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Sufficient internal fixation for occipitocervical (OC) or C1–C2 instability in pediatric patients with Down syndrome is difficult owing to small osseous structures, congenital deformities, and immature ossification. The purpose of this study was to evaluate the clinical outcomes of patients aged 8 years or younger with Down syndrome who underwent OC or C1–C2 fusion using freeze-dried allograft as bone graft substitute. The participants included seven consecutive patients aged 8 years or younger with Down syndrome who were treated for upper cervical disorders with posterior OC or C1–C2 fusion using freeze-dried allografts at our hospital between 2007 and 2016 and had a minimum follow-up of 1 year. Postoperative flexion/extension cervical radiography and computed tomography were repeated at 3 months after surgery before removal of the collar. The modified McCormick scale was used to grade functional status. The seven patients had an age range of 5–8 years (mean: 5.9 years). The mean follow-up period was 36 months (12–120 months). Six patients had os odontoideum and one had basilar invagination. Three patients underwent C1–C2 fusion, and in all cases, bilateral C1 lateral mass screws and bilateral C2 pedicle screws were used. Four patients underwent OC fusion, and in three of these cases, occipital and bilateral pedicle screws were used. One patient underwent reoperation because of occipital screw back-out with autograft; therefore, C2 lamina screws were added to pedicle screws. Solid bony fusion was achieved, and stable constructs were maintained on radiography in all patients, without infection or implant failure. In this study, we used freeze-dried allograft as a bone graft substitute, and we were able to detect bony trabeculae at the graft–recipient interface on lateral cervical radiographs and on reconstructed sagittal computed tomographic images in all patients. These results suggest that use of allograft is effective for treatment of upper cervical spine abnormalities in pediatric patients with Down syndrome.