Additional file 2: Figure S1. of Evidence for L1-associated DNA rearrangements and negligible L1 retrotransposition in glioblastoma multiforme

Structure and detection of L1 mutations in MeCP2 and EGFR. (a) RC-seq versions: Capture probes from version 2 (V2, marked in blue) correspond to two sets of DNA oligonucleotides mapping within the 5'UTR and the 3'UTR of the L1 sequence (UTRs represented as red boxes). Version 3 (V3, marked in green) includes a single LNA probe for each UTR. The 5' end probes capture only the 5' junction of full or nearly full length insertions. The 3' end probes capture both 3' junctions of insertions of all lengths and 5' junctions of heavily truncated insertions. (b) Pre- and post- mutation site sequences for MeCP2: Pre-integration panel shows the sequence at the L1 mutation site as obtained from the human reference genome (GRCh37/hg19). A 58 nt deletion was detected after the L1 mutation (marked in green within box). Post-integration panel shows the 5' and 3' termini sequences of the L1 mutation and flanking genomic region. L1PA2 sequence is marked in red. The 49 additional nucleotides from an Alu are marked in grey. Micro-homology with the pre-integration genomic region is denoted (underlined). Slashes represent L1PA2 sequence not shown. Lowercase indicate mutations versus reference sequences. (c) MeCP2 L1 mutation PCR validation: DNA extracted from different regions of the tumour (denoted from A to G) was used as template for the amplification of MeCP2 5'end L1 junction. No amplification was detected when water was used as template (NTC). (d) Pre- and post- mutation site sequences for EGFR: Pre-integration panel shows the sequence at the L1 insertion site as obtained from the human reference genome (GRCh37/hg19). A 550 nt deletion was detected after the L1 mutation (marked in green within box). Post-integration panel shows the 5' and 3' termini sequences of the L1 mutation and flanking genomic region. L1-Ta sequence is marked in red. Slashes represent genomic or L1-Ta sequence not shown. Lowercase indicate mutations relative to reference sequences (L1-Ta, human reference genome). Untemplated nucleotides are represented in grey. (e) EGFR mutation site PCR validation: DNA extracted from different regions of the tumour (denoted from A to G) was used as template for the amplification of the EGFR 5' end L1 junction. No amplification was detected when water was used as template (NTC) (EPS 2005 kb)