Fig. 6.

Genomic HRD assessment in EC PDX models and public data. A HRD assessment in PDX models. Somatic substitutions, indels, CNAs and SVs are shown for DNA repair related genes, including PTEN and ARID1A (Additional File 1: Table S5, Additional File 2: Table S6). HR-related genes are highlighted in bold. No pathogenic or likely pathogenic germline substitution and indel variants in these genes were detected. HRD sum scores were determined using scarHRD from SNP arrays and WGS data, where available (unable to calculate scores for PDX21 F1 and F2 samples and PDX23 F1 and F4 samples due to noisy arrays). Percentage of Signature 3 was determined with deconstructSigs using COSMIC v2 signatures. Only WGS data is shown for PDX03 and PDX49, where WES and WGS was performed. HRDetect scores were determined only for samples with WGS data. B Mutational signature assignment for TCGA-UCEC and TCGA-UCS cohorts (n=591). Signature assignment was performed using deconstructSigs with 15% minimum signature cut-off. c TCGA-UCEC and TCGA-UCS cases with possible HRD. Cases with pathogenic or likely pathogenic variants in HR-related genes (Additional File 1: Table S5, Additional File 2: Table S7) or cases with Signature 3 detected are included