Next generation sequencing as a follow-up test in an expanded newborn screening programme

Clin Biochem. 2018 Feb:52:48-55. doi: 10.1016/j.clinbiochem.2017.10.016. Epub 2017 Oct 27.

Abstract

Objectives: Contrary to many western European countries, most south-eastern European countries do not have an expanded newborn screening (NBS) program using tandem mass spectrometry. This study would represent one of the first expanded NBS studies in south-eastern Europe and will enable the estimation of the incidences of IEM in Slovenia. We proposed an expanded NBS approach including next-generation sequencing (NGS) as a confirmational analysis.

Design & methods: We conducted a pilot study of expanded NBS for selected inborn errors of metabolism (IEM) in Slovenia including 10,048 NBS cards. We used an approach including tandem mass spectrometry followed by second tier tests including NGS. Based on the NBS results, 85 children were evaluated at a metabolic follow-up; 80 of them were analyzed using NGS.

Results: Altogether, glutaric acidemia type 1 was confirmed in one patient who was a compound heterozygote for two known causative GCDH variants. A patient with suspected very long-chain acyl-CoA dehydrogenase deficiency had negative metabolic follow-up tests, but had two heterozygous ACADVL variants; one known disease-causing variant and one indel, namely c.205-8_205-7delinsGC, that is predicted to be causative. Nine participants had elevated metabolites characteristic of 3-methylcrotonyl-CoA carboxylase deficiency, 2 of them had known causative homozygous variants in MCCC1. The other seven were heterozygous; two had a novel genetic variant c.149_151dupCCA (p.Thr50dup). Cumulative incidences of IEM in Slovenia were similar to other European countries.

Conclusions: NGS proved to be valuable in explaining the abnormal metabolite concentrations in NBS as it enabled the differentiation between affected patients and mere heterozygotes, and it improved the turnaround time of genetic analysis. The results of this study will be instrumental in the routine implementation of expanded NBS in Slovenia.

Keywords: Inborn errors of metabolism; Incidence; Newborn screening; Next generation sequencing.

MeSH terms

  • Acyl-CoA Dehydrogenase, Long-Chain / deficiency
  • Amino Acid Metabolism, Inborn Errors / diagnosis
  • Brain Diseases, Metabolic / diagnosis
  • Carbon-Carbon Ligases / deficiency
  • Congenital Bone Marrow Failure Syndromes
  • Female
  • Follow-Up Studies
  • Glutaryl-CoA Dehydrogenase / deficiency
  • High-Throughput Nucleotide Sequencing / methods
  • Humans
  • Infant, Newborn
  • Lipid Metabolism, Inborn Errors / diagnosis
  • Male
  • Metabolism, Inborn Errors / diagnosis*
  • Mitochondrial Diseases / diagnosis
  • Muscular Diseases / diagnosis
  • Neonatal Screening / methods*
  • Pilot Projects
  • Slovenia
  • Tandem Mass Spectrometry / methods
  • Urea Cycle Disorders, Inborn / diagnosis

Substances

  • Glutaryl-CoA Dehydrogenase
  • Acyl-CoA Dehydrogenase, Long-Chain
  • Carbon-Carbon Ligases

Supplementary concepts

  • 3-methylcrotonyl CoA carboxylase 1 deficiency
  • Glutaric Acidemia I
  • VLCAD deficiency