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Disclaimer: Supplementary materials have been peer-reviewed but not copyedited.

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Supplemental Figure 1. The discovery probability of a novel variant (VAF = 0.01) using pooling designs, with a fixed sequencing cost. The sequencing cost is the same as that of sequencing 200 individuals with 4× coverage, which provides a maximum discovery probability possible at 0.866.

Supplement Figure 2. Comparison in variant detection probability of optimal pooling designs with various cost function, vs. individual designs, over a range of variant allele frequencies. The cost function is the same as in Figure 7.

Supplemental Text 1. The WinBUGS code for the hierarchical model on the pooled NGS data.

Supplemental Table 1. Top 5 optimal pooling designs for a study interested in a variant with VAF = 0.03 and OR = 2, with a specified cost function and fixed constraints on sequencing cost and sample size

Supplemental Table 2. Comparison in variant detection probability of optimal pooling designs with various cost function, vs. individual designs, over a range of variant allele frequencies. The cost function is the same as in Figure 7.

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