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

Area of Science:

• Biochemistry
• Genetics
• Neonatal Medicine

Background:

• Newborn screening (NBS) for primary carnitine deficiency (PCD) faces performance challenges.
• Current NBS methods for PCD exhibit suboptimal accuracy.

Purpose of the Study:

• To evaluate the feasibility of integrating next-generation sequencing (NGS) as a second-tier test for PCD.
• To enhance the diagnostic performance of PCD screening in newborns.

Main Methods:

• Screened 60,070 newborns for inherited metabolic disorders between March and December 2020.
• Selected newborns with free carnitine (C0) levels < 8.5 μmol/L for second-tier genetic testing.
• Utilized NGS for genetic analysis of selected newborns.

Main Results:

• 130 newborns underwent second-tier genetic testing due to low C0 levels.
• 30 newborns (23.08%) carried pathogenic SLC22A5 gene variants; 6 were diagnosed with PCD (incidence 1:10,012).
• The positive predictive value (PPV) reached 20% with the combined MS/MS NBS and second-tier NGS approach.

Conclusions:

• The combination of MS/MS-based NBS and second-tier NGS significantly improves PCD detection.
• This integrated approach effectively reduces false-positive rates in newborn screening for PCD.
• The study demonstrates the value of NGS as a confirmatory test for PCD.