PMC3618227_01
Features of the B3 thymoma.. (A) Preoperative Chest CT-scan showing a mediastinal mass protruding in the left hemithorax. (B) Haematoxylin and Eosin staining of postoperative tumor section showing the lobular aspects typical of B3 thymomas, the almost complete absence of intratumoral thymocytes and the presence of cancer cells characterized by polygonal shape and round nuclei. (C) Whole-genome sequencing results showing (1) Sanger sequencing-confirmed SNVs and INDELs, (2) reference genomic coordinates, (3) copy number gain (green) and loss (red), and (4) structural variations.
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In March 2009, she was referred to the National Cancer Institute (NCI; Bethesda, MD), where a CT scan (Figure 1A) showed no evidence of disease progression with the mediastinal mass measuring 11x6 cm. The pathology report confirmed the diagnosis of B3 thymoma infiltrating the pericardium, lung and the chest wall but with negative bronchial and surgical margins (Figure 1B). Tier 1 mutations (10 SNVs and 2 INDELs) were confirmed using Sanger re-sequencing (Figure 1C). CN estimation from next generation sequencing data agreed with array CGH analysis and revealed CN gain of chromosomes 1q, 5 and 7 and CN loss of chromosomes 3p, 6, 13 and part of chromosome 11q in the autosomal chromosomes (Figure 1C).
t(11;X) translocation.. (A) Schematic illustration of t(11;X); STOP: inframe TAA codon. (B) PCR amplification using primers spanning C11ORF73 exon 2-ODZ1 intron 19 junction (2168T), ODZ1 exon 18-intron 19 junction (ODZ1 int19), GAPDH exons 9 and 10 and introns across exon 3 of an unrelated gene (KIF5C) on genomic and cDNA of the t(11;X)-positive B3 thymoma and a t(11;X)-negative thymoma cDNA. Note that the presence of KIF5C PCR product in the B3 thymoma genomic DNA but not cDNA suggests that the cDNA is free of genomic DNA contamination.
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The predicted transcript resulted from juxtaposition of the two genes in tail-to-tail (3'-3') orientation (Figure 2A). RT-PCR demonstrated the presence of the junction transcript in this t(11:X) B3 thymoma but absence in another thymoma without the t(11;X) translocation (Figure 2B).