The CUX1 gene on 7q22 is disrupted by a fusion event involving CLDN7 on 17p13.1 resulting in a chimeric transcript in 1 sample. (A) Model of the chimeric fusion transcript. The fusion contains the first exon of CUX1 upstream of exons 2-4 of CLDN7. The fusion was identified by 35 RNA-sequencing reads wherein one end of the paired-end reads maps to one gene whereas the mate-pair maps to the other gene (indicated by black bars connected by hyphenated lines). In addition, 89 junction spanning reads (indicated as single bars) were identified that map across the exon-exon boundaries of the fused genes. Sanger sequencing of the PCR product confirmed the fusion. The CLDN7 exons are out of frame with respect to the CUX1 start site, resulting in a premature stop codon. (B) RT-PCR of RNA from t-MN sample T20 confirms the presence of both the CUX1-CLDN7 fusion transcript and native CUX1. K562 cells, which express both endogenous CUX1 and CLDN7, but not the fusion transcript, were used as a control.