A novel classification of small bowel adenocarcinoma based on the hidden genome classifier: a multi-institutional study

Abstract Background Small bowel adenocarcinoma (SBA) is a rare malignancy with poor prognosis. Its clinical and pathologic characteristics are sparse, and few studies have examined its genetic features within the continuum of the gastrointestinal tract. Methods Patients (n = 243) from six institutions with SBA and available tumor tissue underwent targeted tumor sequencing. A hidden genome classifier (HGC) was developed based on analyses of 286 gastroesophageal (foregut) and 286 colorectal (hindgut) cancers. SBA samples were assigned to foregut (n = 61), hindgut (n = 61) or mixed-type (n = 121) lineages using predefined HGC score thresholds. Overall survival (OS) was calculated from 90 days post resection until date of last follow-up for patients who underwent curative-intent resection. Results HGC classified 54% of duodenal and 64% of intestinal-type periampullary tumors as foregut; 56% of jejunal and 68% of ileal tumors were classified as hindgut. Foregut showed amplifications in CDK12, CD3, EGFR, KRAS and cytoband changes at 8p21.1/15q26.3; hindgut harbored APC and KRAS mutations; mixed-type combined features. Median OS was 73 months (95%CI, 53 to 130) after curative-intent resection. The HGC prediction group (hindgut vs mixed-type, HR 2.80, 95%CI, 1.35-5.75) and age (HR 1.03, 95%CI, 1.01-1.05) were associated with decreased survival. Anatomic site was not associated with OS, whereas driver mutations ARID1A, KRAS and TP53 were associated with OS on univariate analysis. Conclusion SBAs display genomic heterogeneity. The novel HGC stratifies these tumors based on homology to foregut or hindgut alterations and may be superior to anatomic location for characterizing pathology. Additional studies are needed to validate and further explore these findings.