Abstract
Non-invasive prenatal testing (NIPT) for common fetal trisomies is effective. However, the usefulness of cell-free DNA testing to detect other chromosomal abnormalities is poorly understood. We analyzed the positive rate at different read depths in next-generation sequencing (NGS) and identified a strategy for fetal copy number variant (CNV) detection in NIPT. Pregnant women who underwent NIPT by NGS at read depths of 4–6 M and fetuses with suspected CNVs were analyzed by amniocentesis and chromosomal microarray analysis (CMA). These fetus samples were re-sequenced at a read depth of 25 M and the positive detection rate was determined. With the increase in read depth, the positive CNV detection rate increased. The positive CNV detection rates at 25 M with small fragments were higher by NGS than by karyotype analysis. Increasing read depth in NGS improves the positive CNV detection rate while lowering the false positive detection rate. NIPT by NGS may be an accurate method of fetal chromosome analysis and reduce the rate of birth defects.
Highlights
Non-invasive prenatal testing (NIPT) calculates the risk of fetal chromosomal aneuploidies by detecting cffDNA circulating in maternal plasma using next-generation sequencing (NGS) technology (Chandrasekharan et al, 2014)
Because of the high incidence of fetal pathogenic copy number variant (CNV) and their severe clinical symptoms, feasibility studies of CNV detection in NIPT, which have been repeatedly proposed by the American College of Medical Genetics and American College of Obstetricians and Gynecologists, are becoming increasingly urgent
We found 20 fetuses (0.42%) with suspected CNVs
Summary
NIPT calculates the risk of fetal chromosomal aneuploidies by detecting cffDNA circulating in maternal plasma using next-generation sequencing (NGS) technology (Chandrasekharan et al, 2014). CNVs are stretches of genomic DNA present as more than or fewer than two copies and can range in size from kilobases to megabases (Mb). They cannot be identified by G-banded chromosome analysis (karyotyping) but can be identified by microarray methodologies and whole genome sequencing analysis (Wang et al, 2017). Peters et al (2011) detected by NIPT a 4.2-Mb microdeletion on chromosome 12 in one fetus and validated it by extracting amniotic fluid and using arraybased comparative genomic hybridization (aCGH). In conjunction with the progress in cffDNA extraction technology and reduction in sequencing cost, it is possible and necessary to detect chromosomal microdeletions, microduplications, and pathogenic CNVs by NIPT on a large scale. The findings of this study could help improve diagnostic accuracy while reducing cost and improving maternal and prenatal health care
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
