Method for quantifying dna fragments in a sample by size
AssigneeThe University of North Carolina at Chapel Hill
InventorsGaorav Gupta, Bhishamjit S. Chera, Sunil Kumar
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Abstract
Disclosed herein are DNA amplification methods for quantifying DNA fragments of a target DNA in a sample by size. This can be used, for example, to detect tumor-derived viral DNA in blood sample and distinguish it from larger viral DNA from non-tumor sources. In particular, disclosed herein are methods of detecting, monitoring or treating a human papilloma virus (HPV)-associated malignancy in a subject that involves detecting a presence or absence of at least one circulating tumor-derived HPV DNA in a sample from the subject. Kits for accomplishing the same are also provided.
Claims1
A method for quantifying DNA fragments in a sample by size comprising:
- (i) fractionating DNA fragments from the sample into droplets at a concentration wherein only 0 or 1 DNA fragments are present in each droplet;
- (ii) amplifying the DNA in each droplet with a combination of primer/probe sets, wherein each primer/probe set is configured to amplify a non-overlapping region of the DNA fragments to produce an amplicon signal;
- and
- (iii) detecting in each droplet the number of amplicon signals;
- wherein the number of amplicon signals is an indication of the minimum size and maximum size of the DNA fragment,
- wherein the minimum size is the maximum distance between the primer/probe sets of the detected amplicons, and
- wherein the maximum size is the maximum distance between the primer/probe sets of the detected amplicons and the primer/probe sets of the adjacent non-overlapping region that was not amplified.
Dependencies are inferred from the claim text.