Fig. 1

Schematic overview on the MGMT promoter region with positioning of exon 1 (ENSG00000170430), promoter-associated CpG island (CGIp) and sequenced amplicon regions; hg19 genomic position is given in bp; relative position of CGIp and amplicons subjected to local deep bisulfite sequencing (MGMTup, MGMTe1 and MGMTi1) are shown as grey bars; MGMTup and MGMTe1 forward primer sequences are highlighted in turquoise, MGMTup and MGMTi1 reverse primer sequences are highlighted in pink; the sequence used for MGMTi1 forward and MGMTe1 reverse primers is highlighted in green; arrows indicate the directionality of primers; exon1 sequence is highlighted in yellow; grey: ambiguously called nucleotides (taken from dbSNP153); red: CpG sites, numbered relative to the TSS