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Supplemental Figure 1: QQ plots of the four RVA tests (CMC, BRV, WSS, and VT) and their extensions (CMC-M, BRV-M, WSS-M, VT-M). Data were generated under the null for 1,000 cases and 1,000 controls for the ALK gene. For the cases and controls, 15% and 5% of the genotypes are missing, respectively. The results are shown for CMC and CMC-M (panel A), BRV and BRV-M (panel B), WSS and WSS-M (panel C) and VT and VT-M (panel D) before and after removing those individuals missing >80% of their variant sites for the analyzed gene region and variant sites missing >10% of their variant calls.

Supplemental Figure 2: Results from the power study were performed with 0% (blue), 5% (black), and 10% (red) missing genotypes completely at random. The y-axis displays the power and the x-axis displays the percent of variants that are causal. The results are shown for the MC4R gene for 1,000 cases and 1,000 controls. The power is displayed for the fixed effect (OR = 3) model with the original RVA tests shown in solid lines and the extended tests in dashed lines. Analysis was performed using CMC and CMC-M (panel A); BRV and BRV-M (panel B); WSS and WSS-M (panel C); and VT and VT-M (panel D).

Supplemental Figure 3: Results from the power study were performed with 0% (blue), 5% (black), and 10% (red) missing genotypes completely at random. The y-axis displays the power and the x-axis displays the percent of variants that are causal. The results are shown for the ALK gene for 1,000 cases and 1,000 controls. The power is displayed for the fixed effect (OR = 3) model with the original RVA tests shown in solid lines and the extended tests in dashed lines. Analysis was performed using CMC and CMC-M (panel A); BRV and BRV-M (panel B); WSS and WSS-M (panel C); and VT and VT-M (panel D).

Supplemental Figure 4: The difference in call-rate between cases and controls for the analysis of the NHBLI-ESP data before filtering. The x-axis displays the absolute difference in call-rate between cases and controls, the y-axis displays the number of genes at which the difference was observed. Overall, there is substantial difference in call-rates between cases and controls. For almost 1,000 genes the difference in call-rate is 100%, implying that the gene was covered by 1 target but not the other.

Supplemental Figure 5: QQ plots of 4 different implementations of the SKAT test. Data were generated under the null for 1,000 cases and 1,000 controls for the ALK gene. For the cases, 0% of the genotypes are missing while for controls 20% of the genotypes are missing.

Supplemental Figure 6: QQ plots of 4 different implementations of the SKAT test. Data were generated under the null for 1,000 cases and 1,000 controls for the ALK gene. For the cases, 15% of the genotypes are missing while for controls 5% of the genotypes are missing.

Supplemental Figure 7: Results from the exome-wide case-control analysis using SKAT. QQ plots of 4 different implementations of the SKAT test are shown. Analysis was performed by assigning 1,000 samples for which the Agilent capture array was used as the “case” group and 1,000 samples for which the Nimblegen capture array was implemented as the “control” group.

Supplemental Figure 8: Results from the power study were performed with 0% (blue), 5% (black), and 10% (red) missing genotypes completely at random. The y-axis displays the power and the x-axis displays the percent of variants that are causal. The results are shown for the MC4R gene for 1,000 cases and 1,000 controls. The power is displayed for the fixed effect (OR = 3) model with the uncorrected SKAT test shown in solid lines and the SKAT-M implementation in dashed lines.

Supplemental Figure 9: Results from the power study were performed with 0% (blue), 5% (black), and 10% (red) missing genotypes completely at random. The y-axis displays the power and the x-axis displays the percent of variants that are causal. The results are shown for the ALK gene for 1,000 cases and 1,000 controls. The power is displayed for the fixed effect (OR = 3) model with the uncorrected SKAT test shown in solid lines and the SKAT-M implementation in dashed lines.

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