title: Microarray analysis of cell-free fetal DNA in amniotic fluid: a prenatal molecular karyotype.
abstract: Metaphase karyotype analysis of fetal cells obtained by amniocentesis or chorionic villus sampling is the current standard for prenatal cytogenetic diagnosis, particularly for the detection of trisomy 21. We previously demonstrated that large quantities of cell-free fetal DNA (cffDNA) are easily extracted from amniotic fluid (AF). In this study, we explored potential clinical applications of AF cffDNA by testing its ability to hybridize to DNA microarrays for comparative genomic hybridization (CGH) analysis. cffDNA isolated from 11 male fetuses showed significantly increased hybridization signals on SRY and decreased signals on X-chromosome markers, compared with female reference DNA. cffDNA isolated from six female fetuses showed the reverse when compared with male reference DNA. cffDNA from three fetuses with trisomy 21 had increased hybridization signals on the majority of the chromosome 21 markers, and cffDNA from a fetus with monosomy X (Turner syndrome) had decreased hybridization signals on most X-chromosome markers, compared with euploid female reference DNA. These results indicate that cffDNA extracted from AF can be analyzed using CGH microarrays to correctly identify fetal sex and aneuploidy. This technology facilitates rapid screening of samples for whole-chromosome changes and may augment standard karyotyping techniques by providing additional molecular information.
authors.affiliation: Division of Newborn Medicine, Department of Pediatrics, Tufts-New England Medical Center, Tufts University School of Medicine, Boston, MA 02111, USA.
authors.forename: Paige B
authors.initials: PB
authors.lastname: Larrabee
authors.forename: Kirby L
authors.initials: KL
authors.lastname: Johnson
authors.forename: Ekaterina
authors.initials: E
authors.lastname: Pestova
authors.forename: Madhuri
authors.initials: M
authors.lastname: Lucas
authors.forename: Kim
authors.initials: K
authors.lastname: Wilber
authors.forename: Erik S
authors.initials: ES
authors.lastname: LeShane
authors.forename: Umadevi
authors.initials: U
authors.lastname: Tantravahi
authors.forename: Janet M
authors.initials: JM
authors.lastname: Cowan
authors.forename: Diana W
authors.initials: DW
authors.lastname: Bianchi
mesh_terms: D000649:Amniocentesis; D000653:Amniotic Fluid / Q000378:metabolism*; D000782:Aneuploidy; D002474:Cell-Free System; D002824:Chorionic Villi / Q000378:metabolism; D015193:Chorionic Villi Sampling; D002891:Chromosomes, Human, Pair 21; D041321:Chromosomes, Human, X; D041322:Chromosomes, Human, Y; D003582:Cytogenetics; D004247:DNA; D005260:Female; D005821:Genetic Techniques; D006801:Humans; D007621:Karyotyping; D008297:Male; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis; D011247:Pregnancy; D014424:Turner Syndrome / Q000235:genetics
chemical_list: D004247:DNA