A bioinformatics tool called LOHHLA enables precise measurement of allele-specific HLA copy number, improving the accuracy of neoantigen prediction and revealing how immune escape contributes to tumor evolution in non-small-cell lung cancer (NSCLC). LOHHLA identifies HLA loss of heterozygosity (LOH) in 40% of early-stage NSCLCs, which is associated with a high subclonal neoantigen burden, APOBEC-mediated mutagenesis, upregulation of cytolytic activity, and PD-L1 positivity. HLA LOH is an immune escape mechanism subject to strong selection pressures. LOHHLA allows for the identification of which specific HLA allele is lost, which is not possible with conventional tools. HLA LOH occurs subclonally in many NSCLCs and is enriched in metastatic sites, suggesting it is a later event in tumor evolution. HLA LOH is associated with an increased mutation burden and subclonal neoantigen burden, indicating it may facilitate immune evasion. HLA LOH is linked to immune editing and is associated with an enrichment of subclonal mutations. Tumors with HLA LOH show increased PD-L1 staining and immune activation signatures. HLA LOH may be a common mechanism of immune evasion in lung cancer evolution, and its identification could have implications for immunotherapy approaches targeting neoantigens. LOHHLA provides a more accurate estimation of HLA loss and may help in identifying neoantigens that are likely to elicit an effective T cell response. The study highlights the importance of HLA LOH in tumor evolution and its potential role in immune evasion and resistance to immunotherapy.A bioinformatics tool called LOHHLA enables precise measurement of allele-specific HLA copy number, improving the accuracy of neoantigen prediction and revealing how immune escape contributes to tumor evolution in non-small-cell lung cancer (NSCLC). LOHHLA identifies HLA loss of heterozygosity (LOH) in 40% of early-stage NSCLCs, which is associated with a high subclonal neoantigen burden, APOBEC-mediated mutagenesis, upregulation of cytolytic activity, and PD-L1 positivity. HLA LOH is an immune escape mechanism subject to strong selection pressures. LOHHLA allows for the identification of which specific HLA allele is lost, which is not possible with conventional tools. HLA LOH occurs subclonally in many NSCLCs and is enriched in metastatic sites, suggesting it is a later event in tumor evolution. HLA LOH is associated with an increased mutation burden and subclonal neoantigen burden, indicating it may facilitate immune evasion. HLA LOH is linked to immune editing and is associated with an enrichment of subclonal mutations. Tumors with HLA LOH show increased PD-L1 staining and immune activation signatures. HLA LOH may be a common mechanism of immune evasion in lung cancer evolution, and its identification could have implications for immunotherapy approaches targeting neoantigens. LOHHLA provides a more accurate estimation of HLA loss and may help in identifying neoantigens that are likely to elicit an effective T cell response. The study highlights the importance of HLA LOH in tumor evolution and its potential role in immune evasion and resistance to immunotherapy.