Comparison of Four Screening Markers [(C16 + C18:1)/C2, C14/C3, C12/C0, and C12/C2] for Carnitine Palmitoyltransferase II Deficiency in the Nationwide Newborn Screening Program in Japan

False-positive results are known to occur frequently in newborn screening (NBS) for carnitine palmitoyltransferase II (CPT II) deficiency, highlighting the need to identify appropriate screening markers. The present study aimed to compare the performance of two markers currently used in NBS for CPT II deficiency, (C16 + C18:1)/C2 and C14/C3, with two promising alternative markers, C12/C0 and C12/C2. We analyzed non-patient data from the 2023 fiscal year NBS program together with patient data for CPT II deficiency and very-long-chain acyl-CoA dehydrogenase deficiency derived from previously reported case series. Marker performance was assessed using precision–recall curves, including an analysis in which patients with the myopathic form of CPT II deficiency who passed NBS using (C16 + C18:1)/C2 and C14/C3 were reclassified as true positives. The area under the precision–recall curve values for C12/C2 and C14/C3 were 0.711 (95% confidence interval, 0.492–0.923) and 0.569 (0.341–0.779), respectively, indicating superior performance compared with the other markers. When cases with the myopathic form of CPT II deficiency were included as true positives, the performance of all markers decreased markedly. Although some patients with the myopathic form are still likely to be missed, C12/C2 appears to be an effective marker for reducing false-positive results.