A. SPECIFIC AIMS Diagnostic Dilemma in the Differential Diagnosis of a Suspicious Thyroid Nodule. Although fine needle aspiration (FNA) cytology is the best diagnostic tool in the differential diagnosis of a thyroid nodule, it often cannot differentiate a benign from a malignant lesion. Consequently, a majority of patients with thyroid nodules require surgery because of a suspicious, but not definite, diagnosis of malignancy. Because the surgical management for benign and malignant thyroid nodules differs, patients with suspicious FNAs may be treated in a less than ideal way surgically. Some patients with benign lesions may undergo unnecessary surgery and some with malignant lesions may require a second operation for completion thyroidectomy once a diagnosis of malignancy is rendered on permanent histological section. Research Premise Although others and we have documented various genetic alterations in thyroid neoplasms, no specific alteration(s) can reliably distinguish benign from malignant lesions. We propose that specific gene expression patterns are associated with the various thyroid tumor types and that these unique expression patterns can be capitalized upon to differentiate one tumor type from another. We therefore propose to genotype by microarray analysis the benign and malignant thyroid lesions that can and often do present as "suspicious" lesions on FNA cytology. [To that end we have performed microarray analysis on 63 thyroid tumors and have selected a set of 11 genes that best discriminate benign from malignant in 4 of 8 thyroid tumor sub-types. These data will be validated and expanded to include 4 additional thyroid tumor sub-types. A panel of candidate, discriminating genes will then be validated by real time RT-PCR and in situ hybridization (ISH) of thyroid tumors, followed by both immunohistochemistry (IHC) of tissue microarrays and, immunocytochemistry (ICC) of cell blocks Prepared from thyroid cell lines and FNA samples.] The ultimate and future goal would then be to apply these results to the differential diagnosis of suspicious thyroid FNA samples in order to improve the clinical management of patients with this diagnosis. To accomplish these goals we propose the following: Specific Aim 1: To genomically define by microarray analysis benign and malignant thyroid tumors. Specific Aim 2: To validate the candidate gene sets selected in Aim 1 by real-time quantitative RT-PCR and, [in situ hybridization ISH]. Specific Aim 3: To develop immunohistochemical (IHC) assays for genes validated in Aim 2, validate these by tissue microarrays analysis (TMA) of thyroid tumors and [cell blocks prepared from paraffin-embedded thyroid cell lines, and perform immunocytochemical (ICC) assays to cell blocks prepared from FNA samples.]