Shallow Whole-Genome Sequencing (sWGS) Identifies a Copy Number-High Subset of TP53-Mutated Multiple-Classifier...

TP53-mutated "multiple-classifier" endometrial carcinomas represent a diagnostically challenging subgroup within current molecular classification algorithms. Although these tumors are assigned to POLE-mutated or mismatch repair-deficient categories according to the current European Society of Gynaecological Oncology/International Federation of Gynaecology and Obstetrics-based algorithms, their biological heterogeneity remains incompletely characterized. Herein, we retrospectively analyzed TP53-mutated multiple-classifier endometrial carcinomas identified through routine molecular profiling at our institution between 2022 and 2025 using an integrated histopathological, immunohistochemical, targeted sequencing, and shallow whole-genome sequencing (sWGS) approach. Copy number alteration (CNA)-high (CNA-high) status was defined as ≥5 large-scale genomic alterations corresponding to copy number gains or losses ≥3 Mb within a single chromosomal arm, excluding whole-arm alterations. Among 33 analyzable TP53-mutated multiple-classifier endometrial carcinomas, sWGS identified 12 CNA-high tumors (36.4%) and 21 CNA-low tumors (63.6%). CNA-high tumors were more frequently nonendometrioid, high grade, and advanced stage according to the International Federation of Gynaecology and Obstetrics 2023. They showed higher TP53 variant allele frequencies and higher TP53 variant allele frequency-to-tumor cellularity ratios. After a median follow-up of 12.8 months, recurrences (6/33, 18.2%) and disease-related deaths (3/33, 9.1%) were observed in the CNA-high subgroup, whereas no recurrence or disease-related death was observed among CNA-low patients. These findings indicate that TP53-mutated multiple-classifier endometrial carcinomas comprise biologically distinct subsets that are not fully captured by the current 4-tier The Cancer Genome Atlas-based molecular classification and European Society of Gynaecological Oncology-based risk stratification. In this cohort, sWGS identified a CNA-high group with adverse clinicopathological features and clinical events suggesting a potentially more aggressive clinical course. Integration of genome-wide copy number profiling may therefore refine the biological interpretation of TP53 alterations in multiple-classifier endometrial carcinomas and warrants validation in larger multicenter cohorts.