Clonal Relatedness Index - Practical and Reliable Tool for Establishing Clonal Relatedness in Gastrointestinal, Hepatopancreaticobiliary and Peritoneal Carcinomas.

While accepted as gold standard, conventional morphology and immunohistochemistry-based methods of determining clonal relatedness between two neoplasms are inconclusive in a subset of patients. Though NGS data can be used for this purpose, this approach has not been widely clinically validated for GI/Hepatopancreaticobiliary(HPB)/Peritoneal carcinomas. This study evaluated tumor-specific alterations in 120 paired GI/HPB/peritoneal tumors from 60 patients, previously established as clonal (52) or non-clonal (8) based on their clinicopathologic characteristics. A clonal-relatedness index (CRI) was calculated as proportion of shared over average of total alterations and was compared to phenotype-based clonality prediction. Based on 1508 assessed alterations, median CRI was 0.85 (IQR 0.69-0.95) for clonal and 0.24 (IQR 0.06-0.43) for non-clonal cohorts. CRI ROC analysis yielded AUROC=0.986, 95% CI: 0.962-1.0, p<0.01, with optimal sensitivity (Sn) and specificity (Sp) at CRI=0.53. In the overall cohort, phenotype predicted clonality with Sn=71.2%, Sp=62.5%, and positive predictive value (PPV) of 92.5% (p=1), versus CRI with 96.2%, 100%, and 100% (p<0.001), respectively. In tumors associated with hypermutability, Sn of phenotype dropped to 42.9%, Sp=33.3%, and PPV=60.0% (p=1), whereas CRI maintained Sn=85.7, Sp=100%, and PPV=100% (p= 0.03). CRI performance remained robust in a validation cohort and with addition of alternative genomic alterations. CRI is a practical, clinically accessible, and highly relevant tool that outperforms phenotype-based method and is essential in reliably establishing clonal-relatedness in GI/HPB/peritoneal carcinomas.