Shallow whole-genome sequencing genomic instability score across endometrial cancer subtypes.

Abstract

e17632 Background: Genomic instability (GI) is a hallmark of cancer. In endometrial cancer (EC) the TCGA molecular classification is prognostic. GI scores (GIS) are widely studied and clinically validated in high grade serous ovarian cancer (HGSOC). The distribution and biological significance of GIS scores in EC remain unclear. We aimed to characterize and explore GI across EC subtypes using shallow whole-genome sequencing. Methods: Up to 96 prospective FFPE EC samples were included, mainly presenting endometrioid (72 %), and serous histologies (14.5 %). The remaining 13.5 % include clear cell and mixed histologies. Stage was categorized as follows: I/II (66.7 %) and III/IV (33.3 %). Cases without primary surgery were excluded from survival analysis. Molecular classification frequencies were CNH (22.9%), CNL (39.6 %), MSI-H (30.2 %) and POLE (7.3 %). Libraries were constructed using HyperPlus kit (Roche diagnostics) and sequenced in a NextSeq 2000 (2x100 paired-end) (Illumina) to achieve a 0.5x coverage. Copy-number (CN) calling and GIS were obtained using QDNA and ShallowHRD. Data were further compared with our own GIS in 60 HGSOC (Romero, I ASCO 2025). All the analyses were performed in Python v3.8 and R v.4.3.11. Results: Basic clinical characteristics and sequencing performance parameters are detailed in table 1. In EC, GIS decreasingly ranged from CNH, CNL, MSI-H to POLE (Table 1) showed statistically significant differences between CNH and the rest of molecular subtypes (p=0.00027). Higher GIS also correlated with serous histology (p=4.6*10 -5 ) and worse PFS (P=0.0062). GIS showed consistently lower values in EC than HGSOC (table 1, p<2*10 -16 ). Among CNH group, highest GIS values (q4) had worse PFS and OS (both p=0.05). CN at chromosomic level were evaluated: amplifications in chromosome 1 and 10 were enriched in MSI-H (p=0.0002) and CNL (p=0.0277) groups respectively. Chromosome 1 CN was correlated with endometrioid histology (p=0.007851). Conclusions: Shallow whole-genome sequencing is a valuable approach to characterize GI across EC populations. However, additional GI parameters should be explored to better understand the nature and possible biological sources of GI in EC. Main clinical and sequencing performance parameters of the EC series. Parameter Median [range] Age at diagnosis (years) 62 [40-89] Progression-Free Survival (PFS, months) 17.33 [0-158.367] Overall Survival (PFS, months) 19.55 [0-186.667] Follow-up (months) 19.55 [0-186.667] Total reads 21740865.5 [1169173-347460678] Whole-genome coverage 0.642 [0.024-10.366] Targeted-sequence coverage 2.111 [1.814-208.054] Genome covered (%) 30.519 [0.012-89.132] Genomic Instability Score (GIS) CNH 5 [0-42] CNL 0 [0-14] MSI-H 0 [0-5] POLE 0 [0-2] CE-GIS 1 [0-42] HGSOC-GIS 20 [1-43]