Validation of amplicon-based next generation sequencing panel for second-tier test in newborn screening for inborn errors of metabolism

• Published in: Journal of laboratory medicine 2021-12, Vol.45 (6), p.267-274
• Main Authors: Tsang, Kwok Yeung, Chan, Toby Chun Hei, Yeung, Matthew Chun Wing, Wong, Tsz Ki, Lau, Wan Ting, Mak, Chloe Miu
• Format: Article
• Language: English
• Subjects: Deoxyribonucleic acid; DNA; DNA sequencing; dried blood spot (dbs); Errors; Genes; Genomes; Inborn errors of metabolism; inborn errors of metabolism (iem); Libraries; Medical screening; Metabolism; newborn screening (nbs); next generation sequencing (ngs); Next-generation sequencing; Nucleotide sequence; Quality assurance; Quality control; second-tier test
• ISSN: 2567-9430; 0342-3026; 2567-9449; 1439-0477
• DOI: 10.1515/labmed-2021-0115

Next generation sequencing (NGS) technology has allowed cost-effective massive parallel DNA sequencing. To evaluate the utility of NGS for newborn screening (NBS) of inborn errors of metabolism (IEM), a custom panel was designed to target 87 disease-related genes. The pilot study was primarily proposed for second-tier testing under the NBSIEM program in Hong Kong.The validation of the panel was performed with two reference genomes and an external quality assurance (EQA) sample. Sequencing libraries were synthesized with amplicon-based approach. The libraries were pooled, spiked-in with 2% PhiX DNA as technical control, for 16-plex sequencing runs. Sequenced reads were analyzed using a commercially available pipeline.The average target region coverage was 208× and the fraction of region with target depth ≥20× was 95.7%, with a sensitivity of 91.2%. There were 85 out of 87 genes with acceptable coverage, and EQA result was satisfactory. The turnaround time from DNA extraction to completion of variant calling and quality control (QC) procedures was 2.5 days.The NGS approach with the amplicon-based panel has been validated for analytical performance and is suitable for second-tier NBSIEM test.