Extended Data Figure 5: Targeted sequencing and whole-genome sequencing reveals no recurrent genomic aberrations at the ALK locus.
From: Alternative transcription initiation leads to expression of a novel ALK isoform in cancer
a, Ultra-deep sequencing data of the ALK locus are displayed in IGV. The genomic region around intron 19 reveals several single nucleotide variations (SNVs). However, the vast majority of SNVs at the ALK locus are also found in the general population as they are detected in the pool of normal DNA, which was used as the control (pooled normal, bottom panel). Numerous SNVs are also documented in the Single Nucleotide Polymorphism database (dbSNP; http://www.ncbi.nlm.nih.gov/SNP/). No genomic aberrations were found at the transcription initiation site of ALKATI. Supplementary Table 2 shows the detected SNVs and indels at the ALK locus after filtering out SNPs documented in the dbSNP database. None of the genomic aberrations was found in more than one case, indicating that the expression of ALKATI is probably not caused by alterations of the DNA nucleotide sequence. b, c, Circos plots of the whole-genome sequencing data of MM-15 (b) and ATC-28 (c) illustrating numerous SNV and structural aberrations. Supplementary Table 3 lists the detected single nucleotide polymorphisms, and Supplementary Table 4 the detected structural aberrations. No recurrent genomic aberrations were found at the ALK locus.
