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

Mol Genet Genomic Med. 2024 Sep;12(9):e70003. doi: 10.1002/mgg3.70003.

Abstract

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.

Keywords: free carnitine; newborn screening; next‐generation sequencing; primary carnitine deficiency; second‐tier screening.

MeSH terms

  • Cardiomyopathies / diagnosis
  • Cardiomyopathies / genetics
  • Carnitine* / blood
  • Carnitine* / deficiency
  • Female
  • Genetic Testing* / methods
  • Genetic Testing* / standards
  • High-Throughput Nucleotide Sequencing* / methods
  • High-Throughput Nucleotide Sequencing* / standards
  • Humans
  • Hyperammonemia* / diagnosis
  • Hyperammonemia* / genetics
  • Infant, Newborn
  • Male
  • Muscular Diseases / diagnosis
  • Muscular Diseases / genetics
  • Mutation
  • Neonatal Screening / methods
  • Neonatal Screening / standards
  • Solute Carrier Family 22 Member 5* / genetics

Substances

  • Carnitine
  • Solute Carrier Family 22 Member 5
  • SLC22A5 protein, human

Supplementary concepts

  • Systemic carnitine deficiency