Gene expression subtype analysis of head and neck squamous cell carcinoma for treatment management
AssigneesGeneCentric Therapeutics, Inc., The University of North Carolina at Chapel Hill
InventorsMyla LAI-GOLDMAN, Hawazin FARUKI, Gregory MAYHEW, Charles M. PEROU, David Neil HAYES, Jose ZEVALLOS
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Abstract
Methods are provided for determining a subtype of head and neck squamous cell carcinoma (HNSCC) of an individual by detecting the expression level of at least one subtype classifier selected from a group of genes that are relevant for determining HNSCC subtypes. Also provided herein are methods for determining a suitable treatment and predicting the overall survival and the likelihood of metastasis for the HNSCC patients according to their subtypes.
Claims85
A method of determining a suitable treatment for a head and neck squamous cell carcinoma (HNSCC) patient, the method comprising:
- (a) detecting an expression level of at least one subtype classifier selected from Table 3 or Table 4 in a head and neck tissue sample obtained from the patient;
- and (b) selecting a treatment for the HNSCC patient according to the expression level of the at least one subtype classifier selected from Table 3 or Table 4;
- wherein the detection of the expression level of the subtype classifier specifically identifies a basal (BA), mesenchymal (MS), atypical (AT) or classical (CL) HNSCC subtype, and wherein the patient is HPV negative.
A method of determining whether a HNSCC patient is likely to respond to radiotherapy, the method comprising:
- (a) detecting an expression level of at least one subtype classifier selected from Table 3 or Table 4 in a head and neck tissue sample obtained from the patient, wherein the patient is HPV negative, and wherein the detection of the expression level of the subtype classifier specifically identifies a BA, MS, AT or CL HNSCC subtype;
- (b) determining expression of one or more genes associated with radiotherapy resistance;
- and (c) identifying the HNSCC subtype correlated with radiotherapy resistance.
A method of predicting occult nodal metastasis in a OCSCC patient, the method comprising:
- (a) detecting an expression level of at least one gene selected from Table 3 or Table 4 in a head and neck tissue sample obtained from a patient, wherein the patient is HPV negative, wherein the detection of the expression level of the subtype classifier specifically identifies a BA, MS, AT or CL HNSCC subtype, and wherein identification of the MS subtype is indicative of occult nodal metastasis in the patient.
A method of predicting overall survival in a LSCC patient, the method comprising detecting an expression level of at least one gene selected from Table 3 or Table 4 in a head and neck tissue sample obtained from a patient, wherein the patient is HPV negative, wherein the detection of the expression level of the subtype classifier specifically identifies a BA, MS, AT or CL LSCC subtype, and wherein identification of the LSCC subtype is predictive of the overall survival in the patient.
Dependencies are inferred from the claim text.