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 . A method of determining tissues and/or cell types giving rise to cell free DNA (cfDNA) in a subject, the method comprising:
 isolating cfDNA from a biological sample from the subject, the isolated cfDNA comprising a plurality of cfDNA fragments;   determining a sequence associated with at least a portion of the plurality of cfDNA fragments;   determining a genomic location within a reference genome for at least some cfDNA fragment endpoints of the plurality of cfDNA fragments as a function of the cfDNA fragment sequences; and   determining at least some of the tissues and/or cell types giving rise to the cfDNA fragments as a function of the genomic locations of at least some of the cfDNA fragment endpoints.   
     
     
         2 . The method of  claim 1  wherein the step of determining at least some of the tissues and/or cell types giving rise to the cfDNA fragments comprises comparing the genomic locations of at least some of the cfDNA fragment endpoints to one or more reference maps. 
     
     
         3 . The method of  claim 1  or  claim 2  wherein the step of determining at least some of the tissues and/or cell types giving rise to the cfDNA fragments comprises performing a mathematical transformation on a distribution of the genomic locations of at least some of the cfDNA fragment endpoints. 
     
     
         4 . The method of  claim 3  wherein the mathematical transformation includes a Fourier transformation. 
     
     
         5 . The method of any one of  claims 1  to  4  further comprising determining a score for each of at least some coordinates of the reference genome, wherein the score is determined as a function of at least the plurality of cfDNA fragment endpoints and their genomic locations, and wherein the step of determining at least some of the tissues and/or cell types giving rise to the observed cfDNA fragments comprises comparing the scores to one or more reference map. 
     
     
         6 . The method of  claim 5 , wherein the score for a coordinate represents or is related to the probability that the coordinate is a location of a cfDNA fragment endpoint. 
     
     
         7 . The method of any one of  claims 2  to  6  wherein the reference map comprises a DNase I hypersensitive site dataset generated from at least one cell-type or tissue; or wherein the reference map comprises an RNA expression dataset generated from at least one cell-type or tissue; or wherein the reference map comprises a chromosome conformation map generated from at least one cell-type or tissue; or wherein the reference map comprises a chromatin accessibility map generated from at least one cell-type or tissue. 
     
     
         8 . (canceled) 
     
     
         9 . The method of any one of  claims 2  to  7  wherein the reference map is generated from cfDNA from an animal to which human tissues or cells that have been xenografted. 
     
     
         10 - 11 . (canceled) 
     
     
         12 . The method of any one of  claims 2  to  7  and  9  wherein the reference map comprises sequence data obtained from samples obtained from at least one reference subject. 
     
     
         13 . The method of any one of  claims 2  to  7 ,  9  and  12  wherein the reference map corresponds to at least one cell-type or tissue that is associated with a disease or a disorder or condition. 
     
     
         14 . The method of any one of  claims 2  to  7 ,  9 , and  12  to  13  wherein the reference map comprises positions or spacing of nucleosomes and/or chromatosomes in a tissue or cell type. 
     
     
         15 . The method of any one of  claims 2  to  7 ,  9 , and  12  to  14  wherein the reference map is generated by digesting chromatin obtained from at least one cell-type or tissue with an exogenous nuclease (e.g., micrococcal nuclease). 
     
     
         16 . The method of any one of  claims 2  to  7 ,  9  and  12  to  15 , wherein the reference maps comprise chromatin accessibility data determined by a transposition-based method (e.g., ATAC-seq). 
     
     
         17 . The method of any one of  claims 2  to  7 ,  9  and  12  to  16  wherein the reference maps comprise data associated with positions of a DNA binding and/or DNA occupying protein for a tissue or cell type. 
     
     
         18 . The method of  claim 17  wherein the DNA binding and/or DNA occupying protein is a transcription factor. 
     
     
         19 . The method of  claim 17  or  claim 18  wherein the positions are determined by chromatin immunoprecipitation of a crosslinked DNA-protein complex. 
     
     
         20 . The method of  claim 17  or  claim 18  wherein the positions are determined by treating DNA associated with the tissue or cell type with a nuclease (e.g., DNase-I). 
     
     
         21 . The method of any one of  claims 2  to  7 ,  9  and  12  to  20  wherein the reference map comprises a biological feature related to the positions or spacing of nucleosomes, chromatosomes, or other DNA binding or DNA occupying proteins within a tissue or cell type. 
     
     
         22 . The method of  claim 21  wherein the biological feature is quantitative expression of one or more genes; or wherein the biological feature is presence or absence of one or more histone marks; or wherein the biological feature is hypersensitivity to nuclease cleavage. 
     
     
         23 - 24 . (canceled) 
     
     
         25 . The method of any one of  claims 2  to  7 ,  9 , and  12  to  22  wherein the tissue or cell type used to generate a reference map is a primary tissue from a subject having a disease or disorder or condition. 
     
     
         26 . The method of  claim 25  wherein the disease or disorder or condition is selected from the group consisting of: cancer, normal pregnancy, a complication of pregnancy (e.g., aneuploid pregnancy), myocardial infarction, inflammatory bowel disease, systemic autoimmune disease, localized autoimmune disease, allotransplantation with rejection, allotransplantation without rejection, stroke, and localized tissue damage. 
     
     
         27 . The method of any one of  claims 2  to  7 ,  9  and  12  to  22  wherein the tissue or cell type used to generate a reference map is a primary tissue from a healthy subject; or wherein the tissue or cell type used to generate a reference map is an immortalized cell line; or wherein the tissue or cell type used to generate a reference map is a biopsy from a tumor. 
     
     
         28 - 29 . (canceled) 
     
     
         30 . The method of  claim 12  wherein the sequence data comprises positions of cfDNA fragment endpoints. 
     
     
         31 . The method of  claim 30  wherein the reference subject is healthy; or wherein the reference subject has a disease or disorder or condition. 
     
     
         32 . (canceled) 
     
     
         33 . The method of  claim 31  wherein the disease or disorder or condition is selected from the group consisting of: cancer, normal pregnancy, a complication of pregnancy (e.g., aneuploid pregnancy), myocardial infarction, inflammatory bowel disease, systemic autoimmune disease, localized autoimmune disease, allotransplantation with rejection, allotransplantation without rejection, stroke, and localized tissue damage. 
     
     
         34 . The method of any one of  claims 13  to  22 ,  25  to  27 ,  30  to  31  and  33  wherein the reference map comprises reference scores for at least a portion of coordinates of the reference genome associated with the tissue or cell type. 
     
     
         35 . The method of  claim 34  wherein the reference map comprises a mathematical transformation of the scores. 
     
     
         36 . The method of  claim 34  wherein the scores represent a subset of all reference genomic coordinates associated with the tissue or cell type. 
     
     
         37 . The method of  claim 36  wherein the subset is associated with positions or spacing of nucleosomes and/or chromatosomes; or wherein the subset is associated with transcription start sites and/or transcription end sites; or wherein the subset is associated with binding sites of at least one transcription factor; or wherein the subset is associated with nuclease hypersensitive sites. 
     
     
         38 - 40 . (canceled) 
     
     
         41 . The method of any one of  claims 36  to  37  wherein the subset is additionally associated with at least one orthogonal biological feature. 
     
     
         42 . The method of  claim 41  wherein the orthogonal biological feature is associated with high expression genes; or wherein the orthogonal biological feature is associated with low expression genes. 
     
     
         43 . (canceled) 
     
     
         44 . The method of any one of  claims 35  to  37  and  41  to  42  wherein the mathematical transformation includes a Fourier transformation. 
     
     
         45 . The method of any one of  claims 5  to  7 ,  9 ,  12  to  22 ,  25  to  27 ,  30  to  31 ,  33  to  37 ,  41  to  42 , and  44  wherein at least a subset of the plurality of the scores each has a score above a threshold value. 
     
     
         46 . The method of any one of  claims 1  to  7 ,  9 ,  12  to  22 ,  25  to  27 ,  30  to  31 ,  33  to  37 ,  41  to  42 , and  44  to  45  wherein the step of determining the tissues and/or cell types giving rise to the cfDNA as a function of a plurality of the genomic locations of at least some of the cfDNA fragment endpoints comprises comparing a Fourier transform of the plurality of the genomic locations of at least some of the cfDNA fragment endpoints, or a mathematical transformation thereof, with a reference map. 
     
     
         47 . The method of any one of  claims 1  to  7 ,  9 ,  12  to  22 ,  25  to  27 ,  30 ,  31 ,  33  to  37 ,  41 ,  42 , and  44  to  46  further comprising generating a report comprising a list of the determined tissues and/or cell types giving rise to the isolated cfDNA. 
     
     
         48 . A method of identifying or diagnosing a disease or disorder or condition in a subject, the method comprising:
 isolating cell free DNA (cfDNA) from a biological sample from the subject, the isolated cfDNA comprising a plurality of cfDNA fragments;   determining a sequence associated with at least a portion of the plurality of cfDNA fragments;   determining a genomic location within a reference genome for at least some cfDNA fragment endpoints of the plurality of cfDNA fragments as a function of the cfDNA fragment sequences;   optionally determining at least some of the tissues and/or cell types giving rise to the cfDNA as a function of the genomic locations of at least some of the cfDNA fragment endpoints; and   identifying or diagnosing the disease or disorder or condition as a function of the determined tissues and/or cell types giving rise to the cfDNA.   
     
     
         49 . The method of  claim 48  wherein the optional step of determining the tissues and/or cell types giving rise to the cfDNA comprises comparing the genomic locations of at least some of the cfDNA fragment endpoints to one or more reference maps. 
     
     
         50 . The method of  claim 48  or  claim 49  wherein the step of determining the tissues and/or cell types giving rise to the cfDNA comprises performing a mathematical transformation on a distribution of the genomic locations of at least some of the plurality of the cfDNA fragment endpoints. 
     
     
         51 . The method of  claim 50  wherein the mathematical transformation includes a Fourier transformation. 
     
     
         52 . The method of any one of  claims 48  to  51  further comprising determining a score for each of at least some coordinates of the reference genome, wherein the score is determined as a function of at least the plurality of cfDNA fragment endpoints and their genomic locations. 
     
     
         53 . The method of any one of  claims 52 ,  112  and  113 , wherein the score for a coordinate represents or is related to the probability that the coordinate is a location of a cfDNA fragment endpoint. 
     
     
         54 . The method of any one of  claims 49  to  53  and  112  to  113  wherein the reference map comprises a DNase I hypersensitive site dataset, an RNA expression dataset, expression data, a chromosome conformation map, a chromatin accessibility map, chromatin fragmentation map, or sequence data obtained from samples obtained from at least one reference subject, and corresponding to at least one cell type or tissue that is associated with a disease or a disorder or condition, and/or positions or spacing of nucleosomes and/or chromatosomes in a tissue or cell type. 
     
     
         55 . The method of any one of  claims 49  to  54  and  112  to  114  wherein the reference map is generated by digesting chromatin from at least one cell-type or tissue with an exogenous nuclease (e.g., micrococcal nuclease); or wherein the reference map comprises chromatin accessibility data determined by applying a transposition-based method (e.g., ATAC-seq) to nuclei or chromatin from at least one cell-type or tissue. 
     
     
         56 . (canceled) 
     
     
         57 . The method of any one of  claims 49  to  55  and  112  to  114  wherein the reference maps comprise data associated with positions of a DNA binding and/or DNA occupying protein for a tissue or cell type. 
     
     
         58 . The method of  claim 57  wherein the DNA binding and/or DNA occupying protein is a transcription factor. 
     
     
         59 . The method of  claim 57  or  claim 58  wherein the positions are determined by applying chromatin immunoprecipitation of a crosslinked DNA-protein complex to at least one cell-type or tissue. 
     
     
         60 . The method of  claim 57  or  claim 58  wherein the positions are determined by treating DNA associated with the tissue or cell type with a nuclease (e.g., DNase-I). 
     
     
         61 . The method of any one of  claims 48  to  55 ,  57  to  60 , and  112  to  114  wherein the reference map comprises a biological feature related to the positions or spacing of nucleosomes, chromatosomes, or other DNA binding or DNA occupying proteins within a tissue or cell type. 
     
     
         62 . The method of  claim 61  wherein the biological feature is quantitative expression of one or more genes; or wherein the biological feature is presence or absence of one or more histone marks; or wherein the biological feature is hypersensitivity to nuclease cleavage. 
     
     
         63 - 64 . (canceled) 
     
     
         65 . The method of any one of  claims 49  to  55 ,  57  to  62  and  112  to  114  wherein the tissue or cell type used to generate a reference map is a primary tissue from a subject having a disease or disorder or condition. 
     
     
         66 . The method of  claim 65  wherein the disease or disorder or condition is selected from the group consisting of: cancer, normal pregnancy, a complication of pregnancy (e.g., aneuploid pregnancy), myocardial infarction, inflammatory bowel disease, systemic autoimmune disease, localized autoimmune disease, allotransplantation with rejection, allotransplantation without rejection, stroke, and localized tissue damage. 
     
     
         67 . The method of any one of  claims 49  to  55 ,  57  to  62 ,  65 , and  112  to  114  wherein the tissue or cell type used to generate a reference map is a primary tissue from a healthy subject; or wherein the tissue or cell type used to generate a reference map is an immortalized cell line; or wherein the tissue or cell type used to generate a reference map is a biopsy from a tumor. 
     
     
         68 - 69 . (canceled) 
     
     
         70 . The method of  claim 54  wherein the sequence data obtained from samples obtained from at least one reference subject comprises positions of cfDNA fragment endpoints. 
     
     
         71 . The method of  claim 70  or  114  wherein at least one of the reference subjects is healthy. 
     
     
         72 . The method of  claim 70  or  114  wherein at least one of the reference subjects has a disease or disorder or condition. 
     
     
         73 . The method of  claim 72  wherein the disease or disorder or condition is selected from the group consisting of: cancer, normal pregnancy, a complication of pregnancy (e.g., aneuploid pregnancy), myocardial infarction, inflammatory bowel disease, systemic autoimmune disease, localized autoimmune disease, allotransplantation with rejection, allotransplantation without rejection, stroke, and localized tissue damage. 
     
     
         74 . The method of any one of  claims 54  to  55 ,  57  to  62 ,  65  to  67 ,  70  to  73 , and  114  wherein the reference map comprises cfDNA fragment endpoint probabilities for at least a portion of the reference genome associated with the tissue or cell type. 
     
     
         75 . The method of  claim 74  wherein the reference map comprises a mathematical transformation of the cfDNA fragment endpoint probabilities. 
     
     
         76 . The method of  claim 74  wherein the cfDNA fragment endpoint probabilities represent a subset of all reference genomic coordinates for the tissue or cell type. 
     
     
         77 . The method of  claim 76  wherein the subset is associated with positions or spacing of nucleosomes and/or chromatosomes; wherein the subset is associated with transcription start sites and/or transcription end sites; or wherein the subset is associated with binding sites of at least one transcription factor; or wherein the subset is associated with nuclease hypersensitive sites. 
     
     
         78 - 80 . (canceled) 
     
     
         81 . The method of  claim 76  or  claim 77  wherein the subset is additionally associated with at least one orthogonal biological feature. 
     
     
         82 . The method of  claim 81  wherein the orthogonal biological feature is associated with high expression genes; or wherein the orthogonal biological feature is associated with low expression genes. 
     
     
         83 . (canceled) 
     
     
         84 . The method of any one of  claims 75  to  77  and  81  to  82  wherein the mathematical transformation includes a Fourier transformation. 
     
     
         85 . The method of any one of  claims 52  to  55 ,  57  to  62 ,  65  to  67 ,  70  to  77 ,  81  to  82 ,  84 , and  112  to  114  wherein at least a subset of the plurality of the cfDNA fragment endpoint scores each has a score above a threshold value. 
     
     
         86 . The method of any one of  claims 48  to  55 ,  57  to  62 ,  65  to  67 ,  70  to  77 ,  81  to  82 ,  84  to  85 , and  112  to  114  wherein the step of determining the tissue(s) and/or cell type(s) giving rise to the cfDNA as a function of a plurality of the genomic locations of at least some of the cfDNA fragment endpoints comprises comparing a Fourier transform of the plurality of the genomic locations of at least some of the cfDNA fragment endpoints, or a mathematical transformation thereof, with a reference map. 
     
     
         87 . The method of any one of  claims 48  to  55 ,  57  to  62 ,  65  to  67 ,  70  to  77 ,  81  to  82 ,  84  to  86 , and  112  to  114  wherein the reference map comprises DNA or chromatin fragmentation data corresponding to at least one tissue that is associated with the disease or disorder or condition. 
     
     
         88 . The method of any one of  claims 48  to  55 ,  57  to  62 ,  65  to  67 ,  70  to  77 ,  81  to  82 ,  84  to  87 , and  112  to  114  wherein the reference genome is associated with a human. 
     
     
         89 . The method of any one of  claims 48  to  55 ,  57  to  62 ,  65  to  67 ,  70  to  77 ,  81  to  82 ,  84  to  88 , and  112  to  114  further comprising generating a report comprising a statement identifying or diagnosing the disease or disorder or condition. 
     
     
         90 . The method of  claim 89  wherein the report further comprises a list of the determined tissue(s) and/or cell type(s) giving rise to the isolated cfDNA. 
     
     
         91 . The method of any one of  claims 1  to  7 ,  9 ,  12  to  22 ,  25  to  27 ,  30 ,  31 ,  33  to  37 ,  41 ,  42 ,  44  to  55 ,  57  to  62 ,  65  to  67 ,  70  to  82 , and  84  to  90  wherein the biological sample comprises, consists essentially of, or consists of whole blood, peripheral blood plasma, urine, or cerebral spinal fluid. 
     
     
         92 . The method for determining tissues and/or cell types giving rise to cell-free DNA (cfDNA) in a subject of  claim 1 , comprising:
 (i) generating a fragment endpoint map by obtaining a biological sample from the subject, isolating the cfDNA from the biological sample, and measuring distributions (a), (b) and/or (c) by library construction and massively parallel sequencing of cfDNA;   (ii) generating a reference set of fragment endpoint maps by obtaining a biological sample from control subjects or subjects with known disease or disorder or condition, isolating the cfDNA from the biological sample, measuring distributions (a), (b) and/or (c) by library construction and massively parallel sequencing of cfDNA; and   (iii) determining the tissues and/or cell types giving rise to the cfDNA by comparing the fragment endpoint map derived from the cfDNA to the reference set of fragment endpoint maps;   
       wherein (a), (b) and (c) are:
 (a) the distribution of likelihoods any specific base-pair in a human genome will appear at a terminus of a cfDNA fragment; 
 (b) the distribution of likelihoods that any pair of base-pairs of a human genome will appear as a pair of termini of a cfDNA fragment; and 
 (c) the distribution of likelihoods that any specific base-pair in a human genome will appear in a cfDNA fragment as a consequence of differential nucleosome occupancy. 
 
     
     
         93 . The method for determining tissues and/or cell types giving rise to cell-free DNA in a subject of  claim 1 , comprising:
 (i) generating a fragment endpoint map by obtaining a biological sample from the subject, isolating the cfDNA from the biological sample, and measuring distributions (a), (b) and/or (c) by library construction and massively parallel sequencing of cfDNA;   (ii) generating a reference set of fragment endpoint maps by obtaining a biological sample from control subjects or subjects with known disease or disorder or condition, isolating chromatin from the biological sample, measuring distributions (a), (b) and/or (c) by library construction and massively parallel sequencing of DNA derived from digestion of chromatin; and   (iii) determining the tissues and/or cell types giving rise to the cfDNA by comparing the nucicosomcfragment endpoint map derived from the cfDNA to the reference set of nucleosome maps;   
       wherein (a), (b) and (c) are:
 (a) the distribution of likelihoods any specific base-pair in a human genome will appear at a terminus of a sequenced fragment; 
 (b) the distribution of likelihoods that any pair of base-pairs of a human genome will appear as a pair of termini of a sequenced fragment; and 
 (c) the distribution of likelihoods that any specific base-pair in a human genome will appear in a sequenced fragment as a consequence of differential nucleosome occupancy. 
 
     
     
         94 . The method for identifying or diagnosing a disease or disorder or condition in a subject of  claim 48 , comprising:
 (i) generating a fragment endpoint map by obtaining a biological sample from the subject, isolating cfDNA from the biological sample, and measuring distributions (a), (b) and/or (c) by library construction and massively parallel sequencing of cfDNA;   (ii) generating a reference set of fragment endpoint maps by obtaining a biological sample from control subjects or subjects with known disease or disorder or condition, isolating the cfDNA from the biological sample, measuring distributions (a), (b) and/or (c) by library construction and massively parallel sequencing of cfDNA; and   (iii) determining the clinical condition by comparing the fragment endpoint map derived from the cfDNA to the reference set of fragment endpoint maps;   
       wherein (a), (b) and (c) are:
 (a) the distribution of likelihoods any specific base-pair in a human genome will appear at a terminus of a cfDNA fragment; 
 (b) the distribution of likelihoods that any pair of base-pairs of a human genome will appear as a pair of termini of a cfDNA fragment; and 
 (c) the distribution of likelihoods that any specific base-pair in a human genome will appear in a cfDNA fragment as a consequence of differential nucleosome occupancy. 
 
     
     
         95 . The method for identifying or diagnosing a disease or disorder or condition in a subject, comprising
 (i) generating a fragment endpoint map by obtaining a biological sample from the subject, isolating cfDNA from the biological sample, and measuring distributions (a), (b) and/or (c) by library construction and massively parallel sequencing of cfDNA;   (ii) generating a reference set of nucleosome maps by obtaining a biological sample from control subjects or subjects with known disease or disorder or condition, isolating chromatin from the biological sample, measuring distributions (a), (b) and/or (c) by library construction and massively parallel sequencing of DNA derived from digestion of chromatin; and   (iii) determining the tissue-of-origin composition of the cfDNA by comparing the fragment endpoint map derived from the cfDNA to the reference set of nucleosome maps;   
       wherein (a), (b) and (c) are:
 (a) the distribution of likelihoods any specific base-pair in a human genome will appear at a terminus of a sequenced fragment; 
 (b) the distribution of likelihoods that any pair of base-pairs of a human genome will appear as a pair of termini of a sequenced fragment; and 
 (c) the distribution of likelihoods that any specific base-pair in a human genome will appear in a sequenced fragment as a consequence of differential nucleosome occupancy. 
 
     
     
         96 . The method of any one of  claims 92 - 95 , wherein the fragment endpoint map of the subject is generated by:
 purifying the cfDNA isolated from the biological sample;   constructing a library by adaptor ligation and optionally PCR amplification; and   sequencing at least a portion of the resulting library.   
     
     
         97 . The method of  claim 92  and  94 , wherein at least one of the reference set of fragment endpoint maps are generated by:
 purifying cfDNA isolated from the biological sample from control subjects; 
 constructing a library by adaptor ligation and optionally PCR amplification; and 
 sequencing at least a portion of the resulting library. 
 
     
     
         98 . The method of any one of  claims 92 - 95 , wherein distribution (a), (b) or (c), or a mathematical transformation of one of these distributions, is subjected to Fourier transformation in contiguous windows, followed by quantitation of intensities for frequency ranges that are associated with nucleosome occupancy, in order to summarize the extent to which nucleosomes exhibit structured positioning within each contiguous window. 
     
     
         99 . The method of any one of  claims 92 - 95 , where distribution (a), (b) or (c), or a mathematical transformation of one of these distributions, is calculated for a subset of the genome. 
     
     
         100 . The method of claim,  99  wherein the subset comprises coordinates, within the reference genome, that are associated with the binding of at least one transcription factor in at least one cell type or tissue, or are associated with DNasel hypersensitive, or are associated with transcription start sites, or are associated with topologically associated domains. 
     
     
         101 . (canceled) 
     
     
         102 . The method of  claim 99 , wherein the subset is defined by tissue-specific data e.g. tissue-specific DNase I hypersensitivity. 
     
     
         103 . The method of any one of  claims 92 - 95 , further comprising step of statistical signal processing for comparing additional nucleosome map(s) to the reference set. 
     
     
         104 . The method of any one of  claims 92 - 95 , in which the comparison in (iii) comprises clustering by principal components analysis (PCA) or by hierarchical clustering. 
     
     
         105 . The method of  claim 94  or  claim 95  wherein the disease or disorder or condition is selected from the group consisting of: cancer, normal pregnancy, a complication of pregnancy (e.g., aneuploidy pregnancy), myocardial infarction, inflammatory bowel disease, systemic autoimmune disease, localized autoimmune disease, allotransplantation with rejection, allotransplantation without rejection, stroke, and localized tissue damage. 
     
     
         106 . The method of  claim 105 , wherein the biological sample comprises, consists essentially of, or consists of whole blood, peripheral blood plasma, urine, or cerebral spinal fluid. 
     
     
         107 . (canceled) 
     
     
         108 . The method of any one of  claims 1  to  7 ,  9 ,  12  to  22 ,  25  to  27 ,  30 ,  31 ,  33  to  37 ,  41 ,  42 ,  44  to  55 ,  57  to  62 ,  65  to  67 ,  70  to  82 ,  84  to  100 ,  102  to  106 , and  112  to  114  further comprising assigning a proportion to each of the one or more tissues or cell types determined to be contributing to cfDNA. 
     
     
         109 . The method of  claim 108  wherein the proportion assigned to each of the one or more determined tissues or cell types is based at least in part on the absolute magnitude of correlation, or on the change in correlation relative to cfDNA from a healthy subject or subjects. 
     
     
         110 . The method of  claim 108  or  claim 109 , wherein the correlation is based at least in part on a comparison of a mathematical transformation of the distribution of cfDNA fragment endpoints from the biological sample with the reference map associated with the determined tissue or cell type. 
     
     
         111 . The method of  claims 108  to  110 , wherein the proportion assigned to each of the one or more determined tissues or cell types is based on a mixture model. 
     
     
         112 . The method of any one of  claims 48  to  52  wherein the step of identifying or diagnosing the disease or disorder or condition comprises comparing the scores to one or more reference map. 
     
     
         113 . The method of any one of  claims 48  to  52  and  112  wherein the step of determining at least some of the tissues and/or cell types giving rise to the observed cfDNA fragments comprises comparing the scores to one or more reference map. 
     
     
         114 . The method of any one of  claims 49  to  53  and  112  to  113  wherein the reference map comprises sequence data obtained from samples obtained from at least one reference subject. 
     
     
         115 . The method of any one of  claims 92 - 95 , where distribution (a), (b), or (c), or a mathematical transformation of one of these distributions, is calculated for a subset of the genome.