Design and Statistical Analysis of Pooled Next Generation Sequencing for Rare Variants

Figure 1

Empirical power at the a level of 5% for the parametric bootstrap (PB) test as a function of the difference of the allele frequency between cases and controls under various sequencing error rates, numbers of pools, and depths of sequencing coverage for testing association. Sample size was set at 500 cases and 500 controls. The minor allele frequencies (MAF) of controls were set at 0.01 and 0.5, sequencing error rates (e) were set at 0.005 and 0.01; and numbers of pools were set at 2, 10, and 40. Lines with different colors indicate the power of the PB test under different depths of coverage, which are compared to that of the Fisher’s exact test (read line) based on the true individual genotypes (FT).