Noninvasive prenatal aneuploidy testing of chromosomes 13, 18, 21, X, and Y, using targeted sequencing of polymorphic loci

ABSTRACT Objective This study aims to develop a noninvasive prenatal test on the basis of the analysis of cell‐free DNA in maternal blood to detect fetal aneuploidy at chromosomes 13, 18, 21, X, and Y. Methods A total of 166 samples from pregnant women, including 11 trisomy 21, three trisomy 18, two trisomy 13, two 45,X, and two 47,XXY samples, were analyzed using an informatics‐based method. Cell‐free DNA from maternal blood was isolated, amplified using a multiplex polymerase chain reaction (PCR) assay targeting 11 000 single nucleotide polymorphisms on chromosomes 13, 18, 21, X, and Y in a single reaction, and sequenced. A Bayesian‐based maximum likelihood statistical method was applied to determine the chromosomal count of the five chromosomes interrogated in each sample, along with a sample‐specific calculated accuracy for each test result. Results The algorithm correctly reported the chromosome copy number at all five chromosomes in 145 samples that passed a DNA quality test, for a total of 725/725 correct calls. The average calculated accuracy for these samples was 99.92%. Twenty‐one samples did not pass the DNA quality test. Conclusions This informatics‐based method noninvasively detected fetuses with trisomy 13, 18, and 21, 45,X, and 47,XXY with high sample‐specific calculated accuracies for each individual chromosome and across all five chromosomes. © 2012 John Wiley & Sons, Ltd.