Multispecimen Genomic Profiling Reveals Inter-Specimen Heterogeneity and Supports Ascites as a Complementary Biospecimen in Pseudomyxoma Peritonei

Background: Pseudomyxoma peritonei (PMP) is a rare peritoneal malignancy with limited genomic data across different biospecimen types. The extent to which ascites and plasma reflect tissue-detected genomic alterations remains incompletely characterized. This study compared genomic profiles across tumor tissue, ascites, and plasma and explored KRAS-defined molecular features in PMP. Methods: Sixty patients with pathologically confirmed PMP were retrospectively included. Next-generation sequencing (NGS) data were available from tumor tissue in 57 patients, ascites in 40, and plasma in 28, with overlapping specimen availability. Cross-specimen genomic concordance was evaluated in 37 patients with matched tissue–ascites samples, including 28 patients with matched tissue, ascites, and plasma. Exploratory analyses were performed to characterize genomic and pathway-level features across KRAS-defined subgroups. Results: In tumor tissue, KRAS (66.7%), GNAS (31.6%), and TP53 (21.1%) were the most frequently altered genes. Among 28 patients with matched tissue, ascites, and plasma, patient-level concordance was 35.7%. At the mutation level, ascites showed higher tissue-referenced positive percentage agreement (PPA) than plasma (93.1% vs. 36.2%). In the expanded cohort of 37 matched tissue–ascites pairs, ascites achieved a tissue-referenced PPA of 94.2% and revealed additional alterations not detected in the corresponding tissue samples. Exploratory KRAS mutation stratification identified G12D (35.0%), G12X (32.5%), and KRAS-wild-type (wt) (17.5%) tumors as the predominant subgroups. KRAS-mutant tumors harbored more detected genomic alterations and potentially clinically actionable alterations than KRAS-wt tumors. Wnt and PI3K pathway alterations were more commonly observed in the G12D and G12X subgroups, respectively, whereas canonical oncogenic pathway alterations were less frequent in KRAS-wt tumors. Conclusions: PMP exhibits substantial genomic heterogeneity across patients and biospecimen types. Ascites cfDNA showed high concordance with tissue and captured additional genomic alterations, suggesting that ascitic fluid may serve as a complementary source for molecular profiling in PMP. KRAS-defined subgroups exhibited distinct genomic characteristics, although their clinical relevance requires further validation in larger, well-characterized cohorts.