title: Disease specific characteristics of fetal epigenetic markers for non-invasive prenatal testing of trisomy 21.
abstract: BACKGROUND
  Non-invasive prenatal testing of trisomy 21 (T21) is being actively investigated using fetal-specific epigenetic markers (EPs) that are present in maternal plasma. Recently, 12 EPs on chromosome 21 were identified based on tissue-specific epigenetic characteristics between placenta and blood, and demonstrated excellent clinical performance in the non-invasive detection of fetal T21. However, the disease-specific epigenetic characteristics of the EPs have not been established. Therefore, we validated the disease-specific epigenetic characteristics of these EPs for use in non-invasive detection of fetal T21.
  
  
  METHODS
  We performed a high-resolution tiling array analysis of human chromosome 21 using a methyl-CpG binding domain-based protein (MBD) method with whole blood samples from non-pregnant normal women, whole blood samples from pregnant normal women, placenta samples of normal fetuses, and placenta samples of T21 fetuses. Tiling array results were validated by bisulfite direct sequencing and qPCR.
  
  
  RESULTS
  Among 12 EPs, only four EPs were confirmed to be hypermethylated in normal placenta and hypomethylated in blood. One of these four showed a severe discrepancy in the methylation patterns of T21 placenta samples, and another was located within a region of copy number variations. Thus, two EPs were confirmed to be potential fetal-specific markers based on their disease-specific epigenetic characteristics. The array results of these EPs were consisted with the results obtained by bisulfite direct sequencing and qPCR. Moreover, the two EPs were detected in maternal plasma.
  
  
  CONCLUSIONS
  We validated that two EPs have the potential to be fetal-specific EPs which is consistent with their disease-specific epigenetic characteristics. The findings of this study suggest that disease-specific epigenetic characteristics should be considered in the development of fetal-specific EPs for non-invasive prenatal testing of T21.
authors.forename: Ji Hyae
authors.initials: JH
authors.lastname: Lim
authors.forename: Da Eun
authors.initials: DE
authors.lastname: Lee
authors.forename: So Yeon
authors.initials: SY
authors.lastname: Park
authors.forename: Do Jin
authors.initials: DJ
authors.lastname: Kim
authors.forename: Hyun Kyong
authors.initials: HK
authors.lastname: Ahn
authors.forename: You Jung
authors.initials: YJ
authors.lastname: Han
authors.forename: Moon Young
authors.initials: MY
authors.lastname: Kim
authors.affiliation: Laboratory of Medical Genetics, Medical Research Institute, Cheil General Hospital and Women's Healthcare Center, Seoul, Korea. hmryu@yahoo.com.
authors.forename: Hyun Mee
authors.initials: HM
authors.lastname: Ryu
mesh_terms: D000328:Adult; D001483:Base Sequence; D015415:Biomarkers / Q000378:metabolism; D018899:CpG Islands / Q000235:genetics; D056915:DNA Copy Number Variations / Q000235:genetics; D019175:DNA Methylation / Q000235:genetics; D004314:Down Syndrome / Q000175:diagnosis* / Q000235:genetics*; D044127:Epigenesis, Genetic; D005260:Female; D005333:Fetus / Q000378:metabolism*; D006801:Humans; D008297:Male; D008969:Molecular Sequence Data; D020411:Oligonucleotide Array Sequence Analysis; D016133:Polymerase Chain Reaction; D011247:Pregnancy; D011296:Prenatal Diagnosis; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA
chemical_list: D015415:Biomarkers