Next-generation sequencing of newborn screening genes: the accuracy of short-read mapping

Trier, Cassandra Nicole; Fournous, Ghislain; Strand, Janne; Stray-Pedersen, Asbjørg; Pettersen, Rolf D.; Rowe, Alexander D.

doi:10.1038/s41525-020-00142-z

Cited by 17 publications

(11 citation statements)

References 57 publications

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“…Technological challenges with short-read NGS technologies remain significant in highly homologous genomic regions, such as pseudogenes or paralogous genes and need to be considered when implemented in screening programs [95]. There is a technological challenge with the paralogous genes or pseudogenes due to the failure of the short reads in mapping to the specific gene [96].…”

Section: Is It Visible That Nucleic Acid Sequencing Will Replace the ...mentioning

confidence: 99%

Insights into National Laboratory Newborn Screening and Future Prospects

Mujamammi

2022

Medicina

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Newborn screening (NBS) is a group of tests that check all newborns for certain rare conditions, covering several genetic or metabolic disorders. The laboratory NBS is performed through blood testing. However, the conditions that newborn babies are screened for vary from one country to another. Since NBS began in the 1960s, technological advances have enabled its expansion to include an increasing number of disorders, and there is a national trend to further expand the NBS program. The use of mass spectrometry (MS) for the diagnosis of inborn errors of metabolism (IEM) obviously helps in the expansion of the screening panels. This technology allows the detection of different metabolic disorders at one run, replacing the use of traditional techniques. Analysis of the targeted pathogenic gene variant is a routine application in the molecular techniques for the NBS program as a confirmatory testing to the positive laboratory screening results. Recently, a lot of molecular investigations, such as next generation sequencing (NGS), have been introduced in the routine NBS program. Nowadays, NGS techniques are widely used in the diagnosis of IMD where its results are rapid, confirmed and reliable, but, due to its uncertainties and the nature of IEM, it necessitates a holistic approach for diagnosis. However, various characteristics found in NGS make it a potentially powerful tool for NBS. A range of disorders can be analyzed with a single assay directly, and samples can reduce costs and can largely be automated. For the implementation of a robust technology such as NGS in a mass NBS program, the main focus should not be just technologically biased; it should also be tested for its long- and short-term impact on the family and the child. The crucial question here is whether large-scale genomic sequencing can provide useful medical information beyond what current NBS is already providing and at what economical and emotional cost? Currently, the topic of newborn genome sequencing as a public health initiative remains argumentative. Thus, this article seeks the answer to the question: NGS for newborn screening- are we there yet?

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Section: Is It Visible That Nucleic Acid Sequencing Will Replace the ...mentioning

confidence: 99%

Insights into National Laboratory Newborn Screening and Future Prospects

Mujamammi

2022

Medicina

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“…Diagnostic accuracy may be improved by using various strategies, for example, applying different read length to genes with high homology to improve variant calling. 69 As aforementioned, WGS-based screening would circumvent many of the shortfalls of WES, but it has its own limitations. Rigorous quality assurance activities are required to ensure appropriate test performance, 2 including participation in internal and external quality control programs.…”

Section: Many Forms Of Iei Can Be Managed With Preventative and Suppomentioning

confidence: 99%

An appraisal of the Wilson & Jungner criteria in the context of genomic-based newborn screening for inborn errors of immunity

King

Notarangelo

Hammarström

2021

Journal of Allergy and Clinical Immunology

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Wilson and Jungner's recommendations for population-based screening have been used to guide decisions regarding candidate disease inclusion in newborn screening programs for the past 50 years. The advent of genomic-based technologies, including next-generation sequencing and its potential application to newborn screening, along with a changing landscape in terms of modern clinical practice and ethical, social, and legal considerations has led to a call for review of these criteria. Inborn errors of immunity (IEI) are a heterogeneous group of more than 450 genetically determined disorders of immunity, which are associated with significant morbidity and mortality, particularly where diagnosis and treatment are delayed. We argue that in addition to screening for severe combined immunodeficiency disease, which has already been initiated in several countries, other clinically significant IEI should be screened for at birth. Because of disease heterogeneity and identifiable genetic targets, a next-generation sequencing-based screening approach would be most suitable. A combination of worldwide experience and technological advances has improved our ability to diagnose and effectively treat patients with IEI. Considering IEI in the context of updated recommendations for population-based screening supports their potential inclusion as disease targets in newborn screening programs.

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“…Elective genomic testing (Lu et al, 2019) as an adjunct or replacement for newborn screening is being studied (Adhikari et al, 2020; Ceyhan‐Birsoy et al, 2019; Roman et al, 2020; Trier et al, 2020). The genetic diseases found at this website represent a useful starting point for programs planning to use genomic testing for newborn screening.…”

Section: Discussionmentioning

confidence: 99%

An online compendium of treatable genetic disorders

Bick

Dimmock

et al. 2020

American J of Med Genetics Pt C

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More than 4,000 genes have been associated with recognizable Mendelian/monogenic diseases. When faced with a new diagnosis of a rare genetic disorder, health care providers increasingly turn to internet resources for information to understand the disease and direct care. Unfortunately, it can be challenging to find information concerning treatment for rare diseases as key details are scattered across a number of authoritative websites and numerous journal articles. The website and associated mobile device application described in this article begin to address this challenge by providing a convenient, readily available starting point to find treatment information. The site, http://rx-genes.com (https://www.rx-genes.com/), is focused on those conditions where the treatment is directed against the mechanism of the disease and thereby alters the natural history of the disease. The website currently contains 633 disease entries that include references to disease information and treatment guidance, a brief summary of treatments, the inheritance pattern, a disease frequency (if known), nonmolecular confirmatory testing (if available), and a link to experimental treatments. Existing entries are continuously updated, and new entries are added as novel treatments appear in the literature.

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Next-generation sequencing of newborn screening genes: the accuracy of short-read mapping

Cited by 17 publications

References 57 publications

Insights into National Laboratory Newborn Screening and Future Prospects

Insights into National Laboratory Newborn Screening and Future Prospects

An appraisal of the Wilson & Jungner criteria in the context of genomic-based newborn screening for inborn errors of immunity

An online compendium of treatable genetic disorders

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