Incorporating Next‐Generation Sequencing as a Second‐Tier Test for Primary Carnitine Deficiency.

Background: Newborn screening (NBS) for primary carnitine deficiency (PCD) has poor performance. This study aimed to evaluate the feasibility of incorporating next‐generation sequencing (NGS) as a second‐tier PCD test. Methods: Between March and December 2020, 60,070 newborns were screened for inherited metabolic disorders. Newborns with free carnitine (C0) levels below 8.5 μmol/L were selected for second‐tier genetic testing. Results: In total, 130 (0.22%) newborns with low C0 levels underwent second‐tier genetic testing, 87 (66.92%) had positive genetic testing results, and 30 (23.08%) carried pathogenic variants of the SLC22A5 gene. Six newborns were diagnosed with PCD. The incidence of PCD was approximately 1 in 1:10,012 newborns. The PPV reached 20% after combining with second‐tier NGS. Of the eight variants identified in patients with PCD, the three most common variants were c.760C>T (p.Arg254*), c.51C>G (p.Phe17Leu), and c.1400C>G (p.Ser467Cys). The C0 levels of patients with PCD were significantly lower than those of PCD carriers (p = 0.0026) and PCD‐negative individuals (p = 0.0005). Conclusions: Our results showed that the PPV reached 20% after combining with second‐tier NGS. The MS/MS‐based NBS and second‐tier NGS combination can effectively reduce the false‐positive rate and detect PCD in patients. [ABSTRACT FROM AUTHOR]