Noninvasive prenatal testing (NIPT) is now clinically available for screening fetal subchromosomal copy number variations (CNVs).
The sensitivity of NIPT for CNVs is challenging to calculate in clinical settings because the number of the missed cases is unknown. This is attributable to the fact that CNV phenotypes can be invisible, mild, or progressive at birth, meaning that some cases require longitudinal follow-up to be identified.
The positive predictive value (PPV) of NIPT for genome-wide CNVs is 32% to 47%, which is comparable with the PPV for trisomy 13 (43.9%–53%).
Four critical factors affect the clinical validity of NIPT for detecting subchromosomal CNVs: fetal fraction, sequencing depth, CNV size, and technical variability of the CNV region. Increasing the fetal fraction and sequencing depth improves the NIPT detection rate of subchromosomal CNVs.
In 1997, the detection of male DNA in peripheral blood samples from women bearing male fetuses proved that fetal DNA circulates in maternal plasma and serum
. Circulating “fetal” cell-free DNA (cfDNA), which is mainly released from the placenta into maternal circulation, is used in noninvasive prenatal testing (NIPT). Currently, NIPT is primarily used to screen for 3 fetal aneuploidies, trisomy 21, trisomy 18, and trisomy 13, and its performance in detecting these has been well studied in both high-risk and low-risk populations . The high sensitivity, low false-positive rate, and high positive predictive value (PPV) of NIPT have led to its widespread clinical adoption. In recent years, NIPT has revolutionized the prenatal screening landscape and become a routine test in Belgium and the Netherlands ,
Researchers and clinicians have great interest in applying NIPT to screen subchromosomal copy number variations (CNVs) in addition to the 3 traditionally screened aneuploidies. In this review, the authors focus on the current status, development, and challenges of using NIPT to screen fetal subchromosomal CNVs in pregnancies.
Subchromosomal Copy Number Variations
Subchromosomal CNVs are abnormalities in which sections of the genome are deleted (loss) or duplicated (gain). They are relatively common in prenatal diagnosis. Wapner and coauthors
used chromosomal microarray analysis (CMA) to reveal that 2.5% of samples with normal karyotypes had a microdeletion or microduplication of clinical significance. Based on low-coverage genome sequencing, Wang and colleagues
reported that 5.3% of pregnant women undergoing prenatal diagnosis had pathogenic/likely pathogenic CNVs.
Subchromosomal CNVs are associated with severe phenotypes, including structural anomalies, intellectual disability, developmental delay, and autism spectrum disorders
. Some presentations, such as structural anomalies, are detectable by ultrasound scans; however, neurologic or neurocognitive features are undetectable via prenatal ultrasound scans. Currently, there are no screening options to identify CNVs at the prenatal stage . To fill this gap, the use of NIPT to screen subchromosomal CNVs is becoming more popular in clinics , ,.
Noninvasive Prenatal Testing for Subchromosomal Copy Number Variations
NIPT can detect aneuploidies through either targeted or random (genome-wide) sequencing, both of which are also technically feasible approaches for detecting subchromosomal CNVs
. The targeted approach relies on the amplification of informative single-nucleotide polymorphisms (SNPs) ; that is, a targeted SNP-based NIPT is designed to detect a preselected region. In comparison, genome-wide NIPT randomly sequences and analyzes all chromosomes, which has the inherent advantage of detecting CNVs anywhere in the genome instead of only in targeted regions.
Selected Copy Number Variations
A handful of selected CNVs with well-defined, severe phenotypes is included in the NIPT screening panel ( Table 1 ), including DiGeorge syndrome (22q11.2 deletion), Prader-Willi and Angelman syndromes (15q11.2-q13 deletion), 1p36 deletion syndrome, Cri-du-chat syndrome (terminal 5p deletion), Jacobsen syndrome (terminal 11q deletion), Wolf-Hirschhorn syndrome (terminal 4p deletion), and Langer-Giedion syndrome (8q24 deletion)
. Five of these conditions (DiGeorge syndrome, Prader-Willi/Angelman syndromes, 1p36 deletion syndrome, and Cri-du-chat syndrome) are the best validated and most reported , , . The remaining conditions, including Jacobsen syndrome, Wolf-Hirschhorn syndrome, and Langer-Giedion syndrome, are rarely reported .