title: Array-CGH analysis of cell-free fetal DNA in 10 mL of amniotic fluid supernatant.
abstract: BACKGROUND
  Previously, we showed that analysis of amniotic fluid (AF) supernatant cell-free fetal (cff) DNA using DNA microarrays (array-CGH) allows for detection of whole chromosome differences between test and reference DNA. Subsequent technical advances have increased both the yield and quality of extracted cffDNA. Here we determined whether array-CGH using smaller volumes of both fresh and frozen AF cffDNA could identify fetal aneuploidy.
  
  
  METHODS
  CffDNA was extracted from 10 mL of residual AF supernatant. The test AF samples (n = 10) included one with a normal karyotype, and nine with the following fetal aneuploidies: trisomies 13 (n = 1), 18 (n = 3), 21 (n = 2), trisomy 9 mosaicism (47,XX,+ 9[18]/46,XX[2]), triploidy (69,XXY) and Turner syndrome (45,X).
  
  
  RESULTS
  Array-CGH using AF cffDNA from aneuploid fetuses, compared to euploid reference AF cffDNA, detected whole chromosome aneuploidy in 8 of 9 cases tested, including the case of trisomy 9 mosaicism. The case of triploidy was not detected.
  
  
  CONCLUSIONS
  CffDNA extracted from 10 mL AF supernatant can be analyzed using array-CGH to correctly identify human chromosome abnormalities. This technology allows for rapid screening of AF samples for whole chromosomal changes by using routinely discarded supernatant, and may augment standard prenatal karyotyping techniques by providing additional molecular information.
authors.affiliation: Division of Genetics, Department of Pediatrics, Tufts-New England Medical Center, Boston, MA, USA.
authors.forename: Olav
authors.initials: O
authors.lastname: Lapaire
authors.forename: Xin-Yan
authors.initials: XY
authors.lastname: Lu
authors.forename: Kirby L
authors.initials: KL
authors.lastname: Johnson
authors.forename: Zina
authors.initials: Z
authors.lastname: Jarrah
authors.forename: Helene
authors.initials: H
authors.lastname: Stroh
authors.forename: Janet M
authors.initials: JM
authors.lastname: Cowan
authors.forename: Umadevi
authors.initials: U
authors.lastname: Tantravahi
authors.forename: Diana W
authors.initials: DW
authors.lastname: Bianchi
mesh_terms: D000653:Amniotic Fluid / Q000737:chemistry*; D004247:DNA / Q000032:analysis*; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis; D011003:Ploidies; D011296:Prenatal Diagnosis / Q000379:methods*; D013048:Specimen Handling; D014314:Trisomy / Q000175:diagnosis*; D014424:Turner Syndrome / Q000175:diagnosis
chemical_list: D004247:DNA