Methods of determining tissues and/or cell types giving rise to cell-free dna, and methods of identifying a disease or disorder using same

Abstract

The present disclosure provides methods of determining one or more tissues and/or cell-types contributing to cell-free DNA (“cfDNA”) in a biological sample of a subject. In some embodiments, the present disclosure provides a method of identifying a disease or disorder in a subject as a function of one or more determined more tissues and/or cell-types contributing to cfDNA in a biological sample from the subject.

1 - 111 . (canceled) 
     
     
         112 . A method of identifying or diagnosing a disease, disorder, or condition in a human, the method comprising:
 isolating cell free DNA (cfDNA) from a biological sample from the human, the isolated cfDNA comprising a plurality of cfDNA fragments;   constructing a sequencing library from the plurality of cfDNA fragments;   determining a sequence associated with at least a portion of the plurality of cfDNA fragments;   aligning the sequences of the portion of the plurality of the cfDNA fragments to a reference genome to generate the outer alignment coordinates within the reference genome for each fragment;   calculating the frequency of occurrence for each outer alignment coordinate of the plurality of cfDNA fragments;   producing a fragment endpoint map comprising frequencies of the genomic locations of the outer alignment coordinates of the plurality of cfDNA fragments;   isolating cfDNA from a first set of reference samples and a second set of reference samples, the isolated cfDNA from the first set of reference samples comprising a plurality of cfDNA fragments from one or more healthy reference humans and the isolated cfDNA from the second set of reference samples comprising a plurality of cfDNA fragments from one or more reference humans with the disease, disorder, or condition in common;   constructing a first set of sequencing libraries and a second set of sequencing libraries from the plurality of cfDNA fragments isolated from the first set of reference samples and the second set of reference samples, respectively;   determining a sequence associated with at least a portion of the plurality of cfDNA fragments isolated from the first set of reference samples and the second set of reference samples;   aligning the sequences of the portion of the plurality of the cfDNA fragments from the first and second sets of reference samples to the reference genome to generate the outer alignment coordinates, within the reference genome, for each fragment;   calculating the frequency of occurrence for each outer alignment coordinate in the first and second reference samples;   producing a first reference fragment endpoint map and a second reference fragment endpoint map, each comprising frequencies of the genomic locations of the outer alignment coordinates of the plurality of cfDNA fragments isolated from the first set of reference samples and the second set of reference samples, and   calculating a first Pearson correlation between the fragment endpoint map and the first reference fragment endpoint map and a second Pearson correlation between the fragment endpoint map and the second reference fragment endpoint map; and   identifying or diagnosing the disease, disorder, or condition if the second Pearson correlation is stronger in magnitude than the first Pearson correlation.   
     
     
         113 . The method of  claim 112 , wherein the disease, disorder, or condition is selected from the group consisting of: cancer, normal pregnancy, a complication of pregnancy, myocardial infarction, inflammatory bowel disease, systemic autoimmune disease, localized autoimmune disease, allotransplantation with rejection, allotransplantation without rejection, stroke, and localized tissue damage. 
     
     
         114 . The method of  claim 112 , further comprising generating a report comprising a statement identifying or diagnosing the disease, disorder, or condition. 
     
     
         115 . The method of  claim 112 , wherein the biological sample comprises, consists essentially of, or consists of whole blood, peripheral blood plasma, urine, or cerebral spinal fluid. 
     
     
         116 . The method of  claim 113 , wherein the disease, disorder, or condition is cancer. 
     
     
         117 . The method of  claim 116 , wherein the cancer is hepatocellular carcinoma, ductal carcinoma in situ breast cancer or metastatic breast adenocarcinoma, or lung squamous cell carcinoma. 
     
     
         118 . The method of  claim 113 , wherein the disease, disorder, or condition is pregnancy or a complication of pregnancy.