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Volumn 112, Issue 40, 2015, Pages E5503-E5512

Plasma DNA tissue mapping by genome-wide methylation sequencing for noninvasive prenatal, cancer, and transplantation assessments

Author keywords

Circulating tumor DNA; Epigenetics; Liquid biopsy; Noninvasive prenatal testing; Transplantation monitoring

Indexed keywords

ARTICLE; B LYMPHOCYTE; BONE MARROW TRANSPLANTATION; CANCER GENETICS; CANCER PATIENT; CONTROLLED STUDY; COPY NUMBER VARIATION; DNA METHYLATION; DNA SEQUENCE; FEMALE; FOLLICULAR LYMPHOMA; GENE MAPPING; GENETIC MARKER; GRAFT RECIPIENT; HUMAN; HUMAN TISSUE; LEUKOCYTE; LIVER CELL CARCINOMA; LIVER TRANSPLANTATION; NON INVASIVE PROCEDURE; PLACENTA; PLASMA; PREGNANT WOMAN; PRIORITY JOURNAL; ADULT; ALGORITHM; BLOOD; CHEMISTRY; FETUS; GENETICS; LIVER; LIVER TUMOR; METABOLISM; MIDDLE AGED; NEUTROPHIL; PATHOLOGY; PREGNANCY; PROCEDURES; T LYMPHOCYTE; TISSUE TRANSPLANTATION;

EID: 84943375035     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1508736112     Document Type: Article
Times cited : (548)

References (48)
  • 1
    • 0342618532 scopus 로고    scopus 로고
    • Presence of fetal DNA in maternal plasma and serum
    • Lo YMD, et al (1997) Presence of fetal DNA in maternal plasma and serum. Lancet 350 (9076):485-487.
    • (1997) Lancet , vol.350 , Issue.9076 , pp. 485-487
    • Lo, Y.M.D.1
  • 2
    • 58149490683 scopus 로고    scopus 로고
    • Noninvasive prenatal diagnosis of fetal chromosomal aneuploidy by massively parallel genomic sequencing of DNA in maternal plasma
    • Chiu RWK, et al (2008) Noninvasive prenatal diagnosis of fetal chromosomal aneuploidy by massively parallel genomic sequencing of DNA in maternal plasma. Proc Natl Acad Sci USA 105(51):20458-20463.
    • (2008) Proc Natl Acad Sci USA , vol.105 , Issue.51 , pp. 20458-20463
    • Chiu, R.W.K.1
  • 3
    • 84902304410 scopus 로고    scopus 로고
    • Noninvasive prenatal diagnosis of congenital adrenal hyperplasia using cell-free fetal DNA in maternal plasma
    • New MI, et al (2014) Noninvasive prenatal diagnosis of congenital adrenal hyperplasia using cell-free fetal DNA in maternal plasma. J Clin Endocrinol Metab 99(6):E1022-E1030.
    • (2014) J Clin Endocrinol Metab , vol.99 , Issue.6 , pp. E1022-E1030
    • New, M.I.1
  • 4
    • 84896691791 scopus 로고    scopus 로고
    • DNA sequencing versus standard prenatal aneuploidy screening
    • Bianchi DW, et al; CARE Study Group (2014) DNA sequencing versus standard prenatal aneuploidy screening. N Engl J Med 370(9):799-808.
    • (2014) N Engl J Med , vol.370 , Issue.9 , pp. 799-808
    • Bianchi, D.W.1
  • 5
    • 78751683468 scopus 로고    scopus 로고
    • Non-invasive prenatal assessment of trisomy 21 by multiplexed maternal plasma DNA sequencing: Large scale validity study
    • Chiu RWK, et al (2011) Non-invasive prenatal assessment of trisomy 21 by multiplexed maternal plasma DNA sequencing: Large scale validity study. BMJ 342:c7401.
    • (2011) BMJ , vol.342
    • Chiu, R.W.K.1
  • 6
    • 84898825445 scopus 로고    scopus 로고
    • Integration of noninvasive prenatal prediction of fetal blood group into clinical prenatal care
    • Clausen FB (2014) Integration of noninvasive prenatal prediction of fetal blood group into clinical prenatal care. Prenat Diagn 34(5):409-415.
    • (2014) Prenat Diagn , vol.34 , Issue.5 , pp. 409-415
    • Clausen, F.B.1
  • 7
    • 84944161591 scopus 로고    scopus 로고
    • Noninvasive prenatal testing using a novel analysis pipeline to screen for all autosomal fetal aneuploidies improves pregnancy management
    • Bayindir B, et al (2015) Noninvasive prenatal testing using a novel analysis pipeline to screen for all autosomal fetal aneuploidies improves pregnancy management. Eur J Hum Genet, 10.1038/ejhg.2014.282.
    • (2015) Eur J Hum Genet
    • Bayindir, B.1
  • 8
    • 0033559576 scopus 로고    scopus 로고
    • Quantitative analysis of cell-free Epstein-Barr virus DNA in plasma of patients with nasopharyngeal carcinoma
    • Lo YMD, et al (1999) Quantitative analysis of cell-free Epstein-Barr virus DNA in plasma of patients with nasopharyngeal carcinoma. Cancer Res 59(6):1188-1191.
    • (1999) Cancer Res , vol.59 , Issue.6 , pp. 1188-1191
    • Lo, Y.M.D.1
  • 9
    • 63449103435 scopus 로고    scopus 로고
    • Single-molecule detection of epidermal growth factor receptor mutations in plasma by microfluidics digital PCR in non-small cell lung cancer patients
    • Yung TKF, et al (2009) Single-molecule detection of epidermal growth factor receptor mutations in plasma by microfluidics digital PCR in non-small cell lung cancer patients. Clin Cancer Res 15(6):2076-2084.
    • (2009) Clin Cancer Res , vol.15 , Issue.6 , pp. 2076-2084
    • Yung, T.K.F.1
  • 10
    • 84870312106 scopus 로고    scopus 로고
    • Detection of chromosomal alterations in the circulation of cancer patients with whole-genome sequencing
    • Leary RJ, et al (2012) Detection of chromosomal alterations in the circulation of cancer patients with whole-genome sequencing. Sci Transl Med 4(162):162ra154.
    • (2012) Sci Transl Med , vol.4 , Issue.162
    • Leary, R.J.1
  • 11
    • 84872020299 scopus 로고    scopus 로고
    • Cancer genome scanning in plasma: Detection of tumorassociated copy number aberrations, single-nucleotide variants, and tumoral heterogeneity by massively parallel sequencing
    • Chan KCA, et al (2013) Cancer genome scanning in plasma: Detection of tumorassociated copy number aberrations, single-nucleotide variants, and tumoral heterogeneity by massively parallel sequencing. Clin Chem 59(1):211-224.
    • (2013) Clin Chem , vol.59 , Issue.1 , pp. 211-224
    • Chan, K.C.A.1
  • 12
    • 84877579861 scopus 로고    scopus 로고
    • Non-invasive analysis of acquired resistance to cancer therapy by sequencing of plasma DNA
    • Murtaza M, et al (2013) Non-invasive analysis of acquired resistance to cancer therapy by sequencing of plasma DNA. Nature 497 (7447):108-112.
    • (2013) Nature , vol.497 , Issue.7447 , pp. 108-112
    • Murtaza, M.1
  • 13
    • 0032474260 scopus 로고    scopus 로고
    • Presence of donor-specific DNA in plasma of kidney and livertransplant recipients
    • Lo YMD, et al (1998) Presence of donor-specific DNA in plasma of kidney and livertransplant recipients. Lancet 351 (9112):1329-1330.
    • (1998) Lancet , vol.351 , Issue.9112 , pp. 1329-1330
    • Lo, Y.M.D.1
  • 14
    • 79955037043 scopus 로고    scopus 로고
    • Universal noninvasive detection of solid organ transplant rejection
    • Snyder TM, Khush KK, Valantine H.A., Quake S.R. (2011) Universal noninvasive detection of solid organ transplant rejection. Proc Natl Acad Sci USA 108(15):6229-6234.
    • (2011) Proc Natl Acad Sci USA , vol.108 , Issue.15 , pp. 6229-6234
    • Snyder, T.M.1    Khush, K.K.2    Valantine, H.A.3    Quake, S.R.4
  • 15
    • 1942501800 scopus 로고    scopus 로고
    • Detection of cell free placental DNA in maternal plasma: Direct evidence from three cases of confined placental mosaicism
    • Masuzaki H, et al (2004) Detection of cell free placental DNA in maternal plasma: Direct evidence from three cases of confined placental mosaicism. J Med Genet 41(4):289-292.
    • (2004) J Med Genet , vol.41 , Issue.4 , pp. 289-292
    • Masuzaki, H.1
  • 16
    • 84904035928 scopus 로고    scopus 로고
    • A pregnancy with discordant fetal and placental chromosome 18 aneuploidies revealed by invasive and noninvasive prenatal diagnosis
    • Chen C, et al (2014) A pregnancy with discordant fetal and placental chromosome 18 aneuploidies revealed by invasive and noninvasive prenatal diagnosis. Reprod Biomed Online 29(1):136-139.
    • (2014) Reprod Biomed Online , vol.29 , Issue.1 , pp. 136-139
    • Chen, C.1
  • 17
    • 84896371874 scopus 로고    scopus 로고
    • Detection of circulating tumor DNA in early- and latestage human Malignancies
    • Bettegowda C, et al (2014) Detection of circulating tumor DNA in early- and latestage human malignancies. Sci Transl Med 6(224):224ra24.
    • (2014) Sci Transl Med , vol.6 , Issue.224
    • Bettegowda, C.1
  • 18
    • 0036177799 scopus 로고    scopus 로고
    • Predominant hematopoietic origin of cell-free DNA in plasma and serum after sex-mismatched bone marrow transplantation
    • Lui YYN, et al (2002) Predominant hematopoietic origin of cell-free DNA in plasma and serum after sex-mismatched bone marrow transplantation. Clin Chem 48(3):421-427.
    • (2002) Clin Chem , vol.48 , Issue.3 , pp. 421-427
    • Lui, Y.Y.N.1
  • 19
    • 84863230684 scopus 로고    scopus 로고
    • Nonhematopoietically derived DNA is shorter than hematopoietically derived DNA in plasma: A transplantation model
    • Zheng YW, et al (2012) Nonhematopoietically derived DNA is shorter than hematopoietically derived DNA in plasma: A transplantation model. Clin Chem 58(3):549-558.
    • (2012) Clin Chem , vol.58 , Issue.3 , pp. 549-558
    • Zheng, Y.W.1
  • 20
    • 84856555311 scopus 로고    scopus 로고
    • A DNA methylation fingerprint of 1628 human samples
    • Fernandez AF, et al (2012) A DNA methylation fingerprint of 1628 human samples. Genome Res 22(2):407-419.
    • (2012) Genome Res , vol.22 , Issue.2 , pp. 407-419
    • Fernandez, A.F.1
  • 21
    • 84923362619 scopus 로고    scopus 로고
    • Integrative analysis of 111 reference human epigenomes
    • Kundaje A, et al; Roadmap Epigenomics Consortium (2015) Integrative analysis of 111 reference human epigenomes. Nature 518 (7539):317-330.
    • (2015) Nature , vol.518 , Issue.7539 , pp. 317-330
    • Kundaje, A.1
  • 22
    • 84860637797 scopus 로고    scopus 로고
    • DNA methylation arrays as surrogate measures of cell mixture distribution
    • Houseman EA, et al (2012) DNA methylation arrays as surrogate measures of cell mixture distribution. BMC Bioinformatics 13:86.
    • (2012) BMC Bioinformatics , vol.13 , pp. 86
    • Houseman, E.A.1
  • 23
    • 26844478953 scopus 로고    scopus 로고
    • Detection of the placental epigenetic signature of the maspin gene in maternal plasma
    • Chim SSC, et al (2005) Detection of the placental epigenetic signature of the maspin gene in maternal plasma. Proc Natl Acad Sci USA 102(41):14753-14758.
    • (2005) Proc Natl Acad Sci USA , vol.102 , Issue.41 , pp. 14753-14758
    • Chim, S.S.C.1
  • 24
    • 84887080693 scopus 로고    scopus 로고
    • Noninvasive prenatal methylomic analysis by genomewide bisulfite sequencing of maternal plasma DNA
    • Lun FMF, et al (2013) Noninvasive prenatal methylomic analysis by genomewide bisulfite sequencing of maternal plasma DNA. Clin Chem 59(11):1583-1594.
    • (2013) Clin Chem , vol.59 , Issue.11 , pp. 1583-1594
    • Lun, F.M.F.1
  • 25
    • 84908086526 scopus 로고    scopus 로고
    • Epigenome-wide DNA methylation assay reveals placental epigenetic markers for noninvasive fetal single-nucleotide polymorphism genotyping in maternal plasma
    • Ou X, et al (2014) Epigenome-wide DNA methylation assay reveals placental epigenetic markers for noninvasive fetal single-nucleotide polymorphism genotyping in maternal plasma. Transfusion 54(10):2523-2533.
    • (2014) Transfusion , vol.54 , Issue.10 , pp. 2523-2533
    • Ou, X.1
  • 26
    • 84935828551 scopus 로고    scopus 로고
    • Whole genome bisulfite sequencing of cell-free DNA and its cellular contributors uncovers placenta hypomethylated domains
    • Jensen TJ, et al (2015) Whole genome bisulfite sequencing of cell-free DNA and its cellular contributors uncovers placenta hypomethylated domains. Genome Biol 16(1):78.
    • (2015) Genome Biol , vol.16 , Issue.1 , pp. 78
    • Jensen, T.J.1
  • 27
    • 0032893755 scopus 로고    scopus 로고
    • Detection of aberrant p16 methylation in the plasma and serum of liver cancer patients
    • Wong IH, et al (1999) Detection of aberrant p16 methylation in the plasma and serum of liver cancer patients. Cancer Res 59(1):71-73.
    • (1999) Cancer Res , vol.59 , Issue.1 , pp. 71-73
    • Wong, I.H.1
  • 28
    • 84888119068 scopus 로고    scopus 로고
    • Noninvasive detection of cancer-associated genome-wide hypomethylation and copy number aberrations by plasma DNA bisulfite sequencing
    • Chan KCA, et al (2013) Noninvasive detection of cancer-associated genome-wide hypomethylation and copy number aberrations by plasma DNA bisulfite sequencing. Proc Natl Acad Sci USA 110(47):18761-18768.
    • (2013) Proc Natl Acad Sci USA , vol.110 , Issue.47 , pp. 18761-18768
    • Chan, K.C.A.1
  • 29
    • 80052918929 scopus 로고    scopus 로고
    • Directional DNA methylation changes and complex intermediate states accompany lineage specificity in the adult hematopoietic compartment
    • Hodges E, et al (2011) Directional DNA methylation changes and complex intermediate states accompany lineage specificity in the adult hematopoietic compartment. Mol Cell 44(1):17-28.
    • (2011) Mol Cell , vol.44 , Issue.1 , pp. 17-28
    • Hodges, E.1
  • 30
    • 78650207098 scopus 로고    scopus 로고
    • Maternal plasma DNA sequencing reveals the genome-wide genetic and mutational profile of the fetus
    • Lo YMD, et al (2010) Maternal plasma DNA sequencing reveals the genome-wide genetic and mutational profile of the fetus. Sci Transl Med 2(61):61ra91.
    • (2010) Sci Transl Med , vol.2 , Issue.61
    • Lo, Y.M.D.1
  • 31
    • 84926492837 scopus 로고    scopus 로고
    • Cell-free DNA analysis for noninvasive examination of trisomy
    • Norton ME, et al (2015) Cell-free DNA analysis for noninvasive examination of trisomy. N Engl J Med 372(17):1589-1597.
    • (2015) N Engl J Med , vol.372 , Issue.17 , pp. 1589-1597
    • Norton, M.E.1
  • 32
    • 84877806778 scopus 로고    scopus 로고
    • Establishment of tumor-specific copy number alterations from plasma DNA of patients with cancer
    • Heitzer E, et al (2013) Establishment of tumor-specific copy number alterations from plasma DNA of patients with cancer. Int J Cancer 133(2):346-356.
    • (2013) Int J Cancer , vol.133 , Issue.2 , pp. 346-356
    • Heitzer, E.1
  • 33
    • 84876269433 scopus 로고    scopus 로고
    • Noninvasive prenatal molecular karyotyping from maternal plasma
    • Yu SCY, et al (2013) Noninvasive prenatal molecular karyotyping from maternal plasma. PLoS One 8(4):e60968.
    • (2013) PLoS One , vol.8 , Issue.4
    • Yu, S.C.Y.1
  • 34
    • 84903776814 scopus 로고    scopus 로고
    • Circulating cell-free DNA enables noninvasive diagnosis of heart transplant rejection
    • De Vlaminck I., et al (2014) Circulating cell-free DNA enables noninvasive diagnosis of heart transplant rejection. Sci Transl Med 6(241):241ra77.
    • (2014) Sci Transl Med , vol.6 , Issue.241
    • De Vlaminck, I.1
  • 35
    • 84937459187 scopus 로고    scopus 로고
    • Noninvasive prenatal testing and incidental detection of occult maternal Malignancies
    • Bianchi DW, et al (2015) Noninvasive prenatal testing and incidental detection of occult maternal malignancies. JAMA 314(2):162-169.
    • (2015) JAMA , vol.314 , Issue.2 , pp. 162-169
    • Bianchi, D.W.1
  • 36
    • 84943394447 scopus 로고    scopus 로고
    • Presymptomatic identification of cancers in pregnant women during noninvasive prenatal testing
    • Amant F, et al (2015) Presymptomatic identification of cancers in pregnant women during noninvasive prenatal testing. JAMA Oncol, 10.1001/jamaoncol.2015.1883.
    • (2015) JAMA Oncol
    • Amant, F.1
  • 37
    • 84888118119 scopus 로고    scopus 로고
    • Detection and mapping of 5-methylcytosine and 5-hydroxymethylcytosine with nanopore MspA
    • Laszlo AH, et al (2013) Detection and mapping of 5-methylcytosine and 5-hydroxymethylcytosine with nanopore MspA. Proc Natl Acad Sci USA 110(47):18904-18909.
    • (2013) Proc Natl Acad Sci USA , vol.110 , Issue.47 , pp. 18904-18909
    • Laszlo, A.H.1
  • 38
    • 84942927070 scopus 로고    scopus 로고
    • Noninvasive prenatal testing by nanopore sequencing of maternal plasma DNA: Feasibility assessment
    • Cheng SH, et al (2015) Noninvasive prenatal testing by nanopore sequencing of maternal plasma DNA: Feasibility assessment. Clin Chem 61(1):172-181.
    • (2015) Clin Chem , vol.61 , Issue.1 , pp. 172-181
    • Cheng, S.H.1
  • 39
    • 0037447089 scopus 로고    scopus 로고
    • mRNA of placental origin is readily detectable in maternal plasma
    • Ng EKO, et al (2003) mRNA of placental origin is readily detectable in maternal plasma. Proc Natl Acad Sci USA 100(8):4748-4753.
    • (2003) Proc Natl Acad Sci USA , vol.100 , Issue.8 , pp. 4748-4753
    • Ng, E.K.O.1
  • 40
    • 84903731165 scopus 로고    scopus 로고
    • Maternal plasma RNA sequencing for genome-wide transcriptomic profiling and identification of pregnancy-associated transcripts
    • Tsui NBY, et al (2014) Maternal plasma RNA sequencing for genome-wide transcriptomic profiling and identification of pregnancy-associated transcripts. Clin Chem 60(7):954-962.
    • (2014) Clin Chem , vol.60 , Issue.7 , pp. 954-962
    • Tsui, N.B.Y.1
  • 41
    • 84901049709 scopus 로고    scopus 로고
    • Noninvasive in vivo monitoring of tissue-specific global gene expression in humans
    • Koh W, et al (2014) Noninvasive in vivo monitoring of tissue-specific global gene expression in humans. Proc Natl Acad Sci USA 111(20):7361-7366.
    • (2014) Proc Natl Acad Sci USA , vol.111 , Issue.20 , pp. 7361-7366
    • Koh, W.1
  • 42
    • 40449127919 scopus 로고    scopus 로고
    • Detection and characterization of placental microRNAs in maternal plasma
    • Chim SSC, et al (2008) Detection and characterization of placental microRNAs in maternal plasma. Clin Chem 54(3):482-490.
    • (2008) Clin Chem , vol.54 , Issue.3 , pp. 482-490
    • Chim, S.S.C.1
  • 43
    • 63149121152 scopus 로고    scopus 로고
    • Circulating microRNAs, potential biomarkers for drug-induced liver injury
    • Wang K, et al (2009) Circulating microRNAs, potential biomarkers for drug-induced liver injury. Proc Natl Acad Sci USA 106(11):4402-4407.
    • (2009) Proc Natl Acad Sci USA , vol.106 , Issue.11 , pp. 4402-4407
    • Wang, K.1
  • 44
    • 84903304809 scopus 로고    scopus 로고
    • Methy-pipe: An integrated bioinformatics pipeline for whole genome bisulfite sequencing data analysis
    • Jiang P, et al (2014) Methy-Pipe: An integrated bioinformatics pipeline for whole genome bisulfite sequencing data analysis. PLoS One 9(6):e100360.
    • (2014) PLoS One , vol.9 , Issue.6
    • Jiang, P.1
  • 45
    • 0036079158 scopus 로고    scopus 로고
    • The human genome browser at UCSC
    • Kent WJ, et al (2002) The human genome browser at UCSC. Genome Res 12(6):996-1006.
    • (2002) Genome Res , vol.12 , Issue.6 , pp. 996-1006
    • Kent, W.J.1
  • 46
    • 59149084538 scopus 로고    scopus 로고
    • The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores
    • Irizarry RA, et al (2009) The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores. Nat Genet 41(2):178-186.
    • (2009) Nat Genet , vol.41 , Issue.2 , pp. 178-186
    • Irizarry, R.A.1
  • 48
    • 79959937504 scopus 로고    scopus 로고
    • Noninvasive prenatal diagnosis of fetal trisomy 18 and trisomy 13 by maternal plasma DNA sequencing
    • Chen EZ, et al (2011) Noninvasive prenatal diagnosis of fetal trisomy 18 and trisomy 13 by maternal plasma DNA sequencing. PLoS One 6(7):e21791.
    • (2011) PLoS One , vol.6 , Issue.7
    • Chen, E.Z.1


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