Second-tier genetics improves newborn screening accuracy for SCID and other T cell deficiencies

Newborn screening (NBS) based on quantifying T cell receptor excision circles (TRECs) is highly sensitive for detecting severe combined immunodeficiency (SCID), but frequently results in false-positive referrals. These referrals contribute to parental distress, increased clinical workload, additional interventions, and costs. To increase the positive predictive value (PPV) for SCID and other T cell deficiencies with a genetic cause, we evaluated next-generation sequencing (NGS) as second-tier testing after TREC analysis. Targeted sequencing was performed on dried blood spots of 68 newborns referred from TREC-based NBS, and results were integrated with collected long-term follow-up data. A safety net algorithm was applied to maintain high sensitivity for SCID by directly referring newborns with profoundly reduced TRECs, increasing the PPV from 22% to 55% without missing patients with severe immunological phenotypes. Therefore, the clinical impact of not identifying non-severe T cell lymphopenia patients without a genetic diagnosis appears limited. These results demonstrate that second-tier NGS in TREC-based NBS improves screening accuracy for SCID and other T cell deficiencies.