Methods of quantifying cell-free DNA

1. A method of quantifying chimeric cfDNA in a sample from a patient, the method comprising:

(a) providing a cell-free DNA (cfDNA) sample from a blood, serum or plasma sample obtained from a patient;

(b) performing a multiplex digital PCR comprising at least a first amplification and a second amplification on the cfDNA sample to determine a correction factor to correct for the degree of fragmentation in the cfDNA sample to provide the fraction of cfDNA that can be amplified for an amplified product of a defined size, wherein the first amplification targets a first single copy genomic locus in the patient genome and results in production of a first amplicon; and a second amplification targets a second single copy genomic locus in the patient genome and results in production of a second amplicon, wherein the first and second amplicon differ in length by at least 50 base pairs;

(c) determining the proportion of the first or the second amplicon in the total amplified product from the digital PCR of step (b) to provide the correction factor for the fraction of the cfDNA sample that can be amplified, and

(d) correcting a diagnostic digital PCR performed on the cfDNA sample using the correction factor determined in step (c) to quantify the level of chimeric DNA.

2. The method of claim 1 , wherein step (b) further comprises an amplification reaction that targets DNA that was added to the blood, serum, or plasma sample prior to extraction.

3. The method of claim 1 , wherein the first and second amplicons differ in length by 100 nucleotides or more.

4. The method of claim 1 , wherein the longer of the first and second amplicons is from 150 to 400 base pairs in length and the shorter of the first and the second amplicons is from 50 to 150 base pairs in length.

5. The method of claim 1 , wherein the cfDNA sample is from a transplant patient.

6. The method of claim 1 , wherein the cfDNA sample is from a cancer patient.

7. The method of claim 1 , wherein the cfDNA sample is from a pregnant patient.

8. The method of claim 1 , wherein the patient is a human.