High Incidence of Severe Combined Immunodeficiency Disease in Saudi Arabia Detected Through Combined T Cell Receptor Excision Circle and Next Generation Sequencing of Newborn Dried Blood Spots

Abstract

Severe combined immunodeficiency disease (SCID) is the most severe form of primary immunodeficiency disorders (PID). T-cell receptor excision circle (TREC) copy number analysis is an efficient tool for population-based newborn screening (NBS) for SCID and other T cell lymphopenias. We sought to assess the incidence of SCID among Saudi newborn population and examine the feasibility of using targeted next generation sequencing PID gene panel (T-NGS PID) on DNA isolated from dried blood spots (DBSs) in routine NBS programs as a mutation screening tool for samples with low TREC count. Punches from 8,718 DBS collected on Guthrie cards were processed anonymously for the TREC assay. DNA was extracted from samples with confirmed low TREC count, then screened for 22q11.2 deletion syndrome by real-time polymerase chain reaction and for mutations in PID-related genes by T-NGS PID panel. Detected mutations were confirmed by Sanger sequencing. Sixteen out of the 8,718 samples were confirmed to have low TREC copy number. Autosomal recessive mutations in AK2, JAK3, and MTHFD1 were confirmed in three samples. Two additional samples were positive for the 22q11.2 deletion syndrome. In this study, we provide evidence for high incidence of SCID among Saudi population (1/2,906 live births) and demonstrate the feasibility of using T-NGS PID panel on DNA extracted from DBSs as a new reliable, rapid, and cost-effective mutation screening method for newborns with low TREC assay, which can be implemented as part of NBS programs for SCID.

Development of a Population-Based Newborn Screening Method for Severe Combined Immunodeficiency in Manitoba, Canada

“…This methodology could also be implemented in other Canadian provinces where these 2 founder mutations are also present in their Mennonite [14] and Indigenous communities [15] or can be adapted to other populations with their own specific founder mutations when there are false negative results with TRECS alone. Our approach is also conceptually similar to that described recently by Al-Mousa et al [7] using a Targeted-NGS [T-NGS] Primary Immunodeficiency panel in their Saudi population with a very high frequency of SCID. However, their approach is different from ours as T-NGS is a second tier mutation screening tool on DBS from Saudi newborns ascertained by low TREC assays.…”

“…Since then several countries including Israel [4], Taiwan [5] and one Canadian province of Ontario [6] have introduced newborn screening for SCID. Many others are conducting pilot projects or have proposals being considered [7][8][9][10]. The most widely used newborn screening test for SCID is the quantification of T-cell receptor excision circles (TREC) [11].…”

Newborn Screening for Primary Immunodeficiencies: The Gaps, Challenges, and Outlook for Developing Countries

“…Maternal drug history is important since maternal intake of azathioprine was associated with low KREC level in offspring (24,25). In addition, ethnic differences in cutoff levels of TRECs and KRECs exist and remain to be studied on a larger scale [ (20,23,(26)(27)(28)(29)(30); Figure 1].…”

“…The mean age of diagnosis is 2 years in the MENA region (32). A pilot study on NBS using TRECs and KRECs in Saudi Arabia showed an increase in the number of patients diagnosed to have SCID reaching an incidence of 1 in 2,906 live births (29), which is a much higher incidence than in California (1/65,000) live birth (41). This highlights the importance of implementing NBS for the early detection of SCID in MENA region countries.…”

Recurrent Demyelinating Episodes as Sole Manifestation of Inherited CD59 Deficiency

“…Genomic DNA was extracted from whole blood using EZ1 DNA Blood 200-μL Kit (Qiagen). Targeted NGS was performed using a primary immunodeficiency gene panel 4 and Ion Torrent PGM sequencer (ThermoFisher) with an average coverage of 130X.…”