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Flowers M, Dickson A, Miller MJ, Spector E, Enns GM, Baudet H, Pasquali M, Racacho L, Sadre-Bazzaz K, Wen T, Fogarty M, Fernandez R, Weaver MA, Feigenbaum A, Graham BH, Mao R. Specifications of the ACMG/AMP guidelines for ACADVL variant interpretation. Mol Genet Metab 2023; 140:107668. [PMID: 37549443 PMCID: PMC10811274 DOI: 10.1016/j.ymgme.2023.107668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 07/24/2023] [Accepted: 07/25/2023] [Indexed: 08/09/2023]
Abstract
Very long-chain acyl-CoA dehydrogenase (VLCAD) deficiency (VLCADD) is a relatively common inborn error of metabolism, but due to difficulty in accurately predicting affected status through newborn screening, molecular confirmation of the causative variants by sequencing of the ACADVL gene is necessary. Although the ACMG/AMP guidelines have helped standardize variant classification, ACADVL variant classification remains disparate due to a phenotype that can be nonspecific, the possibility of variants that produce late-onset disease, and relatively high carrier frequency, amongst other challenges. Therefore, an ACADVL-specific variant curation expert panel (VCEP) was created to facilitate the specification of the ACMG/AMP guidelines for VLCADD. We expect these guidelines to help streamline, increase concordance, and expedite the classification of ACADVL variants.
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Affiliation(s)
- May Flowers
- Invitae Corporation, San Francisco, CA 94103, USA
| | - Alexa Dickson
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Marcus J Miller
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Elaine Spector
- Department of Pathology, University of Colorado School of Medicine, Aurora, CO 80045, USA; Section of Clinical Genetics and Metabolism, Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Gregory Mark Enns
- Division of Medical Genetics, Department of Pediatrics, Lucile Packard Children's Hospital, Stanford University, Stanford, CA 94304, USA
| | - Heather Baudet
- Department of Genetics, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Marzia Pasquali
- Department of Pathology, University of Utah, Salt Lake City, UT 84112, USA; ARUP Laboratories, Salt Lake City, UT 84108, USA
| | - Lemuel Racacho
- Department of Medical Genetics, Alberta Children's Hospital, Calgary, Alberta T3B6A8, Canada
| | | | - Ting Wen
- ARUP Laboratories, Salt Lake City, UT 84108, USA
| | | | - Raquel Fernandez
- American College of Medical Genetics and Genomics, Bethesda, MD 20814, USA
| | - Meredith A Weaver
- American College of Medical Genetics and Genomics, Bethesda, MD 20814, USA
| | - Annette Feigenbaum
- Department of Pediatrics, Division of Genetics, Rady Children's Hospital and The University of California, San Diego, CA 92123, USA
| | - Brett H Graham
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Rong Mao
- Department of Pathology, University of Utah, Salt Lake City, UT 84112, USA; ARUP Laboratories, Salt Lake City, UT 84108, USA.
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Liang NSY, Watts-Dickens A, Chitayat D, Babul-Hirji R, Chakraborty P, Hayeems RZ. Parental Preferences for Expanded Newborn Screening: What Are the Limits? CHILDREN (BASEL, SWITZERLAND) 2023; 10:1362. [PMID: 37628361 PMCID: PMC10453746 DOI: 10.3390/children10081362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 08/02/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023]
Abstract
The use of next-generation sequencing technologies such as genomic sequencing in newborn screening (NBS) could enable the detection of a broader range of conditions. We explored parental preferences and attitudes towards screening for conditions for which varying types of treatment exist with a cross-sectional survey completed by 100 parents of newborns who received NBS in Ontario, Canada. The survey included four vignettes illustrative of hypothetical screening targets, followed by questions assessing parental attitudes. Chi-square tests were used to compare frequency distributions of preferences. Results show that most parents supported NBS for conditions for which only supportive interventions are available, but to a significantly lesser degree than those with disease-specific treatments (99% vs. 82-87%, p ≤ 0.01). For conditions without an effective treatment, the type of supportive care and age of onset of the condition did not significantly alter parent perceptions of risks and benefits. Parents are interested in expanded NBS for conditions with only supportive interventions in childhood, despite lower levels of perceived benefit for the child and greater anticipated anxiety from screen-positive results. These preferences suggest that the expansion of NBS may require ongoing deliberation of perceived benefits and risks and enhanced approaches to education, consent, and support.
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Affiliation(s)
- Nicole S. Y. Liang
- Department of Genetic Counselling, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Abby Watts-Dickens
- Department of Genetic Counselling, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - David Chitayat
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Riyana Babul-Hirji
- Department of Genetic Counselling, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | | | - Robin Z. Hayeems
- Child Health Evaluative Sciences, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
- Health Policy, Management and Evaluation, University of Toronto, ON M5T 3M6, Canada
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D’Annibale OM, Koppes EA, Sethuraman M, Bloom K, Mohsen AW, Vockley J. Characterization of exonic variants of uncertain significance in very long-chain acyl-CoA dehydrogenase identified through newborn screening. J Inherit Metab Dis 2022; 45:529-540. [PMID: 35218577 PMCID: PMC9090957 DOI: 10.1002/jimd.12492] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 02/20/2022] [Accepted: 02/22/2022] [Indexed: 11/06/2022]
Abstract
Very long-chain acyl-CoA dehydrogenase deficiency (VLCADD) is an autosomal recessive disease resulting from mutations in the ACADVL gene and is among the disorders tested for in newborn screening (NBS). Confirmatory sequencing following suspected VLCADD NBS results often identifies variants of uncertain significance (VUS) in the ACADVL gene, leading to uncertainty of diagnosis and providing effective treatment regimen. Currently, ACADVL has >300 VUSs in the ClinVar database that requiring characterization to determine potential pathogenicity. In this study, CRISPR/Cas9 genome editing was used to knock out ACADVL in HEK293T cells, and targeted deletion was confirmed by droplet digital polymerase chain reaction (PCR). No VLCAD protein was detected and an 84% decrease in enzyme activity using the electron transfer flavoprotein fluorescence reduction assay and C21-CoA as substrate was observed compared to control. Plasmids containing control or variant ACADVL coding sequence were transfected into the ACADVL null HEK293T. While transfection of control ACADVL restored VLCAD protein and enzyme activity, cells expressing the VLCAD Val283Ala mutant had 18% VLCAD enzyme activity and reduced protein compared to control. VLCAD Ile420Leu, Gly179Arg, and Gln406Pro produced protein comparable to control but 25%, 4%, and 5% VLCAD enzyme activity, respectively. Leu540Pro and Asp570_Ala572dup had reduced VLCAD protein and 10% and 3% VLCAD enzyme activity, respectively. VLCADD fibroblasts containing the same variations had decreased VLCAD protein and activity comparable to the transfection experiments. Generating ACADVL null HEK293T cell line allowed functional studies to determine pathogenicity of ACADVL exonic variants. This approach can be applied to multiple genes for other disorders identified through NBS.
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Affiliation(s)
- Olivia M. D’Annibale
- Division of Genetic and Genomic Medicine, Department of Pediatrics, University of Pittsburgh School of Medicine, and UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA 15224
- Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA 15261
| | - Erik A. Koppes
- Division of Genetic and Genomic Medicine, Department of Pediatrics, University of Pittsburgh School of Medicine, and UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA 15224
| | - Meena Sethuraman
- University of Pittsburgh School of Medicine, Pittsburgh, PA 15261
| | - Kaitlyn Bloom
- Division of Genetic and Genomic Medicine, Department of Pediatrics, University of Pittsburgh School of Medicine, and UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA 15224
| | - Al-Walid Mohsen
- Division of Genetic and Genomic Medicine, Department of Pediatrics, University of Pittsburgh School of Medicine, and UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA 15224
- Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA 15261
| | - Jerry Vockley
- Division of Genetic and Genomic Medicine, Department of Pediatrics, University of Pittsburgh School of Medicine, and UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA 15224
- Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA 15261
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Xiang J, Zhang H, Sun X, Zhang J, Xu Z, Sun J, Peng Z. Utility of Whole Genome Sequencing for Population Screening of Deafness-Related Genetic Variants and Cytomegalovirus Infection in Newborns. Front Genet 2022; 13:883617. [PMID: 35571039 PMCID: PMC9099144 DOI: 10.3389/fgene.2022.883617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 04/07/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Hearing loss affects approximately two out of every 1,000 newborns. Genetic factors and congenital cytomegalovirus (CMV) infections account for around 90% of the etiology. The purpose of this study was to develop and test a whole genome sequencing (WGS) approach to detect deafness-related genetic variants and CMV infections simultaneously in newborns.Method: Deafness-related genes causing congenital or childhood hearing loss were curated and selected for newborn screening. Nine dried blood spots from newborns with known genetic variants (n = 6) or CMV infections (n = 3) were employed to develop and validate the WGS testing and analytic pipeline. We then pilot tested the WGS analysis on 51 de-identified clinical samples.Results: 92 gene-disease pairs were selected for screening hearing loss in newborns. In the validation test, WGS accurately detected all types of genetic variants, including single nucleotide variations, insertions/deletions, and copy number variations in the nuclear or mitochondrial genome. Sequence reads mapping to the CMV reference genome were discovered in CMV infected samples. In the pilot test, WGS identified nine out of 51 (18%) newborns carrying pathogenic variants associated with deafness.Conclusion: WGS can simultaneously detect genetic variants and CMV infections in dried blood spot specimens from newborns. Our study provides proof of principle that genome sequencing can be a promising alternative for newborn screening of hearing loss.
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Affiliation(s)
- Jiale Xiang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | | | | | - Junqing Zhang
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, China
| | - Zhenpeng Xu
- BGI-Wuhan Clinical Laboratories, BGI-Shenzhen, Wuhan, China
| | - Jun Sun
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, China
| | - Zhiyu Peng
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
- *Correspondence: Zhiyu Peng,
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Bains S, Dotzler SM, Krijger C, Giudicessi JR, Ye D, Bikker H, Rohatgi RK, Tester DJ, Bos JM, Wilde AAM, Ackerman MJ. A phenotype-enhanced variant classification framework to decrease the burden of missense variants of uncertain significance in type 1 long QT syndrome. Heart Rhythm 2021; 19:435-442. [PMID: 34798354 DOI: 10.1016/j.hrthm.2021.11.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 11/10/2021] [Accepted: 11/11/2021] [Indexed: 12/16/2022]
Abstract
BACKGROUND Pathogenic/likely pathogenic (P/LP) variants in the KCNQ1-encoded Kv7.1 potassium channel cause type 1 long QT syndrome (LQT1). Despite the revamped 2015 American College of Medical Genetics (ACMG) variant interpretation guidelines, the burden of KCNQ1 variants of uncertain significance (VUS) in patients with LQTS remains ∼30%. OBJECTIVE The purpose of this study was to determine whether a phenotype-enhanced (PE) variant classification approach could reduce the VUS burden in LQTS genetic testing. METHODS Retrospective analysis was performed on 79 KCNQ1 missense variants in 356 patients from Mayo Clinic and an independent cohort of 42 variants in 225 patients from Amsterdam University Medical Center (UMC). Each variant was classified initially using the ACMG guidelines and then readjudicated using a PE-ACMG framework that incorporated the LQTS clinical diagnostic Schwartz score plus 4 "LQT1-defining features": broad-based/slow upstroke T waves, syncope/seizure during exertion, swimming-associated events, and a maladaptive LQT1 treadmill stress test. RESULTS According to the ACMG guidelines, Mayo Clinic variants were classified as follows: 17 of 79 P variants (22%), 34 of 79 LP variants (43%), and 28 of 79 VUS (35%). Similarly, for Amsterdam UMC, the variant distribution was 9 of 42 P variants (22%), 14 of 42 LP variants (33%), and 19 of 42 variants VUS (45%). After PE-ACMG readjudication, the total VUS burden decreased significantly from 28 (35%) to 13 (16%) (P = .0007) for Mayo Clinic and from 19 (45%) to 12 (29%) (P = .02) for Amsterdam UMC. CONCLUSION Phenotype-guided variant adjudication decreased significantly the VUS burden of LQT1 case-derived KCNQ1 missense variants in 2 independent cohorts. This study demonstrates the value of incorporating LQT1-specific phenotype/clinical data to aid in the interpretation of KCNQ1 missense variants identified during genetic testing for LQTS.
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Affiliation(s)
- Sahej Bains
- Medical Scientist Training Program, Mayo Clinic, Rochester, Minnesota; Department of Molecular Pharmacology and Experimental Therapeutics, Windland Smith Rice Sudden Death Genomics Laboratory, Mayo Clinic, Rochester, Minnesota
| | - Steven M Dotzler
- Medical Scientist Training Program, Mayo Clinic, Rochester, Minnesota; Department of Molecular Pharmacology and Experimental Therapeutics, Windland Smith Rice Sudden Death Genomics Laboratory, Mayo Clinic, Rochester, Minnesota
| | - Christian Krijger
- Department of Experimental Cardiology, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - John R Giudicessi
- Department of Cardiovascular Medicine, Division of Heart Rhythm Services, Windland Smith Rice Genetic Heart Rhythm Clinic, Mayo Clinic, Rochester, Minnesota
| | - Dan Ye
- Department of Molecular Pharmacology and Experimental Therapeutics, Windland Smith Rice Sudden Death Genomics Laboratory, Mayo Clinic, Rochester, Minnesota
| | - Hennie Bikker
- Department of Human Genetics, University of Amsterdam, Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - Ram K Rohatgi
- Department of Pediatric and Adolescent Medicine (Division of Pediatric Cardiology), Mayo Clinic, Rochester, Minnesota
| | - David J Tester
- Department of Molecular Pharmacology and Experimental Therapeutics, Windland Smith Rice Sudden Death Genomics Laboratory, Mayo Clinic, Rochester, Minnesota; Department of Cardiovascular Medicine, Division of Heart Rhythm Services, Windland Smith Rice Genetic Heart Rhythm Clinic, Mayo Clinic, Rochester, Minnesota; Department of Pediatric and Adolescent Medicine (Division of Pediatric Cardiology), Mayo Clinic, Rochester, Minnesota
| | - J Martijn Bos
- Department of Molecular Pharmacology and Experimental Therapeutics, Windland Smith Rice Sudden Death Genomics Laboratory, Mayo Clinic, Rochester, Minnesota; Department of Cardiovascular Medicine, Division of Heart Rhythm Services, Windland Smith Rice Genetic Heart Rhythm Clinic, Mayo Clinic, Rochester, Minnesota; Department of Pediatric and Adolescent Medicine (Division of Pediatric Cardiology), Mayo Clinic, Rochester, Minnesota
| | - Arthur A M Wilde
- Department of Experimental Cardiology, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands; Department of Cardiology, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Michael J Ackerman
- Department of Molecular Pharmacology and Experimental Therapeutics, Windland Smith Rice Sudden Death Genomics Laboratory, Mayo Clinic, Rochester, Minnesota; Department of Cardiovascular Medicine, Division of Heart Rhythm Services, Windland Smith Rice Genetic Heart Rhythm Clinic, Mayo Clinic, Rochester, Minnesota; Department of Pediatric and Adolescent Medicine (Division of Pediatric Cardiology), Mayo Clinic, Rochester, Minnesota.
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6
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Elmonem MA, van den Heuvel LP. Editorial: Newborn Screening for Inborn Errors of Metabolism: Is It Time for a Globalized Perspective Based on Genetic Screening? Front Genet 2021; 12:758142. [PMID: 34589119 PMCID: PMC8473867 DOI: 10.3389/fgene.2021.758142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 08/23/2021] [Indexed: 12/23/2022] Open
Affiliation(s)
- Mohamed A Elmonem
- Department of Clinical and Chemical Pathology, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Lambertus P van den Heuvel
- Department of Pediatric Nephrology & Development and Regeneration, KU Leuven, Leuven, Belgium.,Department of Pediatric Nephrology, Radboud University Medical Centre, Nijmegen, Netherlands
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D'Annibale OM, Koppes EA, Alodaib AN, Kochersperger C, Karunanidhi A, Mohsen AW, Vockley J. Characterization of variants of uncertain significance in isovaleryl-CoA dehydrogenase identified through newborn screening: An approach for faster analysis. Mol Genet Metab 2021; 134:29-36. [PMID: 34535384 PMCID: PMC8578405 DOI: 10.1016/j.ymgme.2021.08.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 08/24/2021] [Accepted: 08/24/2021] [Indexed: 11/18/2022]
Abstract
INTRODUCTION Clinical standard of care for newborn screening (NBS) is acylcarnitine metabolites quantitation by tandem mass spectrometry (MS/MS) from dried blood spots. Follow up sequencing often results in identification of one or more variants of uncertain significance (VUS). Isovaleric acidemia (IVA) is an autosomal recessive inborn error of metabolism caused by deficiency of isovaleryl-CoA dehydrogenase (IVDH) in the Leu catabolism pathway. Many IVD mutations are characterized as VUS complicating IVA clinical diagnoses and treatment. We present a testing platform approach to confirm the functional implication of VUS identified in newborns with IVA applicable to multiple inborn errors of metabolism identified by NBS. METHODS An IVD null HEK293T cell culture model was generated by using a dual sgRNA CRISPR/Cas9 genome-editing strategy targeting IVD exons 2-3. Clonal cell lines were confirmed by a combination of genomic breakpoint sequencing and droplet digital PCR. The IVD null model had no IVDH antigen signal and 96% reduction in IVDH enzyme activity. The IVD null model was transfected with vectors containing control or variant IVD and functional assays were performed to determine variant pathogenicity. RESULTS c.149G > C (p.Arg50Pro; precursor numbering), c.986T > C (p.Met329Thr), and c.1010G > A (p.Arg337Gln), c.1179del394 f. mutant proteins had reduced IVDH protein and activity. c.932C > T (p.Ala311Val), c.707C > T (p.Thr236Ile), and c.1232G > A (p.Arg411Gln) had stable IVDH protein, but no enzyme activity. c.521T > G (p.Val174Gly) had normal IVDH protein and activity. IVD variant transfection results confirmed results from IVA fibroblasts containing the same variants. CONCLUSIONS We have developed an IVD null HEK293T cell line to rapidly allow determination of VUS pathogenicity following identification of novel alleles by clinical sequencing following positive NBS results for suspected IVA. We suggest similar models can be generated via genome-editing for high throughput assessment of VUS function for a multitude of inborn errors of metabolism and can ideally supplement NBS programs.
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Affiliation(s)
- Olivia M D'Annibale
- Division of Genetic and Genomic Medicine, Department of Pediatrics, University of Pittsburgh School of Medicine, and UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA; Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA 15261, USA
| | - Erik A Koppes
- Division of Genetic and Genomic Medicine, Department of Pediatrics, University of Pittsburgh School of Medicine, and UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Ahmad N Alodaib
- Division of Genetic and Genomic Medicine, Department of Pediatrics, University of Pittsburgh School of Medicine, and UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA; Department of Clinical Genomics, Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Catherine Kochersperger
- Division of Genetic and Genomic Medicine, Department of Pediatrics, University of Pittsburgh School of Medicine, and UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Anuradha Karunanidhi
- Division of Genetic and Genomic Medicine, Department of Pediatrics, University of Pittsburgh School of Medicine, and UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Al-Walid Mohsen
- Division of Genetic and Genomic Medicine, Department of Pediatrics, University of Pittsburgh School of Medicine, and UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA; Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA 15261, USA
| | - Jerry Vockley
- Division of Genetic and Genomic Medicine, Department of Pediatrics, University of Pittsburgh School of Medicine, and UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA; Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA 15261, USA.
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8
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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.
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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.)
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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.
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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
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10
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Guenzel AJ, Hall PL, Scott AI, Lam C, Chang IJ, Thies J, Ferreira CR, Pichurin P, Laxen W, Raymond K, Gavrilov DK, Oglesbee D, Rinaldo P, Matern D, Tortorelli S. The low excretor phenotype of glutaric acidemia type I is a source of false negative newborn screening results and challenging diagnoses. JIMD Rep 2021; 60:67-74. [PMID: 34258142 PMCID: PMC8260482 DOI: 10.1002/jmd2.12217] [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: 02/17/2021] [Revised: 03/23/2021] [Accepted: 03/25/2021] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Glutaric acidemia type I (GA1) is an organic acidemia that is often unrecognized in the newborn period until patients suffer an acute encephalopathic crisis, which can be mistaken for nonaccidental trauma. Presymptomatic identification of GA1 patients is possible by newborn screening (NBS). However, the biochemical "low-excretor" (LE) phenotype with nearly normal levels of disease metabolites can be overlooked, which may result in untreated disease and irreversible neurological sequelae. The LE phenotype is also a potential source of false negative (FN) NBS results that merits further investigation. METHODS Samples from six LE GA1 patients were analyzed by biochemical and molecular methods and newborn screen outcomes were retrospectively investigated. RESULTS Five LE GA1 patients were identified that had normal NBS results and three of these presented clinically with GA1 symptoms. One additional symptomatic patient was identified who did not undergo screening. Semiquantitative urine organic acid analysis was consistent with a GA1 diagnosis in two (33%) of the six patients, while plasma glutarylcarnitine was elevated in four (67%) of the six and urine glutarylcarnitine was elevated in four (80%) of five patients. Five GCDH variants were identified in these patients; three of which have not been previously linked to the biochemical LE phenotype. CONCLUSIONS The data presented here raise awareness of potential FN NBS results for LE GA1 patients. The LE phenotype is not protective against adverse clinical outcomes, and the possibility of FN NBS results calls for high vigilance amongst clinicians, even in the setting of a normal NBS result.
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Affiliation(s)
- Adam J. Guenzel
- Biochemical Genetics Laboratory, Mayo ClinicRochesterMinnesotaUSA
| | | | - Anna I. Scott
- Biochemical Genetics LaboratorySeattle Children's HospitalSeattleWashingtonUSA
| | - Christina Lam
- Division of Genetic Medicine, Department of PediatricsUniversity of Washington and Seattle Children's HospitalSeattleWashingtonUSA
| | - Irene J. Chang
- Division of Genetic Medicine, Department of PediatricsUniversity of Washington and Seattle Children's HospitalSeattleWashingtonUSA
| | - Jenny Thies
- Division of Genetic Medicine, Department of PediatricsUniversity of Washington and Seattle Children's HospitalSeattleWashingtonUSA
| | | | - Pavel Pichurin
- Division of Clinical GenomicsMayo ClinicRochesterMinnesotaUSA
| | - William Laxen
- Biochemical Genetics Laboratory, Mayo ClinicRochesterMinnesotaUSA
| | - Kimiyo Raymond
- Biochemical Genetics Laboratory, Mayo ClinicRochesterMinnesotaUSA
| | | | - Devin Oglesbee
- Biochemical Genetics Laboratory, Mayo ClinicRochesterMinnesotaUSA
| | - Piero Rinaldo
- Biochemical Genetics Laboratory, Mayo ClinicRochesterMinnesotaUSA
| | - Dietrich Matern
- Biochemical Genetics Laboratory, Mayo ClinicRochesterMinnesotaUSA
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11
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Development of Strategies to Decrease False Positive Results in Newborn Screening. Int J Neonatal Screen 2020; 6:ijns6040084. [PMID: 33147868 PMCID: PMC7712114 DOI: 10.3390/ijns6040084] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 10/27/2020] [Accepted: 10/31/2020] [Indexed: 01/11/2023] Open
Abstract
The expansion of national newborn screening (NBS) programmes has provided significant benefits in the diagnosis and early treatment of several rare, heritable conditions, preventing adverse health outcomes for most affected infants. New technological developments have enabled the implementation of testing panel covering over 50 disorders. Consequently, the increment of false positive rate has led to a high number of healthy infants recalled for expensive and often invasive additional testing, opening a debate about the harm-benefit ratio of the expanded newborn screening. The false-positive rate represents a challenge for healthcare providers working in NBS systems. Here, we give an overview on the most commonly used strategies for decreasing the adverse effects due to inconclusive screening results. The focus is on NBS performance improvement through the implementation of analytical methods, the application of new and more informative biomarkers, and by using post-analytical interpretive tools. These strategies, used as part of the NBS process, can to enhance the positive predictive value of the test and reduce the parental anxiety and healthcare costs related to the unnecessary tests and procedures.
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12
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Giudicessi JR, Lieve KVV, Rohatgi RK, Koca F, Tester DJ, van der Werf C, Martijn Bos J, Wilde AAM, Ackerman MJ. Assessment and Validation of a Phenotype-Enhanced Variant Classification Framework to Promote or Demote RYR2 Missense Variants of Uncertain Significance. CIRCULATION-GENOMIC AND PRECISION MEDICINE 2020; 12:e002510. [PMID: 31112425 DOI: 10.1161/circgen.119.002510] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Background Many rare, potentially pathogenic, RYR2 variants identified in individuals with clinically definite catecholaminergic polymorphic ventricular tachycardia are classified ambiguously as variants of uncertain significance (VUS). We aimed to determine if a phenotype-enhanced variant classification approach could reduce the burden of RYR2 VUS encountered during clinical genetic testing. Methods This retrospective study was conducted in 84 RYR2-positive individuals from the Mayo Clinic (Rochester, MN) and validated in 149 RYR2-positive individuals from Amsterdam University Medical Center (Amsterdam, NL). Using a newly developed diagnostic scorecard, the pretest clinical probability of catecholaminergic polymorphic ventricular tachycardia was determined for all RYR2-positive individuals. Each RYR2 variant was then readjudicated using a phenotype-enhanced American College of Medical Genetics approach that incorporates new criteria that reflect the phenotypic strength associated with each individual RYR2 variant. Results Overall, 72 distinct RYR2 variants were identified among the 84 Mayo Clinic (39 unique) and 149 Amsterdam University Medical Center (30 unique) cases. Three variants were present in both cohorts. American College of Medical Genetics guidelines classified 47% of all RYR2 variants as VUS. In the Mayo Clinic cohort, readjudication using amended phenotype-enhanced American College of Medical Genetics standards dropped the VUS rate significantly (20/42 [48%] versus 3/42 [7%]; P<0.001) with 13/20 (65%) RYR2 VUS promoted to likely pathogenic and 4/20 (20%) demoted to likely benign. A similar drop in VUS rate (14/33 [42%] versus 3/33 [9%]; P=0.001) was observed in the Amsterdam University Medical Center validation cohort with 10/14 (71%) RYR2 VUS promoted to likely pathogenic and 1/14 (7%) demoted to likely benign. Conclusions This multicenter study illustrates the potential utility of phenotype-enhanced variant classification in catecholaminergic polymorphic ventricular tachycardia.
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Affiliation(s)
- John R Giudicessi
- Department of Cardiovascular Medicine (Clinician-Investigator Training Program) (J.R.G.)
| | - Krystien V V Lieve
- Amsterdam UMC, University of Amsterdam, Heart Center and Department of Clinical and Experimental Cardiology, Amsterdam Cardiovascular Sciences, The Netherlands (K.V.V.L., F.K., C.v.d.W., A.A.M.W.)
| | - Ram K Rohatgi
- Department of Pediatric and Adolescent Medicine (Division of Pediatric Cardiology) (R.K.R.)
| | - Faruk Koca
- Amsterdam UMC, University of Amsterdam, Heart Center and Department of Clinical and Experimental Cardiology, Amsterdam Cardiovascular Sciences, The Netherlands (K.V.V.L., F.K., C.v.d.W., A.A.M.W.)
| | - David J Tester
- Departments of Cardiovascular Medicine (Division of Heart Rhythm Services), Pediatrics (Division of Pediatric Cardiology), and Molecular Pharmacology and Experimental Therapeutics (Windland Smith Rice Sudden Death Genomics Laboratory), Mayo Clinic, Rochester, MN (D.J.T., J.M.B., M.J.A.)
| | - Christian van der Werf
- Amsterdam UMC, University of Amsterdam, Heart Center and Department of Clinical and Experimental Cardiology, Amsterdam Cardiovascular Sciences, The Netherlands (K.V.V.L., F.K., C.v.d.W., A.A.M.W.)
| | - J Martijn Bos
- Departments of Cardiovascular Medicine (Division of Heart Rhythm Services), Pediatrics (Division of Pediatric Cardiology), and Molecular Pharmacology and Experimental Therapeutics (Windland Smith Rice Sudden Death Genomics Laboratory), Mayo Clinic, Rochester, MN (D.J.T., J.M.B., M.J.A.)
| | - Arthur A M Wilde
- Amsterdam UMC, University of Amsterdam, Heart Center and Department of Clinical and Experimental Cardiology, Amsterdam Cardiovascular Sciences, The Netherlands (K.V.V.L., F.K., C.v.d.W., A.A.M.W.)
| | - Michael J Ackerman
- Departments of Cardiovascular Medicine (Division of Heart Rhythm Services), Pediatrics (Division of Pediatric Cardiology), and Molecular Pharmacology and Experimental Therapeutics (Windland Smith Rice Sudden Death Genomics Laboratory), Mayo Clinic, Rochester, MN (D.J.T., J.M.B., M.J.A.)
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13
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Li M, Yang Q, Yi S, Qin Z, Luo J, Fan X. Two novel mutations in DNAJC12 identified by whole-exome sequencing in a patient with mild hyperphenylalaninemia. Mol Genet Genomic Med 2020; 8:e1303. [PMID: 32519510 PMCID: PMC7434608 DOI: 10.1002/mgg3.1303] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 04/22/2020] [Accepted: 04/23/2020] [Indexed: 12/23/2022] Open
Abstract
Background Recently hyperphenylalaninemia (HPA) caused by variants in DNAJC12 was reported and this suggested a new strategy for diagnosis. But DNAJC12‐associated HPA is a rare in Chinese population so far. Methods The clinical information and blood samples from the patient and his family members were collected and analyzed. Whole‐exome sequencing (WES) was used to identify the causative gene. Results We reported a newborn patient with HPA, having excluded the causes in common genes associated with HPA. By using whole‐exome sequencing, novel compound heterozygosity mutations in DNAJC12 were found, namely c.306C>G (p.His102Gln) and c.182delA (p.Lys61Argfs*6). Administering a diet with low phenylalanine combined with tetrahydrobiopterin and neurotransmitter precursors were shown to be effective in preventing neurodevelopmental delay for these patients. Conclusion Our finding confirms the diagnosis of DNAJC12‐associated HPA and suggests that genetic detection of DNAJC12 should be considered when newborn screening results are positive for HPA.
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Affiliation(s)
- Mengting Li
- Department of Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Qi Yang
- Department of Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Sheng Yi
- Department of Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Zailong Qin
- Department of Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Jingsi Luo
- Department of Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Xin Fan
- Department of Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China.,Department of Pediatric, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
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14
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Gavrilov DK, Piazza AL, Pino G, Turgeon C, Matern D, Oglesbee D, Raymond K, Tortorelli S, Rinaldo P. The Combined Impact of CLIR Post-Analytical Tools and Second Tier Testing on the Performance of Newborn Screening for Disorders of Propionate, Methionine, and Cobalamin Metabolism. Int J Neonatal Screen 2020; 6:33. [PMID: 33073028 PMCID: PMC7423003 DOI: 10.3390/ijns6020033] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 04/07/2020] [Indexed: 12/13/2022] Open
Abstract
The expansion of the recommend uniform screening panel to include more than 50 primary and secondary target conditions has resulted in a substantial increase of false positive results. As an alternative to subjective manipulation of cutoff values and overutilization of molecular testing, here we describe the performance outcome of an algorithm for disorders of methionine, cobalamin, and propionate metabolism that includes: (1) first tier screening inclusive of the broadest available spectrum of markers measured by tandem mass spectrometry; (2) integration of all results into a score of likelihood of disease for each target condition calculated by post-analytical interpretive tools created byCollaborative Laboratory Integrated Reports (CLIR), a multivariate pattern recognition software; and (3) further evaluation of abnormal scores by a second tier test measuring homocysteine, methylmalonic acid, and methylcitric acid. This approach can consistently reduce false positive rates to a <0.01% level, which is the threshold of precision newborn screening. We postulate that broader adoption of this algorithm could lead to substantial savings in health care expenditures. More importantly, it could prevent the stress and anxiety experienced by many families when faced with an abnormal newborn screening result that is later resolved as a false positive outcome.
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Affiliation(s)
- Dimitar K Gavrilov
- Biochemical Genetics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA; (A.L.P.); (G.P.); (C.T.); (D.M.); (D.O.); (K.R.); (S.T.); (P.R.)
| | - Amy L Piazza
- Biochemical Genetics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA; (A.L.P.); (G.P.); (C.T.); (D.M.); (D.O.); (K.R.); (S.T.); (P.R.)
| | - Gisele Pino
- Biochemical Genetics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA; (A.L.P.); (G.P.); (C.T.); (D.M.); (D.O.); (K.R.); (S.T.); (P.R.)
| | - Coleman Turgeon
- Biochemical Genetics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA; (A.L.P.); (G.P.); (C.T.); (D.M.); (D.O.); (K.R.); (S.T.); (P.R.)
| | - Dietrich Matern
- Biochemical Genetics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA; (A.L.P.); (G.P.); (C.T.); (D.M.); (D.O.); (K.R.); (S.T.); (P.R.)
| | - Devin Oglesbee
- Biochemical Genetics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA; (A.L.P.); (G.P.); (C.T.); (D.M.); (D.O.); (K.R.); (S.T.); (P.R.)
| | - Kimiyo Raymond
- Biochemical Genetics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA; (A.L.P.); (G.P.); (C.T.); (D.M.); (D.O.); (K.R.); (S.T.); (P.R.)
| | - Silvia Tortorelli
- Biochemical Genetics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA; (A.L.P.); (G.P.); (C.T.); (D.M.); (D.O.); (K.R.); (S.T.); (P.R.)
| | - Piero Rinaldo
- Biochemical Genetics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA; (A.L.P.); (G.P.); (C.T.); (D.M.); (D.O.); (K.R.); (S.T.); (P.R.)
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15
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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.
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16
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Powell CM. What Genomic Sequencing Can Offer Universal Newborn Screening Programs. Hastings Cent Rep 2019; 48 Suppl 2:S18-S19. [PMID: 30133725 DOI: 10.1002/hast.878] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Massively parallel sequencing, also known as next-generation sequencing, has the potential to significantly improve newborn screening programs in the United States and around the world. Compared to genetic tests whose use is well established, sequencing allows for the analysis of large amounts of DNA, providing more comprehensive and rapid results at a lower cost. It is already being used in limited ways by some public health newborn screening laboratories in the United States and other countries-and it is under study for broader and more widespread use, including as a core part of newborn screening programs. Sequencing technology has the potential to significantly improve these essential public health programs. For many of the conditions that newborns are already screened for, sequencing can return more specific and more sensitive results. The technology could also enable newborn screening programs to expand the list of rare pediatric conditions that they look for, thereby identifying more infants who can benefit from immediate care.
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17
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Value of genetic analysis for confirming inborn errors of metabolism detected through the Spanish neonatal screening program. Eur J Hum Genet 2019; 27:556-562. [PMID: 30626930 DOI: 10.1038/s41431-018-0330-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 11/16/2018] [Accepted: 11/27/2018] [Indexed: 11/09/2022] Open
Abstract
The present work describes the value of genetic analysis as a confirmatory measure following the detection of suspected inborn errors of metabolism in the Spanish newborn mass spectrometry screening program. One hundred and forty-one consecutive DNA samples were analyzed by next-generation sequencing using a customized exome sequencing panel. When required, the Illumina extended clinical exome panel was used, as was Sanger sequencing or transcriptional profiling. Biochemical tests were used to confirm the results of the genetic analysis. Using the customized panel, the metabolic disease suspected in 83 newborns (59%) was confirmed. In three further cases, two monoallelic variants were detected for two genes involved in the same biochemical pathway. In the remainder, either a single variant or no variant was identified. Given the persistent absence of biochemical alterations, carrier status was assigned in 39 cases. False positives were recorded for 11. In five cases in which the biochemical pattern was persistently altered, further genetic analysis allowed the detection of two variants affecting the function of BCAT2, ACSF3, and DNAJC12, as well as a second, deep intronic variant in ETFDH or PTS. The present results suggest that genetic analysis using extended next-generation sequencing panels can be used as a confirmatory test for suspected inborn errors of metabolism detected in newborn screening programs. Biochemical tests can be very helpful when a diagnosis is unclear. In summary, simultaneous genomic and metabolomic analyses can increase the number of inborn errors of metabolism that can be confirmed following suggestive newborn screening results.
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18
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Vidal-Folch N, Milosevic D, Majumdar R, Gavrilov D, Matern D, Raymond K, Rinaldo P, Tortorelli S, Abraham RS, Oglesbee D. A Droplet Digital PCR Method for Severe Combined Immunodeficiency Newborn Screening. J Mol Diagn 2018; 19:755-765. [PMID: 28826609 DOI: 10.1016/j.jmoldx.2017.05.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 05/11/2017] [Accepted: 05/30/2017] [Indexed: 11/16/2022] Open
Abstract
Severe combined immunodeficiency (SCID) benefits from early intervention via hematopoietic cell transplantation to reverse T-cell lymphopenia (TCL). Newborn screening (NBS) programs use T-cell receptor excision circle (TREC) levels to detect SCID. Real-time quantitative PCR is often performed to quantify TRECs in dried blood spots (DBSs) for NBS. Yet, real-time quantitative PCR has inefficiencies necessitating normalization, repeat analyses, or standard curves. To address these issues, we developed a multiplex, droplet digital PCR (ddPCR) method for measuring absolute TREC amounts in one DBS punch. TREC and RPP30 levels were simultaneously measured with a Bio-Rad AutoDG and QX200 ddPCR system. DBSs from 610 presumed-normal, 29 lymphocyte-profiled, and 10 clinically diagnosed infants (1 X-linked SCID, 1 RAG1 Omenn syndrome, and other conditions) were tested. Control infants showed 14 to 474 TREC copies/μL blood. SCID infants, and other TCL conditions, had ≤15 TREC copies/μL. The ddPCR lower limit of quantitation was 14 TREC copies/μL, and the limit of detection was 4 TREC copies/μL. Intra-assay and interassay imprecision was <20% CV for DBSs at 54 to 60 TREC copies/μL. Testing 29 infants with known lymphocyte profiles resulted in a sensitivity of 88.9% and a specificity of 100% at TRECs <20 copies/μL. We developed a multiplex ddPCR method for the absolute quantitation of DBS TRECs that can detect SCID and other TCL conditions associated with absent or low TRECs and validated this method for NBS.
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Affiliation(s)
- Noemi Vidal-Folch
- Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, Minnesota
| | - Dragana Milosevic
- Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, Minnesota
| | - Ramanath Majumdar
- Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, Minnesota
| | - Dimitar Gavrilov
- Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, Minnesota; Department of Clinical Genomics, Mayo Clinic College of Medicine, Rochester, Minnesota
| | - Dietrich Matern
- Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, Minnesota; Department of Clinical Genomics, Mayo Clinic College of Medicine, Rochester, Minnesota; Department of Pediatric and Adolescent Medicine, Mayo Clinic College of Medicine, Rochester, Minnesota
| | - Kimiyo Raymond
- Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, Minnesota; Department of Clinical Genomics, Mayo Clinic College of Medicine, Rochester, Minnesota
| | - Piero Rinaldo
- Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, Minnesota; Department of Clinical Genomics, Mayo Clinic College of Medicine, Rochester, Minnesota; Department of Pediatric and Adolescent Medicine, Mayo Clinic College of Medicine, Rochester, Minnesota
| | - Silvia Tortorelli
- Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, Minnesota; Department of Clinical Genomics, Mayo Clinic College of Medicine, Rochester, Minnesota
| | - Roshini S Abraham
- Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, Minnesota; Department of Allergy and Immunology, Mayo Clinic College of Medicine, Rochester, Minnesota
| | - Devin Oglesbee
- Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, Minnesota; Department of Clinical Genomics, Mayo Clinic College of Medicine, Rochester, Minnesota.
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Chakravorty S, Hegde M. Inferring the effect of genomic variation in the new era of genomics. Hum Mutat 2018; 39:756-773. [PMID: 29633501 DOI: 10.1002/humu.23427] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 03/20/2018] [Accepted: 03/28/2018] [Indexed: 12/11/2022]
Abstract
Accurate and detailed understanding of the effects of variants in the coding and noncoding regions of the genome is the next big challenge in the new genomic era of personalized medicine, especially to tackle newer findings of genetic and phenotypic heterogeneity of diseases. This is necessary to resolve the gene-variant-disease relationship, the pathogenic variant spectrum of genes, pathogenic variants with variable clinical consequences, and multiloci diseases. In turn, this will facilitate patient recruitment for relevant clinical trials. In this review, we describe the trends in research at the intersection of basic and clinical genomics aiming to (a) overcome molecular diagnostic challenges and increase the clinical utility of next-generation sequencing (NGS) platforms, (b) elucidate variants associated with disease, (c) determine overall genomic complexity including epistasis, complex inheritance patterns such as "synergistic heterozygosity," digenic/multigenic inheritance, modifier effect, and rare variant load. We describe the newly emerging field of integrated functional genomics, in vivo or in vitro large-scale functional approaches, statistical bioinformatics algorithms that support NGS genomics data to interpret variants for timely clinical diagnostics and disease management. Thus, facilitating the discovery of new therapeutic or biomarker options, and their roles in the future of personalized medicine.
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Affiliation(s)
- Samya Chakravorty
- Department of Human Genetics, Emory University School of Medicine, Whitehead Biomedical Research Building Suite 301, Atlanta, Georgia
| | - Madhuri Hegde
- Department of Human Genetics, Emory University School of Medicine, Whitehead Biomedical Research Building Suite 301, Atlanta, Georgia
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20
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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.
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Chakravorty S, Hegde M. Gene and Variant Annotation for Mendelian Disorders in the Era of Advanced Sequencing Technologies. Annu Rev Genomics Hum Genet 2017; 18:229-256. [PMID: 28415856 DOI: 10.1146/annurev-genom-083115-022545] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Comprehensive annotations of genetic and noncoding regions and corresponding accurate variant classification for Mendelian diseases are the next big challenge in the new genomic era of personalized medicine. Progress in the development of faster and more accurate pipelines for genome annotation and variant classification will lead to the discovery of more novel disease associations and candidate therapeutic targets. This ultimately will facilitate better patient recruitment in clinical trials. In this review, we describe the trends in research at the intersection of basic and clinical genomics that aims to increase understanding of overall genomic complexity, complex inheritance patterns of disease, and patient-phenotype-specific genomic associations. We describe the emerging field of translational functional genomics, which integrates other functional "-omics" approaches that support next-generation sequencing genomic data in order to facilitate personalized diagnostics, disease management, biomarker discovery, and medicine. We also discuss the utility of this integrated approach for diagnostic clinics and medical databases and its role in the future of personalized medicine.
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Affiliation(s)
- Samya Chakravorty
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia 30322;
| | - Madhuri Hegde
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia 30322;
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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.
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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
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23
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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.
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24
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Reassessment of Genomic Sequence Variation to Harmonize Interpretation for Personalized Medicine. Am J Hum Genet 2016; 99:1140-1149. [PMID: 27843123 DOI: 10.1016/j.ajhg.2016.09.015] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 09/21/2016] [Indexed: 01/25/2023] Open
Abstract
Accurate interpretation of DNA sequence variation is a prerequisite for implementing personalized medicine. Discrepancies in interpretation between testing laboratories impede the effective use of genetic test results in clinical medicine. To better understand the underpinnings of these discrepancies, we quantified differences in variant classification internally over time and those between our diagnostic laboratory and other laboratories and resources. We assessed the factors that contribute to these discrepancies and those that facilitate their resolution. Our process resolved 72% of nearly 300 discrepancies between pairs of laboratories to within a one-step classification difference and identified key sources of data that facilitate changes in variant interpretation. The identification and harmonization of variant discrepancies will maximize the clinical use of genetic information; these processes will be fostered by the accumulation of additional population data as well as the sharing of data between diagnostic laboratories.
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