Human papilloma virus as predictor of cancer prognosis

A kit for assessing a subject having a squamous cell carcinoma of the head and neck (HNSCC), containing methods for determining whether a subject is HPV+ or HPV−, and to accordingly identify an appropriate therapeutic agent to treat the HNSCC;

• wherein said kit comprises at least one or more of the following detection agents:
• (i) one or more PCR primers for detecting an HPV in a sample from the subject;
• (ii) one or more probes for detecting an HPV in a sample from the subject;
• (iii) one or more antibodies for detecting an HPV protein in a sample from the subject.

A system or device for producing a report recording the presence or absence of HPV in a patient, said system or device comprising one or more of the following:

• (i) a component for containing a sample from a subject;
• (ii) a detection component capable of identifying the presence or absence of a HPV;
• and
• (iii) a means for outputting a report.

A method for determining the likely effectiveness of a therapeutic option for a subject with cancer, said method comprising the steps of:

• (1) subjecting a subject sample to a sequencing device for producing a genotype report, said sequencing device comprising one or more of the following:
• (i) a component for containing a sample;
• (ii) a detection component capable of identifying the presence or absence of a mutant gene;
• and
• (iii) a means for outputting a report;
• (2) identifying the sequence, alternation or mutation of a mutant gene;
• (3) determining the acceptability of a therapeutic option based on step (2);
• (4) determining the advisability of applying the therapeutic option based on step (3);
• and
• (5) providing a report of potential or suggested therapeutic options based on the determination of steps (3) and (4).

A method for screening for an agent that inhibits the expression or activity of a mutant gene comprising:

• determining if a sample is HPV− or HPV+;
• contacting the sample with a candidate agent;
• and
• detecting a change in a parameter associated with a cell cycle gene chosen from CDKN2A, CDKN2B, CCNE1, CCND1, CCND2, CCND3, CDK4 or CDK6, or a gene described in Table 1 or Table 4.

A method of evaluating a patient or a patient population, comprising:

• identifying, selecting, or obtaining information or knowledge that the patient or patient population has participated in a clinical trial;
• acquiring information or knowledge of the presence of HPV in the patient or patient population;
• acquiring genotype information of the subject that identifies a mutant gene as being present in the patient;
• acquiring a sequence for a nucleic acid molecule described in Table 1 or Table 4;
• or
• detecting the presence of a mutant nucleic acid or polypeptide in the subject;
• wherein the absence of HPV in the patient identifies the patient or patient population as a candidate to receive treatment with a CDK inhibitor;
• and
• wherein the presence of HPV identifies the patient or patient population as a candidate to receive treatment with an anti-cancer agent other than a CDK inhibitor.