Fig. 3

Representative example of intragenic complex rearrangements generating EML4-ALK fusion transcripts from case 4. A DNA sequencing reads indicating EML4 (intron13)-ALK (intron3) fusion and ALK (intron19)-ALK (intron3) fusion regions were visualized by the IGV software. B RNA sequencing reads indicating EML4-ALK fusion regions were visualized by the IGV software. C Possible schematic diagram of genomic rearrangements involving the fusion breakpoints in DNA and RNA level. DNA-based NGS detected that intron 13 of EML4 fused with intron 3 of ALK, and intron 3 of ALK jointed to intron 19 of ALK with a 9-bp insertion. RNA-based NGS detected the canonical fusion transcript joining EML4 exon 13 to ALK exon 20. Red dashed lines indicate fusion breakpoints and red arrows indicate direction of transcription. D Positive ALK FISH pattern with separate red and green signals. E Positive ALK expression detected by IHC assay