Estimate of the contemporary live-birth prevalence of recurrent 22q11.2 deletions: a cross-sectional analysis from population-based newborn screening

Abstract

Background: Although pathogenic 22q11.2 deletions are an important cause of developmental delays and lifelong disease burden, their variable and complex clinical expression contributes to under-recognition, delayed molecular diagnosis and uncertainty about prevalence. We sought to estimate the contemporary live-birth prevalence of typical 22q11.2 deletions using a population-based newborn screening sample and to examine data available for associated clinical features.

Methods: Using DNA available from an unbiased sample of about 12% of all dried blood spots collected for newborn screening in Ontario between January 2017 and September 2018, we prospectively screened for 22q11.2 deletions using multiplex quantitative polymerase chain reaction assays and conducted independent confirmatory studies. We used cross-sectional analyses to compare available clinical and T-cell receptor excision circle (TREC, used in newborn screening for severe combined immunodeficiency) data between samples with and without 22q11.2 deletions.

Results: The estimated minimum prevalence of 22q11.2 deletions was 1 in 2148 (4.7 per 10 000) live births (95% confidence interval [CI] 2.5 to 7.8 per 10 000), based on a total of 30 074 samples screened, with 14 having confirmed 22q11.2 deletions. Of term singletons, samples with 22q11.2 deletions had significantly younger median maternal age (25.5 v. 32.0 yr, difference -6.5 yr, 95% CI -7 to -2 yr), a greater proportion with small birth weight for gestational age (odds ratio 7.00, 95% CI 2.36 to 23.18) and lower median TREC levels (108.9 v. 602.5 copies/3 μL, p < 0.001).

Interpretation: These results indicate that the 22q11.2 deletion syndrome is one of the most common of rare genetic conditions and may be associated with relatively younger maternal ages and with prenatal growth abnormalities. The findings support the public health importance of early - prenatal and neonatal - diagnosis that would enable prompt screening for and management of well-known actionable features associated with 22q11.2 deletions.

Figure 1:

Illustration of the common 22q11.2 deletion (about 3 megabases [Mb]) and the rarer proximal nested 22q11.2 deletions (about 2 Mb and about 1.5 Mb), as well as the approximate positions of genes for probes used to detect these deletions: 3 primary screening quantitative real-time polymerase chain reaction (qPCR) probes (UFD1L, COMT, CRKL, bold font, single asterisk), 15 genes for confirmatory multiplex ligation-dependent probe amplification studies (16 probes, including 2 at TBX1, and flanking probes at USP18 and HIC2), and 1 secondary screening qPCR probe (TBX1, 2 asterisks). Also shown are the relative positions of the low copy repeat (LCR) sequences (segmental duplications) that predispose this complex genomic region to de novo 22q11.2 deletion events at gametogenesis, and probes (N25 and TUPLE1) commonly used for targeted fluorescence in situ hybridization (FISH) studies that cannot determine the length of deletions. Clinical genome-wide microarray, the current standard for detecting pathogenic copy number variation,, provides information on deletion length and extent. Note: Cen = centromere.

Figure 2:

(A) Severe combined immunodeficiency screening results showing distribution of T-cell receptor excision circle (TREC) copies/3 μL for term singleton newborn screening samples, by 22q11.2 deletion status. For the term singleton subsample, the majority (7/13, 54%) of the 22q11.2 deletion group had fewer than 200 TREC copies/3 μL (about the 3rd percentile), whereas the greatest proportion of the remaining population-based group (13 297 [50%] of 26 435) had at least 600 TREC copies/3 μL. (B) Subset of term singleton newborn screening samples with lowest TREC values (< 200 copies/3 μL). Shown here are detailed distribution results for samples from the term singleton subsample. Overall, there were 859 with fewer than 200 TREC copies/3 μL, 7 with confirmed 22q11.2 deletion and 852 from the remaining population-based group. The dashed horizontal lines indicate where the scale changes for fine gradations: below 10, each mark on the y axis indicates 1 individual, and above 10, each mark on the y axis indicates 10 individuals. Six (46%) of the overall 13 term singleton samples with a confirmed 22q11.2 deletion had no more than 100 TREC copies/3 μL (to the left of the vertical dashed line), compared with 81 (0.3%) of the remaining population-based group (n = 26 435, p < 0.001). Currently, 100 TREC copies/3 μL is the cut-off in Ontario to undergo a secondary, more accurate TREC assay for final reporting of severe combined immunodeficiency identified by newborn screening.