Noninvasive prenatal screening of fetal aneuploidy without massively parallel sequencing

Abstract

BACKGROUND: Noninvasive prenatal screening (NIPS) using plasma cell-free DNA has gained tremendous popularity in the clinical assessment of fetal aneuploidy. Most, if not all, of these tests rely on complex and expensive massively parallel sequencing (MPS) techniques, hindering the use of NIPS as a common screening procedure. METHODS: We have developed and optimized an MPSindependent noninvasive genetic test that can rapidly detect fetal aneuploidy at considerably lower costs. We used the high-throughput ligation-dependent probe amplification (HLPA) assay with standard z score statistics to identify the minute copy number change of targeted chromosomal regions. HLPA was modified from multiplex ligation-dependent probe amplification to allow quantification of up to 200 genomic loci in a single multiplex PCR. As a proof of principle, we conducted Down syndrome screening in 1182 women with singleton pregnancies [maternal age (SD): 32.7 (4.6)] using whole-genome sequencing-based NIPS and our method. RESULTS: Nineteen fetuses with trisomy 21 were detected by both methods and confirmed by karyotyping of amniotic fluid. Overall, our method showed 100.0% sensitivity (19/19) and 99.7% specificity (1076/1079) in trisomy 21 screening, generating a positive predictive value of 86.4% (19/22) and a 7.1% (84/1182) no-call rate. CONCLUSIONS: Our technique potentially opens new avenues for the development of inexpensive, yet effective, prenatal aneuploidy tests. The simplicity and accuracy of this method make it a good candidate for clinical implementation as a standard screening procedure.