ETV6-FLT3 fusion genes and predicted protein structure. (A) RACE-PCR (3′-rapid amplification of cDNA ends) for ETV6 was performed with mRNA derived from patient 1 as described previously.8 Sequencing of RACE-PCR products revealed an in-frame fusion between ETV6 exon 4 and a truncated FLT3 exon 14 in patient 1 with insertion of a 16-bp sequence derived from ETV6 intron 4. The ETV6-FLT3 fusion gene was confirmed by RT-PCR. (B) Sequencing of RACE-PCR products revealed an in-frame fusion between ETV6 exon 5 and FLT3 exon 14 in patient 2 with insertion of a 6-bp sequence, probably derived from ETV6 intron 5. Interestingly, base pair number 2 (or 3) of FLT3 exon 14 was deleted in the fusion gene to retain the open-reading frame (underscored). The ETV6-FLT3 fusion gene was confirmed by RT-PCR. (C) The predicted ETV6-FLT3 protein of patient 1 retained the TK domain of FLT3. TM indicates transmembrane domain; PTK domain, protein-TK domain. Break point of patient 1 is indicated by a dashed line; the ETV6 break point of patient 2 as determined by RT-PCR and sequencing with primers TELFLT/f1&2 and TELFLT/r1&2 (supplemental Table 1, available on the Blood Web site; see the Supplemental Materials link at the top of the online article) is shown by a solid line, whereas its complete fusion protein is not shown.
