Figure 5.

Serial Dilution of an Abnormal iPSC Line to Establish Detection Sensitivity

(A) Mean log R ratio (LRR, in red) and B-allele frequency (BAF, in blue) in the six dilution states (0%, 6.25%, 12.5%, 25%, 50%, and 100%). Notably, the AAB/ABB trisomy specific BAF signal (the two blue horizontal bands) transitions to the diploid AB BAF signal (single blue band) as the amount of abnormal cell line in the assay decreases. The black arrows highlight the heterozygous SNP band as it changes from the AAB and ABB genotype (two blue bands) to the AB genotype (one blue band). The disappearance of the double-band AAB/ABB genotype to the single-band AB genotype indicates the failure of the assay to detect the difference between abnormal trisomic and normal diploid DNA, and thus we estimate the sensitivity of the array to be between 12.5% and 25%.

(B) Plot displaying the mean BAF distance for chromosomes 12, 13, 14, 17, and 20 across the six dilution states. High BAF mean distance indicates a trisomic state, while a lower value signifies normal diploid DNA.

See also Table S4. Genomic Position of All Variants in Trisomic Chromosomes, Related to Figure 5, Table S5. Log R Ratio for All Variants in Trisomic Chromosomes, Related to Figure 5, Table S6. B-Allele Frequency for All Variants in Trisomic Chromosomes, Related to Figure 5.