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

Abstract

Provided herein are methods and computer-readable storage media related to cell-free DNA and uses thereof to determine risk of a condition, such as transplant rejection or cancer, in a subject.

1 . A method of assessing a risk in a subject, the method comprising:
 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;   determining an allele of each of the plurality of loci;   selecting at least one informative locus from the plurality of loci based on the determining of the allele;   calculating an estimated allele frequency of a first allele at the at least one informative locus using a statistical distribution;   determining an amount of cell-free DNA not native to the subject in the cell-free DNA based on the estimated allele frequency; and   determining a risk in the subject based on the determined amount of the cell-free DNA not native to the subject in the cell-free DNA.   
     
     
         2 . The method of  claim 1 , wherein the subject is a recipient of a transplant, and the risk is a risk associated with the transplant. 
     
     
         3 . The method of  claim 2 , wherein the risk associated with the transplant is risk of transplant rejection, an anatomical problem with the transplant or injury to the transplant. 
     
     
         4 . The method of  claim 3 , wherein the injury to the transplant is initial or ongoing injury. 
     
     
         5 . The method of  claim 3 , wherein the risk associated with the transplant is indicative of the severity of the injury. 
     
     
         6 . The method of  claim 2 , wherein the risk associated with the transplant is a risk of having or developing a systemic disease. 
     
     
         7 . The method of  claim 6 , wherein the systemic disease is inflammation, infection or sepsis. 
     
     
         8 . The method of  claim 1 , wherein the cell-free DNA not native to the subject is donor-specific cell-free DNA. 
     
     
         9 . The method of  claim 1 , wherein the subject has or is at risk of having a cancer, and the risk is a risk associated with the cancer. 
     
     
         10 . The method of  claim 9 , wherein the risk associated with the cancer is the presence or absence of the cancer, recurrence of the cancer or metastasis of the cancer. 
     
     
         11 . The method of  claim 9 , wherein the cell-free DNA not native to the subject is cancer-specific cell-free DNA. 
     
     
         12 . The method of  claim 1 , further comprising:
 extracting the cell-free DNA from the biological sample.   
     
     
         13 . The method of  claim 11 , wherein:
 the first allele comprises a minor allele.   
     
     
         14 . The method of  claim 1 , wherein the at least one informative locus is selected by:
 detecting the first allele and a second allele at a locus; and   determining that the first nucleic acids are homozygous for the second allele at the at least one informative locus and the second nucleic acids are heterozygous or homozygous for the first allele at the at least one informative locus.   
     
     
         15 .- 47 . (canceled) 
     
     
         48 . A method of treatment of a subject, the method comprising:
 determining an amount of cell-free DNA not native to the subject in cell-free DNA extracted from a biological sample from the subject;   determining a risk in the subject based on the determined amount of the cell-free DNA not native to the subject; and   administering a therapy, or providing information about a therapy, to the subject based on the determined risk.   
     
     
         49 .- 81 . (canceled) 
     
     
         82 . A method of assessing a risk of a systemic disease in a recipient of a transplant, the method comprising:
 quantifying the amount of cell-free DNA extracted from a biological sample obtained from the recipient of a transplant; and   determining a risk of a systemic disease in the recipient of a transplant based on the determined amount of the cell-free DNA.   
     
     
         83 .- 103 . (canceled) 
     
     
         104 . A method of treatment of a recipient of a transplant, the method comprising:
 quantifying the amount of cell-free DNA extracted from a biological sample obtained from the recipient of a transplant;   determining a risk of a systemic disease in the recipient of a transplant based on the determined amount of the cell-free DNA; and   administering a therapy, or providing information about a therapy, to the recipient of a transplant based on the determined risk.   
     
     
         105 .- 117 . (canceled) 
     
     
         118 . A method of evaluating a subject, comprising:
 calculating a value for a Predictive Model of Formula 1, Formula 2 or Formula 3; and   assessing the condition of the recipient of a transplant.   
     
     
         119 .- 133 . (canceled) 
     
     
         134 . At least one computer-readable storage medium storing computer-executable instructions that, when executed by at least one processor, cause a computing device to perform a method comprising:
 (a) determining an allele of each of a plurality of loci;   selecting at least one informative locus from the plurality of loci based on the determining of the allele;   calculating an estimated allele frequency of a first allele at the at least one informative locus using a statistical distribution;   determining an amount of cell-free DNA not native to a subject in the cell-free DNA based on the estimated allele frequency; and   determining a risk in the subject based on the determined amount of the cell-free DNA not native to the subject in the cell-free DNA;   (b) determining an amount of cell-free DNA not native to a subject in cell-free DNA extracted from a biological sample from the subject; and   determining a risk in the subject based on the determined amount of the cell-free DNA not native to the subject;   (c) quantifying an amount of cell-free DNA extracted from a biological sample obtained from a recipient of a transplant; and   determining a risk of a systemic disease in the recipient of a transplant based on the determined amount of cell-free DNA; or   (d) calculating a value for the Predictive Model of Formula 1, Formula 2, or Formula 3.   
     
     
         135 .- 157 . (canceled) 
     
     
         158 . 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; 
   (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, or adjusting the anti-rejection therapy or a therapeutic agent that treats a systemic disease administered to the subject based on the determined amount of the cell-free DNA not native to the subject.