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Fanconi anemia (FA) is a chromosomal instability disorder with a very high risk of developing head and neck squamous cell carcinoma (HNSCC), most notably after hematopoietic stem cell transplantation (HSCT).In the current study, the authors reported 13 cases of HNSCC in FA patients who underwent HSCT at the Saint Louis Hospital between 1976 and 2007.The median age of the patients at time of HSCT was 9.7 years. All patients received irradiation-based conditioning before HSCT and all developed extensive chronic graft versus host disease (GVHD). HNSCC was diagnosed at a median interval of 10 years after HSCT, mainly in numerous sites within the oral cavity (11 patients). Lymph node involvement was diagnosed in 4 patients. The TNM classification was: T1 in 6 patients, T2 in 2 patients, T3 in 2 patients, and T4 in 3 patients. Treatment was comprised of surgery in 10 patients, with clear surgical margins reported in 7 (including cervical lymph node dissection in 6 patients). Surgery was performed in addition to other treatments in only 2 patients (radiotherapy or cryotherapy). For the remaining 3 patients, treatment consisted in radiotherapy (2 patients) or chemotherapy (1 patient). Disease progression while receiving therapy was observed in 5 patients and 5 other patients developed disease recurrence between 3.5 and 23.7 months after treatment. Death occurred in 11 patients. At the time of last follow-up, only 2 patients were alive without any disease between 9 and 23 months after diagnosis.HNSCC developing in FA patients after HSCT is associated with a very poor prognosis. A systematic surveillance of the oral cavity is essential to permit early surgery, which to the authors' knowledge remains the only curative treatment for a minority of patients. It is very important to attempt to prevent this cancer by reducing chronic GVHD and using conditioning without irradiation. Cancer 2008. © 2008 American Cancer Society.