Cancer Education. Chordoma is a rare cancerous (malignant) primary bone tumor that usually occurs along the spine. Chordoma most often occurs in the base of the spine (sacrum) or in the base of the skull.Chordomas form from small remnants of the notochord, a coil of cells in the embryo that develops into the spinal cord.A chordoma may occur at any age but is most common in adults.hordoma most often occurs in the base of the spine (sacrum) or in the base of the skull. Chordomas form from small remnants of the notochord, a coil of cells in the embryo that develops into the spinal cord.