Patent Document ID: 9057108
Application ID: 13611584
Patent Flag: 1

Claim One:
1. A method of identifying the origin of a neoplasm of unknown primary comprising: obtaining a sample of a neoplasm; analyzing morphology of the sample to distinguish between solid and liquid tumor types; testing the solid sample for cytokeratin expression to determine if the solid sample is cytokeratin positive or negative; performing immunohistochemistry on the cytokeratin positive sample to differentiate between carcinoma, mesothelioma and germ cell tumors; performing immunohistochemistry on the carcinoma sample to differentiate between subclasses of carcinomas wherein the subclasses of carcinoma are selected from the group consisting of adenocarcinoma, squamous cell carcinoma, urothelial carcinoma, and neuroendocrine carcinoma; applying a hierarchal microarray gene expression classifier to gene expression data from the carcinoma sample to verify differentiation between the subclasses of the carcinomas wherein the hierarchal gene expression classifier is comprised of top tier classifiers and second tier classifiers; assigning the carcinoma sample to one of the subclasses of carcinoma based on comparing the immunohistochemistry and the top tier classifier results; applying the second tier classifier to gene expression data from the carcinoma sample to assign a primary site of origin to the carcinoma sample; and administering a treatment to the patient according to the subclass of carcinoma assigned to the carcinoma sample; wherein the top tier classifiers differentiate between the subclasses of the carcinomas wherein the subclasses of carcinoma are selected from the group consisting of adenocarcinoma, squamous cell carcinoma, urothelial carcinoma, and neuroendocrine carcinoma; wherein the top tier classifiers for adenocarcinoma use gene expression data selected from the group of genes consisting of hexokinase domain containing 1 (HKDC1), malectin (KIAA0152), calmodulin-like 4 (CALML4), amiloride binding protein 1 (ABP1), tripartite motif-containing 15 (TRIM15), hepatocyte nuclear factor 4 gamma (HNF4G), and crystallin lambda 1 (CRYL1).