Validation of Copy Number Variants Detection from Pregnant Plasma Using Low-Pass Whole-Genome Sequencing in Noninvasive Prenatal Testing-Like Settings

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.

Copy Number Variant Detection with Low-Coverage Whole-Genome Sequencing Represents a Viable Alternative to the Conventional Array-CGH

“…The assay originated from a basic NIPT test focused on noninvasive prenatal screening for the three most common trisomies. Later, the development continued by adding the detection of sex chromosome aneuploidies and five selected microdeletions, and most recently it has been advanced to a whole-genome scan for chromosomal microaberrations [ 18 , 24 , 25 ]. The common link between all these tests is the method based on low-coverage, whole-genome sequencing.…”

“…In this paper, we present GenomeScreen—a low-coverage, whole-genome NGS-based CNV detection method and estimate its accuracy in theoretical and in silico settings. This method is partially based on the previously published non-invasive prenatal testing (NIPT) CNV detection method [ 18 , 19 ]. The main differences are the parameters of the reported CNVs—in the NIPT setting, the CNVs corresponding to more than 5% fetal fraction and at least 3 Mb in size were reported.…”

Copy number variant detection with low-coverage whole-genome sequencing is a viable alternative to the traditional array-CGH

“…GenomeScreen test is a result of evolving laboratory methods and bioinformatic tools validated in our laboratory and is currently available commercially. The genesis of the assay has begun with a basic NIPT test focused on noninvasive prenatal screening for three most common trisomies, continued with the addition of sex chromosomes aneuploidies, five selected microdeletions detection, and most recently moved to whole-genome scan for chromosomal microaberrations [18,24,25]. The common link between all these tests is the method based on low-coverage whole-genome sequencing.…”

“…We present GenomeScreen - low-coverage whole-genome NGS based CNV detection method (based on the previously published NIPT CNV detection method [9,10]) and estimate its accuracy in theoretical and in-silico settings. Furthermore, we compare its sensitivity to the more conventional aCGH method on 106 laboratory prepared clinical samples.…”

“…We present GenomeScreen – a low-coverage whole-genome NGS-based CNV detection method and estimate its accuracy in theoretical and in-silico settings. This method is partially based on the previously published NIPT CNV detection method [18,19]. The main differences are the parameters of reported CNVs - in the NIPT setting, CNVs corresponding to more than 5% fetal fraction and at least 3Mb in size were reported, here we focus on full (non-mosaic) aberrations with much shorter length (100 kb and larger).…”