Validation of a SNP-based non-invasive prenatal test to detect the fetal 22q11.2 deletion in maternal plasma samples

Abstract

IntroductionNon-invasive prenatal testing (NIPT) for aneuploidy using cell-free DNA in maternal plasma has been widely adopted. Recently, NIPT coverage has expanded to detect subchromosomal abnormalities including the 22q11.2 deletion. Validation of a SNP-based NIPT for detection of 22q11.2 deletions demonstrating a high sensitivity (97.8%) and specificity (99.75%) has been reported. We sought to further demonstrate the performance of a revised version of the test in a larger set of pregnancy plasma samples.MethodsBlood samples from pregnant women (10 with 22q11.2-deletion‒affected fetuses and 390 negative controls) were successfully analyzed using a revised SNP-based NIPT for the 22q11.2 deletion. The sensitivity and specificity of the assay were measured.ResultsSensitivity of the assay was 90% (9/10), and specificity of the assay was 99.74% (389/390), with a corresponding false positive-rate of 0.26%.DiscussionThe data presented in this study add to the growing body of evidence demonstrating the ability of the SNP-based NIPT to detect 22q11.2 deletions with high sensitivity and specificity.

The Genetics and Epigenetics of 22q11.2 Deletion Syndrome

“…Innovations in whole genome sequencing and DNA-based microarrays also make possible an accurate diagnosis of 22q11.2del in the developing fetus using maternal blood sampling (Yatsenko et al, 2015;Schmid et al, 2017). These non-invasive prenatal tests are very sensitive and have low false positive discovery rates (Ravi et al, 2018). Improvements in sequencing limited amounts of fetal DNA from maternal sampling is moving the field to 1 st trimester screening (Srinivasan et al, 2013;Helgeson et al, 2015) (ClinicalTrials.gov Identifier: NCT03375359).…”

“…DiGeorge syndrome is first suggested following newborn screens for detecting the levels T-cell receptor excision circles (TRECs) as a measure of T cell output from the thymus ( Table 1) (Botto et al, 2003;Kobrynski and Sullivan, 2007;Mcdonald-Mcginn et al, 2015). Low TRECs can be an indicator of DiGeorge syndrome, with the diagnosis of 22q11.2del subsequently established by FISH or chromosomal microarray technologies (Kwan et al, 2014;Van Der Spek et al, 2015;Schmid et al, 2017;Ravi et al, 2018). The heterogeneous congenital problems for 22q11.2del patients arise from defective remodeling of the pharyngeal region during embryogenesis (Sullivan, 2004;Bassett et al, 2005;Kobrynski and Sullivan, 2007;Fung et al, 2015;Guna et al, 2015;Mcdonald-Mcginn et al, 2015;Baldini et al, 2016).…”

Chromosome 22q11.2 deletion syndrome and DiGeorge syndrome

“…This was recently piloted for 22q11.2del. Additional efforts based on cell‐free DNA from maternal serum have been developed that utilize single nucleotide polymorphism arrays and multiplex PCR . Further assessment of sensitivity and specificity will be critical as these are offered commercially.…”

Noninvasive screening by cell‐free DNA for 22q11.2 deletion: Benefits, limitations, and challenges

“…Targeted and genome‐wide cfDNA tests have both been proposed as a screening tests for the detection of panels of microdeletions and microduplications, in particular for 22q11.2DS due to this syndrome's prevalence and clinical importance (Table ) …”

“…Analytic validation of test performance has been reported on artificial samples and real plasma samples for three targeted technologies: single nucleotide polymorphisms‐based (SNP‐based), digital analysis of selected regions (DANSR), and targeted capture enrichment assay (TCEA) technologies (Table ) . Results from experiments with artificial samples created by spiking plasma/genomic samples to simulate cfDNA should be considered with caution as these samples may not reflect the analytical performance of real plasma samples.…”