title: Noninvasive prenatal methylomic analysis by genomewide bisulfite sequencing of maternal plasma DNA.
abstract: BACKGROUND
  Epigenetic mechanisms play an important role in prenatal development, but fetal tissues are not readily accessible. Fetal DNA molecules are present in maternal plasma and can be analyzed noninvasively.
  
  
  METHODS
  We applied genomewide bisulfite sequencing via 2 approaches to analyze the methylation profile of maternal plasma DNA at single-nucleotide resolution. The first approach used maternal blood samples and polymorphic differences between the mother and fetus to analyze the fetal methylome across the genome. The second approach used the methylation profile of maternal blood cells and the fractional fetal DNA concentration in maternal plasma to deduce the placental methylomic profile from maternal plasma DNA-sequencing data.
  
  
  RESULTS
  Because of the noninvasive nature of these approaches, we were able to serially assess the methylation profiles of fetal, placental, and maternal plasma with maternal blood samples collected in the first and third trimesters and after delivery. Gestation-related changes were observed. The fetal methylation profile deduced from maternal plasma data resembled that of the placental methylome, both on a genomewide level and per CpG site. Imprinted genes and differentially methylated regions were identified from the maternal plasma data. We demonstrated one potential clinical application of maternal plasma bisulfite sequencing with the successful detection of fetal trisomy 21.
  
  
  CONCLUSIONS
  We successfully analyzed fetal and placental methylomes on a genomewide scale, noninvasively and serially. This development offers a powerful method for research, biomarker discovery, and clinical testing for pregnancy-related disorders.
authors.affiliation: Centre for Research into Circulating Fetal Nucleic Acids, Li Ka Shing Institute of Health Sciences, and.
authors.forename: Fiona M F
authors.initials: FM
authors.lastname: Lun
authors.forename: Rossa W K
authors.initials: RW
authors.lastname: Chiu
authors.forename: Kun
authors.initials: K
authors.lastname: Sun
authors.forename: Tak Y
authors.initials: TY
authors.lastname: Leung
authors.forename: Peiyong
authors.initials: P
authors.lastname: Jiang
authors.forename: K C Allen
authors.initials: KC
authors.lastname: Chan
authors.forename: Hao
authors.initials: H
authors.lastname: Sun
authors.forename: Y M Dennis
authors.initials: YM
authors.lastname: Lo
mesh_terms: D002891:Chromosomes, Human, Pair 21 / Q000235:genetics; D004247:DNA / Q000097:blood / Q000235:genetics*; D019175:DNA Methylation; D004314:Down Syndrome / Q000175:diagnosis; D044127:Epigenesis, Genetic; D005260:Female; D005333:Fetus; D056426:Genetic Loci; D015894:Genome, Human; D006801:Humans; D007202:Indicators and Reagents; D010920:Placenta / Q000737:chemistry; D011110:Polymorphism, Genetic; D011247:Pregnancy; D011296:Prenatal Diagnosis; D017422:Sequence Analysis, DNA; D013447:Sulfites
chemical_list: D007202:Indicators and Reagents; D013447:Sulfites; D004247:DNA; C009279:sodium bisulfite