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Fig. 1 | Molecular Cancer

Fig. 1

From: Targeted next-generation sequencing of circulating free DNA enables non-invasive tumor detection in myxoid liposarcomas

Fig. 1

Mutational profiling of myxoid liposarcomas. A 51 MLS tumors and two MLS cell lines (402-91 and 1765-92) were sequenced with an MLS specific lockdown panel. Chromosomal translocations could be detected in 49/51 tumors (1 - 49) and both cell lines (C1, C2) and occurred between DDIT3 and FUS in 87.7% and between DDIT3 and EWSR1 in 8.3%. Breakpoints clustered to several distinct regions within DDIT3 and FUS but were not restricted to a single site. For 36 tumors, both breakpoints of the reciprocal translocation could be determined. Arrows depict the sites where the chromosomal breaks occurred. Areas with an increased likelihood of chromosomal breaks are colored in blue. Breakpoints were annotated to homo sapiens (human) genome assembly GRCh38 (hg38). B For 36 tumors, where both breakpoints could be sequenced, loss or gain of DNA during the translocation event could be determined and specifically mapped to either DDIT3 or FUS. A mean loss of 7 bp (SD 64 bp) occurred on chromosome 12 (DDIT3) and of 11 bp (SD 73 bp) on chromosome 16 (FUS). There was considerable intertumor variability. Each symbol of the graph represents one tumor, with the largest gain of 282 bp on chromosome 16 and the biggest deletion of 138 bp on chromosome 12. C Point mutations occurred most commonly in the TERT promoter region (73%) and PIK3CA (33%). Only one tumor showed an additional point mutation in TET2 and one tumor analyzed for intratumor heterogeneity (tumor 2 in Fig. 1 D) displayed two mutations in PTEN. TERT promoter mutations were all detected at the well-known hotspot locations C228T and C250T, with a prevalence of 61% and 12% of all analyzed tumors respectively. PIK3CA mutations occurred at well-known hotspot mutations in exon 9 (c.1624G > A, c.1633G > A, c.1633G > C, c1634A > G) and exon 20 (c.3140A > G) but also at less commonly annotated positions in exon 5 (c.1035 T > A) and exon 8 (c. 1345C > A). D To determine intratumor heterogeneity of MLS, 20 individual samples of tumor 1 were taken at uniform distances and 10 samples were taken from tumor 2. Each sample was analyzed separately with the standard panel. The individual tumor-specific breakpoints identified before (Fig. 1 A) were detectable in all samples. There were no TERT promoter mutations in tumor 1, however PIK3CA mutations were present in 3/20 samples. Two showed a hotspot mutation in exon 9 (chr3:179,218,294; c.1624G > A) and one samples had a hotspot mutation in exon 20 (chr3:179,234,297; c.3140A > G). In tumor 2, TERT promoter mutations were present in all samples, however nine samples contained the C250T and one sample the C228T mutations. PIK3CA mutations were even more diverse. 6/10 samples contained a PIK3CA mutation. Of these samples three showed the well-known hotspot mutation in exon 9 (chr3:179,218,304; c.1634A > G) and the remaining three the hotspot mutation in exon 20 (chr3:179,234,297; c.3140A > G). A deletion (c.388del) and a point mutation in (c.377C > A) were identified in PTEN. The intratumor heterogeneity of PIK3CA, PTEN and the TERT promoter point towards multiple subclones which emerge from a tumor ancestor that initially acquired the characteristic t (12;16) driver translocation. Depicted is the tumor (red), which was reconstructed from the patients’ MRI scans. The black lines depict how the tumor was sectioned for histopathologic assessment. Although the samples were taken at uniform distances throughout the tumor, the exact location of each sample within the tumor cannot be determined due to the retrospective nature of the study

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