Array-CGH analysis of cell-free fetal DNA in 10 mL of amniotic fluid supernatant

• Published in: Prenatal diagnosis Vol. 27; no. 7; pp. 616 - 621
• Main Authors: Lapaire, Olav, Lu, Xin-Yan, Johnson, Kirby L., Jarrah, Zina, Stroh, Helene, Cowan, Janet M., Tantravahi, Umadevi, Bianchi, Diana W.
• Format: Journal Article
• Language: English
• Published: Chichester, UK John Wiley & Sons, Ltd 01.07.2007; Wiley
• Subjects: Amniotic Fluid - chemistry; amniotic fluid supernatant; array-CGH; Biological and medical sciences; cell-free fetal DNA; DNA - analysis; Fundamental and applied biological sciences. Psychology; Gynecology. Andrology. Obstetrics; Humans; Management. Prenatal diagnosis; Medical sciences; Molecular and cellular biology; Oligonucleotide Array Sequence Analysis; Ploidies; Pregnancy. Fetus. Placenta; prenatal diagnosis; Prenatal Diagnosis - methods; Specimen Handling; Trisomy - diagnosis; Turner Syndrome - diagnosis; Andrology; amniotic fluid supernatant; Prenatal Diagnosis; Gynecology; Supernatant; cell-free fetal DNA; array-CGH; Fetal cell; DNA; Amniotic fluid; Genetics; Array-based Comparative Genomic Hybridisation; Cell free system
• ISSN: 0197-3851; 1097-0223
• DOI: 10.1002/pd.1752

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. Copyright © 2007 John Wiley & Sons, Ltd.