Figure 1: Somatic pseudogenes.
From: Processed pseudogenes acquired somatically during cancer development
(a) A somatic FOPNL pseudogene in a non-small cell lung cancer. Sequencing reads from high-coverage whole-genome shotgun sequencing of the tumour reveal a series of split reads (red) crossing the four canonical exon–exon splice junctions in the gene. In addition, read pairs map to adjacent exons with an insert size larger than expected (light brown). At either end of the gene, read pairs linking to chr7 could be identified, revealing that the FOPNL pseudogene is inserted into intron 11 of the SND1 gene in the opposite orientation with an intact polyA tail and a target-site duplication of 10 bp. (b) A somatic ARHGEF9 pseudogene in a non-small cell lung cancer. The insertion was confirmed as somatic by PCR (Supplementary Fig. 2) and capillary sequencing across an exon–exon junction and insertion site.
