Application of a next-generation sequencing (NGS) panel in newborn screening efficiently identifies inborn disorders of neonates

Abstract

Background Newborn screening (NBS) has been implemented for neonatal inborn disorders using various technology platforms, but false-positive and false-negative results are still common. In addition, target diseases of NBS are limited by suitable biomarkers. Here we sought to assess the feasibility of further improving the screening using next-generation sequencing technology. Methods We designed a newborn genetic sequencing (NBGS) panel based on multiplex PCR and next generation sequencing to analyze 134 genes of 74 inborn disorders, that were validated in 287 samples with previously known mutations. A retrospective cohort of 4986 newborns was analyzed and compared with the biochemical results to evaluate the performance of this panel. Results The accuracy of the panel was 99.65% with all samples, and 154 mutations from 287 samples were 100% detected. In 4986 newborns, a total of 113 newborns were detected with biallelic or hemizygous mutations, of which 36 newborns were positive for the same disorder by both NBGS and conventional NBS (C-NBS) and 77 individuals were NBGS positive/C-NBS negative. Importantly, 4 of the 77 newborns were diagnosed currently including 1 newborn with methylmalonic acidemia, 1 newborn with primary systemic carnitine deficiency and 2 newborns with Wilson’s disease. A total of 1326 newborns were found to be carriers with an overall carrier rate of 26.6%. Conclusion Analysis based on next generation sequencing could effectively identify neonates affected with more congenital disorders. Combined with C-NBS, this approach may improve the early and accurate identification of neonates with inborn disorders. Our study lays the foundation for prospective studies and for implementing NGS-based analysis in NBS.

Mutation spectrum of thalassemia among pre‐pregnant adults in the Jiangsu Province by capillary electrophoresis‐based multiplex PCR assay

“…Compared with traditional strategy for thalassemia carrier screening, NGS allows the generation of vast amounts of genomic data in order to reveal the genetic constitution of people and reduce the residual risks. Additionally, NGS continuously accumulates data on the variant lists based on new findings and reclassification, yielding high‐quality genotype calls and acceptable false‐positive and false‐negative rates (Fridman et al., 2020; Huang et al., 2022; Komlosi et al., 2018). However, NGS may identify many variants of uncertain significance, which is still a big challenge for many clinical laboratories (Vrijenhoek et al., 2015).…”

Determining the characteristics of genetic disorders that predict inclusion in newborn genomic sequencing programs

“…We included gene lists from 19 research studies: BabyDetect 20 , BabyScreen+ 16 , BabySeq2 17 , BeginNGS 18,21 , Chen et al 2023 22 , Early Check 23 , FirstSteps, the Generation study, gnSTAR 24,25 , GUARDIAN study, Jian et al 2022 26 , Lee et al 2019 27 , Luo et al 2020 28 , NeoExome 29 , NeoSeq 30 , NESTS 31 , NewbornsInSA, Progetto Genoma Puglia, and Wang et al 2023 32 . In two studies (GUARDIAN study and Early Check 23 ), participants receive testing for a gene list focused on conditions with effective treatments and have the option to be tested for an expanded gene list.…”

Newborn Screening of Primary Carnitine Deficiency: An Overview of Worldwide Practices and Pitfalls to Define an Algorithm before Expansion of Newborn Screening in France

“…To our knowledge, India still struggles to initiate a nationwide NBS program, and other Asian Pacific or Central Asia countries have not included PCD to their program to date [ 57 ]. The high incidence of PCD in Asian populations, along with the development of Next Generation Sequencing, have led to the emergence of a systematic study of the SLC22A5 gene as a second-tier testing after phenotypic screening [ 58 , 59 , 60 ].…”