1
|
King JR, Grill K, Hammarström L. Genomic-Based Newborn Screening for Inborn Errors of Immunity: Practical and Ethical Considerations. Int J Neonatal Screen 2023; 9:ijns9020022. [PMID: 37092516 PMCID: PMC10123688 DOI: 10.3390/ijns9020022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 03/27/2023] [Accepted: 03/29/2023] [Indexed: 04/25/2023] Open
Abstract
Inborn errors of immunity (IEI) are a group of over 450 genetically distinct conditions associated with significant morbidity and mortality, for which early diagnosis and treatment improve outcomes. Newborn screening for severe combined immunodeficiency (SCID) is currently underway in several countries, utilising a DNA-based technique to quantify T cell receptor excision circles (TREC) and kappa-deleting recombination excision circles (KREC). This strategy will only identify those infants with an IEI associated with T and/or B cell lymphopenia. Other severe forms of IEI will not be detected. Up-front, first-tier genomic-based newborn screening has been proposed as a potential approach by which to concurrently screen infants for hundreds of monogenic diseases at birth. Given the clinical, phenotypic and genetic heterogeneity of IEI, a next-generation sequencing-based newborn screening approach would be suitable. There are, however, several ethical, legal and social issues which must be evaluated in detail prior to adopting a genomic-based newborn screening approach, and these are discussed herein in the context of IEI.
Collapse
Affiliation(s)
- Jovanka R King
- Department of Allergy & Clinical Immunology, Women's and Children's Hospital Network, North Adelaide, SA 5006, Australia
- Immunology Directorate, SA Pathology, Adelaide, SA 5000, Australia
- Robinson Research Institute and Discipline of Paediatrics, School of Medicine, University of Adelaide, North Adelaide, SA 5006, Australia
| | - Kalle Grill
- Department of Historical, Philosophical and Religious Studies, Umeå University, SE-90187 Umeå, Sweden
| | - Lennart Hammarström
- Department of Biosciences and Nutrition, Neo, Karolinska Institutet, SE-14183 Huddinge, Sweden
| |
Collapse
|
2
|
Kingsmore SF, Smith LD, Kunard CM, Bainbridge M, Batalov S, Benson W, Blincow E, Caylor S, Chambers C, Del Angel G, Dimmock DP, Ding Y, Ellsworth K, Feigenbaum A, Frise E, Green RC, Guidugli L, Hall KP, Hansen C, Hobbs CA, Kahn SD, Kiel M, Van Der Kraan L, Krilow C, Kwon YH, Madhavrao L, Le J, Lefebvre S, Mardach R, Mowrey WR, Oh D, Owen MJ, Powley G, Scharer G, Shelnutt S, Tokita M, Mehtalia SS, Oriol A, Papadopoulos S, Perry J, Rosales E, Sanford E, Schwartz S, Tran D, Reese MG, Wright M, Veeraraghavan N, Wigby K, Willis MJ, Wolen AR, Defay. T. A genome sequencing system for universal newborn screening, diagnosis, and precision medicine for severe genetic diseases. Am J Hum Genet 2022; 109:1605-1619. [PMID: 36007526 PMCID: PMC9502059 DOI: 10.1016/j.ajhg.2022.08.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/01/2022] [Indexed: 12/31/2022] Open
Abstract
Newborn screening (NBS) dramatically improves outcomes in severe childhood disorders by treatment before symptom onset. In many genetic diseases, however, outcomes remain poor because NBS has lagged behind drug development. Rapid whole-genome sequencing (rWGS) is attractive for comprehensive NBS because it concomitantly examines almost all genetic diseases and is gaining acceptance for genetic disease diagnosis in ill newborns. We describe prototypic methods for scalable, parentally consented, feedback-informed NBS and diagnosis of genetic diseases by rWGS and virtual, acute management guidance (NBS-rWGS). Using established criteria and the Delphi method, we reviewed 457 genetic diseases for NBS-rWGS, retaining 388 (85%) with effective treatments. Simulated NBS-rWGS in 454,707 UK Biobank subjects with 29,865 pathogenic or likely pathogenic variants associated with 388 disorders had a true negative rate (specificity) of 99.7% following root cause analysis. In 2,208 critically ill children with suspected genetic disorders and 2,168 of their parents, simulated NBS-rWGS for 388 disorders identified 104 (87%) of 119 diagnoses previously made by rWGS and 15 findings not previously reported (NBS-rWGS negative predictive value 99.6%, true positive rate [sensitivity] 88.8%). Retrospective NBS-rWGS diagnosed 15 children with disorders that had been undetected by conventional NBS. In 43 of the 104 children, had NBS-rWGS-based interventions been started on day of life 5, the Delphi consensus was that symptoms could have been avoided completely in seven critically ill children, mostly in 21, and partially in 13. We invite groups worldwide to refine these NBS-rWGS conditions and join us to prospectively examine clinical utility and cost effectiveness.
Collapse
Affiliation(s)
- Stephen F. Kingsmore
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA,Keck Graduate Institute, Claremont, CA 91711, USA,Corresponding author
| | - Laurie D. Smith
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA
| | | | - Matthew Bainbridge
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | - Sergey Batalov
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | - Wendy Benson
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | - Eric Blincow
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | - Sara Caylor
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | - Christina Chambers
- Department of Pediatrics, University of California San Diego, San Diego, CA 92093, USA
| | | | - David P. Dimmock
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | - Yan Ding
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | - Katarzyna Ellsworth
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | - Annette Feigenbaum
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA,Department of Pediatrics, University of California San Diego, San Diego, CA 92093, USA
| | - Erwin Frise
- Fabric Genomics, Inc., Oakland, CA 94612, USA
| | - Robert C. Green
- Mass General Brigham, Broad Institute, Ariadne Labs and Harvard Medical School, Boston, MA 02115, USA
| | - Lucia Guidugli
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | | | - Christian Hansen
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | - Charlotte A. Hobbs
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | | | - Mark Kiel
- Genomenon Inc., Ann Arbor, MI 48108, USA
| | - Lucita Van Der Kraan
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | | | - Yong H. Kwon
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | - Lakshminarasimha Madhavrao
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | - Jennie Le
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | | | - Rebecca Mardach
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA,Department of Pediatrics, University of California San Diego, San Diego, CA 92093, USA
| | | | - Danny Oh
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | - Mallory J. Owen
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | | | - Gunter Scharer
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA
| | | | - Mari Tokita
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | | | - Albert Oriol
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | | | - James Perry
- Rady Children’s Hospital, San Diego, CA 92123, USA,Department of Pediatrics, University of California San Diego, San Diego, CA 92093, USA
| | - Edwin Rosales
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | - Erica Sanford
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA
| | | | - Duke Tran
- Illumina, Inc., San Diego, CA 92122, USA
| | | | - Meredith Wright
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | - Narayanan Veeraraghavan
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | - Kristen Wigby
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA,Department of Pediatrics, University of California San Diego, San Diego, CA 92093, USA
| | - Mary J. Willis
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA
| | | | - Thomas Defay.
- Alexion, Astra Zeneca Rare Disease, Boston, MA 02210, USA
| |
Collapse
|
3
|
Rahimzadeh V, Friedman JM, de Wert G, Knoppers BM. Exome/Genome-Wide Testing in Newborn Screening: A Proportionate Path Forward. Front Genet 2022; 13:865400. [PMID: 35860465 PMCID: PMC9289115 DOI: 10.3389/fgene.2022.865400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 05/27/2022] [Indexed: 11/20/2022] Open
Abstract
Population-based newborn screening (NBS) is among the most effective public health programs ever launched, improving health outcomes for newborns who screen positive worldwide through early detection and clinical intervention for genetic disorders discovered in the earliest hours of life. Key to the success of newborn screening programs has been near universal accessibility and participation. Interest has been building to expand newborn screening programs to also include many rare genetic diseases that can now be identified by exome or genome sequencing (ES/GS). Significant declines in sequencing costs as well as improvements to sequencing technologies have enabled researchers to elucidate novel gene-disease associations that motivate possible expansion of newborn screening programs. In this paper we consider recommendations from professional genetic societies in Europe and North America in light of scientific advances in ES/GS and our current understanding of the limitations of ES/GS approaches in the NBS context. We invoke the principle of proportionality—that benefits clearly outweigh associated risks—and the human right to benefit from science to argue that rigorous evidence is still needed for ES/GS that demonstrates clinical utility, accurate genomic variant interpretation, cost effectiveness and universal accessibility of testing and necessary follow-up care and treatment. Confirmatory or second-tier testing using ES/GS may be appropriate as an adjunct to conventional newborn screening in some circumstances. Such cases could serve as important testbeds from which to gather data on relevant programmatic barriers and facilitators to wider ES/GS implementation.
Collapse
Affiliation(s)
- Vasiliki Rahimzadeh
- Stanford Center for Biomedical Ethics, Stanford University, Stanford, CA, United States
- *Correspondence: Vasiliki Rahimzadeh,
| | - Jan M. Friedman
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Guido de Wert
- Department of Health, Ethics and Society, Maastricht University, Maastricht, Netherlands
| | | |
Collapse
|
4
|
Kingsmore SF. Dispatches from Biotech beginning BeginNGS: Rapid newborn genome sequencing to end the diagnostic and therapeutic odyssey. AMERICAN JOURNAL OF MEDICAL GENETICS. PART C, SEMINARS IN MEDICAL GENETICS 2022; 190:243-256. [PMID: 36218021 PMCID: PMC9588745 DOI: 10.1002/ajmg.c.32005] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/29/2022] [Accepted: 08/29/2022] [Indexed: 01/11/2023]
Abstract
In this Dispatch from Biotech, we briefly review the urgent need for extensive expansion of newborn screening (NBS) by genomic sequencing, and the reasons why early attempts had limited success. During the next decade transformative developments will continue in society and in the pharmaceutical, biotechnology, informatics, and medical sectors that enable prompt addition of genetic disorders to NBS by rapid whole genome sequencing (rWGS) upon introduction of new therapies that qualify them according to the Wilson and Jungner criteria (Wilson, J. M. G., & Jungner, G., World Health Organization. (1968). Principles and Practice of Screening for Disease. World Health Organization. Retrieved from https://apps.who.int/iris/handle/10665/37650). Herein we describe plans, progress, and clinical trial designs for BeginNGS (Newborn Genome Sequencing to end the diagnostic and therapeutic odyssey), a new international, pre-competitive, public-private consortium that proposes to implement a self-learning healthcare delivery system for screening all newborns for over 400 hundred genetic diseases, diagnostic confirmation, implementation of effective treatment, and acceleration of orphan drug development. We invite investigators and stakeholders worldwide to join the consortium in a prospective, multi-center, international trial of the clinical utility and cost effectiveness of BeginNGS.
Collapse
Affiliation(s)
- Stephen F. Kingsmore
- Rady Children's Institute for Genomic Medicine, Rady Children's HospitalSan DiegoCaliforniaUSA
| | | |
Collapse
|
5
|
Implementation of Hospital-Based Supplemental Duchenne Muscular Dystrophy Newborn Screening (sDMDNBS): A Pathway to Broadening Adoption. Int J Neonatal Screen 2021; 7:ijns7040077. [PMID: 34842620 PMCID: PMC8629008 DOI: 10.3390/ijns7040077] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 10/29/2021] [Accepted: 11/08/2021] [Indexed: 12/14/2022] Open
Abstract
Duchenne muscular dystrophy (DMD) is not currently part of mandatory newborn screening, despite the availability of a test since 1975. In the absence of screening, a DMD diagnosis is often not established in patients until 3-6 years of age. During this time, irreversible muscle degeneration takes place, and clinicians agree that the earlier therapy is initiated, the better the long-term outcome. With recent availability of FDA-approved DMD therapies, interest has renewed for adoption by state public health programs, but such implementation is a multiyear process. To speed access to approved therapies, we implemented a unique, hospital-based program offering parents of newborns an optional, supplemental DMD newborn screen (NBS) via a two-tiered approach: utilizing a creatine kinase (CK) enzyme assay coupled with rapid targeted next-generation sequencing (tNGS) for the DMD gene (using a Whole-Exome Sequencing (WES) assay). The tNGS/WES assay integrates the ability to detect both point mutations and large deletion/duplication events. This tiered newborn screening approach allows for the opportunity to improve treatment and outcomes, avoid the diagnostic delays, and diminish healthcare disparities. To implement this screening algorithm through hospitals in a way that would ultimately be acceptable to public health laboratories, we chose an FDA-approved CK-MM immunoassay to avoid the risks of false-negative/-positive results. Because newborn CK values can be affected due to non-DMD-related causes such as birth trauma, a confirmatory repeat CK assay on a later dried blood spot (DBS) collection has been proposed. Difficulties associated with non-routine repeat DBS collection, including the tracking and recall of families, and the potential creation of parental anxiety associated with false-positive results, can be avoided with this algorithm. Whereas a DMD diagnosis is essentially ruled out by the absence of detected DMD sequence abnormalities, a subsequent CK would still be warranted to confirm resolution of the initial elevation, and thus the absence of non-DMD muscular dystrophy or other pathologies. To date, we have screened over 1500 newborns (uptake rate of ~80%) by a CK-MM assay, and reflexed DMD tNGS in 29 of those babies. We expect the experience from this screening effort will serve as a model that will allow further expansion to other hospital systems until a universal public health screening is established.
Collapse
|
6
|
Ruiz-Schultz N, Asay B, Rohrwasser A. Scalable Newborn Screening Solutions: Bioinformatics and Next-Generation Sequencing. Int J Neonatal Screen 2021; 7:ijns7040063. [PMID: 34698050 PMCID: PMC8544371 DOI: 10.3390/ijns7040063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 08/25/2021] [Accepted: 09/23/2021] [Indexed: 11/20/2022] Open
Abstract
Expansion of the newborn disorder panel requires the incorporation of new testing modalities. This is especially true for disorders lacking robust biomarkers for detection in primary screening methods and for disorders requiring genotyping or sequencing as a second-tier and/or diagnostic test. In this commentary, we discuss how next-generation sequencing (NGS) methods can be used as a secondary testing method in NBS. Additionally, we elaborate on the importance of genomic variant repositories for the annotation and interpretation of variants. Barriers to the incorporation of NGS and bioinformatics within NBS are discussed, and ideas for a regional bioinformatics model and shared variant repository are presented as potential solutions.
Collapse
|
7
|
Nisar H, Wajid B, Shahid S, Anwar F, Wajid I, Khatoon A, Sattar MU, Sadaf S. Whole-genome sequencing as a first-tier diagnostic framework for rare genetic diseases. Exp Biol Med (Maywood) 2021; 246:2610-2617. [PMID: 34521224 DOI: 10.1177/15353702211040046] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Rare diseases affect nearly 300 million people globally with most patients aged five or less. Traditional diagnostic approaches have provided much of the diagnosis; however, there are limitations. For instance, simply inadequate and untimely diagnosis adversely affects both the patient and their families. This review advocates the use of whole genome sequencing in clinical settings for diagnosis of rare genetic diseases by showcasing five case studies. These examples specifically describe the utilization of whole genome sequencing, which helped in providing relief to patients via correct diagnosis followed by use of precision medicine.
Collapse
Affiliation(s)
- Haseeb Nisar
- Office of Research, Innovation and Commercialization, University of Management and Technology, Lahore 54000, Pakistan.,School of Biochemistry & Biotechnology, University of the Punjab, Lahore 54000, Pakistan
| | - Bilal Wajid
- Department of Electrical Engineering, University of Engineering and Technology, Lahore 54000, Pakistan.,Ibn Sina Research & Development Division, Sabz-Qalam, Lahore 54000, Pakistan.,Department of Computer Sciences, University of Management and Technology, Lahore 54000, Pakistan
| | - Samiah Shahid
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore 54000, Pakistan
| | - Faria Anwar
- Out Patient Department, Mayo Hospital, Lahore 54000, Pakistan
| | - Imran Wajid
- Ibn Sina Research & Development Division, Sabz-Qalam, Lahore 54000, Pakistan
| | - Asia Khatoon
- School of Biochemistry & Biotechnology, University of the Punjab, Lahore 54000, Pakistan
| | - Mian Usman Sattar
- Institute of Social Sciences, Istanbul Commerce University, Istanbul, Turkey
| | - Saima Sadaf
- School of Biochemistry & Biotechnology, University of the Punjab, Lahore 54000, Pakistan
| |
Collapse
|
8
|
Lund AM, Wibrand F, Skogstrand K, Bækvad-Hansen M, Gregersen N, Andresen BS, Hougaard DM, Dunø M, Olsen RKJ. Use of Molecular Genetic Analyses in Danish Routine Newborn Screening. Int J Neonatal Screen 2021; 7:ijns7030050. [PMID: 34449524 PMCID: PMC8395600 DOI: 10.3390/ijns7030050] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/19/2021] [Accepted: 07/22/2021] [Indexed: 12/20/2022] Open
Abstract
Historically, the analyses used for newborn screening (NBS) were biochemical, but increasingly, molecular genetic analyses are being introduced in the workflow. We describe the application of molecular genetic analyses in the Danish NBS programme and show that second-tier molecular genetic testing is useful to reduce the false positive rate while simultaneously providing information about the precise molecular genetic variant and thus informing therapeutic strategy and easing providing information to parents. When molecular genetic analyses are applied as second-tier testing, valuable functional data from biochemical methods are available and in our view, such targeted NGS technology should be implemented when possible in the NBS workflow. First-tier NGS technology may be a promising future possibility for disorders without a reliable biomarker and as a general approach to increase the adaptability of NBS for a broader range of genetic diseases, which is important in the current landscape of quickly evolving new therapeutic possibilities. However, studies on feasibility, sensitivity, and specificity are needed as well as more insight into what views the general population has towards using genetic analyses in NBS. This may be sensitive to some and could have potentially negative consequences for the NBS programme.
Collapse
Affiliation(s)
- Allan Meldgaard Lund
- Center for Inherited Metabolic Disorders, Departments of Clinical Genetics and Pediatrics, Copenhagen University Hospital, 2100 Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
- Correspondence: ; Fax: +45-35454072
| | - Flemming Wibrand
- Metabolic Laboratory, Department of Clinical Genetics, Copenhagen University Hospital, 2100 Copenhagen, Denmark;
| | - Kristin Skogstrand
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institute, 2300 Copenhagen, Denmark; (K.S.); (M.B.-H.); (D.M.H.)
| | - Marie Bækvad-Hansen
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institute, 2300 Copenhagen, Denmark; (K.S.); (M.B.-H.); (D.M.H.)
| | - Niels Gregersen
- Research Unit for Molecular Medicine, Department of Clinical Medicine, Aarhus University and Aarhus University Hospital, 8200 Aarhus, Denmark; (N.G.); (R.K.J.O.)
| | - Brage Storstein Andresen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark;
| | - David M. Hougaard
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institute, 2300 Copenhagen, Denmark; (K.S.); (M.B.-H.); (D.M.H.)
| | - Morten Dunø
- Molecular Genetics Laboratory, Department of Clinical Genetics, Copenhagen University Hospital, 2100 Copenhagen, Denmark;
| | - Rikke Katrine Jentoft Olsen
- Research Unit for Molecular Medicine, Department of Clinical Medicine, Aarhus University and Aarhus University Hospital, 8200 Aarhus, Denmark; (N.G.); (R.K.J.O.)
| |
Collapse
|
9
|
Abstract
IMPORTANCE Genomic newborn screening (gNBS) may optimize the health and well-being of children and families. Screening programs are required to be evidence based, acceptable, and beneficial. OBJECTIVES To identify what has been discovered following the reporting of the first gNBS pilot projects and to provide a summary of key points for the design of gNBS. EVIDENCE REVIEW A systematic literature review was performed on April 14, 2021, identifying 36 articles that addressed the following questions: (1) what is the interest in and what would be the uptake of gNBS? (2) what diseases and genes should be included? (3) what is the validity and utility of gNBS? and (4) what are the ethical, legal, and social implications? Articles were only included if they generated new evidence; all opinion pieces were excluded. FINDINGS In the 36 articles included, there was high concordance, except for gene disease inclusion, which was highly variable. Key findings were the need for equitable access, appropriate educational materials, and informed and flexible consent. The process for selecting genes for testing should be transparent and reflect that parents value the certainty of prediction over actionability. Data should be analyzed in a way that minimizes uncertainty and incidental findings. The expansion of traditional newborn screening (tNBS) to identify more life-threatening and treatable diseases needs to be balanced against the complexity of consenting parents of newborns for genomic testing as well as the risk that overall uptake of tNBS may decline. The literature reflected that the right of a child to self-determination should be valued more than the possibility of the whole family benefiting from a newborn genomic test. CONCLUSIONS AND RELEVANCE The findings of this systematic review suggest that implementing gNBS will require a nuanced approach. There are gaps in our knowledge, such as the views of diverse populations, the capabilities of health systems, and health economic implications. It will be essential to rigorously evaluate outcomes and ensure programs can evolve to maximize benefit.
Collapse
Affiliation(s)
- Lilian Downie
- Murdoch Children’s Research Institute, Melbourne, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Jane Halliday
- Murdoch Children’s Research Institute, Melbourne, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Sharon Lewis
- Murdoch Children’s Research Institute, Melbourne, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - David J. Amor
- Murdoch Children’s Research Institute, Melbourne, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
- Royal Children’s Hospital, Melbourne, Victoria, Australia
- Victorian Clinical Genetics Services, Melbourne, Victoria, Australia
| |
Collapse
|
10
|
Woerner AC, Gallagher RC, Vockley J, Adhikari AN. The Use of Whole Genome and Exome Sequencing for Newborn Screening: Challenges and Opportunities for Population Health. Front Pediatr 2021; 9:663752. [PMID: 34350142 PMCID: PMC8326411 DOI: 10.3389/fped.2021.663752] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 06/07/2021] [Indexed: 01/01/2023] Open
Abstract
Newborn screening (NBS) is a population-based program with a goal of reducing the burden of disease for conditions with significant clinical impact on neonates. Screening tests were originally developed and implemented one at a time, but newer methods have allowed the use of multiplex technologies to expand additions more rapidly to standard panels. Recent improvements in next-generation sequencing are also evolving rapidly from first focusing on individual genes, then panels, and finally all genes as encompassed by whole exome and genome sequencing. The intersection of these two technologies brings the revolutionary possibility of identifying all genetic disorders in newborns, allowing implementation of therapies at the optimum time regardless of symptoms. This article reviews the history of newborn screening and early studies examining the use of whole genome and exome sequencing as a screening tool. Lessons learned from these studies are discussed, along with technical, ethical, and societal challenges to broad implementation.
Collapse
Affiliation(s)
- Audrey C Woerner
- Department of Pediatrics, University of Pittsburgh Medical Center Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Renata C Gallagher
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA, United States
| | - Jerry Vockley
- Department of Pediatrics, University of Pittsburgh Medical Center Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States.,Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, United States
| | - Aashish N Adhikari
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, United States.,Artificial Intelligence Lab, Illumina Inc, Foster City, CA, United States
| |
Collapse
|
11
|
Williams WA, Ross LF. The Harms of Carrier Status Identification: A Cautionary Warning Against Newborn Sequencing. J Pediatr 2020; 224:22-23. [PMID: 32417254 DOI: 10.1016/j.jpeds.2020.05.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 05/08/2020] [Indexed: 11/30/2022]
Affiliation(s)
| | - Lainie Friedman Ross
- Department of Pediatrics, MacLean Center for Clinical Medical Ethics, Institute for Translational Medicine, University of Chicago, Chicago, Illinois.
| |
Collapse
|
12
|
Parad RB, Kaler SG, Mauceli E, Sokolsky T, Yi L, Bhattacharjee A. Targeted next generation sequencing for newborn screening of Menkes disease. Mol Genet Metab Rep 2020; 24:100625. [PMID: 32714836 PMCID: PMC7378272 DOI: 10.1016/j.ymgmr.2020.100625] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 06/18/2020] [Indexed: 11/17/2022] Open
Abstract
Purpose Population-based newborn screening (NBS) allows early detection and treatment of inherited disorders. For certain medically-actionable conditions, however, NBS is limited by the absence of reliable biochemical signatures amenable to detection by current platforms. We sought to assess the analytic validity of an ATP7A targeted next generation DNA sequencing assay as a potential newborn screen for one such disorder, Menkes disease. Methods Dried blood spots from control or Menkes disease subjects (n = 22) were blindly analyzed for pathogenic variants in the copper transport gene, ATP7A. The analytical method was optimized to minimize cost and provide rapid turnaround time. Results The algorithm correctly identified pathogenic ATP7A variants, including missense, nonsense, small insertions/deletions, and large copy number variants, in 21/22 (95.5%) of subjects, one of whom had inconclusive diagnostic sequencing previously. For one false negative that also had not been detected by commercial molecular laboratories, we identified a deep intronic variant that impaired ATP7A mRNA splicing. Conclusions Our results support proof-of-concept that primary DNA-based NBS would accurately detect Menkes disease, a disorder that fulfills Wilson and Jungner screening criteria and for which biochemical NBS is unavailable. Targeted next generation sequencing for NBS would enable improved Menkes disease clinical outcomes, establish a platform for early identification of other unscreened disorders, and complement current NBS by providing immediate data for molecular confirmation of numerous biochemically screened condition.
Collapse
Affiliation(s)
- Richard B Parad
- Department of Pediatric Newborn Medicine, Brigham & Women's Hospital, Harvard Medical School, Boston, MA, United States of America
| | - Stephen G Kaler
- Section on Translational Neuroscience, Molecular Medicine Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, United States of America.,Center for Gene Therapy, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, United States of America
| | - Evan Mauceli
- Parabase Genomics, Inc., Boston, MA, United States of America
| | - Tanya Sokolsky
- Parabase Genomics, Inc., Boston, MA, United States of America.,Baebies, Inc., Durham, NC, United States of America
| | - Ling Yi
- Section on Translational Neuroscience, Molecular Medicine Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, United States of America
| | - Arindam Bhattacharjee
- Parabase Genomics, Inc., Boston, MA, United States of America.,Baebies, Inc., Durham, NC, United States of America
| |
Collapse
|
13
|
Lee Yu HL, Fan TW, Hsing IM. Oligonucleotide hybridization with magnetic separation assay for multiple SNP phasing. Anal Chim Acta X 2020; 5:100050. [PMID: 33117988 PMCID: PMC7587028 DOI: 10.1016/j.acax.2020.100050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 04/09/2020] [Accepted: 04/14/2020] [Indexed: 10/29/2022] Open
Abstract
Since humans have two copies of each gene, multiple mutations in different loci may or may not be found on the same strand of DNA (i.e., inherited from one parent). When a person is heterozygous at more than one position, the placement of these mutations, also called the haplotype phase, (i.e., cis for the same strand and trans for different strands) can result in the expression of different amount and type of proteins. In this work, we described an enzyme-free method to phase two single nucleotide polymorphisms (SNPs) using two fluorophore/quencher-labelled probes, where one of which was biotinylated. The fluorescence signal was obtained twice: first, after the addition of the labelled probes and second, after the addition of the magnetic beads. The first signal was shown to be proportional to the total number of SNP A and SNP B present in the target analyte, while the second signal showed a marked decrease of the fluorescence signal from the non-biotinylated probe when the SNPs were in trans, showing that the probe immobilized on the magnetic bead selectively captures targets with SNPs in a cis configuration. We then mimic the nature of the human genome which consists of two haplotype copies of each gene, and showed that 250 nM of the 10 possible pairs of haplotypes could be differentiated using a combination of fluorescence microscopy and fluorescence detection.
Collapse
Affiliation(s)
- Henson L. Lee Yu
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Tsz Wing Fan
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - I-Ming Hsing
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| |
Collapse
|
14
|
Smith LD, Bainbridge MN, Parad RB, Bhattacharjee A. Second Tier Molecular Genetic Testing in Newborn Screening for Pompe Disease: Landscape and Challenges. Int J Neonatal Screen 2020; 6:32. [PMID: 32352041 PMCID: PMC7189780 DOI: 10.3390/ijns6020032] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 04/03/2020] [Indexed: 02/06/2023] Open
Abstract
Pompe disease (PD) is screened by a two tier newborn screening (NBS) algorithm, the first tier of which is an enzymatic assay performed on newborn dried blood spots (DBS). As first tier enzymatic screening tests have false positive results, an immediate second tier test on the same sample is critical in resolving newborn health status. Two methodologies have been proposed for second tier testing: (a) measurement of enzymatic activities such as of Creatine/Creatinine over alpha-glucosidase ratio, and (b) DNA sequencing (a molecular genetics approach), such as targeted next generation sequencing. (tNGS). In this review, we discuss the tNGS approach, as well as the challenges in providing second tier screening and follow-up care. While tNGS can predict genotype-phenotype effects when known, these advantages may be diminished when the variants are novel, of unknown significance or not discoverable by current test methodologies. Due to the fact that criticisms of screening algorithms that utilize tNGS are based on perceived complexities, including variant detection and interpretation, we clarify the actual limitations and present the rationale that supports optimizing a molecular genetic testing approach with tNGS. Second tier tNGS can benefit clinical decision-making through the use of the initial NBS DBS punch and rapid turn-around time methodology for tNGS, that includes copy number variant analysis, variant effect prediction, and variant 'cut-off' tools for the reduction of false positive results. The availability of DNA sequence data will contribute to the improved understanding of genotype-phenotype associations and application of treatment. The ultimate goal of second tier testing should enable the earliest possible diagnosis for the earliest initiation of the most effective clinical interventions in infants with PD.
Collapse
Affiliation(s)
- Laurie D. Smith
- Department of Pediatrics, UNC Hospitals, Chapel Hill, NC 27599, USA;
- Laboratory Services Division, Baebies, Inc., Durham, NC 27709, USA
| | - Matthew N. Bainbridge
- Codified Genomics, Houston, TX 77004, USA;
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Richard B. Parad
- Department of Pediatric Newborn Medicine, Brigham & Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | | |
Collapse
|
15
|
Singh R, Chopra S, Graham C, Langer M, Ng R, Ullal AJ, Pamula VK. Emerging Approaches for Fluorescence-Based Newborn Screening of Mucopolysaccharidoses. Diagnostics (Basel) 2020; 10:E294. [PMID: 32403245 PMCID: PMC7277946 DOI: 10.3390/diagnostics10050294] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 05/06/2020] [Accepted: 05/07/2020] [Indexed: 11/23/2022] Open
Abstract
Interest in newborn screening for mucopolysaccharidoses (MPS) is growing, due in part to ongoing efforts to develop new therapies for these disorders and new screening assays to identify increased risk for the individual MPSs on the basis of deficiency in the cognate enzyme. Existing tests for MPSs utilize either fluorescence or mass spectrometry detection methods to measure biomarkers of disease (e.g., enzyme function or glycosaminoglycans) using either urine or dried blood spot (DBS) samples. There are currently two approaches to fluorescence-based enzyme function assays from DBS: (1) manual reaction mixing, incubation, and termination followed by detection on a microtiter plate reader; and (2) miniaturized automation of these same assay steps using digital microfluidics technology. This article describes the origins of laboratory assays for enzyme activity measurement, the maturation and clinical application of fluorescent enzyme assays for MPS newborn screening, and considerations for future expansion of the technology.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Vamsee K. Pamula
- Baebies, Inc., P.O. Box 14403, Durham, NC 27709, USA; (R.S.); (S.C.); (C.G.); (M.L.); (R.N.); (A.J.U.)
| |
Collapse
|
16
|
Ibarra-González I, Fernández-Lainez C, Guillén-López S, López-Mejía L, Belmont-Matínez L, Sokolsky TD, Amin VR, Kitchener RL, Vela-Amieva M, Naylor EW, Bhattacharjee A. Molecular analysis using targeted next generation DNA sequencing and clinical spectrum of Mexican patients with isovaleric acidemia. Clin Chim Acta 2020; 501:216-221. [DOI: 10.1016/j.cca.2019.10.041] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 10/07/2019] [Accepted: 10/28/2019] [Indexed: 10/25/2022]
|
17
|
A pediatric perspective on genomics and prevention in the twenty-first century. Pediatr Res 2020; 87:338-344. [PMID: 31578042 DOI: 10.1038/s41390-019-0597-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 09/18/2019] [Indexed: 12/19/2022]
Abstract
We present evidence from diverse disciplines and populations to identify the current and emerging role of genomics in prevention from both medical and public health perspectives as well as key challenges and potential untoward consequences of increasing the role of genomics in these endeavors. We begin by comparing screening in healthy populations (newborn screening), with testing in symptomatic populations, which may incidentally identify secondary findings and at-risk relatives. Emerging evidence suggests that variants in genes subject to the reporting of secondary findings are more common than expected in patients who otherwise would not meet the criteria for testing and population testing for variants in these genes may more precisely identify discrete populations to target for various prevention strategies starting in childhood. Conversely, despite its theoretical promise, recent studies attempting to demonstrate benefits of next-generation sequencing for newborn screening have instead demonstrated numerous barriers and pitfalls to this approach. We also examine the special cases of pharmacogenomics and polygenic risk scores as examples of ways genomics can contribute to prevention amongst a broader population than that affected by rare Mendelian disease. We conclude with unresolved questions which will benefit from future investigations of the role of genomics in disease prevention.
Collapse
|
18
|
Abstract
Next generation DNA sequencing (NGS) has the potential to improve the diagnostic and prognostic utility of newborn screening programmes. This study assesses the feasibility of automating NGS on dried blood spot (DBS) DNA in a United Kingdom National Health Service (UK NHS) laboratory. An NGS panel targeting the entire coding sequence of five genes relevant to disorders currently screened for in newborns in the UK was validated on DBS DNA. An automated process for DNA extraction, NGS and bioinformatics analysis was developed. The process was tested on DBS to determine feasibility, turnaround time and cost. The analytical sensitivity of the assay was 100% and analytical specificity was 99.96%, with a mean 99.5% concordance of variant calls between DBS and venous blood samples in regions with ≥30× coverage (96.8% across all regions; all variant calls were single nucleotide variants (SNVs), with indel performance not assessed). The pipeline enabled processing of up to 1000 samples a week with a turnaround time of four days from receipt of sample to reporting. This study concluded that it is feasible to automate targeted NGS on routine DBS samples in a UK NHS laboratory setting, but it may not currently be cost effective as a first line test.
Collapse
|
19
|
Lee H, Lim J, Shin JE, Eun HS, Park MS, Park KI, Namgung R, Lee JS. Implementation of a Targeted Next-Generation Sequencing Panel for Constitutional Newborn Screening in High-Risk Neonates. Yonsei Med J 2019; 60:1061-1066. [PMID: 31637888 PMCID: PMC6813152 DOI: 10.3349/ymj.2019.60.11.1061] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 09/13/2019] [Accepted: 09/23/2019] [Indexed: 11/27/2022] Open
Abstract
PURPOSE Newborn screening (NBS) programs are important for appropriate management of susceptible neonates to prevent serious clinical problems. Neonates admitted to neonatal intensive care units (NICU) are at a potentially high risk of false-positive results, and repetitive NBS after total parenteral nutrition is completely off results in delayed diagnosis. Here, we present the usefulness of a targeted next-generation sequencing (TNGS) panel to complement NBS for early diagnosis in high-risk neonates. MATERIALS AND METHODS The TNGS panel covered 198 genes associated with actionable genetic and metabolic diseases that are typically included in NBS programs in Korea using tandem mass spectrometry. The panel was applied to 48 infants admitted to the NICU of Severance Children's Hospital between May 2017 and September 2017. The infants were not selected for suspected metabolic disorders. RESULTS A total of 13 variants classified as likely pathogenic or pathogenic were detected in 11 (22.9%) neonates, including six genes (DHCR7, PCBD1, GAA, ALDOB, ATP7B, and GBA) associated with metabolic diseases not covered in NBS. One of the 48 infants was diagnosed with an isobutyl-CoA dehydrogenase deficiency, and false positive results of tandem mass screening were confirmed in two infants using the TNGS panel. CONCLUSION The implementation of TNGS in conjunction with conventional NBS can allow for better management of and earlier diagnosis in susceptible infants, thus preventing the development of critical conditions in these sick infants.
Collapse
Affiliation(s)
- Hyunjoo Lee
- Division of Clinical Genetics, Department of Pediatrics, Severance Children's Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Joohee Lim
- Division of Neonatology, Department of Pediatrics, Severance Children's Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Jeong Eun Shin
- Division of Neonatology, Department of Pediatrics, Severance Children's Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Ho Sun Eun
- Division of Neonatology, Department of Pediatrics, Severance Children's Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Min Soo Park
- Division of Neonatology, Department of Pediatrics, Severance Children's Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Kook In Park
- Division of Neonatology, Department of Pediatrics, Severance Children's Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Ran Namgung
- Division of Neonatology, Department of Pediatrics, Severance Children's Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Jin Sung Lee
- Division of Clinical Genetics, Department of Pediatrics, Severance Children's Hospital, Yonsei University College of Medicine, Seoul, Korea.
| |
Collapse
|
20
|
Milko LV, O’Daniel JM, DeCristo DM, Crowley SB, Foreman AKM, Wallace KE, Mollison LF, Strande NT, Girnary ZS, Boshe LJ, Aylsworth AS, Gucsavas-Calikoglu M, Frazier DM, Vora NL, Roche MI, Powell BC, Powell CM, Berg JS. An Age-Based Framework for Evaluating Genome-Scale Sequencing Results in Newborn Screening. J Pediatr 2019; 209:68-76. [PMID: 30851990 PMCID: PMC6535354 DOI: 10.1016/j.jpeds.2018.12.027] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Revised: 10/24/2018] [Accepted: 12/06/2018] [Indexed: 12/19/2022]
Abstract
OBJECTIVE To assess the performance of a standardized, age-based metric for scoring clinical actionability to evaluate conditions for inclusion in newborn screening and compare it with the results from other contemporary methods. STUDY DESIGN The North Carolina Newborn Exome Sequencing for Universal Screening study developed an age-based, semiquantitative metric to assess the clinical actionability of gene-disease pairs and classify them with respect to age of onset or timing of interventions. This categorization was compared with the gold standard Recommended Uniform Screening Panel and other methods to evaluate gene-disease pairs for newborn genomic sequencing. RESULTS We assessed 822 gene-disease pairs, enriched for pediatric onset of disease and suspected actionability. Of these, 466 were classified as having childhood onset and high actionability, analogous to conditions selected for the Recommended Uniform Screening Panel core panel. Another 245 were classified as having childhood onset and low to no actionability, 25 were classified as having adult onset and high actionability, 19 were classified as having adult onset and low to no actionability, and 67 were excluded due to controversial evidence and/or prenatal onset. CONCLUSIONS This study describes a novel method to facilitate decisions about the potential use of genomic sequencing for newborn screening. These categories may assist parents and physicians in making informed decisions about the disclosure of results from voluntary genomic sequencing in children.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Natasha T. Strande
- Department of Genetics, UNC Chapel Hill,Department of Pathology and Laboratory Medicine, UNC Chapel Hill
| | - Zahra S. Girnary
- Department of Genetics, UNC Chapel Hill,current affiliation: Mission Fullerton Genetics Center, Asheville, NC
| | - Lacey J. Boshe
- Department of Genetics, UNC Chapel Hill,current affiliation: School of Medicine, UNC Chapel Hill
| | - Arthur S. Aylsworth
- Department of Pediatrics, Division of Genetics and Metabolism, UNC Chapel Hill
| | | | - Dianne M. Frazier
- Department of Pediatrics, Division of Genetics and Metabolism, UNC Chapel Hill
| | - Neeta L. Vora
- Department of Obstetrics and Gynecology, UNC Chapel Hill
| | - Myra I. Roche
- Department of Genetics, UNC Chapel Hill,Department of Pediatrics, Division of Genetics and Metabolism, UNC Chapel Hill
| | | | - Cynthia M. Powell
- Department of Pediatrics, Division of Genetics and Metabolism, UNC Chapel Hill
| | | |
Collapse
|
21
|
Bick D, Jones M, Taylor SL, Taft RJ, Belmont J. Case for genome sequencing in infants and children with rare, undiagnosed or genetic diseases. J Med Genet 2019; 56:783-791. [PMID: 31023718 PMCID: PMC6929710 DOI: 10.1136/jmedgenet-2019-106111] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 03/19/2019] [Indexed: 01/01/2023]
Abstract
Up to 350 million people worldwide suffer from a rare disease, and while the individual diseases are rare, in aggregate they represent a substantial challenge to global health systems. The majority of rare disorders are genetic in origin, with children under the age of five disproportionately affected. As these conditions are difficult to identify clinically, genetic and genomic testing have become the backbone of diagnostic testing in this population. In the last 10 years, next-generation sequencing technologies have enabled testing of multiple disease genes simultaneously, ranging from targeted gene panels to exome sequencing (ES) and genome sequencing (GS). GS is quickly becoming a practical first-tier test, as cost decreases and performance improves. A growing number of studies demonstrate that GS can detect an unparalleled range of pathogenic abnormalities in a single laboratory workflow. GS has the potential to deliver unbiased, rapid and accurate molecular diagnoses to patients across diverse clinical indications and complex presentations. In this paper, we discuss clinical indications for testing and historical testing paradigms. Evidence supporting GS as a diagnostic tool is supported by superior genomic coverage, types of pathogenic variants detected, simpler laboratory workflow enabling shorter turnaround times, diagnostic and reanalysis yield, and impact on healthcare.
Collapse
Affiliation(s)
- David Bick
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Marilyn Jones
- Rady Children's Hospital San Diego, San Diego, California, USA
| | | | | | | |
Collapse
|
22
|
Málaga DR, Brusius-Facchin AC, Siebert M, Pasqualim G, Saraiva-Pereira ML, Souza CFMD, Schwartz IVD, Matte U, Giugliani R. Sensitivity, advantages, limitations, and clinical utility of targeted next-generation sequencing panels for the diagnosis of selected lysosomal storage disorders. Genet Mol Biol 2019; 42:197-206. [PMID: 30985853 PMCID: PMC6687342 DOI: 10.1590/1678-4685-gmb-2018-0092] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 10/18/2018] [Indexed: 01/22/2023] Open
Abstract
Lysosomal storage disorders (LSDs) constitute a heterogeneous group of
approximately 50 genetic disorders. LSDs diagnosis is challenging due to
variability in phenotype penetrance, similar clinical manifestations, and a high
allelic heterogeneity. A powerful tool for the diagnosis of the disease could
reduce the “diagnostic odyssey” for affected families, leading to an appropriate
genetic counseling and a better outcome for current therapies, since enzyme
replacement therapies have been approved in Brazil for Gaucher, Fabry, and Pompe
diseases, and are under development for Niemann-Pick Type B. However,
application of next-generation sequencing (NGS) technology in the clinical
diagnostic setting requires a previous validation phase. Here, we assessed the
application of this technology as a fast, accurate, and cost-effective method to
determine genetic diagnosis in selected LSDs. We have designed two panels for
testing simultaneously 11 genes known to harbor casual mutations of LSDs. A
cohort of 58 patients was used to validate those two panels, and the clinical
utility of these gene panels was tested in four novel cases. We report the
assessment of a NGS approach as a new tool in the diagnosis of LSDs in our
service.
Collapse
Affiliation(s)
- Diana Rojas Málaga
- Postgraduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.,Medical Genetics Service, Hospital de Clinicas de Porto Alegre, Porto Alegre, RS, Brazil
| | | | - Marina Siebert
- Experimental Research Center, Hospital de Clinicas de Porto Alegre, Porto Alegre, RS, Brazil
| | - Gabriela Pasqualim
- Postgraduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.,Experimental Research Center, Hospital de Clinicas de Porto Alegre, Porto Alegre, RS, Brazil.,Gene Therapy Center, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
| | - Maria Luiza Saraiva-Pereira
- Postgraduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.,Medical Genetics Service, Hospital de Clinicas de Porto Alegre, Porto Alegre, RS, Brazil.,Department of Biochemistry, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Carolina F M de Souza
- Medical Genetics Service, Hospital de Clinicas de Porto Alegre, Porto Alegre, RS, Brazil
| | - Ida V D Schwartz
- Postgraduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.,Medical Genetics Service, Hospital de Clinicas de Porto Alegre, Porto Alegre, RS, Brazil.,Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Ursula Matte
- Postgraduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.,Experimental Research Center, Hospital de Clinicas de Porto Alegre, Porto Alegre, RS, Brazil.,Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Roberto Giugliani
- Postgraduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.,Medical Genetics Service, Hospital de Clinicas de Porto Alegre, Porto Alegre, RS, Brazil.,Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| |
Collapse
|
23
|
Mortensen Ó, Lydersen LN, Apol KD, Andorsdóttir G, Steig BÁ, Gregersen NO. Using dried blood spot samples from a trio for linked-read whole-exome sequencing. Eur J Hum Genet 2019; 27:980-988. [PMID: 30765883 PMCID: PMC6777531 DOI: 10.1038/s41431-019-0343-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 12/21/2018] [Accepted: 01/05/2019] [Indexed: 01/22/2023] Open
Abstract
Long-term collection of dried blood spot (DBS) samples through newborn screening may have retrospective and prospective advantages, especially in combination with advanced analytical techniques. This work concerns whether linked-reads may overcome some of the limitations of short-read sequencing of DBS samples, such as performing molecular phasing. We performed whole-exome sequencing of DNA extracted from DBS and corresponding whole blood (WB) reference samples, belonging to a trio with unaffected parents and a proband affected by primary carnitine deficiency (PCD). For the DBS samples we were able to phase >21% of the genes under 100 kb, >40% of the SNPs, and the longest phase block was >72 kb. Corresponding results for the WB reference samples was >85%, >75%, and >915 kb, respectively. Concerning the PCD causing variant (rs72552725:A > G) in the SLC22A5 gene we observe full genotype concordance between DBS and WB for all three samples. Furthermore, we were able to phase all variants within the SLC22A5 gene in the proband’s WB data, which shows that linked-read sequencing may replace the trio information for haplotype detection. However, due to smaller molecular lengths in the DBS data only small phase blocks were observed in the proband’s DBS sample. Therefore, further optimisation of the DBS workflow is needed in order to explore the full potential of DBS samples as a test bed for molecular phasing.
Collapse
Affiliation(s)
- Ólavur Mortensen
- FarGen, The Genetic Biobank of the Faroe Islands, Tórshavn, Faroe Islands
| | | | | | | | - Bjarni Á Steig
- General Medical Department, National Hospital of the Faroe Islands, Tórshavn, Faroe Islands
| | | |
Collapse
|
24
|
Peng G, Shen P, Gandotra N, Le A, Fung E, Jelliffe-Pawlowski L, Davis RW, Enns GM, Zhao H, Cowan TM, Scharfe C. Combining newborn metabolic and DNA analysis for second-tier testing of methylmalonic acidemia. Genet Med 2018; 21:896-903. [PMID: 30209273 PMCID: PMC6416784 DOI: 10.1038/s41436-018-0272-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 08/03/2018] [Indexed: 11/27/2022] Open
Abstract
Purpose Improved second-tier tools are needed to reduce false-positive outcomes in newborn screening (NBS) for inborn metabolic disorders on the Recommended Universal Screening Panel (RUSP). Methods We designed an assay for multiplex sequencing of 72 metabolic genes (RUSPseq) from newborn dried blood spots. Analytical and clinical performance was evaluated in 60 screen-positive newborns for methylmalonic acidemia (MMA) reported by the California Department of Public Health NBS program. Additionally, we trained a Random Forest machine learning classifier on NBS data to improve prediction of true and false-positive MMA cases. Results Of 28 MMA patients sequenced, we found two pathogenic or likely pathogenic (P/LP) variants in a MMA-related gene in 24 patients, and one pathogenic variant and a variant of unknown significance (VUS) in 1 patient. No such variant combinations were detected in MMA false positives and healthy controls. Random Forest–based analysis of the entire NBS metabolic profile correctly identified the MMA patients and reduced MMA false-positive cases by 51%. MMA screen-positive newborns were more likely of Hispanic ethnicity. Conclusion Our two-pronged approach reduced false positives by half and provided a reportable molecular finding for 89% of MMA patients. Challenges remain in newborn metabolic screening and DNA variant interpretation in diverse multiethnic populations.
Collapse
Affiliation(s)
- Gang Peng
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA.,Department of Biostatistics, Yale University School of Public Health, New Haven, CT, USA
| | - Peidong Shen
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA
| | - Neeru Gandotra
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Anthony Le
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Eula Fung
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Laura Jelliffe-Pawlowski
- Department of Epidemiology and Biostatistics, University of California San Francisco School of Medicine, San Francisco, CA, USA
| | - Ronald W Davis
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA
| | - Gregory M Enns
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Hongyu Zhao
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA.,Department of Biostatistics, Yale University School of Public Health, New Haven, CT, USA
| | - Tina M Cowan
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Curt Scharfe
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA.
| |
Collapse
|
25
|
Shearer AE, Frees K, Kolbe DL, Smith RJH. Comprehensive Genetic Testing for Deafness from Fresh and Archived Dried Blood Spots. Otolaryngol Head Neck Surg 2018; 159:1058-1060. [PMID: 30149782 DOI: 10.1177/0194599818797291] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Comprehensive genetic testing has become integral in the evaluation of children with deafness, but the amount of blood required to obtain DNA can be prohibitive in newborns. Dried blood spots (DBSs) are routinely collected and would provide an alternative source of DNA. Our objective was to evaluate the use of DBSs for comprehensive genetic testing for deafness. DNA derived from fresh and archived DBS samples was compared with DNA from whole blood. We performed next-generation sequencing of all known deafness genes in 4 DBS samples: 2 positive controls, an unknown sample, and a negative control. The DBS-derived DNA was of sufficient quantity and quality for clinical testing. In the 2 positive control samples, pathogenic variants were identified; in the negative control, no pathogenic variants were found; and in the unknown sample, homozygous deletion of the OTOA gene was identified as the cause of deafness. This pilot study shows that comprehensive genetic testing for deafness is feasible with fresh and/or archived DBSs.
Collapse
Affiliation(s)
- A Eliot Shearer
- Department of Otolaryngology-Head and Neck Surgery, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA.,Molecular Otolaryngology and Renal Research Laboratories, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Kathy Frees
- Molecular Otolaryngology and Renal Research Laboratories, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Diana L Kolbe
- Molecular Otolaryngology and Renal Research Laboratories, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Richard J H Smith
- Department of Otolaryngology-Head and Neck Surgery, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA.,Molecular Otolaryngology and Renal Research Laboratories, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA.,Interdepartmental PhD Program in Genetics, University of Iowa, Iowa City, Iowa, USA
| |
Collapse
|
26
|
Li N, Yu P, Rao B, Deng Y, Guo Y, Huang Y, Ding L, Zhu J, Yang H, Wang J, Guo J, Chen F, Liu Z. Molecular genetics of tetrahydrobiopterin deficiency in Chinese patients. J Pediatr Endocrinol Metab 2018; 31:911-916. [PMID: 30001213 DOI: 10.1515/jpem-2018-0037] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Accepted: 05/14/2018] [Indexed: 11/15/2022]
Abstract
Background The overall incidence of hyperphenylalaninemia (HPA) in China is 1:11,763, with tetrahydrobiopterin (BH4) deficiency accounting for 8.55% of patients with HPA in the mainland. Much progress has been made in the diagnosis and treatment of BH4 deficiency with the introduction of neonatal screening in China. However, the screening rate is still low and screening is not universally available. Methods A total of 44 BH4-deficient patients were enrolled in this study, of which 39 were diagnosed with BH4 deficiency, while the remaining five showed typical characteristics of BH4 deficiency at a later period. The entire coding regions and adjacent intronic regions of GCH1, PTS, PCBD1 and QDPR genes were analyzed using target sequencing. Results Nineteen (n=19) different mutations in the PTS gene including four novel mutations and one mutation in QDPR were identified. p.P87S, p.D96N, IVS1-291A>G, p.N52S, p.K91R, p.V56M, p.T106M and p.F40GfsX53 in PTS were the prevalent mutations with ≥3% relative frequency. The mutation p.R221X in the QDPR gene was found with relatively lower frequencies (2.27%). The remaining 12 mutations in PTS were found at relative frequencies of 1.14%. Conclusions The results could be of value for genetic counseling and prenatal diagnosis in the patients' families and for the molecular diagnosis of BH4 deficiencies. Furthermore, four novel mutations expand and improve the PTS mutation database.
Collapse
Affiliation(s)
- Nana Li
- National Center for Birth Defects Monitoring, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, P.R. China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, P.R. China
| | - Ping Yu
- National Center for Birth Defects Monitoring, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, P.R. China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, P.R. China
| | - Bin Rao
- BGI-Shenzhen, Shenzhen, P.R. China.,China National GeneBank, BGI-Shenzhen, Shenzhen, P.R. China
| | - Ying Deng
- National Center for Birth Defects Monitoring, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Yixiong Guo
- National Center for Birth Defects Monitoring, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Yushan Huang
- BGI-Shenzhen, Shenzhen, P.R. China.,China National GeneBank, BGI-Shenzhen, Shenzhen, P.R. China
| | - Lijie Ding
- BGI-Shenzhen, Shenzhen, P.R. China.,China National GeneBank, BGI-Shenzhen, Shenzhen, P.R. China
| | - Jun Zhu
- National Center for Birth Defects Monitoring, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, P.R. China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, P.R. China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, P.R. China.,James D. Watson Institute of Genome Sciences, Hangzhou, P.R. China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen, P.R. China.,James D. Watson Institute of Genome Sciences, Hangzhou, P.R. China
| | - Jian Guo
- BGI-Shenzhen, Building 11, Beishan Industrial Zone, Yantian, Shenzhen, Guangdong, P.R. China, Phone: 86-15914038192.,BGI-Shenzhen, Building 11, Beishan Industrial Zone, Yantian, Shenzhen, Guangdong, P.R. China, Phone: 86-13428735579.,China National GeneBank, BGI-Shenzhen, Shenzhen, Guangdong, P.R. China
| | - Fang Chen
- BGI-Shenzhen, Building 11, Beishan Industrial Zone, Yantian, Shenzhen, Guangdong, P.R. China, Phone: 86-15914038192.,BGI-Shenzhen, Building 11, Beishan Industrial Zone, Yantian, Shenzhen, Guangdong, P.R. China, Phone: 86-13428735579.,China National GeneBank, BGI-Shenzhen, Shenzhen, Guangdong, P.R. China
| | - Zhen Liu
- National Center for Birth Defects Monitoring, West China Second University Hospital, Sichuan University, 20, Section 3, Ren Min South Road, Chengdu, Sichuan, P.R. China, Phone: 86-028-85502490, Fax: 86-028-85501386.,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, P.R. China
| |
Collapse
|
27
|
Holm IA, Agrawal PB, Ceyhan-Birsoy O, Christensen KD, Fayer S, Frankel LA, Genetti CA, Krier JB, LaMay RC, Levy HL, McGuire AL, Parad RB, Park PJ, Pereira S, Rehm HL, Schwartz TS, Waisbren SE, Yu TW, Green RC, Beggs AH. The BabySeq project: implementing genomic sequencing in newborns. BMC Pediatr 2018; 18:225. [PMID: 29986673 PMCID: PMC6038274 DOI: 10.1186/s12887-018-1200-1] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 06/27/2018] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND The greatest opportunity for lifelong impact of genomic sequencing is during the newborn period. The "BabySeq Project" is a randomized trial that explores the medical, behavioral, and economic impacts of integrating genomic sequencing into the care of healthy and sick newborns. METHODS Families of newborns are enrolled from Boston Children's Hospital and Brigham and Women's Hospital nurseries, and half are randomized to receive genomic sequencing and a report that includes monogenic disease variants, recessive carrier variants for childhood onset or actionable disorders, and pharmacogenomic variants. All families participate in a disclosure session, which includes the return of results for those in the sequencing arm. Outcomes are collected through review of medical records and surveys of parents and health care providers and include the rationale for choice of genes and variants to report; what genomic data adds to the medical management of sick and healthy babies; and the medical, behavioral, and economic impacts of integrating genomic sequencing into the care of healthy and sick newborns. DISCUSSION The BabySeq Project will provide empirical data about the risks, benefits and costs of newborn genomic sequencing and will inform policy decisions related to universal genomic screening of newborns. TRIAL REGISTRATION The study is registered in ClinicalTrials.gov Identifier: NCT02422511 . Registration date: 10 April 2015.
Collapse
Affiliation(s)
- Ingrid A. Holm
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, MA USA
- Department of Pediatrics, Harvard Medical School, Boston, MA USA
| | - Pankaj B. Agrawal
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, MA USA
- Department of Pediatrics, Harvard Medical School, Boston, MA USA
- Division of Newborn Medicine, Boston Children’s Hospital, Boston, MA USA
| | - Ozge Ceyhan-Birsoy
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, MA USA
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA USA
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Kurt D. Christensen
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, MA USA
- Harvard Medical School, Boston, MA USA
| | - Shawn Fayer
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, MA USA
| | - Leslie A. Frankel
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX USA
- Department of Psychological, Health and Learning Sciences, University of Houston College of Education, Houston, TX USA
| | - Casie A. Genetti
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, MA USA
| | - Joel B. Krier
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, MA USA
- Harvard Medical School, Boston, MA USA
| | - Rebecca C. LaMay
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, MA USA
| | - Harvey L. Levy
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, MA USA
- Department of Pediatrics, Harvard Medical School, Boston, MA USA
| | - Amy L. McGuire
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX USA
| | - Richard B. Parad
- Department of Pediatrics, Harvard Medical School, Boston, MA USA
- Division of Newborn Medicine, Boston Children’s Hospital, Boston, MA USA
- Department of Pediatric Newborn Medicine, Brigham and Women’s Hospital, Boston, MA USA
| | - Peter J. Park
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, MA USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA USA
| | - Stacey Pereira
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX USA
| | - Heidi L. Rehm
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, MA USA
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA USA
- The Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Talia S. Schwartz
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, MA USA
| | - Susan E. Waisbren
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, MA USA
- Department of Pediatrics, Harvard Medical School, Boston, MA USA
| | - Timothy W. Yu
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, MA USA
- Department of Pediatrics, Harvard Medical School, Boston, MA USA
- The Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Robert C. Green
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, MA USA
- Harvard Medical School, Boston, MA USA
- The Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Alan H. Beggs
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, MA USA
- Department of Pediatrics, Harvard Medical School, Boston, MA USA
| |
Collapse
|
28
|
Ko JM, Park KS, Kang Y, Nam SH, Kim Y, Park I, Chae HW, Lee SM, Lee KA, Kim JW. A New Integrated Newborn Screening Workflow Can Provide a Shortcut to Differential Diagnosis and Confirmation of Inherited Metabolic Diseases. Yonsei Med J 2018; 59:652-661. [PMID: 29869463 PMCID: PMC5990675 DOI: 10.3349/ymj.2018.59.5.652] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 04/16/2018] [Accepted: 04/19/2018] [Indexed: 12/17/2022] Open
Abstract
PURPOSE We developed a new workflow design which included results from both biochemical and targeted gene sequencing analysis interpreted comprehensively. We then conducted a pilot study to evaluate the benefit of this new approach in newborn screening (NBS) and demonstrated the efficiency of this workflow in detecting causative genetic variants. MATERIALS AND METHODS Ten patients in Group 1 were diagnosed clinically using biochemical assays only, and 10 newborns in Group 2 were diagnosed with suspected inherited metabolic disease (IMD) in NBS. We applied NewbornDiscovery (SD Genomics), an integrated workflow design that encompasses analyte-phenotype-gene, single nucleotide variant/small insertion and deletion/copy number variation analyses along with clinical interpretation of genetic variants related to each participant's condition. RESULTS A molecular genetic diagnosis was established in 95% (19/20) of individuals. In Group 1, 13 and 7 of 20 alleles were classified as pathogenic and likely pathogenic, respectively. In Group 2, 11 and 6 of 17 alleles with identified causative variants were pathogenic and likely pathogenic, respectively. There were no variants of uncertain significance. For each individual, the NewbornDiscovery and biochemical analysis results reached 100% concordance, since the single newborn testing negative for causative genetic variant in Group 2 showed a benign clinical course. CONCLUSION This integrated diagnostic workflow resulted in a high yield. This approach not only enabled early confirmation of specific IMD, but also detected conditions not included in the current NBS.
Collapse
Affiliation(s)
- Jung Min Ko
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul National University College of Medicine, Seoul, Korea
| | | | | | | | - Yoonjung Kim
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea
| | | | - Hyun Wook Chae
- Department of Pediatrics, Yonsei University College of Medicine, Seoul, Korea
| | - Soon Min Lee
- Department of Pediatrics, Yonsei University College of Medicine, Seoul, Korea
| | - Kyung A Lee
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea.
| | - Jong Won Kim
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.
| |
Collapse
|
29
|
Abstract
Newborn screening in the United States is an important public health measure to provide early detection for specified disorders when early treatment is both possible and beneficial. As technology improves, newborn screening can be offered for many more conditions. In the past 10 years, screening has expanded to include severe combined immunodeficiency, congenital heart disease, lysosomal storage disease, and X-linked adrenoleukodystrophy. This article reviews the current state of newborn screening with updates on recent developments. [Pediatr Ann. 2018;47(5):e187-e190.].
Collapse
|
30
|
Abstract
Newborn screening programs aim to achieve presymptomatic diagnosis of treatable disorders allowing for early initiation of medical care to prevent or reduce significant morbidity and mortality. Many of the conditions included in the newborn screening panels are inborn errors of metabolism; however, screening for endocrine, hematologic, immunologic, and cardiovascular diseases, and hearing loss is also included in many panels. Newborn screening tests are not diagnostic and therefore diagnostic testing is needed to confirm or exclude the suspected diagnosis. Further advancement in technology is expected to allow continuous expansion of newborn screening.
Collapse
|
31
|
Next generation sequencing as a follow-up test in an expanded newborn screening programme. Clin Biochem 2017; 52:48-55. [PMID: 29111448 DOI: 10.1016/j.clinbiochem.2017.10.016] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 10/23/2017] [Accepted: 10/23/2017] [Indexed: 02/08/2023]
Abstract
OBJECTIVES Contrary to many western European countries, most south-eastern European countries do not have an expanded newborn screening (NBS) program using tandem mass spectrometry. This study would represent one of the first expanded NBS studies in south-eastern Europe and will enable the estimation of the incidences of IEM in Slovenia. We proposed an expanded NBS approach including next-generation sequencing (NGS) as a confirmational analysis. DESIGN & METHODS We conducted a pilot study of expanded NBS for selected inborn errors of metabolism (IEM) in Slovenia including 10,048 NBS cards. We used an approach including tandem mass spectrometry followed by second tier tests including NGS. Based on the NBS results, 85 children were evaluated at a metabolic follow-up; 80 of them were analyzed using NGS. RESULTS Altogether, glutaric acidemia type 1 was confirmed in one patient who was a compound heterozygote for two known causative GCDH variants. A patient with suspected very long-chain acyl-CoA dehydrogenase deficiency had negative metabolic follow-up tests, but had two heterozygous ACADVL variants; one known disease-causing variant and one indel, namely c.205-8_205-7delinsGC, that is predicted to be causative. Nine participants had elevated metabolites characteristic of 3-methylcrotonyl-CoA carboxylase deficiency, 2 of them had known causative homozygous variants in MCCC1. The other seven were heterozygous; two had a novel genetic variant c.149_151dupCCA (p.Thr50dup). Cumulative incidences of IEM in Slovenia were similar to other European countries. CONCLUSIONS NGS proved to be valuable in explaining the abnormal metabolite concentrations in NBS as it enabled the differentiation between affected patients and mere heterozygotes, and it improved the turnaround time of genetic analysis. The results of this study will be instrumental in the routine implementation of expanded NBS in Slovenia.
Collapse
|
32
|
Cho Y, Lee CH, Jeong EG, Kim MH, Hong JH, Ko Y, Lee B, Yun G, Kim BJ, Jung J, Jung J, Lee JS. Prevalence of Rare Genetic Variations and Their Implications in NGS-data Interpretation. Sci Rep 2017; 7:9810. [PMID: 28851938 PMCID: PMC5574920 DOI: 10.1038/s41598-017-09247-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 07/21/2017] [Indexed: 12/30/2022] Open
Abstract
Next-generation sequencing (NGS) technology has improved enough to discover mutations associated with genetic diseases. Our study evaluated the feasibility of targeted NGS as a primary screening tool to detect causal variants and subsequently predict genetic diseases. We performed parallel computations on 3.7-megabase-targeted regions to detect disease-causing mutations in 103 participants consisting of 81 patients and 22 controls. Data analysis of the participants took about 6 hours using local databases and 200 nodes of a supercomputer. All variants in the selected genes led on average to 3.6 putative diseases for each patient while variants restricted to disease-causing genes identified the correct disease. Notably, only 12% of predicted causal variants were recorded as causal mutations in public databases: 88% had no or insufficient records. In this study, most genetic diseases were caused by rare mutations and public records were inadequate. Most rare variants, however, were not associated with genetic diseases. These data implied that novel, rare variants should not be ignored but interpreted in conjunction with additional clinical data. This step is needed so appropriate advice can be given to primary doctors and parents, thus fulfilling the purpose of this method as a primary screen for rare genetic diseases.
Collapse
Affiliation(s)
- Yangrae Cho
- Syntekabio Incorporated, Techno-2ro B-512, Yuseong-gu, Daejeon, 34025, Republic of Korea
- DFTBA, CALS, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Chul-Ho Lee
- Department of Clinical Genetics, Department of Pediatrics, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Eun-Goo Jeong
- Syntekabio Incorporated, Techno-2ro B-512, Yuseong-gu, Daejeon, 34025, Republic of Korea
| | - Min-Ho Kim
- Syntekabio Incorporated, Techno-2ro B-512, Yuseong-gu, Daejeon, 34025, Republic of Korea
| | - Jong Hui Hong
- Syntekabio Incorporated, Techno-2ro B-512, Yuseong-gu, Daejeon, 34025, Republic of Korea
| | - Younhee Ko
- Department of Clinical Genetics, Department of Pediatrics, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
- Department of Biomedical Engineering, Hankuk University of Foreign Studies, Yongin-si, Gyeonggi-do, 17035, Republic of Korea
| | - Bomnun Lee
- Syntekabio Incorporated, Techno-2ro B-512, Yuseong-gu, Daejeon, 34025, Republic of Korea
| | - Gilly Yun
- Syntekabio Incorporated, Techno-2ro B-512, Yuseong-gu, Daejeon, 34025, Republic of Korea
| | - Byong Joon Kim
- Syntekabio Incorporated, Techno-2ro B-512, Yuseong-gu, Daejeon, 34025, Republic of Korea
| | - Jongcheol Jung
- Syntekabio Incorporated, Techno-2ro B-512, Yuseong-gu, Daejeon, 34025, Republic of Korea
| | - Jongsun Jung
- Syntekabio Incorporated, Techno-2ro B-512, Yuseong-gu, Daejeon, 34025, Republic of Korea.
| | - Jin-Sung Lee
- Department of Clinical Genetics, Department of Pediatrics, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea.
| |
Collapse
|
33
|
Peer-Zada AA, Al-Asmari AM. Excessive homozygosity identified by chromosomal microarray at a known GCDH mutation locus correlates with brain MRI abnormalities in an infant with glutaric aciduria. Clin Case Rep 2017; 5:1303-1308. [PMID: 28781846 PMCID: PMC5538054 DOI: 10.1002/ccr3.1054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 04/06/2017] [Indexed: 11/12/2022] Open
Abstract
Herein, we report a conceptually novel clinical case highlighting the diagnostic implications of excessive homozygosity and its correlation with brain MRI abnormalities in an infant with GA1. The case also points a need for an extra amount of caution to be exercised when evaluating patients with “negative exomes.”
Collapse
Affiliation(s)
- Abdul Ali Peer-Zada
- Molecular Pathology (Genetics) Section Pathology and Clinical Laboratory Medicine Administration King Fahad Medical City Riyadh Saudi Arabia
| | - Ali M Al-Asmari
- Department of Pediatrics Medical Genetics Section King Fahad Medical City Riyadh Saudi Arabia
| |
Collapse
|
34
|
Powis Z, Hart A, Cherny S, Petrik I, Palmaer E, Tang S, Jones C. Clinical diagnostic exome evaluation for an infant with a lethal disorder: genetic diagnosis of TARP syndrome and expansion of the phenotype in a patient with a newly reported RBM10 alteration. BMC MEDICAL GENETICS 2017; 18:60. [PMID: 28577551 PMCID: PMC5455125 DOI: 10.1186/s12881-017-0426-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 05/22/2017] [Indexed: 11/11/2022]
Abstract
Background Diagnostic Exome Sequencing (DES) has been shown to be an effective tool for diagnosis individuals with suspected genetic conditions. Case Presentation We report a male infant born with multiple anomalies including bilateral dysplastic kidneys, cleft palate, bilateral talipes, and bilateral absence of thumbs and first toes. Prenatal testing including chromosome analysis and microarray did not identify a cause for the multiple congenital anomalies. Postnatal diagnostic exome studies (DES) were utilized to find a molecular diagnosis for the patient. Exome sequencing of the proband, mother, and father showed a previously unreported maternally inherited RNA binding motif protein 10 (RBM10) c.1352_1353delAG (p.E451Vfs*66) alteration. Mutations in RBM10 are associated with TARP syndrome, an X-linked recessive disorder originally described with cardinal features of talipes equinovarus, atrial septal defect, Robin sequence, and persistent left superior vena cava. Conclusion DES established a molecular genetic diagnosis of TARP syndrome for a neonatal patient with a poor prognosis in whom traditional testing methods were uninformative and allowed for efficient diagnosis and future reproductive options for the parents. Other reported cases of TARP syndrome demonstrate significant variability in clinical phenotype. The reported features in this infant including multiple hemivertebrae, imperforate anus, aplasia of thumbs and first toes have not been reported in previous patients, thus expanding the clinical phenotype for this rare disorder. Electronic supplementary material The online version of this article (doi:10.1186/s12881-017-0426-3) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Zöe Powis
- Ambry Genetics, 15 Argonaut, Aliso Viejo, CA, 92656, USA.
| | - Alexa Hart
- Rush University Medical Center, Chicago, IL, USA
| | - Sara Cherny
- Rush University Medical Center, Chicago, IL, USA
| | - Igor Petrik
- Ambry Genetics, 15 Argonaut, Aliso Viejo, CA, 92656, USA
| | - Erika Palmaer
- Ambry Genetics, 15 Argonaut, Aliso Viejo, CA, 92656, USA
| | - Sha Tang
- Ambry Genetics, 15 Argonaut, Aliso Viejo, CA, 92656, USA
| | | |
Collapse
|
35
|
Lalani SR. Current Genetic Testing Tools in Neonatal Medicine. Pediatr Neonatol 2017; 58:111-121. [PMID: 28277305 DOI: 10.1016/j.pedneo.2016.07.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 05/13/2016] [Accepted: 07/08/2016] [Indexed: 12/31/2022] Open
Abstract
With the growing understanding of the magnitude of genetic diseases in newborns and equally rapid advancement of tools used for genetic diagnoses, healthcare providers must have a sufficient knowledge base to both recognize and evaluate genetic diseases in the neonatal period. Genetic assessment has become an essential aspect of medicine, and professionals need to know when genetic evaluation is indispensable. Much progress has been made in recent years in utilizing massively parallel sequencing for rapid diagnosis of genetic conditions in neonates. Next-generation sequencing is increasingly being used for noninvasive prenatal diagnosis, and it may become an essential component of newborn screening. This review will define some basic genetic terms and concepts, explain the gamut of genetic testing available for early diagnosis of genetic diseases, and describe some common chromosomal abnormalities, genomic disorders, and single-gene diseases relevant to neonatal medicine.
Collapse
Affiliation(s)
- Seema R Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
| |
Collapse
|
36
|
Friedman JM, Cornel MC, Goldenberg AJ, Lister KJ, Sénécal K, Vears DF. Genomic newborn screening: public health policy considerations and recommendations. BMC Med Genomics 2017; 10:9. [PMID: 28222731 PMCID: PMC5320805 DOI: 10.1186/s12920-017-0247-4] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 02/14/2017] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The use of genome-wide (whole genome or exome) sequencing for population-based newborn screening presents an opportunity to detect and treat or prevent many more serious early-onset health conditions than is possible today. METHODS The Paediatric Task Team of the Global Alliance for Genomics and Health's Regulatory and Ethics Working Group reviewed current understanding and concerns regarding the use of genomic technologies for population-based newborn screening and developed, by consensus, eight recommendations for clinicians, clinical laboratory scientists, and policy makers. RESULTS Before genome-wide sequencing can be implemented in newborn screening programs, its clinical utility and cost-effectiveness must be demonstrated, and the ability to distinguish disease-causing and benign variants of all genes screened must be established. In addition, each jurisdiction needs to resolve ethical and policy issues regarding the disclosure of incidental or secondary findings to families and ownership, appropriate storage and sharing of genomic data. CONCLUSION The best interests of children should be the basis for all decisions regarding the implementation of genomic newborn screening.
Collapse
Affiliation(s)
- Jan M. Friedman
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
- Child & Family Research Institute, Vancouver, Canada
| | - Martina C. Cornel
- Section Clinical Genetics, Department of Clinical Genetics, VU University Medical Center, Amsterdam, Holland
- EMGO Institute for Health and Care Research, VU University Medical Center, Amsterdam, Holland
| | - Aaron J. Goldenberg
- The Center for Genetic Research Ethics and Law, Department of Bioethics, Case Western Reserve University, Cleveland, OH USA
| | - Karla J. Lister
- Office of Population Health Genomics, Public Health Division, Department of Health, Government of Western Australia, Perth, Australia
| | - Karine Sénécal
- Centre of Genomics and Policy, Department of Human Genetics, McGill University, Montreal, Canada
| | - Danya F. Vears
- Centre for Biomedical Ethics and Law, Department of Public Health and Primary Care, KU Leuven, Leuven, Belgium
| |
Collapse
|
37
|
Park KJ, Park S, Lee E, Park JH, Park JH, Park HD, Lee SY, Kim JW. A Population-Based Genomic Study of Inherited Metabolic Diseases Detected Through Newborn Screening. Ann Lab Med 2017; 36:561-72. [PMID: 27578510 PMCID: PMC5011110 DOI: 10.3343/alm.2016.36.6.561] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 05/11/2016] [Accepted: 06/27/2016] [Indexed: 01/29/2023] Open
Abstract
Background A newborn screening (NBS) program has been utilized to detect asymptomatic newborns with inherited metabolic diseases (IMDs). There have been some bottlenecks such as false-positives and imprecision in the current NBS tests. To overcome these issues, we developed a multigene panel for IMD testing and investigated the utility of our integrated screening model in a routine NBS environment. We also evaluated the genetic epidemiologic characteristics of IMDs in a Korean population. Methods In total, 269 dried blood spots with positive results from current NBS tests were collected from 120,700 consecutive newborns. We screened 97 genes related to NBS in Korea and detected IMDs, using an integrated screening model based on biochemical tests and next-generation sequencing (NGS) called NewbornSeq. Haplotype analysis was conducted to detect founder effects. Results The overall positive rate of IMDs was 20%. We identified 10 additional newborns with preventable IMDs that would not have been detected prior to the implementation of our NGS-based platform NewbornSeq. The incidence of IMDs was approximately 1 in 2,235 births. Haplotype analysis demonstrated founder effects in p.Y138X in DUOXA2, p.R885Q in DUOX2, p.Y439C in PCCB, p.R285Pfs*2 in SLC25A13, and p.R224Q in GALT. Conclusions Through a population-based study in the NBS environment, we highlight the screening and epidemiological implications of NGS. The integrated screening model will effectively contribute to public health by enabling faster and more accurate IMD detection through NBS. This study suggested founder mutations as an explanation for recurrent IMD-causing mutations in the Korean population.
Collapse
Affiliation(s)
- Kyoung Jin Park
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul, Korea
| | | | | | - Jong Ho Park
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul, Korea
| | - June Hee Park
- Samsung Biomedical Research Institute, Samsung Medical Center, Seoul, Korea
| | - Hyung Doo Park
- Department of Laboratory Medicine & Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Soo Youn Lee
- Department of Laboratory Medicine & Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jong Won Kim
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul, Korea.,Department of Laboratory Medicine & Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.
| |
Collapse
|
38
|
Berg JS, Agrawal PB, Bailey DB, Beggs AH, Brenner SE, Brower AM, Cakici JA, Ceyhan-Birsoy O, Chan K, Chen F, Currier RJ, Dukhovny D, Green RC, Harris-Wai J, Holm IA, Iglesias B, Joseph G, Kingsmore SF, Koenig BA, Kwok PY, Lantos J, Leeder SJ, Lewis MA, McGuire AL, Milko LV, Mooney SD, Parad RB, Pereira S, Petrikin J, Powell BC, Powell CM, Puck JM, Rehm HL, Risch N, Roche M, Shieh JT, Veeraraghavan N, Watson MS, Willig L, Yu TW, Urv T, Wise AL. Newborn Sequencing in Genomic Medicine and Public Health. Pediatrics 2017; 139:e20162252. [PMID: 28096516 PMCID: PMC5260149 DOI: 10.1542/peds.2016-2252] [Citation(s) in RCA: 140] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/15/2016] [Indexed: 12/20/2022] Open
Abstract
The rapid development of genomic sequencing technologies has decreased the cost of genetic analysis to the extent that it seems plausible that genome-scale sequencing could have widespread availability in pediatric care. Genomic sequencing provides a powerful diagnostic modality for patients who manifest symptoms of monogenic disease and an opportunity to detect health conditions before their development. However, many technical, clinical, ethical, and societal challenges should be addressed before such technology is widely deployed in pediatric practice. This article provides an overview of the Newborn Sequencing in Genomic Medicine and Public Health Consortium, which is investigating the application of genome-scale sequencing in newborns for both diagnosis and screening.
Collapse
Affiliation(s)
| | - Pankaj B Agrawal
- Divisions of Newborn Medicine and
- Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | | | - Alan H Beggs
- Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | | | - Amy M Brower
- American College of Medical Genetics and Genomics, Bethesda, Maryland
| | - Julie A Cakici
- Rady Children's Institute for Genomic Medicine, San Diego, California
| | | | - Kee Chan
- Chicago School of Public Health, University of Illinois, Chicago, Illinois
| | | | - Robert J Currier
- Genetic Disease Screening Program, California Department of Public Health, Sacramento, California
| | - Dmitry Dukhovny
- Department of Pediatrics and Division of Neonatology, Oregon Health & Science University, Portland, Oregon
| | | | | | - Ingrid A Holm
- Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | | | - Galen Joseph
- Department of Anthropology, History, and Social Medicine
| | | | | | - Pui-Yan Kwok
- Institute for Human Genetics
- Cardiovascular Research Institute, and Department of Dermatology
| | - John Lantos
- Department of Pediatrics, Children's Mercy Hospital, Kansas City, Missouri
| | - Steven J Leeder
- Department of Pediatrics, Children's Mercy Hospital, Kansas City, Missouri
| | - Megan A Lewis
- RTI International, Research Triangle Park, North Carolina
| | - Amy L McGuire
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, Texas; and
| | | | | | - Richard B Parad
- Department of Pediatric Newborn Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Stacey Pereira
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, Texas; and
| | - Joshua Petrikin
- Department of Pediatrics, Children's Mercy Hospital, Kansas City, Missouri
| | | | - Cynthia M Powell
- Pediatrics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina
| | - Jennifer M Puck
- Department of Pediatrics, University of California, San Francisco, California
| | | | | | - Myra Roche
- Pediatrics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina
| | - Joseph T Shieh
- Institute for Human Genetics
- Department of Pediatrics, Benioff Children's Hospital, and
| | | | - Michael S Watson
- American College of Medical Genetics and Genomics, Bethesda, Maryland
| | - Laurel Willig
- Department of Pediatrics, Children's Mercy Hospital, Kansas City, Missouri
| | - Timothy W Yu
- Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Tiina Urv
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland
| | | |
Collapse
|
39
|
Newborn screening: a review of history, recent advancements, and future perspectives in the era of next generation sequencing. Curr Opin Pediatr 2016; 28:694-699. [PMID: 27552071 DOI: 10.1097/mop.0000000000000414] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
PURPOSE OF REVIEW The purpose of this review is to summarize the development and recent advancements of newborn screening. RECENT FINDINGS Early initiation of medical care has modified the outcome for many disorders that were previously associated with high morbidity (such as cystic fibrosis, primary immune deficiencies, and inborn errors of metabolism) or with significant neurodevelopmental disabilities (such as phenylketonuria and congenital hypothyroidism). The new era of mass spectrometry and next generation sequencing enables the expansion of the newborn screen panel, and will help to address technical issues such as turnaround time, and decreasing false-positive and false-negative rates for the testing. SUMMARY The newborn screening program is a successful public health initiative that facilitates early diagnosis of treatable disorders to reduce long-term morbidity and mortality.
Collapse
|
40
|
Array comparative genomic hybridization and genomic sequencing in the diagnostics of the causes of congenital anomalies. J Appl Genet 2016; 58:185-198. [PMID: 27858254 DOI: 10.1007/s13353-016-0376-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 10/19/2016] [Accepted: 11/03/2016] [Indexed: 12/17/2022]
Abstract
The aim of this review is to provide the current state of knowledge about the usefulness of modern genetic technologies in uncovering the causality of isolated and multiple congenital anomalies. Array comparative genomic hybridization and next-generation sequencing have revolutionized the clinical approach to patients with these phenotypes. Both technologies enable early diagnosis, especially in clinically challenging newborn populations, and help to uncover genetic defects associated with various phenotypes. The application of both complementary methods could assist in identifying many variants that may simultaneously be involved in the development of a number of isolated or multiple congenital anomalies. Both technologies carry serious variant misinterpretation risks as well. Therefore, the methods of variant classification and accessible variant databases are mentioned. A useful strategy of clinical genetic testing with the application of both methodologies is presented. Finally, future directions and challenges are briefly commented on in this review.
Collapse
|
41
|
Abstract
As part of the "Grand Convergence: Aligning Technologies and Realities in Global Health" Collection, Cyril Engmann and colleagues discuss promising innovations that have the potential to move the RMNCH agenda forward.
Collapse
|
42
|
Berg JS, Powell CM. Potential Uses and Inherent Challenges of Using Genome-Scale Sequencing to Augment Current Newborn Screening. Cold Spring Harb Perspect Med 2015; 5:cshperspect.a023150. [PMID: 26438605 DOI: 10.1101/cshperspect.a023150] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Since newborn screening (NBS) began in the 1960s, technological advances have enabled its expansion to include an increasing number of disorders. Recent developments now make it possible to sequence an infant's genome relatively quickly and economically. Clinical application of whole-exome and whole-genome sequencing is expanding at a rapid pace but presents many challenges. Its utility in NBS has yet to be demonstrated and its application in the pediatric population requires examination, not only for potential clinical benefits, but also for the unique ethical challenges it presents.
Collapse
Affiliation(s)
- Jonathan S Berg
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7264
| | - Cynthia M Powell
- Departments of Pediatrics and Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7264
| |
Collapse
|
43
|
Utility of whole-genome sequencing for detection of newborn screening disorders in a population cohort of 1,696 neonates. Genet Med 2015; 18:221-30. [PMID: 26334177 DOI: 10.1038/gim.2015.111] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 06/26/2015] [Indexed: 01/29/2023] Open
Abstract
PURPOSE To assess the potential of whole-genome sequencing (WGS) to replicate and augment results from conventional blood-based newborn screening (NBS). METHODS Research-generated WGS data from an ancestrally diverse cohort of 1,696 infants and both parents of each infant were analyzed for variants in 163 genes involved in disorders included or under discussion for inclusion in US NBS programs. WGS results were compared with results from state NBS and related follow-up testing. RESULTS NBS genes are generally well covered by WGS. There is a median of one (range: 0-6) database-annotated pathogenic variant in the NBS genes per infant. Results of WGS and NBS in detecting 28 state-screened disorders and four hemoglobin traits were concordant for 88.6% of true positives (n = 35) and 98.9% of true negatives (n = 45,757). Of the five infants affected with a state-screened disorder, WGS identified two whereas NBS detected four. WGS yielded fewer false positives than NBS (0.037 vs. 0.17%) but more results of uncertain significance (0.90 vs. 0.013%). CONCLUSION WGS may help rule in and rule out NBS disorders, pinpoint molecular diagnoses, and detect conditions not amenable to current NBS assays.
Collapse
|
44
|
Alamillo CL, Powis Z, Farwell K, Shahmirzadi L, Weltmer EC, Turocy J, Lowe T, Kobelka C, Chen E, Basel D, Ashkinadze E, D'Augelli L, Chao E, Tang S. Exome sequencing positively identified relevant alterations in more than half of cases with an indication of prenatal ultrasound anomalies. Prenat Diagn 2015; 35:1073-8. [PMID: 26147564 DOI: 10.1002/pd.4648] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
OBJECTIVE Exome sequencing is a successful option for diagnosing individuals with previously uncharacterized genetic conditions, however little has been reported regarding its utility in a prenatal setting. The goal of this study is to describe the results from a cohort of fetuses for which exome sequencing was performed. METHODS We performed a retrospective analysis of the first seven cases referred to our laboratory for exome sequencing following fetal demise or termination of pregnancy. All seven pregnancies had multiple congenital anomalies identified by level II ultrasound. Exome sequencing was performed on trios using cultured amniocytes or products of conception from the affected fetuses. RESULTS Relevant alterations were identified in more than half of the cases (4/7). Three of the four were categorized as 'positive' results, and one of the four was categorized as a 'likely positive' result. The provided diagnoses included osteogenesis imperfecta II (COL1A2), glycogen storage disease IV (GBE1), oral-facial-digital syndrome 1 (OFD1), and RAPSN-associated fetal akinesia deformation sequence. CONCLUSION This data suggests that exome sequencing is likely to be a valuable diagnostic testing option for pregnancies with multiple congenital anomalies detected by prenatal ultrasound; however, additional studies with larger cohorts of affected pregnancies are necessary to confirm these findings.
Collapse
Affiliation(s)
| | - Zöe Powis
- Ambry Genetics, Aliso Viejo, CA, USA
| | | | | | | | - John Turocy
- Genetics Department, Kaiser Permanente, Clovis, CA, USA
| | - Thomas Lowe
- Thomas Lowe, MD, Private Practice, Boca Raton, FL, USA
| | | | - Emily Chen
- Genetics Department, Kaiser Permanente, San Francisco, CA, USA
| | - Donald Basel
- Division of Genetics, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Elena Ashkinadze
- Division of Maternal-Fetal Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | | | - Elizabeth Chao
- Ambry Genetics, Aliso Viejo, CA, USA.,Department of Pediatrics, University of California Irvine, Irvine, CA, USA
| | - Sha Tang
- Ambry Genetics, Aliso Viejo, CA, USA
| |
Collapse
|
45
|
|