We first applied the Davies-Bouldin (DB) validity index [29] to verify that relative ASE = 2 is an appropriate threshold for AEI analysis. Our analysis showed the lowest DB index was at the threshold between ASE = 1.78 and ASE = 3.48 for rs16969968 (Figure 2a). The lowest DB index for rs615470 was at the threshold between ASE = 1.29 and ASE = 2.23 (Figure 3a). After excluding samples that failed in ASE assays and those with <90% genotyping success rate, 30 subjects showed more than 2-fold difference in relative ASE (AEI-positive) quantified with rs16969968; 14 subjects had ASE <2 and were determined to be AEI-negative (Figure 2b). Using ANOVA analysis, we detected strongly significant difference in relative ASE between AEI-positive and AEI-negative subsets (p-value = 1.85×10−18). With assay of rs615470, there were 39 AEI-positive subjects with 2.2-7.1-fold difference in relative ASE which is significantly different (p-value = 1.94×10−9) from the relative ASE in the AEI-negative subset (6 subjects) (Figure 3b).
