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AssigneeRutgers, The State University of New Jersey
InventorsBassel Ghaddar, Subhajyoti De
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Disclosed herein are methods of identifying and treating subjects with cancer, and methods of predicting a survival outcome in a subject with cancer, such as pancreatic cancer. In one aspect, the application provides methods for detecting the presence of cancer or infectious disease in a subject by collecting and analyzing sequencing information from the subject, such as by performing single cell RNA sequencing analysis of individual cells obtained from a sample from the subject. In a further aspect, the application provides methods for detecting the presence of cancer or infectious disease in a subject by determining microbial diversity and/or assessing the presence or absence of particular microbes in individual cells from the subject as compared to a control. Also provided are methods of determining T-cell microenvironment reaction, for example by sequencing nucleic acid molecules in individual T-cells obtained from the subject.
A method of treating a subject having or suspected of having pancreatic cancer, comprising:
2-3. (canceled)
A method of determining T-cell microenvironment reaction in a subject, comprising sequencing nucleic acid molecules in individual T-cells obtained from the subject, determining the expression level of one or more of the genes of Table 2 in the individual T-cells, and comparing the expression level of the one or more genes of Table 2 in the individual T-cells to a control using a random forest model, thereby classifying the individual T-cells as infection microenvironment reactive or tumor microenvironment reactive.
A method of identifying a microbe or virus in a sample, comprising:
(canceled)
14-16. (canceled)
(canceled)
21-22. (canceled)
28-29. (canceled)
31-33. (canceled)
35-37. (canceled)
Dependencies are inferred from the claim text.