Molecular diagnosis of Down syndrome using quantitative APEX-2 microarrays.
OBJECTIVE
To develop a new rapid and high-throughput microarray-based prenatal diagnostic test for the detection of trisomy 21 (T21).


METHODS
The T21 arrayed primer extension-2 (APEX-2) assay discriminates between trisomy and euploid DNA samples by comparing the signal intensities of allelic fractions of heterozygous single nucleotide polymorphisms (SNPs) after APEX reaction. After preliminary validation using DNA samples from Down syndrome patients, we analyzed DNA samples from cultured and uncultured amniocytes and chorionic villus for 90 SNPs with high heterozygosity from the 21(q21.1q22.2) region. Differences in allelic ratios of heterozygous SNPs in normal and T21 individuals were verified by t-test.


RESULTS
Analysis of the T21 APEX-2 assay results revealed that 90 SNPs were sufficient for reliable discrimination between T21 and euploid DNA samples (P≤0.05 for one or both strands). Using 134 clinical samples from cultured or uncultured fetal cells, both the sensitivity and the specificity of the assay were 100%.


CONCLUSIONS
Our study provides a proof of principle demonstration of the use of the modified APEX-2 assay as a new, fast and reliable method for prenatal diagnosis of fetal T21.
Oitmaa
Eneli
E
Estonian Biocentre, Tartu, Estonia. eneli@asperbio.com
Peters
Maire
M
Vaidla
Kadri
K
Andreson
Reidar
R
Mägi
Reedik
R
Slavin
Georgi
G
Velthut
Agne
A
Tõnisson
Neeme
N
Reimand
Tiia
T
Remm
Maido
M
Schneider
Marion
M
Ounap
Katrin
K
Salumets
Andres
A
Metspalu
Andres
A
D000465:Algorithms; D004247:DNA / Q000032:analysis / Q000378:metabolism; D017931:DNA Primers; D003937:Diagnosis, Differential; D004314:Down Syndrome / Q000175:diagnosis* / Q000235:genetics; D005260:Female; D005333:Fetus / Q000378:metabolism; D006801:Humans; D046228:Microarray Analysis / Q000379:methods*; D008954:Models, Biological; D025202:Molecular Diagnostic Techniques / Q000379:methods*; D021141:Nucleic Acid Amplification Techniques / Q000379:methods*; D020641:Polymorphism, Single Nucleotide; D011247:Pregnancy
D017931:DNA Primers; D004247:DNA