Expanding the Scope of Noninvasive Prenatal Testing: Detection of Fetal Microdeletion Syndromes

There are noninvasive prenatal testing (NIPT) approaches using cell-free DNA in the maternal circulation to detect those women at high risk of trisomy 21, trisomy 18, trisomy 13, and sex chromosomal abnormalities. This study estimates the success of a single-nucleotide polymorphism (SNP) approach to analyzing maternal cell-free DNA in detecting 5 fetal microdeletion syndromes. Genomic DNA was isolated from 40 characterized cell lines for initial validation studies to show that SNP-targeted assay could detect the presence of 22q11.2, 1p36, cri-du-chat, Angelman, and Prader-Willi deletions. A cohort of 496 test samples, including 352 unaffected pregnancy plasmas, 111 artificial DNA mixtures representing microdeletions, and 6 maternal plasma samples from women pregnant with a fetus with a microdeletion were studied. All samples, as well as maternal and, if available, paternal samples, were sequenced and underwent targeted multiplex polymerase chain reaction. The NExt Generation Aneuploidy Test using SNPs algorithm analyzed the data and predicted fetal copy number for microdeletion regions of interest. Of the 358 pregnancy samples, 335 passed QC metrics, and for 23 (6.4%), the algorithm did not return a result. One of the 6 affected pregnancy plasmas (22q11.2) was reported as a false negative. Overall detection rates were 100% for all except for the 22q11.2 deletion at 97.8% (45/46). Cri-du-chat syndrome had a false-positive rate of 0.24% (1/419), and 22q11.2 had a false-positive rate of 0.76% (3/397). The results confirmed the SNP-based approach could detect the microdeletions accurately in all 5 specific syndromes studied. Because clinically relevant duplications and microdeletions occur in more than 1% of all pregnancies, approaches to identifying these abnormal pregnancies should be studied.