Abstract
Detection of copy number variants as an integral part of noninvasive prenatal testing is increasingly used in clinical practice worldwide. We performed validation on plasma samples from 34 pregnant women with known aberrations using cell-free DNA sequencing to evaluate the sensitivity for copy number variants (CNV) detection using an in-house CNV fraction-based detection algorithm. The sensitivity for CNVs smaller than 3 megabases (Mb), larger than 3Mb, and overall was 78.57%, 100%, and 90.6%, respectively. Regarding the fetal fraction, detection sensitivity in the group with a fetal fraction of less than 10% was 57.14%, whereas there was 100% sensitivity in the group with fetal fraction exceeding 10%. The assay is also capable of indicating whether the origin of an aberration is exclusively fetal or fetomaternal/maternal. This validation demonstrated that a CNV fraction-based algorithm was applicable and feasible in clinical settings as a supplement to testing for common trisomies 21, 18, and 13.
Highlights
The application of noninvasive prenatal testing (NIPT) has increased dramatically from fetal sex determination to whole fetal genome sequencing
We performed a technical validation of cell-free DNA low-coverage whole-genome sequencing in
We performed a technical validation of cell-free low-coverage whole-genome sequencing combination with a copy number variants (CNV)
Summary
The application of noninvasive prenatal testing (NIPT) has increased dramatically from fetal sex determination to whole fetal genome sequencing. This is a consequence of rapidly evolving Next. Detection of common trisomies 21, 18, and 13 has become routine, as the sensitivity has reached over 99% for worldwide NIPT. The applied approaches include either whole-genome or a targeted approach [1,2] as the application of NIPT is rapidly expanding beyond whole chromosomes, including quantitative sub-chromosomal aberrations, known as copy number variants (CNVs). The incidence of CNVs is independent of maternal age [3], and prenatal detection of pathogenic CNVs would, benefit all pregnant women. The widespread implementation of CNV detection in standard prenatal screening is limited, as the detection sensitivity is still under investigation
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