An Integrated Solution for Application of Next-Generation Sequencing in Newborn Screening

Next-generation sequencing (NGS) has greatly improved the diagnostic process for hereditary diseases, and incorporation of NGS into newborn screening (NBS) programs for more actionable diseases has been widely discussed. The aim of this study was to evaluate an integrated solution for application of NGS in newborn screening.

An NGS panel targeting 155 genes related to inborn errors of metabolism, hearing loss, severe combined immunodeficiency, congenital hypothyroidism, and other actionable genetic diseases, was designed. An all-in-one library preparation strategy was developed to combine multiplex PCR target enrichment and sample barcoding. A clinical genetic analysis system was assembled to facilitate bioinformatics analysis and reporting. The integrated solution was validated using 160 samples with known variants.

The end-to-end time from DNA isolation to sequencing was approximately 34 hours, and bioinformatics analysis pipeline took 4 hours for 160 samples in parallel. This allowed reporting of results on day 3. All known variants were confirmed by the NGS workflow, and two large insertion/deletions were additionally detected in two cases with previously clinically but not genetically confirmed diseases.

The integrated solution for application of NGS in NBS provided reasonable turnaround time to meet the NBS timeframe and could be implemented at scale.