Figure 2

Structure of FGF4 duplication and monoallelic expression of FGF4 mRNA. (A) Schematic representation of the structure of FGF4 duplication in two quadruple WT cases. In GIST400 (left panel), the genomic region between FGF4-3UTR and the upstream region of AP003555.2 was duplicated in tandem, producing the fusion gene FGF4-3UTR/AP003555.2-upstr. In GIST401 (right panel), the genomic region between CCND1 and AP003555.2 was duplicated, inverted and inserted into the 3′UTR of FGF4, producing the fusion gene FGF4-3UTR/CCND1-upstr. Duplicated regions are shown in violet. Genes are indicated by yellow arrows, depending on their transcriptional direction. The FGF4 copy involved in the fusion is shown in red. Breakpoint sequence and position on the genome are shown for each fusion: sequences corresponding to FGF4-3UTR are shown in red (+ or − marks indicated if the sequence maps on the positive or negative strand). (B) Plot (in the left) showing the coverage per base of FGF4 mRNA in the two quadruple WT cases carrying FGF4-3UTR fusion. The FGF4 region retained in the fusion gene is highlighted in yellow. As a comparison, coverage of a quadruple WT without fusion (GIST133) is shown (lower panel). A relevant drop in coverage was detected in the cases carrying FGF4-3UTR fusion after the breakpoint of each case (indicated by a black bar). On the right, a box plot shows the coverage depth of exon 3 in FGF4 before and after the fusion breakpoint. (C) Bar plot showing the allelic fraction (%) of two SNPs located at the FGF4 locus (specifically rs3168175 in the 3′UTR and rs9666584 in the 5′UTR) at the DNA and mRNA levels in two quadruple WT GISTs (GIST127 and GIST133), indicating that FGF4 expression is monoallelic.