Aneuploidy detection in mixed DNA samples by methylation-sensitive amplification and microarray analysis.
BACKGROUND
Cell-free fetal nucleic acid, believed to be derived from the placenta/trophoblast, is present in the plasma of pregnant women; however, its use for predictive genetic testing has been severely limited because the circulating fetal DNA is present in a small quantity and mixed with a much larger quantity of maternal DNA. Methods for detecting fetal aneuploidy from the cell-free fetal DNA in plasma are highly sought after, but proposed methods must take into account the small quantity and highly contaminated nature of the available fetal DNA.


METHODS
We developed a method for methylation-sensitive amplification of DNA suitable for use with small (approximately 1 ng) samples. We used this method in conjunction with 2-color microarray analysis with a custom-made array to investigate whether relative amplification, and hence relative methylation, could be evaluated for a large number of genomic loci.


RESULTS
Microarray assessment of genomic methylation accurately predicted the degree of methylation measured with bisulfite-conversion PCR and confirmed that DNA from first-trimester trophoblast was generally hypomethylated compared with whole-blood DNA. With a series of 3 samples in which 1 ng of DNA from a trisomic first trimester placenta was mixed with 9 ng of chromosomally normal peripheral blood DNA, we observed that the microarray signal associated with the trisomic chromosome was significantly different from that of the other chromosomes (P < 0.001).


CONCLUSIONS
This method has potential to be used for noninvasive detection of fetal aneuploidy.
Department of Obstetrics, Gynecology and Reproductive Sciences, University of Vermont, Burlington, VT 05405, USA.
Lucia
L
Brown
Gregory
G
Brown
Pamela
P
Vacek
Stephen
S
Brown
D000293:Adolescent; D000328:Adult; D000782:Aneuploidy; D004247:DNA / Q000097:blood* / Q000235:genetics; D019175:DNA Methylation; D005260:Female; D005333:Fetus / Q000378:metabolism*; D056426:Genetic Loci; D006801:Humans; D008431:Maternal-Fetal Exchange; D020411:Oligonucleotide Array Sequence Analysis / Q000295:instrumentation / Q000379:methods*; D010920:Placenta / Q000378:metabolism*; D011247:Pregnancy; D011296:Prenatal Diagnosis / Q000379:methods*; D055815:Young Adult
D004247:DNA