Background: Non-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 anomalies including the 22q11.2 deletion. Previous validation studies of a SNP-based NIPT for detection of 22q11.2 deletions demonstrated high sensitivity (>95%) and specificity (>99.5%). Here, we validated a revised version of this test in a cohort of pregnancy plasma samples.
Materials and Methods: Blood samples were obtained from pregnant women with known 22q11.2 status. Ten positive control samples and 390 negative control samples were analyzed using a revised SNP-based NIPT for the 22q11.2 deletion. Samples were amplified and sequenced using pooled primer sets that included 1,351 SNPs spanning a 2.91Mb section of the 22q11.2 region. A risk score was assigned to all samples using a proprietary algorithm. The algorithm’s confidence threshold was raised to 0.95 and “high-risk” samples with deletion of the maternal haplotype were reflexively sequenced at high depth of read (14×106 reads/sample). The sensitivity and specificity of the assay were measured.
Results: Sensitivity of the assay was 90% (9/10), and specificity of 99.74% (389/390), with a corresponding false positive-rate of 0.26% were reported.
Conclusions: This validation of the revised SNP-based assay in a cohort of pregnancy plasma samples demonstrates a high sensitivity and specificity for detection of the 22q11.2 deletion. Given the benefits of early intervention in patients with the 22q11.2 deletion and the high incidence of the condition, this SNP-based methodology provides a valuable addition to current population-wide prenatal screening approaches.