Long-distance polymerase chain reaction targeting genomic DNA to detect <i>ALK</i> fusion genes with various partners in ALK+ hematological tumors

We developed genomic DNA-targeting long-distance polymerase chain reaction (LD-PCR) to detect ALK fusion genes with various partner genes in ALK+ hematological tumors. DNA was obtained from 3 anaplastic large cell lymphoma (ALCL) cases with NPM1::ALK, 2 ALCL cases with ATIC::ALK, 1 ALCL case with TRAF1::ALK, 1 ALK+ large B-cell lymphoma case with CLTC::ALK, 1 acute myeloid leukemia case with RANBP2::ALK, and 5 additional ALK+ ALCL cases, in which the ALK fusion gene had not been characterized. Forward primers were designed for exons of NPM1, TPM3, ATIC, TRAF1, TFG, CLTC, and RANBP2 and a reverse primer for ALK exon 20. We obtained PCR products representing the fusion sequences in 8 cases with known partners using the corresponding primer combination. For 5 ALCL cases with uncharacterized fusion genes, we performed LD-PCR using combinations of the forward primers for the 7 genes and ALK reverse primer. The results showed that ALK fused to ATIC in 3, TRAF1 in 1, and TFG in 1. A total of 13 ALK breakpoints were randomly distributed within intron 19 and those of the NPM1, ATIC, and TRAF1 genes were located within introns 4, 7, and 6, respectively, without creating subclusters or recurrent breakpoints. This study indicates that LD-PCR can effectively detect the ALK fusion gene in the majority of ALK+ ALCL cases and is useful for rapid diagnosis of the disease.