Genomic features of patients harboring HLA-I LOH
Based on SNV data, we further investigated mutations in 1021 cancer genes within HLA-I LOH subtypes. Results showed that TP53 ,LRP1B , EGFR , KRAS , and PIK3CA were the most frequently altered genes in advanced pan-cancer cohort (Fig.4D). Among these genes, the alteration frequencies of TP53 , EGFR , andLRP1B in the HLA-I LOH group were significantly higher than that in HLA-I stable group (p<0.001 for TP53 , p<0.01 for EGFR and p<0.05 for LRP1B , Fig.4D). However, as the distribution of EGFR mutation across cancer types biased in NSCLC patients (220/242 [90.9%]) while the incidence of HLA-I LOH in NSCLC cohort differed from the average incidence in pan-cancer cohort (Fig.2C), the difference in pan-cancerEGFR mutation between HLA-I LOH and HLA-I stable group might not reflect the relationship between EGFR alteration and HLA-I LOH. In contrast, there was no significant difference in EGFRalteration frequency between the HLA-I LOH and HLA-I stable group in NSCLC cohort (Supplementary Figure 4C).