D cases reclassified by the model as compared to the null expectation. The area of the diamond for each odds ratio is proportional to the total number of reclassified individuals in the AMP-T2D-GENES test sample (total N assessed=17,206; see Supplementary Table 9 for model-specific reclassification sample sizes). Error bars indicate 95% confidence intervals of the odds ratios.