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Next-generation sequencing (NGS)

Hum Pathol. 2019 May;87:83-94.

Targeted next-generation sequencing of well-differentiated rectal, gastric, and appendiceal neuroendocrine tumors to identify potential targets.

Park HY, Kwon MJ, Kang HS, Kim YJ, Kim NY, Kim MJ, Min KW, Choi KC, Nam ES, Cho SJ, Park HR, Min SK, Seo J, Choe JY, Lee HK.

Rectal neuroendocrine tumors (NETs) are the most common gastrointestinal (GI) NETs with an uncertain malignant potential despite their small size. There are limited data about driver mutations in rectal NETs, which may explain the tumors' unexpected behavior or common histologic morphology with other GI-NETs. Here, we investigated the clinically and pathologically relevant mutations of rectal and nonrectal NETs and compared the frequency and clinical significance of detected mutations between them. We sequenced 84 primary GI-NETs (69 rectal, 7 gastric, 5 appendiceal, and 3 sigmoid colon NETs) and 3 metastatic GI-NETs using targeted next-generation sequencing. Twenty-one rectal NETs (30.4%) showed at least 1 mutation in 24 cancer-related genes; the most common mutations were TP53 (10.1%) and FBXW7 (7.2%), of which 73% were pathogenic/likely pathogenic mutations. TP53 (p.R337C and p.R213*), PTEN (p.W111*, p.Q214*), CDKN2A (p.W110*), FBXW7 (p.R465H), and AKT1 (p.R23Q) were repetitive mutations found exclusively in rectal NETs, whereas SMAD4 (p.R361C) and STK11 (p.D176N) were repetitive mutations found only in gastric NETs. PTEN (p.G129K), EGFR (p.E709K), and KIT (p.V555I) were shared mutations between rectal and appendiceal NETs, whereas SMAD4 (p.R361C), ALK (p.G1202R), VHL (p.Q132*), and IDH1 (p.R132H) were concurrently detected between rectal and gastric NETs. GI-NETs with higher histologic grades, lymphovascular invasion, or recurrence tended to have higher numbers of mutation variants than other tumors; however, there was no significant difference. In conclusion, rectal NETs commonly carried pathogenic/likely pathogenic mutations. Because most mutations were identified in nonhotspot positions, next-generation sequencing is useful in identifying potential drug targets in rectal NETs.

Schematic overview of overall mutational profile of 84 primary GI-NETs, followed by targeted NGS and analysis

Locations of SMAD4 (A), FBXW7 (B), and IDH1 (C) mutations. Numbers in circles represent cases with corresponding mutation. Blank circles represent presence of a single mutation case. Upper portions show cases in the present study, and lower portions show cases in previous cancer genome studies archived in cBioPortal.

BSchematic overview of histologic findings of repetitive mutations in both codons and peptides between rectal NETs and gastric or appendiceal NETs. (A, B, D, J-N: original magnification, ×100; C, E-I: ×40; O: ×200).