مقالات پذیرفته شده در نهمین کنگره بین المللی زیست پزشکی
The application of next-generation sequencing technologies in newborn screening
The application of next-generation sequencing technologies in newborn screening
Behdokht Fathi Dizaji,1,*
1. Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
Introduction: Newborn screening (NBS) programs have facilitated the early diagnosis, proper intervention, and treatment of several neonatal disorders. However, Screening experiments have their limitations, including the amenability of conditions to screening due to a lack of biomarkers, sensitivity, and specificity. Next-generation sequencing (NGS) may offer the potential to overcome these limitations
Methods: This review provides a summarized overview of the application of (NGS) technologies in newborn screening via searching databases, Google Scholar, ScienceDirect, and PubMed.
Results: Due to advancements in (NGS) technologies and data interpretation, scientists have shown great interest in exploring NGS as a complement to conventional NBS methods. NGS can be classified as: whole genome sequencing (WGS), whole exome sequencing (WES), and targeted gene panel sequencing. To assess the usage of DNA sequencing in NBS, diverse studies are being conducted worldwide. Cereda et al. recruited gene panels to evaluate actionable neonatal/pediatric conditions. DNA was extracted from 34 dried blood samples (DBSs), yielding 500–1500 ng of DNA, with an A260/A280 wavelength ratio of 1.7–1.8. The DNA was then sequenced. Assessing the results of different panels exhibited that DBS from newborns is suitable for utilization in genomic NBS. The (NC NEXUS) project evaluated the use of exome sequencing (ES) in 106 children with metabolic or hearing loss disorders. ES confirmed the previous NBS diagnosis in 88% of children with metabolic disorders and18% of children with hearing loss. In four babies, practical findings that were not identified by traditional NBS were reported. They identified pathogenic variants causing breast/ovarian cancer in two children, a likely pathogenic variant in the gene causing Lowe syndrome in one child, and being a carrier for an average of 1.8 considerable variants per child. Therefore, NGS cannot be utilized without biochemical or phenotypic screening for etiologically heterogeneous conditions. The sequencing of responsible genes for diseases that are screened via traditional NBS may help improve sensitivity and specificity. In the NBSeq study, dried blood specimens of 4.5 million infants for almost all inborn errors of metabolism (IEM) disorders were assessed by WES, whose MS/MS results were positive, but follow-up tests found them healthy. WES showed a sensitivity of 88% and specificity of 98.4%, compared to MS/MS with 99.0% and 99.8%. Consequently, a single WES assay cannot be first-line screen for IEM in neonates. However, complementary to MS/MS provides appropriate, timely, and specific diagnosis, along with reducing false-positive results. The lack of a disease phenotype in NBS may lead to unsuccessful genomic screening. Another study analyzed 159 newborns of BabySeq study to evaluate actionable adult and childhood-onset disease risks through newborn genomic sequencing (nGS). nGS successfully identified carrier status and the risk of these conditions that were not recognized by current newborn screening modalities, the infant’s clinical information, or family history. Provisional results of the (GUARDIAN) study encompassing 4000 newborns from different ethnic and racial groups demonstrated a 3.7% positive screen rate in a well-defined gene panel. Thus, targeted gene panel analysis of a predetermined set of genes in a diverse newborn population is feasible and could expand the scope of newborn screening. One study in China found MeltPro HL assay, which detects 20 variants in four HL-related genes at once, is more suitable for newborn genetic screening in their studied population due to its cost and clinical performance than a targeted NGS analysis for genetic screening of Hearing loss (HL). However, the targeted NGS assay identifies 208 variants in 24 HL genes. Using this assay may substantially improve the diagnosis of the disorder in patients with heterozygous variants. Genome newborn screening of (UKB470K) via exploring 412 severe childhood genetic conditions, 342 genes with 53,855 pathogenic or likely pathogenic variants, was positive in 74% of cases, resulting in 97% false positives. Researchers devised a federated training method based on purifying hyper-selection to detect and remove false-positive variants. They identified that 2.0% of UKB470K adults were positive.
Conclusion: Next-generation sequencing in NBS, provides advantages, including the ability to screen conditions lacking biomarkers, being complementary to common NBS, which increases the sensitivity and specificity of conventional methods. The chance of modifying the disease list. The potential to avoid cofounding factors like metabolic state or gestational age, and data reanalysis. Nevertheless, its application encounters important challenges related to medical, feasibility, accuracy, privacy, consent, equity, and cost.