title: Whole genome bisulfite sequencing of cell-free DNA and its cellular contributors uncovers placenta hypomethylated domains.
abstract: BACKGROUND
  Circulating cell-free fetal DNA has enabled non-invasive prenatal fetal aneuploidy testing without direct discrimination of the maternal and fetal DNA. Testing may be improved by specifically enriching the sample material for fetal DNA. DNA methylation may allow for such a separation of DNA; however, this depends on knowledge of the methylomes of circulating cell-free DNA and its cellular contributors.
  
  
  RESULTS
  We perform whole genome bisulfite sequencing on a set of unmatched samples including circulating cell-free DNA from non-pregnant and pregnant female donors and genomic DNA from maternal buffy coat and placenta samples. We find CpG cytosines within longer fragments are more likely to be methylated. Comparison of the methylomes of placenta and non-pregnant circulating cell-free DNA reveal many of the 51,259 identified differentially methylated regions are located in domains exhibiting consistent placenta hypomethylation across millions of consecutive bases. We find these placenta hypomethylated domains are consistently located within regions exhibiting low CpG and gene density. Differentially methylated regions identified when comparing placenta to non-pregnant circulating cell-free DNA are recapitulated in pregnant circulating cell-free DNA, confirming the ability to detect differential methylation in circulating cell-free DNA mixtures.
  
  
  CONCLUSIONS
  We generate methylome maps for four sample types at single-base resolution, identify a link between DNA methylation and fragment length in circulating cell-free DNA, identify differentially methylated regions between sample groups, and uncover the presence of megabase-size placenta hypomethylated domains.
authors.affiliation: Sequenom Laboratories, 3595 John Hopkins Ct, San Diego, CA, 92121, USA. tjensen@sequenom.com.
authors.forename: Taylor J
authors.initials: TJ
authors.lastname: Jensen
authors.affiliation: Sequenom Laboratories, 3595 John Hopkins Ct, San Diego, CA, 92121, USA. skim@scmmlab.com.
authors.forename: Sung K
authors.initials: SK
authors.lastname: Kim
authors.affiliation: Sequenom Laboratories, 3595 John Hopkins Ct, San Diego, CA, 92121, USA. zzhu@scmmlab.com.
authors.forename: Zhanyang
authors.initials: Z
authors.lastname: Zhu
authors.affiliation: Sequenom Laboratories, 3595 John Hopkins Ct, San Diego, CA, 92121, USA. cchin@scmmlab.com.
authors.forename: Christine
authors.initials: C
authors.lastname: Chin
authors.affiliation: Sequenom Laboratories, 3595 John Hopkins Ct, San Diego, CA, 92121, USA. claudia.gebhard@googlemail.com.
authors.forename: Claudia
authors.initials: C
authors.lastname: Gebhard
authors.affiliation: Sequenom Laboratories, 3595 John Hopkins Ct, San Diego, CA, 92121, USA. tlu@scmmlab.com.
authors.forename: Tim
authors.initials: T
authors.lastname: Lu
authors.affiliation: Sequenom Laboratories, 3595 John Hopkins Ct, San Diego, CA, 92121, USA. cdeciu@scmmlab.com.
authors.forename: Cosmin
authors.initials: C
authors.lastname: Deciu
authors.affiliation: Sequenom Inc., 3595 John Hopkins Ct, San Diego, CA, 92121, USA. dvandenboom@sequenom.com.
authors.forename: Dirk
authors.initials: D
authors.lastname: van den Boom
authors.affiliation: Sequenom Inc., 3595 John Hopkins Ct, San Diego, CA, 92121, USA. mehrich@sequenom.com.
authors.forename: Mathias
authors.initials: M
authors.lastname: Ehrich
mesh_terms: D018899:CpG Islands; D003596:Cytosine / Q000737:chemistry; D004247:DNA / Q000097:blood*; D053938:DNA Fragmentation; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D005260:Female; D005333:Fetus; D015723:Gene Library; D023281:Genomics; D006801:Humans; D047468:Immunoprecipitation; D010920:Placenta / Q000378:metabolism*; D011247:Pregnancy; D017422:Sequence Analysis, DNA; D013447:Sulfites
chemical_list: D013447:Sulfites; D003596:Cytosine; D004247:DNA; C042345:hydrogen sulfite