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Epigenetics Volume 16, 2021 - Issue 6
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Research Paper

Cell-free DNA Methylation and Transcriptomic Signature Prediction of Pregnancies with Adverse Outcomes

Giorgia Del Vecchioa Departments of Pediatrics David Geffen School of Medicine at UCLA, Los Angeles, California, USAORCID Iconhttps://orcid.org/0000-0001-5156-3231View further author information
ORCID Icon,
Qingjiao Lib The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, ChinaView further author information
,
Wenyuan Lic Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California, USAView further author information
,
Shanthie Thamotharana Departments of Pediatrics David Geffen School of Medicine at UCLA, Los Angeles, California, USAView further author information
,
Anela Tosevskad Departments of Molecular, Cellular and Developmental Biology, University of California Los Angeles, California, USAView further author information
,
Marco Morsellid Departments of Molecular, Cellular and Developmental Biology, University of California Los Angeles, California, USAORCID Iconhttps://orcid.org/0000-0003-3351-5791View further author information
ORCID Icon,
Kyunghyun Sunge Department of Radiological Sciences, University of California Los Angeles, California, USAView further author information
,
Carla Janzenf Department of Obstetrics & Gynecology, David Geffen School of Medicine at UCLA, Los Angeles, California, USAORCID Iconhttps://orcid.org/0000-0001-5010-659XView further author information
ORCID Icon,
Xianghong Zhouc Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California, USAView further author information
,
Matteo Pellegrinid Departments of Molecular, Cellular and Developmental Biology, University of California Los Angeles, California, USAView further author information
&
Sherin U. Devaskara Departments of Pediatrics David Geffen School of Medicine at UCLA, Los Angeles, California, USACorrespondence[email protected]
View further author information
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Pages 642-661 | Received 23 Apr 2020, Accepted 10 Aug 2020, Published online: 13 Oct 2020

  • Norton ME, Wapner RJ. Cell-free DNA Analysis for Noninvasive Examination of Trisomy. N Engl J Med. 2015;373:2581–2582.
  • Heazell AE, Hayes DJ, Whitworth M, et al. Biochemical tests of placental function versus ultrasound assessment of fetal size for stillbirth and small-for-gestational-age infants. Cochrane Database Syst Rev. 2019;5:CD012245.
  • Shao X, Liu D, Martin T, et al. Measuring human placental blood flow with multidelay 3D GRASE pseudocontinuous arterial spin labeling at 3T. J Magn Reson Imaging. 2018;47(6):1667–1676.
  • Ngo TTM, Moufarrej MN, Rasmussen M-LH, et al. Noninvasive blood tests for fetal development predict gestational age and preterm delivery. Science. 2018;360(6393):1133–1136.
  • van Boeckel SR, Davidson DJ, Norman JE, et al. Cell-free fetal DNA and spontaneous preterm birth. Reproduction. 2018;155(3):R137–145.
  • Chen P-Y, Chu A, Liao -W-W, et al. Prenatal Growth Patterns and Birthweight Are Associated With Differential DNA Methylation and Gene Expression of Cardiometabolic Risk Genes in Human Placentas: A Discovery-Based Approach. Reprod Sci. 2018;25(4):523–539.
  • Thamotharan S, Chu A, Kempf K, et al. Differential microRNA expression in human placentas of term intra-uterine growth restriction that regulates target genes mediating angiogenesis and amino acid transport. PLoS One. 2017;12(5):e0176493.
  • Sun K, Jiang P, Chan KC, et al. Plasma DNA tissue mapping by genome-wide methylation sequencing for noninvasive prenatal, cancer, and transplantation assessments. Proc Natl Acad Sci U S A. 2015;112(40):E5503–5512.
  • Moss J, Magenheim J, Neiman D, et al. Comprehensive human cell-type methylation atlas reveals origins of circulating cell-free DNA in health and disease. Nat Commun. 2018;9(1):5068.
  • Kang S, Li Q, Chen Q, et al. CancerLocator: non-invasive cancer diagnosis and tissue-of-origin prediction using methylation profiles of cell-free DNA. Genome Biol. 2017;18(1):53.
  • Li W, Li Q, Kang S, et al. CancerDetector: ultrasensitive and non-invasive cancer detection at the resolution of individual reads using cell-free DNA methylation sequencing data. Nucleic Acids Res. 2018;46(15):e89.
  • Ananth CV. Ischemic placental disease: a unifying concept for preeclampsia, intrauterine growth restriction, and placental abruption. Semin Perinatol. 2014;38(3):131–132.
  • Adams T, Yeh C, Bennett-Kunzier N, et al. Long-term maternal morbidity and mortality associated with ischemic placental disease. Semin Perinatol. 2014;38(3):146–150.
  • Practice Bulletin ACOG. No. 190: gestational Diabetes Mellitus. Obstet Gynecol. 2018;131:e49–e64.
  • Practice Bulletin ACOG. No. 202: gestational Hypertension and Preeclampsia. Obstet Gynecol. 2019;133:e1–e25.
  • Dempster AP, Laird NM, Rubin DB. Maximum Likelihood from Incomplete Data via the EM Algorithm. J R Stat Soc Series B Stat Methodol. 1977;39:1–38.
  • Friedman J, Hastie T, and Tibshirani R. Regularization paths for generalized linear models via coordinate descent. Journal of Statistical Software. 2010;33(1):1–22.
  • Sachs MC. plotROC: A tool for plotting ROC curves. J statl softw. 2017;79:1–19.
  • Benjamini Y, Hochberg Y. Controlling the false discovery rate - a practical and powerful approach to multiple testing. J Roy Stat Soc B Met. 1995;57:289–300.
  • Lun FM, Chiu RW, Sun K, et al. Noninvasive Prenatal Methylomic Analysis by Genomewide Bisulfite Sequencing of Maternal Plasma DNA. Clin Chem. 2013;59(11):1583–1594.
  • Hodges E, Smith AD, Kendall J, et al. High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing. Cold Spring Harbor Laboratory Press. 2009;19:1593–1605.
  • Jensen TJ, Kim SK, Zhu Z, et al. Whole genome bisulfite sequencing of cell-free DNA and its cellular contributors uncovers placenta hypomethylated domains. Genome Biol. 2015;15:16–78.
  • Lopez D, Montoya D, Ambrose M, et al. SaVanT: a web-based tool for the sample-level visualization of molecular signatures in gene expression profiles. BMC Genomics. 2017;18–824.
  • Taylor HS. Endometrial cells derived from donor stem cells in bone marrow transplant recipients. Jama. 2004;292(1):81–85.
  • Mints M, Jansson M, Sadeghi B, et al. Endometrial endothelial cells are derived from donor stem cells in a bone marrow transplant recipient. Hum Reprod. 2008;23:139–143.
  • Ikoma T, Kyo S, Maida Y, et al. Bone marrow–derived cells from male donors can compose endometrial glands in female transplant recipients. Am J Obstet Gynecol. 2009;201(6):e1–8.
  • Handwerger S, Freemark M. The roles of placental growth hormone and placental lactogen in the regulation of human fetal growth and development. J Pediatr Endocrinol Metab. 2000;13(4):343–356.
  • Phillips RJ, Fortier MA, Lopez Bernal A. Prostaglandin pathway gene expression in human placenta, amnion and choriodecidua is differentially affected by preterm and term labour and by uterine inflammation. BMC Pregnancy Childbirth. 2014;14(1):241.
  • Baker JR, Jeffery R, May RD, et al. Distinct roles for S100a8 in early embryo development and in the maternal deciduum. Dev Dyn. 2011;240(9):2194–2203.
  • Hjort L, Martino D, Grunnet LG, et al. Gestational diabetes and maternal obesity are associated with epigenome-wide methylation changes in children. JCI Insight. 2018;3(17):e122572.
  • Daskalakis G, Marinopoulos S, Krielesi V, et al. Placental pathology in women with gestational diabetes. Acta Obstetricia et Gynecologica Scandinavica. 2008;87(4):403–407.
  • Edlow AG, Vora NL, Hui L, et al. Maternal obesity affects fetal neurodevelopmental and metabolic gene expression: a pilot study. PLoS One. 2014;9(2):e88661.
  • Mhatre M, Adeli S, Norwitz E, et al. The Effect of Maternal Obesity on Placental Cell-Free DNA Release in a Mouse Model. Reprod Sci. 2019;26(9):1218–1224.
  • Pan W, Ngo TTM, Camunas-Soler J, et al. Simultaneously Monitoring Immune Response and Microbial Infections during Pregnancy through Plasma cfRNA Sequencing. Clin Chem. 2017;63(11):1695–1704.
  • Tal R, Shaikh S, Pallavi P, et al. Adult bone marrow progenitors become decidual cells and contribute to embryo implantation and pregnancy. PLoS Biol. 2019;17(9):e3000421.
  • Lamain-de Ruiter M, Kwee A, Naaktgeboren CA, et al. Van ‘t Zelfde A, van Oirschot CM, Vankan-Buitelaar SA, Vonk MA, Wiegers TA, Zwart JJ, Franx A, Moons KG, Koster MP. External validation of prognostic models to predict risk of gestational diabetes mellitus in one Dutch cohort: prospective multicentre cohort study. BMJ. 2016;354:i4338.
  • De Kat AC, Hirst J, Woodward M, et al. Prediction models for preeclampsia: A systematic review. Pregnancy Hypertens. 2019;16:48–66.
  • Katsi V, Georgountzos G, Kallistratos M, et al. The Role of Statins in Prevention of Preeclampsia: A Promise for the Future? Front Pharmacol. 2017;8:247.
  • Costantine MM, Cleary K, Hebert MF, et al. Safety and pharmacokinetics of pravastatin used for the prevention of preeclampsia in high-risk pregnant women: a pilot randomized controlled trial. Am J Obstet Gynecol. 2016;214(6):e1–720. e17.
  • Marrs CC, Costantine MM. Should We Add Pravastatin to Aspirin for Preeclampsia Prevention in High-risk Women? Clin Obstet Gynecol. 2017;60(1):161–168.
  • Chan KC, Jiang P, Chan CW, et al. Noninvasive detection of cancer-associated genome-wide hypomethylation and copy number aberrations by plasma DNA bisulfite sequencing. Proc Natl Acad Sci U S A. 2013;110(47):18761–18768.
  • Edgar R. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Research. 2002;30(1):207–210.

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