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

Significance Plasma consists of DNA released from multiple tissues within the body. Using genome-wide bisulfite sequencing of plasma DNA, we obtained a bird’s eye view of the identities and contributions of these tissues to the circulating DNA pool. The tissue contributors and their relative proportions are identified by a bioinformatics deconvolution process that draws reference from DNA methylation signatures representative of each tissue type. We validated this approach in pregnant women, cancer patients, and transplant recipients. This method also allows one to identify the tissue of origin of genomic aberrations observed in plasma DNA. This approach has numerous research and diagnostic applications in prenatal testing, oncology, transplantation monitoring, and other fields. Plasma consists of DNA released from multiple tissues within the body. Using genome-wide bisulfite sequencing of plasma DNA and deconvolution of the sequencing data with reference to methylation profiles of different tissues, we developed a general approach for studying the major tissue contributors to the circulating DNA pool. We tested this method in pregnant women, patients with hepatocellular carcinoma, and subjects following bone marrow and liver transplantation. In most subjects, white blood cells were the predominant contributors to the circulating DNA pool. The placental contributions in the plasma of pregnant women correlated with the proportional contributions as revealed by fetal-specific genetic markers. The graft-derived contributions to the plasma in the transplant recipients correlated with those determined using donor-specific genetic markers. Patients with hepatocellular carcinoma showed elevated plasma DNA contributions from the liver, which correlated with measurements made using tumor-associated copy number aberrations. In hepatocellular carcinoma patients and in pregnant women exhibiting copy number aberrations in plasma, comparison of methylation deconvolution results using genomic regions with different copy number status pinpointed the tissue type responsible for the aberrations. In a pregnant woman diagnosed as having follicular lymphoma during pregnancy, methylation deconvolution indicated a grossly elevated contribution from B cells into the plasma DNA pool and localized B cells as the origin of the copy number aberrations observed in plasma. This method may serve as a powerful tool for assessing a wide range of physiological and pathological conditions based on the identification of perturbed proportional contributions of different tissues into plasma.

[1]  J. Garber,et al.  Noninvasive Prenatal Testing and Incidental Detection of Occult Maternal Malignancies. , 2015, JAMA.

[2]  K. Sun,et al.  Noninvasive prenatal testing by nanopore sequencing of maternal plasma DNA: feasibility assessment. , 2015, Clinical chemistry.

[3]  P. Neven,et al.  Presymptomatic Identification of Cancers in Pregnant Women During Noninvasive Prenatal Testing. , 2015, JAMA oncology.

[4]  T. Musci,et al.  Cell-free DNA analysis for noninvasive examination of trisomy. , 2015, The New England journal of medicine.

[5]  Zhanyang Zhu,et al.  Whole genome bisulfite sequencing of cell-free DNA and its cellular contributors uncovers placenta hypomethylated domains , 2014, Genome Biology.

[6]  Michael Q. Zhang,et al.  Integrative analysis of 111 reference human epigenomes , 2015, Nature.

[7]  H. Peeters,et al.  Noninvasive prenatal testing using a novel analysis pipeline to screen for all autosomal fetal aneuploidies improves pregnancy management , 2015, European Journal of Human Genetics.

[8]  D. Liang,et al.  Noninvasive prenatal testing for Wilson disease by use of circulating single-molecule amplification and resequencing technology (cSMART). , 2015, Clinical chemistry.

[9]  Diana Miglioretti,et al.  Cell-free DNA Analysis for Noninvasive Examination of Trisomy. , 2015, The New England journal of medicine.

[10]  D. Cram,et al.  A pregnancy with discordant fetal and placental chromosome 18 aneuploidies revealed by invasive and noninvasive prenatal diagnosis. , 2014, Reproductive biomedicine online.

[11]  P. Jiang,et al.  Maternal plasma RNA sequencing for genome-wide transcriptomic profiling and identification of pregnancy-associated transcripts. , 2014, Clinical chemistry.

[12]  K. Sun,et al.  Methy-Pipe: An Integrated Bioinformatics Pipeline for Whole Genome Bisulfite Sequencing Data Analysis , 2014, PloS one.

[13]  Daniel Bernstein,et al.  Circulating Cell-Free DNA Enables Noninvasive Diagnosis of Heart Transplant Rejection , 2014, Science Translational Medicine.

[14]  W. Koh,et al.  Noninvasive in vivo monitoring of tissue-specific global gene expression in humans , 2014, Proceedings of the National Academy of Sciences.

[15]  F. B. Clausen.  Integration of noninvasive prenatal prediction of fetal blood group into clinical prenatal care. , 2014, Prenatal diagnosis.

[16]  Huan Wang,et al.  Epigenome‐wide DNA methylation assay reveals placental epigenetic markers for noninvasive fetal single‐nucleotide polymorphism genotyping in maternal plasma , 2014, Transfusion.

[17]  T. Jensen,et al.  Whole genome bisulfite sequencing of cell-free DNA and its cellular contributors uncovers placenta hypomethylated domains , 2014, Genome Biology.

[18]  Peiyong Jiang,et al.  Noninvasive prenatal diagnosis of congenital adrenal hyperplasia using cell-free fetal DNA in maternal plasma. , 2014, The Journal of clinical endocrinology and metabolism.

[19]  M. Choti,et al.  Detection of Circulating Tumor DNA in Early- and Late-Stage Human Malignancies , 2014, Science Translational Medicine.

[20]  M. Rochon.  DNA Sequencing Versus Standard Prenatal Aneuploidy Screening , 2014 .

[21]  Kang Zhang,et al.  DNA sequencing versus standard prenatal aneuploidy screening. , 2014, The New England journal of medicine.

[22]  Peiyong Jiang,et al.  Noninvasive detection of cancer-associated genome-wide hypomethylation and copy number aberrations by plasma DNA bisulfite sequencing , 2013, Proceedings of the National Academy of Sciences.

[23]  Peiyong Jiang,et al.  Noninvasive prenatal methylomic analysis by genomewide bisulfite sequencing of maternal plasma DNA. , 2013, Clinical chemistry.

[24]  I. Derrington,et al.  Detection and mapping of 5-methylcytosine and 5-hydroxymethylcytosine with nanopore MspA , 2013, Proceedings of the National Academy of Sciences.

[25]  N. Rosenfeld,et al.  Non-invasive analysis of acquired resistance to cancer therapy by sequencing of plasma DNA , 2013, Nature.

[26]  K. Choy,et al.  Noninvasive Prenatal Molecular Karyotyping from Maternal Plasma , 2013, PloS one.

[27]  M. Speicher,et al.  Establishment of tumor-specific copy number alterations from plasma DNA of patients with cancer , 2013, International journal of cancer.

[28]  Peiyong Jiang,et al.  Cancer genome scanning in plasma: detection of tumor-associated copy number aberrations, single-nucleotide variants, and tumoral heterogeneity by massively parallel sequencing. , 2013, Clinical chemistry.

[29]  G. Parmigiani,et al.  Detection of Chromosomal Alterations in the Circulation of Cancer Patients with Whole-Genome Sequencing , 2012, Science Translational Medicine.

[30]  Devin C. Koestler,et al.  DNA methylation arrays as surrogate measures of cell mixture distribution , 2012, BMC Bioinformatics.

[31]  Yama W. L. Zheng,et al.  Nonhematopoietically derived DNA is shorter than hematopoietically derived DNA in plasma: a transplantation model. , 2012, Clinical chemistry.

[32]  Thomas Lengauer,et al.  A DNA methylation fingerprint of 1628 human samples. , 2011, Genome research.

[33]  S. Rafii,et al.  Directional DNA methylation changes and complex intermediate states accompany lineage specificity in the adult hematopoietic compartment. , 2011, Molecular cell.

[34]  Peiyong Jiang,et al.  Noninvasive Prenatal Diagnosis of Fetal Trisomy 18 and Trisomy 13 by Maternal Plasma DNA Sequencing , 2011, PloS one.

[35]  S. Quake,et al.  Universal noninvasive detection of solid organ transplant rejection , 2011, Proceedings of the National Academy of Sciences.

[36]  Yama W. L. Zheng,et al.  Non-invasive prenatal assessment of trisomy 21 by multiplexed maternal plasma DNA sequencing: large scale validity study , 2011, BMJ : British Medical Journal.

[37]  Yama W. L. Zheng,et al.  Maternal Plasma DNA Sequencing Reveals the Genome-Wide Genetic and Mutational Profile of the Fetus , 2010, Science Translational Medicine.

[38]  Karline Soetaert,et al.  xsample(): An R Function for Sampling Linear Inverse Problems , 2009 .

[39]  Annie Chu,et al.  SOCR Analyses: Implementation and Demonstration of a New Graphical Statistics Educational Toolkit. , 2009, Journal of statistical software.

[40]  L. Hood,et al.  Circulating microRNAs, potential biomarkers for drug-induced liver injury , 2009, Proceedings of the National Academy of Sciences.

[41]  T. Mok,et al.  Single-Molecule Detection of Epidermal Growth Factor Receptor Mutations in Plasma by Microfluidics Digital PCR in Non–Small Cell Lung Cancer Patients , 2009, Clinical Cancer Research.

[42]  A. Feinberg,et al.  Genome-wide methylation analysis of human colon cancer reveals similar hypo- and hypermethylation at conserved tissue-specific CpG island shores , 2008, Nature Genetics.

[43]  C. Cantor,et al.  Noninvasive prenatal diagnosis of fetal chromosomal aneuploidy by massively parallel genomic sequencing of DNA in maternal plasma , 2008, Proceedings of the National Academy of Sciences.

[44]  T. Leung,et al.  Detection and characterization of placental microRNAs in maternal plasma. , 2008, Clinical chemistry.

[45]  Chunming Ding,et al.  Detection of the placental epigenetic signature of the maspin gene in maternal plasma. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[46]  N. Niikawa,et al.  Detection of cell free placental DNA in maternal plasma: direct evidence from three cases of confined placental mosaicism , 2004, Journal of Medical Genetics.

[47]  R. Chiu,et al.  mRNA of placental origin is readily detectable in maternal plasma , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[48]  Tom H. Pringle,et al.  The human genome browser at UCSC. , 2002, Genome research.

[49]  C. Lam,et al.  Predominant hematopoietic origin of cell-free DNA in plasma and serum after sex-mismatched bone marrow transplantation. , 2002, Clinical chemistry.

[50]  S. Leung,et al.  Quantitative analysis of cell-free Epstein-Barr virus DNA in plasma of patients with nasopharyngeal carcinoma. , 1999, Cancer research.

[51]  W. Lau,et al.  Detection of aberrant p16 methylation in the plasma and serum of liver cancer patients. , 1999, Cancer research.

[52]  N. M. Hjelm,et al.  Presence of donor-specific DNA in plasma of kidney and liver-transplant recipients , 1998, The Lancet.

[53]  I. Sargent,et al.  Presence of fetal DNA in maternal plasma and serum , 1997, The Lancet.