Biomarkers in Predicting Response to Treatment in Patients With Newly Diagnosed Stage III or Stage IV Head and Neck Cancer Treated With Carboplatin, Paclitaxel, and Radiation Therapy

OBJECTIVES:

- Determine if gene expression patterns that correlate with treatment response and
survival can be identified using DNA microarrays in patients with newly diagnosed head
and neck squamous cell carcinoma (HNSCC) treated with carboplatin, paclitaxel, and
radiotherapy.

- Determine if protein expression patterns that correlate with treatment response and
survival in HNSCC can be identified using matrix-assisted laser desorption
ionization-time-of-flight mass spectrometry (MALDI-TOFMS).

- Determine if the molecular signature of human papilloma virus-16 infection can be
determined using DNA microarray and MALDI-TOFMS and correlate with gene and protein
expression, treatment response, and survival.

OUTLINE: Tumor tissue samples are analyzed by DNA microarray analysis and validated by
quantitative reverse transcription-polymerase chain reaction (PCR). Protein and gene
expression patterns are analyzed by laser desorption ionization-time-of-flight mass
spectrometry, high performance liquid chromatography, liquid chromatography-tandem mass
spectrometry, and PCR. Samples are also analyzed by tissue microarray and
immunohistochemistry.