Result of Prospective Validation of the Trisomy Test® for the Detection of Chromosomal Trisomies

Abstract

Noninvasive prenatal testing (NIPT) is one of the most common prenatal screening tests used worldwide. Trisomy Test® belongs to NIPT tests based on low-coverage whole-genome sequencing. In our prospective study, 7279 samples of pregnant women collected during approximately two years were analyzed. In this cohort, 117 positive cases for trisomies 21, 18, and 13 were reported. An in-house designed bioinformatic pipeline and proprietary biostatistical approach was used for the detection of trisomies. The pooled sensitivity and specificity of our test reached 99.12% and 99.94%, respectively. The proportion of repeatedly uninformative results after repeated blood draws was 1.11%. Based on the presented results, we can confirm that the Trisomy Test® is fully comparable with other commercial NIPT tests available worldwide.

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

“…The theoretical minimum of reads for predicting a variation with length l c with the desired Z-score ( Z ) is estimated as (see Section 4.2): Standardly, a Z-score of 4 is used in the detection of whole chromosomal aneuploidies [24,25]; however, there are inherently more possible CNVs than whole chromosomal aneuploidies. Thus, the desired Z-score should be much higher in this instance to decrease the number of false positives.…”

“…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.…”

“…Standardly, Z-score of 4 is used in the detection of whole chromosomal aneuploidies [11,12] ; however, there are inherently more possible CNVs as whole chromosomal aneuploidies. Thus, the desired Z-score should be much higher in this instance to decrease the number of false positives.…”

Technical and Methodological Aspects of Cell-Free Nucleic Acids Analyzes

“…With regard to cfNAs applications, even in cases of fragments having different origins, such as fetal NAs in maternal plasma or cancer genomes in patient plasma, entire genomes can be characterized using MPS. Although using highly different read depths, genome-scale high-throughput screening and genotyping of the majority of DNA variant types was reported, from characterization of epigenetic markers of NAs [ 295 , 296 ], through SNVs and a wide range of CNVs [ 297 , 298 , 299 ], including even microsatellites [ 300 ] and chromosomal aneuploidies [ 301 ]. Moreover, highly sensitive MPS approaches may be further modified to achieve even higher sensitivity of detection and quantification of low frequency mutations in plasma, for example using modifications such as the Safe-Sequencing System (Safe-SeqS).…”

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

“…For adapter-ligated DNA library construction, a TruSeq Nano (Illumina, San Diego, CA, USA) kit with an in-house optimized protocol was used as previously published [ 14 , 15 ]. The starting input of cfDNA was typically less than 5 ng (~ 0.1 ng/µl).…”