Dna methylation diagnostic test for breast cancer

Abstract

The present subject matter provides, inter alia, a method of diagnosing invasive ductal cancer or detecting invasive ductal cancer risk in a subject who has ductal carcinoma in situ, a method of treating breast cancer in a subject detected to have invasive ductal cancer or determined to be at risk of invasive ductal cancer, compositions for detecting invasive presence or potential in ductal carcinoma in situ in a subject, and kits including reagents and composition for detecting invasive presence or potential in ductal carcinoma in situ in a subject.

1 . A method of detecting methylation or unmethylation of a ductal carcinoma in situ (DCIS) cell proliferation deoxyribonucleic acid (DNA) molecule of a human subject, the method comprising:
 (i) contacting an isolated DCIS cancer cell proliferation DNA molecule from a breast tissue sample of said subject with a bisulfate salt thereby forming a reacted DCIS cancer cell proliferation DNA molecule; and   (ii) detecting the presence or absence of uracil in said reacted DCIS cancer cell proliferation DNA molecule at a methylation site, wherein said methylation site is at Chromosome 1 (Chr1) position 4714314, Chromosome 3 (Chr3) position 121903470, Chromosome 4 (Chr4) position 44449864, Chromosome 7 (Chr7) position 157477232, Chromosome 12 (Chr12) position 95941925, Chr12 position 129338355, Chromosome 19 (Chr19) 30017283, or Chromosome 20 (Chr20) position 23016002 with respect to human genome assembly hg19,   thereby detecting methylation or unmethylation of said DCIS cancer cell proliferation DNA molecule of said subject.   
     
     
         2 . (canceled) 
     
     
         3 . The method of  claim 1 , further comprising detecting the presence or absence of uracil in a plurality of reacted DCIS cancer cell proliferation DNA molecules at a plurality of methylation sites selected from Chr1 position 4714314, Chr1 position 11413742, Chr1 position 39957798, Chr1 position 46951513, Chr1 position 47904912, Chr1 position 62660691, Chr1 position 63785800, Chr1 position 67600465, Chr1 position 91183172, Chr1 position 166853786, Chr1 position 179545096, Chr1 position 207669851, Chr1 position 237205704, Chr1 position 237205705, Chr1 position 240161215, Chr1 position 240934954, Chromosome 2 (Chr2) position 20870821, Chr2 position 45156764, Chr2 position 74743346, Chr2 position 80549703, Chr2 position 95989474, Chr2 position 105471544, Chr2 position 115919663, Chr2 position 115920004, Chr2 position 118982006, Chr2 position 177001540, Chr3 position 14852857, Chr3 position 121903470, Chr3 position 170303393, Chr3 position 170303422, Chr3 position 170303423, Chr3 position 170303424, Chr3 position 170303425, Chr 4 position 44449864, Chr4 position 54976099, Chr4 position 56023880, Chromosome 5 (Chr5) positon 71014951, Chr5 position 72677229, Chr5 position 87981177, Chr5 position 140743998, Chr5 position 178421786, Chromosome 6 (Chr6) position 41337153, Chr6 position 85484102, Chr6 position 157557787, Chr6 position 160769248, Chr7 position 1282082, Chr7 position 32467637, Chr7 position 71801896, Chr7 position 71801905, Chr7 position 100946148, Chr7 position 100946151, Chr7 position 121957003, Chr7 position 150038502, Chr7 position 157477232, Chr7 position 157477399, Chr7 position 157477401, Chromosome 8 (Chr8) position 9764011, Chr8 position 11566080, Chr8 position 11566102, Chr8 position 11566125, Chr8 position 56015232, Chr8 position 65281933, Chr8 position 145105472, Chromosome 9 (Chr9) position 126780185, Chr9 position 127239956, Chr9 position 140772369, Chromosome 10 (Chr10) position 8076277, Chr10 position 50818610, Chr10 position 77157527, Chr10 position 123778639, Chr10 position 123778640, Chr10 position 124902829, Chr10 position 124909545, Chr10 position 130085373, Chr10 position 134598235, Chr10 position 134599080, Chromosome 11 (Chr11) position 1215978, Chr11 position 9025912, Chr11 position 15963013, Chr11 position 66187593, Chr11 position 71318977, Chr11 position 101453451, Chr12 position 49726711, Chr12 position 50297756, Chr12 position 50297763, Chr12 position 50297768, Chr12 position 50297774, Chr12 position 50297776, Chr12 position 50444766, Chr12 position 75601447, Chr12 position 95941925, Chr12 position 128750309, Chr 12 position 129338355, Chr12 position 129338471, Chromosome 13 (Chr13) position 28502190, Chr13 position 79181509, Chr13 position 92051154, Chr13 position 95363553, Chr13 position 95363592, Chromosome 14 (Chr14) position 29236052, Chr14 position 29236065, Chr14 position 101543886, Chromosome 15 (Chr15) position 29407958, Chr15 position 45403826, Chr15 position 76630094, Chr15 position 89951787, Chromosome 16 position 1255253, Chromosome 17 (Chr17) position 3211643, Chr17 position 30244229, Chr17 position 35294171, Chr17 position 64831307, Chr17 position 74136562, Chr17 position 74865566, Chromosome 18 (Chr18) position 19745047, Chr18 position 19745054, Chr18 position 19747206, Chr18 position 44774403, Chr18 position 55103840, Chr18 position 55106910, Chr18 position 70534832, Chr18 position 72880039, Chr18 position 77547934, Chr19 position 30016170, Chr19 position 30017283, Chr19 position 30717013, Chr19 position 30719659, Chr20 position 1294019, Chr20 position 3073503, Chr20 position 10198305, Chr20 position 23015989, Chr20 position 23016002, Chr20 position 26189258, Chr20 position 48626669, Chr20 position 53092916, Chr20 position 59827619, Chr20 position 59828325, Chromosome 21 (Chr21) position 9825842, Chr21 position 9826150, Chr21 position 9826934, or Chromosome 22 position 43807517 with respect to human genome assembly hg19. 
     
     
         4 . (canceled) 
     
     
         5 . (canceled) 
     
     
         6 . The method of  claim 3 , wherein said plurality of methylation sites comprises at least about 2, 5, or 10 methylation sites with respect to human genome assembly hg19. 
     
     
         7 . The method of  claim 3 , wherein the uracil level of at least one methylation site of said plurality of methylation sites is above a threshold selected from 76.09 for chr1 position 11413742, 78.57 for chr1 240934954, 74.49 for chr10 position 123778639, 79.31 for chr10 position 123778640, 74.47 for chr11 position 1215978, or 83.33 for chr12 position 128750309 with respect to human genome assembly hg19. 
     
     
         8 . The method of  claim 3 , wherein the uracil level of at least one methylation site of said plurality of methylation sites is below a threshold selected from 74.32 for chr1 position 4714314, 63.81 for chr1 position 39957798, 85.11 for chr1 46951513, 73.08 for chr1 position 47904912, 71.20 for chr1 position 62660691, 46.94 for chr1 position 63785800, 42.86 for chr1 position 67600465, 48.28 for chr1 position 91183172, 64.29 for chr1 position 166853786, 88.89 for chr1 position 179545096, 89.29 for chr1 position 207669851, 82.61 for chr1 position 237205704, 78.57 for chr1 position 237205705, 60.00 for chr1 position 240161215, 75.00 for chr10 position 8076277, 76.30 for chr10 position 50818610, 50.43 for chr10 position 77157527, 67.35 for chr10 position 124902829, 80.00 for chr10 position 124909545, 76.74 for chr10 position 130085373, 34.43 for chr10 position 134598235, 79.31 for chr10 position 134599080, 65.85 for chr11 position 9025912, 51.72 for chr11 position 15963013, 80.95 for chr11 position 66187593, 51.52 for chr11 position 71318977, 57.89 for chr11 position 101453451, 60.00 for chr12 position 49726711, 69.81 for chr12 position 50297756, 82.98 for chr12 position 50297763, 81.13 for chr12 position 50297768, 75.47 for chr12 position 50297774, 77.36 for chr12 position 50297776, 54.17 for chr12 position 50444766, 52.00 for chr12 position 75601447, 36.84 for chr12 position 95941925, 57.14 for chr12 position 129338355, 60.71 for chr12 position 129338471, 65.85 for chr13 position 28502190, 79.84 for chr13 position 79181509, 70.70 for chr13 position 92051154, 73.91 for chr13 position 95363553, 78.95 for chr13 position 95363592, 72.36 for chr14 position 29236052, 62.60 for chr14 position 29236065, 92.45 for chr14 position 101543886, 69.84 for chr15 position 29407958, 73.68 for chr15 position 45403826, 62.30 for chr15 position 76630094, 39.68 for chr15 position 89951787, 71.43 for chr17 position 35294171, 56.52 for chr17 position 64831307, 43.48 for chr17 position 74136562, 62.79 for chr17 position 74865566, 67.01 for chr18 position 19745047, 64.10 for chr18 position 19745054, 80.00 for chr18 position 19747206, 68.29 for chr18 position 44774403, 66.20 for chr18 position 55103840, 50.00 for chr18 position 55106910, 66.67 for chr18 position 70534832, 33.33 for chr18 position 77547934, 38.89 for chr19 position 30016170, 60.00 for chr19 position 30017283, 54.24 for chr19 position 30717013, 66.67 for chr19 position 30719659, 12.20 for chr2 position 20870821, 34.25 for chr2 position 45156764, 34.69 for chr2 position 74743346, 28.21 for chr2 position 80549703, 63.64 for chr2 position 105471544, 64.44 for chr2 position 115919663, 79.31 for chr2 position 115920004, 47.06 for chr2 position 118982006, 63.16 for chr2 position 177001540, 55.43 for chr20 position 1294019, 62.96 for chr20 position 3073503, 62.44 for chr20 position 10198305, 80.70 for chr20 position 23015989, 65.59 for chr20 position 23016002, 55.56 for chr20 position 26189258, 36.00 for chr20 position 48626669, 72.13 for chr20 position 53092916, 58.82 for chr20 position 59827619, 76.47 for chr20 position 59828325, 37.32 for chr21 position 9825842, 50.00 for chr21 position 9826150, 53.36 for chr21 position 9826934, 40.68 for chr22 position 43807517, 57.54 for chr3 position 14852857, 71.96 for chr3 position 121903470, 68.63 for chr3 position 170303393, 67.65 for chr3 position 170303422, 81.82 for chr3 position 170303423, 56.52 for chr3 position 170303424, 69.77 for chr3 position 170303425, 78.38 for chr4 position 44449864, 72.00 for chr4 position 54976099, 55.10 for chr4 position 56023880, 65.00 for chr5 position 71014951, 80.82 for chr5 position 72677229, 55.26 for chr5 position 87981177, 71.83 for chr5 position 140743998, 56.25 for chr5 position 178421786, 57.25 for chr6 position 41337153, 68.18 for chr6 position 85484102, 55.56 for chr6 position 157557787, 75.51 for chr6 position 160769248, 70.45 for chr7 position 1282082, 31.03 for chr7 position 32467637, 63.89 for chr7 position 71801896, 63.89 for chr7 position 71801905, 55.17 for chr7 position 100946148, 43.66 for chr7 position 100946151, 75.00 for chr7 position 121957003, 84.83 for chr7 position 150038502, 26.45 for chr7 position 157477232, 71.43 for chr7 position 157477399, 92.59 for chr7 position 157477401, 70.91 for chr8 position 9764011, 85.51 for chr8 position 11566080, 65.22 for chr8 position 11566102, 65.22 for chr8 position 11566125, 53.85 for chr8 position 56015232, 95.00 for chr8 position 65281933, 44.93 for chr8 position 145105472, 85.19 for chr9 position 126780185, 66.96 for chr9 position 127239956, or 84.62 for chr9 position 140772369 with respect to human genome assembly hg19. 
     
     
         9 . The method of  claim 1 , wherein said DCIS cancer cell proliferation comprises cancer cells isolated from a sample obtained by biopsy, by laser capture microdissection, or by surgical resection of DCIS tissue from said subject. 
     
     
         10 . (canceled) 
     
     
         11 . The method of  claim 1 , wherein said subject has undergone lumpectomy, mastectomy, radiation therapy, and/or administration of an active agent. 
     
     
         12 . The method of  claim 11 , wherein said active agent comprises trastuzumab, trastuzumab emtansine, lapatinib, pertuzumab, bevacizumab, tamoxifen, exemestane, anastrozole, letrozole, doxorubicin, epirubicin, cyclophosphamide, docetaxel, paclitaxel, nab paclitaxel, eribulin, everolimus, palbociclib, capecitabine, ixabepilone, methotrexate, or fluorouracil. 
     
     
         13 . (canceled) 
     
     
         14 . (canceled) 
     
     
         15 . The method of  claim 1 , wherein said subject (a) is a woman; (b) is about 30 to about 75 years old; (c) has at least one mutant breast cancer 1 (BRCA1), breast cancer 2 (BRCA2), Partner and localizer of BRCA2 (PALB2), phosphatase and tensin homolog (PTEN), or p53 allele; (d) has a parent, sibling, or child who has been diagnosed with breast cancer; (e) has had atypical ductal hyperplasia or lobular carcinoma in situ; (f) has had previous radiation treatment to the chest or a breast before the age of 30; (g) has received a combination hormone therapy with estrogen and progestin for at least five years; and/or (h) has or has had breast cancer. 
     
     
         16 . (canceled) 
     
     
         17 . (canceled) 
     
     
         18 . (canceled) 
     
     
         19 . (canceled) 
     
     
         20 . (canceled) 
     
     
         21 . (canceled) 
     
     
         22 . (canceled) 
     
     
         23 . (canceled) 
     
     
         24 . (canceled) 
     
     
         25 . (canceled) 
     
     
         26 . (canceled) 
     
     
         27 . (canceled) 
     
     
         28 . (canceled) 
     
     
         29 . (canceled) 
     
     
         30 . (canceled) 
     
     
         31 . (canceled) 
     
     
         32 . A deoxyribonucleic acid at least 5 to 100 nucleotides in length comprising a uracil-containing sequence that is identical to a sequence of at least a 5 contiguous nucleotides within a sequence chosen from SEQ ID NO:1 to SEQ ID NO:242. 
     
     
         33 . The deoxyribonucleic acid of  claim 32 , comprising a uracil-containing sequence that is identical to a sequence of at least 5-10, 10-20, 20-30, 30-40, 40-50, 50-60, 60-70, 70-80, 80-90, 90-100, 100-110, 110-120, 120-130, 130-140, 140-150, 150-160, 160-170, 170-180, 180-190, or 190-200 contiguous nucleotides within said sequence chosen from SEQ ID NO:1 to SEQ ID NO:242. 
     
     
         34 . The deoxyribonucleic acid of  claim 32 , wherein said sequence comprises a methylation site set forth in Table 1 selected from Chr1 position 4714314, Chr1 position 11413742, Chr1 position 39957798, Chr1 position 46951513, Chr1 position 47904912, Chr1 position 62660691, Chr1 position 63785800, Chr1 position 67600465, Chr1 position 91183172, Chr1 position 166853786, Chr1 position 179545096, Chr1 position 207669851, Chr1 position 237205704, Chr1 position 237205705, Chr1 position 240161215, Chr1 position 240934954, Chromosome 2 (Chr2) position 20870821, Chr2 position 45156764, Chr2 position 74743346, Chr2 position 80549703, Chr2 position 95989474, Chr2 position 105471544, Chr2 position 115919663, Chr2 position 115920004, Chr2 position 118982006, Chr2 position 177001540, Chr3 position 14852857, Chr3 position 121903470, Chr3 position 170303393, Chr3 position 170303422, Chr3 position 170303423, Chr3 position 170303424, Chr3 position 170303425, Chr 4 position 44449864, Chr4 position 54976099, Chr4 position 56023880, Chromosome 5 (Chr5) positon 71014951, Chr5 position 72677229, Chr5 position 87981177, Chr5 position 140743998, Chr5 position 178421786, Chromosome 6 (Chr6) position 41337153, Chr6 position 85484102, Chr6 position 157557787, Chr6 position 160769248, Chr7 position 1282082, Chr7 position 32467637, Chr7 position 71801896, Chr7 position 71801905, Chr7 position 100946148, Chr7 position 100946151, Chr7 position 121957003, Chr7 position 150038502, Chr7 position 157477232, Chr7 position 157477399, Chr7 position 157477401, Chromosome 8 (Chr8) position 9764011, Chr8 position 11566080, Chr8 position 11566102, Chr8 position 11566125, Chr8 position 56015232, Chr8 position 65281933, Chr8 position 145105472, Chromosome 9 (Chr9) position 126780185, Chr9 position 127239956, Chr9 position 140772369, Chromosome 10 (Chr10) position 8076277, Chr10 position 50818610, Chr10 position 77157527, Chr10 position 123778639, Chr10 position 123778640, Chr10 position 124902829, Chr10 position 124909545, Chr10 position 130085373, Chr10 position 134598235, Chr10 position 134599080, Chromosome 11 (Chr11) position 1215978, Chr11 position 9025912, Chr11 position 15963013, Chr11 position 66187593, Chr11 position 71318977, Chr11 position 101453451, Chr12 position 49726711, Chr12 position 50297756, Chr12 position 50297763, Chr12 position 50297768, Chr12 position 50297774, Chr12 position 50297776, Chr12 position 50444766, Chr12 position 75601447, Chr12 position 95941925, Chr12 position 128750309, Chr 12 position 129338355, Chr12 position 129338471, Chromosome 13 (Chr13) position 28502190, Chr13 position 79181509, Chr13 position 92051154, Chr13 position 95363553, Chr13 position 95363592, Chromosome 14 (Chr14) position 29236052, Chr14 position 29236065, Chr14 position 101543886, Chromosome 15 (Chr15) position 29407958, Chr15 position 45403826, Chr15 position 76630094, Chr15 position 89951787, Chromosome 16 position 1255253, Chromosome 17 (Chr17) position 3211643, Chr17 position 30244229, Chr17 position 35294171, Chr17 position 64831307, Chr17 position 74136562, Chr17 position 74865566, Chromosome 18 (Chr18) position 19745047, Chr18 position 19745054, Chr18 position 19747206, Chr18 position 44774403, Chr18 position 55103840, Chr18 position 55106910, Chr18 position 70534832, Chr18 position 72880039, Chr18 position 77547934, Chr19 position 30016170, Chr19 position 30017283, Chr19 position 30717013, Chr19 position 30719659, Chr20 position 1294019, Chr20 position 3073503, Chr20 position 10198305, Chr20 position 23015989, Chr20 position 23016002, Chr20 position 26189258, Chr20 position 48626669, Chr20 position 53092916, Chr20 position 59827619, Chr20 position 59828325, Chromosome 21 (Chr21) position 9825842, Chr21 position 9826150, Chr21 position 9826934, or Chromosome 22 position 43807517 with respect to human genome assembly hg19. 
     
     
         35 . The deoxyribonucleic acid of  claim 34 , wherein a plurality of said methylation sites set forth in Table 1 contain a uracil or a cytosine. 
     
     
         36 . A deoxyribonucleic acid chosen from SEQ ID NO:243 to SEQ ID NO:356, wherein said nucleic acid is hybridized to a complementary DNA sequence comprising uridine or cytosine. 
     
     
         37 . The deoxyribonucleic acid of  claim 36 , further comprising an enzyme in a complex with said hybridized complementary DNA sequence. 
     
     
         38 . The deoxyribonucleic acid of  claim 37 , wherein said enzyme is Taq polymerase. 
     
     
         39 . A kit comprising a plurality of nucleic acids each independently comprising SEQ ID NO: 242 to SEQ ID NO:356, wherein each nucleic acid of said plurality is unique. 
     
     
         40 . The kit according to  claim 39 , further comprising: an enzyme, a reagent for deamination of cytosine, a buffer, a vial, a control DNA, a device for collecting a breast tissue sample, device for purification cancer cells from breast tissues, a reagent for isolating DNA, a reagent for labeling DNA, or any combination thereof. 
     
     
         41 . The kit according to  claim 40 , wherein the enzyme comprises a thermostable DNA polymerase enzyme and/or a restriction enzyme. 
     
     
         42 . A system for detecting methylation or unmethylation of a ductal carcinoma in situ (DCIS) cell mass deoxyribonucleic acid (DNA) molecule of a human subject, the system comprising:
 at least one processor; and   at least one memory including program code which when executed by the at least one processor provides operations comprising:   contacting an isolated DCIS cancer cell proliferation DNA molecule from a breast tissue sample of said subject with a bisulfite salt thereby forming a reacted DCIS cancer cell proliferation DNA molecule;   detecting the presence or absence of uracil in said reacted DCIS cancer cell proliferation DNA molecule at a methylation site set forth in Table 1, wherein said methylation site is at Chromosome 1 (Chr1) position 4714314, Chromosome 3 (Chr3) position 121903470, Chromosome 4 (Chr4) position 44449864, Chromosome 7 (Chr7) position 157477232, Chromosome 12 (Chr12) position 95941925, Chr12 position 129338355, Chromosome 19 (Chr19) 30017283, or Chromosome 20 (Chr20) position 23016002 with respect to human genome assembly hg19, thereby detecting methylation or unmethylation of said DCIS cancer cell proliferation DNA molecule of said subject;   generating a diagnosis for said subject based at least in part on the presence or absence of uracil in said reacted DCIS cancer cell proliferation DNA molecule at the methylation site; and   providing, via a user interface, the diagnosis or prognosis for said subject.   
     
     
         43 . (canceled) 
     
     
         44 . The system of  claim 42 , wherein the system is further configured to detect the presence or absence of uracil in a plurality of reacted DCIS cancer cell proliferation DNA molecules at a plurality of methylation sites selected from Chr1 position 4714314, Chr1 position 11413742, Chr1 position 39957798, Chr1 position 46951513, Chr1 position 47904912, Chr1 position 62660691, Chr1 position 63785800, Chr1 position 67600465, Chr1 position 91183172, Chr1 position 166853786, Chr1 position 179545096, Chr1 position 207669851, Chr1 position 237205704, Chr1 position 237205705, Chr1 position 240161215, Chr1 position 240934954, Chromosome 2 (Chr2) position 20870821, Chr2 position 45156764, Chr2 position 74743346, Chr2 position 80549703, Chr2 position 95989474, Chr2 position 105471544, Chr2 position 115919663, Chr2 position 115920004, Chr2 position 118982006, Chr2 position 177001540, Chr3 position 14852857, Chr3 position 121903470, Chr3 position 170303393, Chr3 position 170303422, Chr3 position 170303423, Chr3 position 170303424, Chr3 position 170303425, Chr 4 position 44449864, Chr4 position 54976099, Chr4 position 56023880, Chromosome 5 (Chr5) positon 71014951, Chr5 position 72677229, Chr5 position 87981177, Chr5 position 140743998, Chr5 position 178421786, Chromosome 6 (Chr6) position 41337153, Chr6 position 85484102, Chr6 position 157557787, Chr6 position 160769248, Chr7 position 1282082, Chr7 position 32467637, Chr7 position 71801896, Chr7 position 71801905, Chr7 position 100946148, Chr7 position 100946151, Chr7 position 121957003, Chr7 position 150038502, Chr7 position 157477232, Chr7 position 157477399, Chr7 position 157477401, Chromosome 8 (Chr8) position 9764011, Chr8 position 11566080, Chr8 position 11566102, Chr8 position 11566125, Chr8 position 56015232, Chr8 position 65281933, Chr8 position 145105472, Chromosome 9 (Chr9) position 126780185, Chr9 position 127239956, Chr9 position 140772369, Chromosome 10 (Chr10) position 8076277, Chr10 position 50818610, Chr10 position 77157527, Chr10 position 123778639, Chr10 position 123778640, Chr10 position 124902829, Chr10 position 124909545, Chr10 position 130085373, Chr10 position 134598235, Chr10 position 134599080, Chromosome 11 (Chr11) position 1215978, Chr11 position 9025912, Chr11 position 15963013, Chr11 position 66187593, Chr11 position 71318977, Chr11 position 101453451, Chr12 position 49726711, Chr12 position 50297756, Chr12 position 50297763, Chr12 position 50297768, Chr12 position 50297774, Chr12 position 50297776, Chr12 position 50444766, Chr12 position 75601447, Chr12 position 95941925, Chr12 position 128750309, Chr 12 position 129338355, Chr12 position 129338471, Chromosome 13 (Chr13) position 28502190, Chr13 position 79181509, Chr13 position 92051154, Chr13 position 95363553, Chr13 position 95363592, Chromosome 14 (Chr14) position 29236052, Chr14 position 29236065, Chr14 position 101543886, Chromosome 15 (Chr15) position 29407958, Chr15 position 45403826, Chr15 position 76630094, Chr15 position 89951787, Chromosome 16 position 1255253, Chromosome 17 (Chr17) position 3211643, Chr17 position 30244229, Chr17 position 35294171, Chr17 position 64831307, Chr17 position 74136562, Chr17 position 74865566, Chromosome 18 (Chr18) position 19745047, Chr18 position 19745054, Chr18 position 19747206, Chr18 position 44774403, Chr18 position 55103840, Chr18 position 55106910, Chr18 position 70534832, Chr18 position 72880039, Chr18 position 77547934, Chr19 position 30016170, Chr19 position 30017283, Chr19 position 30717013, Chr19 position 30719659, Chr20 position 1294019, Chr20 position 3073503, Chr20 position 10198305, Chr20 position 23015989, Chr20 position 23016002, Chr20 position 26189258, Chr20 position 48626669, Chr20 position 53092916, Chr20 position 59827619, Chr20 position 59828325, Chromosome 21 (Chr21) position 9825842, Chr21 position 9826150, Chr21 position 9826934, or Chromosome 22 position 43807517 with respect to human genome assembly hg19. 
     
     
         45 . (canceled) 
     
     
         46 . (canceled) 
     
     
         47 . (canceled) 
     
     
         48 . (canceled) 
     
     
         49 . (canceled) 
     
     
         50 . (canceled) 
     
     
         51 . (canceled) 
     
     
         52 . (canceled) 
     
     
         53 . (canceled) 
     
     
         54 . (canceled) 
     
     
         55 . (canceled) 
     
     
         56 . (canceled) 
     
     
         57 . The method of  claim 3 , further comprising:
 (i) detecting a level of uracil of said plurality of methylation sites that is equal to or greater than the level of methylation sites selected from 76.09 for chr1 position 11413742, 78.57 for chr1 240934954, 74.49 for chr10 position 123778639, 79.31 for chr10 position 123778640, 74.47 for chr11 position 1215978, or 83.33 for chr12 position 128750309 with respect to human genome assembly hg19; and   (ii) administering to said subject a treatment to treat or prevent IDC or directing said subject to obtain treatment to treat or prevent IDC, wherein the treatment comprises (a) lumpectomy, mastectomy, radiation therapy, chemotherapy, or hormone therapy; or (b) administering an active agent comprising trastuzumab, trastuzumab emtansine, lapatinib, pertuzumab, bevacizumab, tamoxifen, exemestane, anastrozole, letrozole, doxorubicin, epirubicin, cyclophosphamide, docetaxel, paclitaxel, nab paclitaxel, eribulin, everolimus, palbociclib, capecitabine, ixabepilone, methotrexate, or fluorouracil.   
     
     
         58 . The method of  claim 3 , further comprising:
 (i) detecting a level of uracil of said plurality of methylation sites that is equal to or less than the level of methylation sites selected from 74.32 for chr1 position 4714314, 63.81 for chr1 position 39957798, 85.11 for chr1 46951513, 73.08 for chr1 position 47904912, 71.20 for chr1 position 62660691, 46.94 for chr1 position 63785800, 42.86 for chr1 position 67600465, 48.28 for chr1 position 91183172, 64.29 for chr1 position 166853786, 88.89 for chr1 position 179545096, 89.29 for chr1 position 207669851, 82.61 for chr1 position 237205704, 78.57 for chr1 position 237205705, 60.00 for chr1 position 240161215, 75.00 for chr10 position 8076277, 76.30 for chr10 position 50818610, 50.43 for chr10 position 77157527, 67.35 for chr10 position 124902829, 80.00 for chr10 position 124909545, 76.74 for chr10 position 130085373, 34.43 for chr10 position 134598235, 79.31 for chr10 position 134599080, 65.85 for chr11 position 9025912, 51.72 for chr11 position 15963013, 80.95 for chr11 position 66187593, 51.52 for chr11 position 71318977, 57.89 for chr11 position 101453451, 60.00 for chr12 position 49726711, 69.81 for chr12 position 50297756, 82.98 for chr12 position 50297763, 81.13 for chr12 position 50297768, 75.47 for chr12 position 50297774, 77.36 for chr12 position 50297776, 54.17 for chr12 position 50444766, 52.00 for chr12 position 75601447, 36.84 for chr12 position 95941925, 57.14 for chr12 position 129338355, 60.71 for chr12 position 129338471, 65.85 for chr13 position 28502190, 79.84 for chr13 position 79181509, 70.70 for chr13 position 92051154, 73.91 for chr13 position 95363553, 78.95 for chr13 position 95363592, 72.36 for chr14 position 29236052, 62.60 for chr14 position 29236065, 92.45 for chr14 position 101543886, 69.84 for chr15 position 29407958, 73.68 for chr15 position 45403826, 62.30 for chr15 position 76630094, 39.68 for chr15 position 89951787, 71.43 for chr17 position 35294171, 56.52 for chr17 position 64831307, 43.48 for chr17 position 74136562, 62.79 for chr17 position 74865566, 67.01 for chr18 position 19745047, 64.10 for chr18 position 19745054, 80.00 for chr18 position 19747206, 68.29 for chr18 position 44774403, 66.20 for chr18 position 55103840, 50.00 for chr18 position 55106910, 66.67 for chr18 position 70534832, 33.33 for chr18 position 77547934, 38.89 for chr19 position 30016170, 60.00 for chr19 position 30017283, 54.24 for chr19 position 30717013, 66.67 for chr19 position 30719659, 12.20 for chr2 position 20870821, 34.25 for chr2 position 45156764, 34.69 for chr2 position 74743346, 28.21 for chr2 position 80549703, 63.64 for chr2 position 105471544, 64.44 for chr2 position 115919663, 79.31 for chr2 position 115920004, 47.06 for chr2 position 118982006, 63.16 for chr2 position 177001540, 55.43 for chr20 position 1294019, 62.96 for chr20 position 3073503, 62.44 for chr20 position 10198305, 80.70 for chr20 position 23015989, 65.59 for chr20 position 23016002, 55.56 for chr20 position 26189258, 36.00 for chr20 position 48626669, 72.13 for chr20 position 53092916, 58.82 for chr20 position 59827619, 76.47 for chr20 position 59828325, 37.32 for chr21 position 9825842, 50.00 for chr21 position 9826150, 53.36 for chr21 position 9826934, 40.68 for chr22 position 43807517, 57.54 for chr3 position 14852857, 71.96 for chr3 position 121903470, 68.63 for chr3 position 170303393, 67.65 for chr3 position 170303422, 81.82 for chr3 position 170303423, 56.52 for chr3 position 170303424, 69.77 for chr3 position 170303425, 78.38 for chr4 position 44449864, 72.00 for chr4 position 54976099, 55.10 for chr4 position 56023880, 65.00 for chr5 position 71014951, 80.82 for chr5 position 72677229, 55.26 for chr5 position 87981177, 71.83 for chr5 position 140743998, 56.25 for chr5 position 178421786, 57.25 for chr6 position 41337153, 68.18 for chr6 position 85484102, 55.56 for chr6 position 157557787, 75.51 for chr6 position 160769248, 70.45 for chr7 position 1282082, 31.03 for chr7 position 32467637, 63.89 for chr7 position 71801896, 63.89 for chr7 position 71801905, 55.17 for chr7 position 100946148, 43.66 for chr7 position 100946151, 75.00 for chr7 position 121957003, 84.83 for chr7 position 150038502, 26.45 for chr7 position 157477232, 71.43 for chr7 position 157477399, 92.59 for chr7 position 157477401, 70.91 for chr8 position 9764011, 85.51 for chr8 position 11566080, 65.22 for chr8 position 11566102, 65.22 for chr8 position 11566125, 53.85 for chr8 position 56015232, 95.00 for chr8 position 65281933, 44.93 for chr8 position 145105472, 85.19 for chr9 position 126780185, 66.96 for chr9 position 127239956, or 84.62 for chr9 position 140772369 with respect to human genome assembly hg19; and   (ii) administering to said subject a treatment to treat or prevent DC or directing said subject to obtain treatment to treat or prevent DC, wherein the treatment comprises (a) lumpectomy, mastectomy, radiation therapy, chemotherapy, or hormone therapy; or (b) administering an active agent comprising trastuzumab, trastuzumab emtansine, lapatinib, pertuzumab, bevacizumab, tamoxifen, exemestane, anastrozole, letrozole, doxorubicin, epirubicin, cyclophosphamide, docetaxel, paclitaxel, nab paclitaxel, eribulin, everolimus, palbociclib, capecitabine, ixabepilone, methotrexate, or fluorouracil.