Fig. 3: Allele-specific genomic validation with digital PCR.

a Allele-specific genomic validation was performed using paired tumor and adjacent normal fresh frozen samples. DNA was extracted from each sample. Allele-specific primers were designed specifically for each patient. Digital PCR was performed on each sample to orthogonally determine the allele-specific copy number. b Bar plot showing the allele-specific copy number of the predicted lost allele, relative to RNase P, as measured by dPCR for cell line mixtures of 11 varying tumor purities, with n = 3 technical replicates examined over three independent experiments per tumor purity (tumor purity 2 replicate 3 only had 1 independent experiment; tumor purity 0 and 100 only have 1 technical replicate). The dashed line denotes the expected value for no change in copy number. Asterisks denote a statistically significant difference (p < 0.05) from the copy number in the normal sample with a one-sided Student T test. c Bar plots denoting the HLA allele dPCR copy number relative to the multiplexed RNase P for 8 patient tumor samples with n = 3 technical replicates. The alleles predicted by DASH to be retained are shown on the top plot while the alleles predicted to be deleted are shown on the bottom plot. The dashed gray lines denote the expected copy number of one if there are no copy number alterations. Asterisks denote samples with p-values < 0.05 as determined by a one-sided Student T test. d Bar plots showing the HLA allele dPCR copy number relative to the multiplexed RNAse P for 13 patient tumor samples where both alleles were predicted to be retained with n = 3 technical replicates. Asterisks denote samples with p-values < 0.05 as determined by a one-sided Student T test. 95% confidence intervals are shown in gray. Source data and exact p values are provided with this paper in the Source Data file.