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Background  Metanephric adenoma (MA) is a rare benign renal neoplasm. On occasion, MA can be difficult to differentiate from renal malignancies such as papillary renal cell carcinoma in adults and Wilms̕ tumor in children. Despite recent advancements in tumor genomics, there is limited data available regarding the genetic alterations characteristic of MA. The purpose of this study is to determine the frequency of metanephric adenoma cases exhibiting cytogenetic aberration t (9;15)(p24;q24), and to investigate the association between t (9,15) and  BRAF  mutation in metanephric adenoma.    Methods  This study was conducted on 28 archival formalin fixed paraffin-embedded (FFPE) specimens from patients with pathologically confirmed MA. Tissue blocks were selected for  BRAF  sequencing and fluorescent in situ hybridization (FISH) analysis for chromosomal rearrangement between  KANK1  on chromosome 9 (9p24.3) and  NTRK3  on chromosome 15 (15q25.3), which was previously characterized and described in two MA cases.    Results   BRAF  V600E  mutation was identified in 62% of our cases, 9 (38%) cases were  BRAF  WT , and 4 cases were uninformative. Of the 20 tumors with FISH results, two (10%) were positive for  KANK1-NTRK3  fusion. Both cases were  BRAF  WT  suggesting mutual exclusivity of  BRAF  V600E  and  KANK1-NTRK3  fusion, the first such observation in the literature.    Conclusions  Our data shows that  BRAF  mutation in MA may not be as frequent as suggested in the literature and  KANK-NTRK3  fusions may account for a subset of  BRAF  WT  cases in younger patients. FISH analysis for  KANK1-NTRK3  fusion or conventional cytogenetic analysis may be warranted to establish the diagnosis of MA in morphologically and immunohistochemically ambiguous MA cases lacking  BRAF  mutations.

KANK1-NTRK3 fusions define a subset of BRAF mutation negative renal metanephric adenomas