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Fig. 2 | Mobile DNA

Fig. 2

From: Evidence for L1-associated DNA rearrangements and negligible L1 retrotransposition in glioblastoma multiforme

Fig. 2

Characterisation of a somatic L1 mutation within EGFR. a Patient #8 EGFR mutant allele: a 0.5 kb L1-Ta sequence antisense to EGFR. Direction of transcription is indicated with blue arrow. b L1 mutation magnified view: RC-seq reads detected at the L1 3' terminus (black/red bars). The L1 mutation comprised a truncated fragment of L1 ORF2 (white box) and the 3′UTR without a poly-A tail (red box). A 550 nucleotide deletion at the integration site was also identified (triangle). Primers used for PCR validation are indicated as pink and purple arrows. c Mutation site PCR validation: Region comprising the EGFR-L1 5' junction was detected in patient #8 tumour sample. No amplification was detected when water (NTC) or genomic DNA from blood were used as template. d qRT-PCR measurement of EGFR transcription at its 5'UTR and exon 11-to-12 junction (E 11–12): The relative levels of RNA from both regions were significantly increased in tumour (blue) versus adjacent brain (green) samples. Data for each group were normalised to adjacent brain values, pooled and presented as mean +/− SEM (*p < 0.001, two tailed t-test, df = 10). e Amplified chromosome 7 region including EGFR: mapped read depth in EGFR region. Positions in Mbp are marked across the top horizontal axis. Read depth is reflected by the height of vertical lines as indicated on the vertical axis. Genes present in the amplified region are placed based on the locations of representative transcripts from UCSC Genes (hg19)

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