Molecular and Genomic Profiling of Head and Neck Tumors
Molecular and Genomic Profiling of Head and Neck Tumors
The purpose of this study is to study the genetic profile of head and neck tumors and their
 relationship to treatment response and outcome
Previous research by our group using genetic microarray analysis of HNSCC and normal
 keratinocytes has identified two distinct groups of genetic expression based on clustering
 patterns of a subgroup of genes. Clinical data was summarized for each group and overall,
 patient segregation by gene expression profiling was a better predictor of outcome than
 clinicopathological variables. Further analysis identified 375 genes that discriminate
 between the genotypic subtypes of HNSCC. Overall, our preliminary data has shown that the
 pattern of global gene expression in a HNSCC specimen can be used as a predictor of
 prognosis. We isolated subsets of genes showing the greatest patterns of divergence in gene
 expression. We have also identified 366 over-expressed and 246 underexpressed genes when
 comparing primary tumor to normal surgical margins and have identified a similar number of
 genes whose expression has changed when comparing primary tumor to lymph node metastasis.
 Combining these data sets we have identified genes which consistently increase or decrease
 expression during progression from normal tissue to primary tumor, and subsequently to
 metastatic node. We have selected several candidate genes for subsequent analysis using HNSCC
 tissue arrays. Through DNA microarray analysis and other techniques for looking at genetic
 and molecular characteristics, a more detailed knowledge of the malignant transformation
 process, and alterations with therapy, in these patients may be obtained. This study will
 seek to perform comprehensive molecular and genetic profiling to improve biomarker
 development in HNSCC and correlate this data with patient clinical data. Ultimately it is
 hoped that tumor specific genetic abnormalities may be identified which could provide targets
 for treatment strategies such as gene therapy, immunotherapy, or other interventions.

 Study Objectives:

 To evaluate gene expression patterns in human head and neck squamous cell carcinoma and
 correlate this with treatment response, both surgical and non-surgical.

 To identify a series of diagnostic markers in blood, urine and/or sputum for head and neck
 squamous cell carcinoma and study the mechanism of action of these proteins.
Inclusion Criteria:

 -  actual or suspected malignant or non-malignant tumors of the head and neck

 -  planned biopsy and/or resection, or availability of paraffin embedded or stored frozen
 tumor tissue for non-genetic analysis

 Exclusion Criteria:

 -  insufficient tissue available for both standard diagnostic evaluation and study
 specimen