CDKN2A and chordoma: Common genetic alterations: T gene (brachyury) duplication, CDKN2A/B loss. EGFR amplification. Pathways: EGFR, PDGFβ, IGFR1, mTOR, MET, PI3K. Poorly differentiated chordomas: marked by SMARCB1 deletion and loss of INI1 expression.