Fig. 6.

RNA fusion and DNA break. (A, Middle tracks) RNA-seq read pairs (purple bars) aligned to ALK (Left) and EML4 (Right). Each pair of paired-end reads is linked by a horizontal line. (A, Lower tracks) iMARGI read pairs aligned to the two genes. Red bars: RNA end. Blue bars: DNA end. Thin gray lines: pairing information of iMARGI read pairs. (B) Positive (red) and negative (black) outcomes of detection of EML4-ALK fusion transcripts based on RNA-seq, FuseFISH, and DNA FISH (ALK Break Apart FISH, a DNA rearrangement test) in each cancer sample (column). White box: no measurement. $*$: Detected a partial deletion of ALK gene without rearrangement. (C) FuseFISH images of the no. 37 cancer sample from the EML4 and ALK channels. Arrows: colocalized FISH signals indicating fusion RNA. (Scale bar: 2 $\mathrm{\mu }$m.) (D) A representative image of ALK Break Apart FISH, with colocalized red and yellow signals that indicate integral ALK gene without rearrangement.