Methods for analyzing viral nucleic acid
Provided herein are methods, systems, and computer readable medium for detecting nucleic acid from a pathogen, e.g., virus, e.g., Epstein-Barr virus (EBV), in a cell-free nucleic sample from an individual at risk of a condition, e.g., nasopharyngeal carcinoma (NPC). The methods, systems, and computer readable medium can be used to screen for the presence of the condition, e.g., NPC, using thresholds adjusted based on sample attributes.
1 . A method of screening and treating a subject for a tumor, the method comprising selecting a subject, and based on said selecting, administering a treatment to the subject effective to treat a tumor in the subject, wherein:
a) the selecting comprises (i) receiving results of an assay of a biological sample of the subject measuring an amount of cell-free nucleic acid from an Epstein-Barr Virus (EBV) in the biological sample, and (ii) identifying the amount of EBV cell-free nucleic acid in the biological sample as being above a threshold amount;
b) the threshold amount distinguishes reference biological samples of reference subjects with a known tumor from reference biological samples of reference subjects without the known tumor;
c) the subject and the reference subjects are characterized by one or more of the following:
(i) age above 45 years old;
(ii) smoking status is a smoker; or
(iii) mean outdoor ambient temperature on a day the respective biological samples were collected at a location within 50 km of a location at which the respective biological samples were collected is below 30° C.; and
d) the treatment is selected from the group consisting of: chemotherapy, radiation therapy, surgery, and antibody therapy.
2 . The method of claim 1 , wherein the subject and the reference subjects are characterized by the smoking status of smoker.
3 . The method of claim 2 , wherein the threshold is at least 20% higher than a threshold amount for a non-smoker.
4 . The method of claim 1 , wherein the subject and reference subjects are characterized by age above 45 years old.
5 . The method of claim 4 , wherein the threshold amount is increased by at least 2% for every block of 5 years that the age of the subject is above 45 years old.
6 . The method of claim 1 , wherein the subject and the reference subjects are characterized by the mean outdoor ambient temperature on the day the biological samples were collected at the location within 50 km of a location at which the respective biological samples were collected is below 30° C.
7 . The method of claim 6 , wherein the threshold amount is increased by at least 1% for every block of 3 degrees that the mean outdoor ambient temperature on the day the biological sample of the subject was collected at the location within 50 km of a location at which the biological sample of the subject was collected is below 30° C.
8 . The method of claim 1 , wherein the subject and the reference subjects are characterized by each of the following:
(i) above 45 years old;
(ii) smoking status is a smoker; and
(iii) the mean outdoor ambient temperature on the day the respective biological samples were collected at the location within 50 km of a location at which the biological samples were collected is below 30° C.
9 . The method of claim 1 , wherein the treatment comprises chemotherapy.
10 . The method of claim 1 , wherein the amount of EBV cell-free nucleic acid in the biological sample comprises at least 100 copies of the cell-free nucleic acid from EBV per milliliter (copies/mL).
11 . The method of claim 1 , wherein the selecting further comprises identifying the subject as the source of a second biological sample comprising a second indicator of presence of the tumor.
12 . The method of claim 11 , wherein the second indicator comprises a size of cell-free nucleic acid from the EBV in the second biological sample from the subject.
13 . The method of claim 12 , wherein the second biological sample is identical to the biological sample.
14 . The method of claim 12 , wherein the second biological sample is different from the biological sample.
15 . The method of claim 12 , wherein the second indicator comprises an amount of cell-free nucleic acid from the second biological sample from the subject that is from the EBV and has a size within a given range.
16 . The method of claim 15 , wherein the amount of the cell-free nucleic acid that is from the EBV and has a size within the given range is based on results for massively parallel sequencing of the cell-free nucleic acid from the second biological sample.
17 . The method of claim 1 , wherein the biological sample comprises plasma or serum.
18 . The method of claim 1 , wherein the amount of EBV cell-free nucleic acid in the biological sample is determined by amplification of the cell-free nucleic acid.
19 . The method of claim 18 , wherein the amplification comprises polymerase chain reaction (PCR).
20 . The method of claim 19 , wherein the PCR comprises quantitative PCR (qPCR).
21 . The method of claim 1 , wherein the tumor is nasopharyngeal cancer.
22 . The method of claim 1 , wherein the treatment comprises radiation therapy.
23 . The method of claim 1 , wherein the treatment comprises surgical removal of tumor tissue.
24 . The method of claim 1 , wherein the treatment comprises antibody therapy.
25 . The method of claim 24 , wherein the antibody therapy comprises administering a monoclonal antibody.
26 . The method of claim 24 , wherein the antibody therapy comprises administering bevacizumab, cetuximab, or nivolumab.
27 . The method of claim 1 , wherein the tumor in the subject and the known tumor of the reference subjects comprise a nasopharyngeal cancer.
28 . The method of claim 1 , wherein the tumor in the subject and the known tumor of the reference subjects comprise a lymphoma or a stomach cancer.