Fig. 1: Inference of HLA-I tumor status with LILAC.

a, Representation of the six immune escape pathways considered in the present study alongside their associated genes (adapted from ‘MHC class I and II pathways’, by BioRender.com). The genes considered for each immune escape pathway are depicted in gray. b, Left, workflow of the Hartwig tumor analytical pipeline integrating LILAC. LILAC’s framework is highlighted with red text and a red border. Right, tables showing an illustrative example of LILAC’s allele-specific and global patient reports (partially created with BioRender.com). QC, quality control; BaseQual., basecalling quality score. c, HLA-I typing tumor and germline agreement in Hartwig cohort. d, LILAC’s HLA-I typing validation using Platinum and Yoruban family trios. e, LILAC’s agreement with the HLA-I types from the TRACERx lung cohort¹². f, LILAC’s HLA-I typing experimental validation. g, LILAC and LOH of HLA-I agreement in the TRACERx100 lung cancer cohort.