Methods for detection and differentiation of origin of viral dna
AssigneeThe Johns Hopkins University
InventorsRichard F. Ambinder, Meir Shamay
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Abstract
The invention disclosed herein provides methods for identifying the origin of viral DNA in a sample by detecting the methylation state of at least one CpG site on a target site of the genome of a virus of interest, and determining whether the origin of the viral DNA is from a cell, such as a tumor cell, or a virion, wherein when the methylation state is positive for methylation, the viral DNA is from a cell, and wherein when the methylation state is negative for methylation, the viral DNA is from a virion. Use of these methods for diagnosis or monitoring, and/or treatment of a subject infected with a virus known to cause cancer and related disease are also provided.
Claims14
A method for identifying the origin of viral DNA in a sample comprising:
- a) obtaining a biological sample comprising viral DNA;
- b) purifying the DNA from a);
- c) allowing the DNA from b) to contact at least one or more paramagnetic beads bound with methylCpG binding protein;
- d) detecting the methylation state of at least one CpG site on a target site of the genome of the virus;
- and
- e) determining whether the origin of the viral DNA is from a cell or a virion, wherein when the methylation state of at least one CpG site on the target site is positive for methylation, the viral DNA is from a cell, and wherein when the methylation state of at least one CpG site on the target site is negative for methylation, the viral DNA is from a virion.
A method for identifying the origin of viral DNA in a subject infected with a virus comprising:
- a) obtaining a biological sample comprising viral DNA;
- b) purifying the DNA from a);
- c) allowing the DNA from b) to contact at least one or more paramagnetic beads bound with methylCpG binding protein;
- d) detecting the methylation state of at least one CpG site on a target site of the genome of the virus;
- and
- e) determining whether the origin of the viral DNA is from a cell or a virion, wherein when the methylation state of at least one CpG site on the target site is positive for methylation, the viral DNA is from a cell, and wherein when the methylation state of at least one CpG site on the target site is negative for methylation, the viral DNA is from a virion.
(canceled)
A method of diagnosis of Kaposi's sarcoma in a subject infected with KSHV comprising:
- a) obtaining a biological sample comprising viral DNA from the subject;
- b) purifying the DNA from a);
- c) allowing the DNA from b) to contact at least one or more paramagnetic beads bound with methylCpG binding protein;
- d)) determining whether the origin of the viral DNA is from a cell or a virion wherein when the methylation state of at least one CpG site on the target site is positive for methylation, the viral DNA is from a cell, and wherein when the methylation state of at least one CpG site on the target site is negative for methylation, the viral DNA is from a virion,
- wherein when the methylation state is positive, the patient is diagnosed as having Kaposi's sarcoma.
A method of diagnosis of primary effusion lymphoma in a subject infected with KSHV comprising:
- a) obtaining a biological sample comprising viral DNA from the subject;
- b) purifying the DNA from a);
- c) allowing the DNA from b) to contact at least one or more paramagnetic beads bound with methylCpG binding protein;
- d)) determining whether the origin of the viral DNA is from a cell or a virion wherein when the methylation state of at least one CpG site on the target site is positive for methylation, the viral DNA is from a cell, and wherein when the methylation state of at least one CpG site on the target site is negative for methylation, the viral DNA is from a virion,
- wherein when the methylation state of at least one CpG site on the target site is positive, the patient is diagnosed as having primary effusion lymphoma.
A method of diagnosis of nasopharyngeal cancer in a subject infected with Epstein-Barr Virus comprising:
- a) obtaining a biological sample comprising viral DNA from the subject;
- b) purifying the DNA from a);
- c) allowing the DNA from b) to contact at least one or more paramagnetic beads bound with methylCpG binding protein;
- d) determining whether the origin of the viral DNA is from a cell or a virion wherein when the methylation state is positive for methylation, the viral DNA is from a cell, and wherein when the methylation state is negative for methylation, the viral DNA is from a virion,
- wherein when the methylation state of at least one CpG site on the target site is positive, the patient is diagnosed as having nasopharyngeal cancer.
Dependencies are inferred from the claim text.