Highly sensitive transplant rejection surveillance using targeted detection of donor specific cell free DNA

A method of treatment of a subject, wherein the subject is a recipient of a transplant, the method comprising:

• (a) determining an amount of cell-free DNA not native to the subject based on a method comprising:
• (i) analyzing nucleic acids from cell-free DNA extracted from a biological sample obtained from the subject to identify a plurality of loci, the nucleic acids comprising first nucleic acids of the subject and second nucleic acids not native to the subject;
• (ii) determining an allele of each of the plurality of loci;
• (iii) selecting at least one informative locus from the plurality of loci based on the determining of the allele;
• and
• (iv) calculating an estimated allele frequency of a first allele at the at least one informative locus using a statistical distribution;
• and
• (b) comparing the determined amount of the cell-free DNA not native to the subject to a threshold value of cell-free DNA;
• and
• (c) administering an anti-rejection therapy or a therapeutic agent that treats a systemic disease to the subject when the determined amount of the cell-free DNA not native to the subject is greater than the threshold value of cell-free DNA.