Raw sequence reads of patient with chordoma

Chordoma associated with tuberous sclerosis complex (TSC) is an extremely rare tumor that was described only in 13 cases since 1975. Chordomas themselves are malignant slow-growing bone tumors thought to arise from vestigial or ectopic notochordal tissue. Chordoma associated with TSC differs from chordoma in the general pediatric population on the median age, where the diagnosis of TSC-associated chordomas is 6.2 months, whereas chordoma in the general pediatric population is 12 years. Chordomas are genetically heterogeneous tumors, in which mostly chromosomal instability (CIN), alterations that involve PI3K-AKT signaling pathway genes, and chromatin remodeling genes are seen. Here we present the fourteenth case of chordoma that are associated with TSC. Among biallelic inactivation of TSC1 gene, molecular genetic analysis of tumor sample revealed CIN and involvement of epigenetic regulation genes. In addition, found the involvement of CBX7 and apolipoprotein B editing complex (APOBEC3) genes that were not yet seen in chordomas. We also found amplified KRAS gene which may suggest the ineffectiveness of EGFR monotherapy.