Array-CGH analysis of cell-free fetal DNA in 10 mL of amniotic fluid supernatant.
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.
Lapaire
Olav
O
Division of Genetics, Department of Pediatrics, Tufts-New England Medical Center, Boston, MA, USA.
Lu
Xin-Yan
XY
Johnson
Kirby L
KL
Jarrah
Zina
Z
Stroh
Helene
H
Cowan
Janet M
JM
Tantravahi
Umadevi
U
Bianchi
Diana W
DW
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
D004247:DNA