PMC10176450_01
Schematic diagram of the novel nonreciprocal/reciprocal NTRK3 translocation.
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Molecular testing revealed a novel fusion transcript between exon 13 of NTRK3 and exon 2 of AJUBA, co-existing with a known fusion transcript between exon 4 of ETV6 and exon 14 of NTRK3 ( Figure 1 ). However, this case showed negative cytoplasmic and nuclear staining for pan-TRK ( Supplementary Figure 1 ), which was discordant with NGS and FISH results.
(A) Integrative Genome Viewer (IGV) snapshot of NTRK3-AJUBA fusion; (B) Integrative Genome Viewer (IGV) snapshot of ETV6-NTRK3 fusion.
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Meanwhile, we used Integrative Genome Viewer (IGV) to check and visualize the supporting reads that demonstrate the novel NTRK3-AJUBA fusion ( Figure 2A ) and ETV6-NTRK3 fusion ( Figure 2B ), respectively. The ETV6-NTRK3 fusion protein is predicted to include the PNT domain encoded by ETV6 and the whole protein tyrosine kinase domain encoded by NTRK3 ( Supplementary Figure 2 ).
(A) Sanger sequencing validation of NTRK3-AJUBA fusion and dashed lines (black) indicate breakpoint position; (B) Sanger sequencing validation of ETV6-NTRK3 fusion and dashed lines (black) indicate breakpoint position.
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The results revealed that exon 13 of the NTRK3 gene on chromosome 15 is fused to exon 2 of the AJUBA gene on chromosome 14 ( Figure 3A ) and exon 4 of the ETV6 gene on chromosome 12 is fused to exon 14 of the NTRK3 gene on chromosome 15 ( Figure 3B ).
FISH break-apart assay for NTRK3 gene and separate red and green signals indicating rearrangement.
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Subsequently, fluorescence in situ hybridization (FISH) analysis, using a break-apart assay, confirmed NTRK3 fusion at the genomic level ( Figure 4 ).