Fig. 4: HLA CN analysis and LOH event detection.
a, Comparison of decimal CN estimation of 346 heterozygous HLA-I alleles from the NCI cohort (n = 68 samples) reported by NeoDisc (x axis) and LOHHLA (y axis). b, Comparison of rounded CN estimation of 389 (homozygous and heterozygous) HLA-I alleles from the NCI cohort (n = 68 samples) reported by NeoDisc (x axis) and Sequenza (y axis). c, Sequenza estimation of HLA-I CN (x axis) of all NeoDisc and LOHHLA HLA-I loss calls (n = 17 participants and 37 events; y axis). Colors indicate common and tool-specific calls. d, Tumor content estimation of samples with HLA-I loss calls (n = 37 samples). e, Comparison of rounded CN estimation of 639 (homozygous and heterozygous) HLA-II alleles from the NCI cohort (n = 68 samples) reported by NeoDisc (x axis) and Sequenza (y axis). f, HLA-II CN estimated by Sequenza (x axis) of all NeoDisc HLA-II loss calls (n = 18 samples and 53 events; y axis). g, Tumor content estimation of samples with HLA-II loss calls (n = 53 events). The box plot center lines represent the median. The bounds of the box represent the 25th and 75th percentiles (IQR). The whiskers extend to the smallest and largest values within 1.5× the IQR. Individual dots represent minima and maxima beyond the whiskers. All individual values are shown as dots. h, Comparison of the effect of keeping or discarding lost HLA-I alleles from the ML prioritization on the ranking of immunogenic peptides from the NCI samples with HLA-I loss (n = 5 samples and 8 peptides). In a, b and e, correlation coefficients and P values were calculated using a two-sided Pearson test.
