DETECTION OF ANTI-VIRAL CDR3s IN CANCER

A method of determining overall survival in a subject with an EBV-positive cancer, comprising:

• a) obtaining a biological sample from the subject, wherein the biological sample comprises tumor-infiltrating lymphocytes (TIL);
• b) extracting complementarity determining region 3 (CDR3) amino acid (AA) sequences from the TIL, thereby obtaining extracted TIL CDR3 AA sequences;
• c) obtaining a chemical complementarity score (CS) by interacting known EBV epitopes AA sequences to the extracted TIL CDR3 AA sequences;
• d) calculating the CS;
• and
• e) correlating the CS with overall survival of the subject,
• wherein a high CS is correlated to better overall survival compared to a reference control, wherein the reference control has low CS.

A method of treating an EBV-positive cancer in a subject, comprising:

• a) obtaining a biological sample from the subject, wherein the biological sample comprises tumor-infiltrating lymphocytes (TIL);
• b) extracting complementarity determining region 3 (CDR3) amino acid (AA) sequences from the TIL, thereby obtaining extracted TIL CDR3 AA sequences;
• c) identifying an exact match of extracted TIL CDR3 AA sequences to known anti-EBV CDR3 AA sequences from the biological sample;
• thereby obtaining an exact match anti-EBV TIL CDR3 AA sequence;
• d) correlating presence of the exact match anti-EBV TIL CDR3 AA sequence with overall survival of the subject;
• and
• e) administering a pharmaceutically effective amount of an anti-EBV therapeutic to the subject with a presence of the exact match anti-EBV TIL CDR3 AA sequence,
• wherein the presence of the exact match anti-EBV TIL CDR3 AA sequence in the sample is correlated to better overall survival.