Chordoma associated with tuberous sclerosis complex (TSC)

Chordoma associated with tuberous sclerosis complex (TSC) are an extremely rare tumor that was described only in 13 cases since 1975. Сhordomas themselves are malignant slow-growing bone tumors thought to arise from vestigial or ectopic notochordal tissue. In total, with CMA we found 180 regions with CNVs in the chordoma tumor sample. The longest section was 58,014 kbp long (arr[GRCh38] 9q21.31q34.3(79267492_137281464)x1-2), harboring region 9q34 that includes TSC1 gene. Also, 12 oncogenes including KRAS and CBX7 were in amplified regions and 92 tumor suppressor genes were in regions with loss status. Four genes that participate in epigenetic regulation, - ELP3, GTF3C4, MBD2, and PHF2 were found to be affected. Moreover, members of the APOBEC3 family were amplified. DNA was extracted from FFPE tumor tissues of chordoma from one patient with tuberous sclerosis complex by using GeneRead DNA FFPE kit (Qiagen, cat. № 180134). Copy number variation were analyzed by using OncoScan™ CNV Assay (Thermo Fisher Scientific, USA) on GeneChip Scanner 3000 7G System (Applied Biosystems, USA) according to manufacturer's protocol. No techinal replicates were perfomed.