Extended Data Figure 1: Comparison of the RNA-seq profiles of various ALK transcripts.
From: Alternative transcription initiation leads to expression of a novel ALK isoform in cancer
RNA-seq data are displayed in the Integrative Genomics Viewer (IGV). The grey bars/arrows indicate the sequencing reads. The blue lines connect sequencing reads that are aligned over the splice site of joining exons. a, The ALKATI transcript shows expression of ALK exons 20–29 and of ∼400 bp in intron 19 (blue shaded area). No expression of exon 1–19 or intronic areas, other than in intron 19, are observed. The detailed view illustrates that the sequencing reads align continuously between exon 20 and intron 19 indicating uninterrupted transcription. The 5′-UTR of ALKATI (intron 19) and exon 20–29 are expressed at comparable levels. b, The full-length wild-type ALK transcript shows expression of all ALK exons and only very little expression of the introns. The detailed view displays that the sequencing reads align sharply to the exons, but not to the intron 19 region, which is present in ALKATI (blue shaded area). c, The ALK fusion transcript of a non-small cell lung cancer with an EML4–ALK translocation shows expression of ALK exons 20–29, and little expression of exons 1–19 and all introns. The detailed view illustrates that the transcription starts mainly at exon 20 due to a preserved splice site. Only few reads are aligned to the intron 19 region (blue shaded area). The green-labelled reads highlight chimaeric read pairs indicating the EML4–ALK translocation.
