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Richter F, Rutherford KD, Cooke AJ, Meshkati M, Eddy-Abrams V, Greene D, Kosowsky J, Park Y, Aggarwal S, Burke RJ, Chang W, Connors J, Giannone PJ, Hays T, Khattar D, Polak M, Senaldi L, Smith-Raska M, Sridhar S, Steiner L, Swanson JR, Tauber KA, Barbosa M, Guttmann KF, Turro E. A Deep Intronic PKHD1 Variant Identified by SpliceAI in a Deceased Neonate With Autosomal Recessive Polycystic Kidney Disease. Am J Kidney Dis 2024; 83:829-833. [PMID: 38211685 PMCID: PMC11116050 DOI: 10.1053/j.ajkd.2023.12.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/09/2023] [Accepted: 11/10/2023] [Indexed: 01/13/2024]
Abstract
The etiologies of newborn deaths in neonatal intensive care units usually remain unknown, even after genetic testing. Whole-genome sequencing, combined with artificial intelligence-based methods for predicting the effects of non-coding variants, provide an avenue for resolving these deaths. Using one such method, SpliceAI, we identified a maternally inherited deep intronic PKHD1 splice variant (chr6:52030169T>C), in trans with a pathogenic missense variant (p.Thr36Met), in a newborn who died of autosomal recessive polycystic kidney disease at age 2 days. We validated the deep intronic variant's impact in maternal urine-derived cells expressing PKHD1. Reverse transcription polymerase chain reaction followed by Sanger sequencing showed that the variant causes inclusion of 147bp of the canonical intron between exons 29 and 30 of PKHD1 into the mRNA, including a premature stop codon. Allele-specific expression analysis at a heterozygous site in the mother showed that the mutant allele completely suppresses canonical splicing. In an unrelated healthy control, there was no evidence of transcripts including the novel splice junction. We returned a diagnostic report to the parents, who underwent in vitro embryo selection.
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Affiliation(s)
- Felix Richter
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, New York; Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Kayleigh D Rutherford
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Anisha J Cooke
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Malorie Meshkati
- Division of Newborn Medicine, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Vanessa Eddy-Abrams
- Division of Newborn Medicine, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Daniel Greene
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jordana Kosowsky
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Yeaji Park
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Surabhi Aggarwal
- Division of Neonatology, Department of Pediatrics, Stony Brook Children's Hospital, New York, New York
| | - Rebecca J Burke
- Department of Pediatrics, Penn State Health Milton S. Hershey Medical Center, Hershey, Pennsylvania
| | - Weili Chang
- Department of Neonatology, Pediatrics, East Carolina University, Greenville, North Carolina
| | - Jillian Connors
- Division of Neonatology, The Children's Hospital at Montefiore, Bronx, New York
| | - Peter J Giannone
- Division of Neonatology, Department of Pediatrics, University of Kentucky, Lexington, Kentucky
| | - Thomas Hays
- Division of Neonatology, Department of Pediatrics, Columbia University Irving Medical Center, New York, New York
| | - Divya Khattar
- Division of Neonatology, Department of Pediatrics, University of Kentucky, Lexington, Kentucky
| | - Mark Polak
- Department of Pediatrics, Division of Neonatology, West Virginia University School of Medicine, Morgantown, West Virginia
| | - Liana Senaldi
- Division of Newborn Medicine, Department of Pediatrics, Weill Cornell Medicine, New York-Presbyterian Hospital, New York, New York
| | - Matthew Smith-Raska
- Division of Newborn Medicine, Department of Pediatrics, Weill Cornell Medicine, New York-Presbyterian Hospital, New York, New York
| | - Shanthy Sridhar
- Division of Neonatology, Department of Pediatrics, Stony Brook Children's Hospital, New York, New York
| | - Laurie Steiner
- Department of Pediatrics, University of Rochester, Rochester, New York
| | - Jonathan R Swanson
- Division of Neonatology, Department of Pediatrics, University of Virginia Children's Hospital, Charlottesville, Virginia
| | - Kate A Tauber
- Department of Pediatrics, Albany Medical Center, Albany, New York
| | - Mafalda Barbosa
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, New York; Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Katherine F Guttmann
- Division of Newborn Medicine, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Ernest Turro
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York; Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York.
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Margiotti K, Fabiani M, Cima A, Libotte F, Mesoraca A, Giorlandino C. Prenatal Diagnosis by Trio Clinical Exome Sequencing: Single Center Experience. Curr Issues Mol Biol 2024; 46:3209-3217. [PMID: 38666931 PMCID: PMC11048976 DOI: 10.3390/cimb46040201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Revised: 03/28/2024] [Accepted: 04/03/2024] [Indexed: 04/28/2024] Open
Abstract
Fetal anomalies, characterized by structural or functional abnormalities occurring during intrauterine life, pose a significant medical challenge, with a notable prevalence, affecting approximately 2-3% of live births and 20% of spontaneous miscarriages. This study aims to identify the genetic cause of ultrasound anomalies through clinical exome sequencing (CES) analysis. The focus is on utilizing CES analysis in a trio setting, involving the fetuses and both parents. To achieve this objective, prenatal trio clinical exome sequencing was conducted in 51 fetuseses exhibiting ultrasound anomalies with previously negative results from chromosomal microarray (CMA) analysis. The study revealed pathogenic variants in 24% of the analyzed cases (12 out of 51). It is worth noting that the findings include de novo variants in 50% of cases and the transmission of causative variants from asymptomatic parents in 50% of cases. Trio clinical exome sequencing stands out as a crucial tool in advancing prenatal diagnostics, surpassing the effectiveness of relying solely on chromosomal microarray analysis. This underscores its potential to become a routine diagnostic standard in prenatal care, particularly for cases involving ultrasound anomalies.
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Affiliation(s)
- Katia Margiotti
- Human Genetics Lab, Altamedica Main Centre, Viale Liegi 45, 00198 Rome, Italy; (M.F.); (A.C.); (F.L.); (A.M.); (C.G.)
| | - Marco Fabiani
- Human Genetics Lab, Altamedica Main Centre, Viale Liegi 45, 00198 Rome, Italy; (M.F.); (A.C.); (F.L.); (A.M.); (C.G.)
| | - Antonella Cima
- Human Genetics Lab, Altamedica Main Centre, Viale Liegi 45, 00198 Rome, Italy; (M.F.); (A.C.); (F.L.); (A.M.); (C.G.)
| | - Francesco Libotte
- Human Genetics Lab, Altamedica Main Centre, Viale Liegi 45, 00198 Rome, Italy; (M.F.); (A.C.); (F.L.); (A.M.); (C.G.)
| | - Alvaro Mesoraca
- Human Genetics Lab, Altamedica Main Centre, Viale Liegi 45, 00198 Rome, Italy; (M.F.); (A.C.); (F.L.); (A.M.); (C.G.)
| | - Claudio Giorlandino
- Human Genetics Lab, Altamedica Main Centre, Viale Liegi 45, 00198 Rome, Italy; (M.F.); (A.C.); (F.L.); (A.M.); (C.G.)
- Fetal-Maternal Medical Centre, Altamedica Viale Liegi 45, 00198 Rome, Italy
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3
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Li D, Sun N, Xiang L, Liu J, Wang X, Yang L, Huang S. Neurophysiological Characteristics in Type II and Type III 5q Spinal Muscular Atrophy Patients: Impact of Nusinersen Treatment. Drug Des Devel Ther 2024; 18:953-965. [PMID: 38562520 PMCID: PMC10984209 DOI: 10.2147/dddt.s449066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 03/21/2024] [Indexed: 04/04/2024] Open
Abstract
Objective This study aimed to observe the neurophysiological characteristics of type II and type III 5q spinal muscular atrophy (SMA) patients and the changes in peripheral motor nerve electrophysiology after Nusinersen treatment, as well as the influencing factors. Methods This single-center retrospective case-control study collected clinical data and peripheral motor nerve CMAP parameters from 42 5qSMA patients and 42 healthy controls at the Second Affiliated Hospital of Xi'an Jiaotong University (January 2021 to December 2022). It evaluated changes in motor function and CMAP amplitude before and after Nusinersen treatment. Results Our investigation encompassed all symptomatic and genetically confirmed SMA patients, consisting of 32 type II and 10 type III cases, with a median age of 57 months (29.5 to 96 months). Comparative analysis with healthy controls revealed substantial reductions in CMAP amplitudes across various nerves in both type II and type III patients. Despite the administration of Nusinersen treatment for 6 or 14 months to the entire cohort, discernible alterations in motor nerve amplitudes were not observed, except for a significant improvement in younger patients (≤36 months) at the 14-month mark. Further scrutiny within the type II subgroup unveiled that individuals with a disease duration ≤12 months experienced a noteworthy upswing in femoral nerve amplitude, a statistically significant difference when compared to those with >12 months of disease duration. Conclusion Motor nerve amplitudes were significantly decreased in type II and type III 5q SMA patients compared to healthy controls. Nusinersen treatment showed better improvement in motor nerve amplitudes in younger age groups and those with shorter disease duration, indicating a treatment-time dependence.
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Affiliation(s)
- Dan Li
- Department of Pediatrics, the Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, People’s Republic of China
| | - Na Sun
- Department of Pediatrics, the Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, People’s Republic of China
| | - Li Xiang
- Department of Neurology, the Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, People’s Republic of China
| | - Jingjie Liu
- Department of Neurology, the Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, People’s Republic of China
| | - Xueying Wang
- Department of Pediatrics, the Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, People’s Republic of China
| | - Lin Yang
- Department of Pediatrics, the Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, People’s Republic of China
| | - Shaoping Huang
- Department of Pediatrics, the Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, People’s Republic of China
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Callahan KP, Clayton EW, Lemke AA, Chaudhari BP, Wenger TL, Lyle ANJ, Brothers KB. Ethical and Legal Issues Surrounding Genetic Testing in the NICU. Neoreviews 2024; 25:e127-e138. [PMID: 38425196 PMCID: PMC10998684 DOI: 10.1542/neo.25-3-e127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
Clinicians practicing in a modern NICU are noticing an increase in the proportion of patients who undergo genetic testing as well as changes in the types of genetic testing patients receive. These trends are not surprising given the increasing recognition of the genetic causes of neonatal illness and recent advances in genetic technology. Yet, the expansion of genetic testing in the NICU also raises a number of ethical questions. In this article, we will review the ethical issues raised by genetic testing, with a focus on the practical implications for neonatologists. First, we outline the complexities of measuring benefit, or utility, for neonatal genetic testing. Next, we discuss potential harms such as inequity, unexpected findings, disability biases, and legal risks. Finally, we conclude with a discussion of ethical issues related to consent for genetic testing. Throughout this article, we highlight solutions to challenges toward the ultimate goal of minimizing harms and maximizing the substantial potential benefits of genetic medicine in the NICU.
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Affiliation(s)
- Katharine P. Callahan
- Division of Neonatology, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
- Department of Medical Ethics and Health Policy, The Perelman School of Medicine at the University of Pennsylvania; Philadelphia, Pennsylvania
| | - Ellen W. Clayton
- Center for Biomedical Ethics and Society, Department of Pediatrics, Vanderbilt University Medical Center, and School of Law, Vanderbilt University, Nashville, Tennessee
| | - Amy A. Lemke
- Norton Children’s Research Institute Affiliated with the University of Louisville School of Medicine, Louisville, Kentucky
| | - Bimal P. Chaudhari
- Divisions of Neonatology, Genetics and Genomic Medicine, Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, Ohio
| | - Tara L. Wenger
- Division of Medical Genetics, University of Washington, Seattle, Washington
| | - Allison N. J. Lyle
- Division of Neonatology, Department of Pediatrics, University of Louisville School of Medicine, Louisville, KY
| | - Kyle B. Brothers
- Norton Children’s Research Institute Affiliated with the University of Louisville School of Medicine, Louisville, Kentucky
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Seither K, Thompson W, Suhrie K. A Practical Guide to Whole Genome Sequencing in the NICU. Neoreviews 2024; 25:e139-e150. [PMID: 38425198 DOI: 10.1542/neo.25-3-e139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
The neonatal period is a peak time for the presentation of genetic disorders that can be diagnosed using whole genome sequencing (WGS). While any one genetic disorder is individually rare, they collectively contribute to significant morbidity, mortality, and health-care costs. As the cost of WGS continues to decline and becomes increasingly available, the ordering of rapid WGS for NICU patients with signs or symptoms of an underlying genetic condition is now feasible. However, many neonatal clinicians are not comfortable with the testing, and unfortunately, there is a dearth of geneticists to facilitate testing for every patient that needs it. Here, we will review the science behind WGS, diagnostic capabilities, limitations of testing, time to consider testing, test initiation, interpretation of results, developing a plan of care that incorporates genomic information, and returning WGS results to families.
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Affiliation(s)
- Katelyn Seither
- Division of Neonatal and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, and the Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH
| | - Whitney Thompson
- Division of Neonatal Medicine, and the Department of Clinical Genomics, Mayo Clinic, Rochester, MN
| | - Kristen Suhrie
- Division of Neonatology, Department of Pediatrics, and Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN
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6
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Hoolachan JM, McCallion E, Sutton ER, Çetin Ö, Pacheco-Torres P, Dimitriadi M, Sari S, Miller GJ, Okoh M, Walter LM, Claus P, Wood MJA, Tonge DP, Bowerman M. A transcriptomics-based drug repositioning approach to identify drugs with similar activities for the treatment of muscle pathologies in spinal muscular atrophy (SMA) models. Hum Mol Genet 2024; 33:400-425. [PMID: 37947217 PMCID: PMC10877467 DOI: 10.1093/hmg/ddad192] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 10/08/2023] [Accepted: 11/03/2023] [Indexed: 11/12/2023] Open
Abstract
Spinal muscular atrophy (SMA) is a genetic neuromuscular disorder caused by the reduction of survival of motor neuron (SMN) protein levels. Although three SMN-augmentation therapies are clinically approved that significantly slow down disease progression, they are unfortunately not cures. Thus, complementary SMN-independent therapies that can target key SMA pathologies and that can support the clinically approved SMN-dependent drugs are the forefront of therapeutic development. We have previously demonstrated that prednisolone, a synthetic glucocorticoid (GC) improved muscle health and survival in severe Smn-/-;SMN2 and intermediate Smn2B/- SMA mice. However, long-term administration of prednisolone can promote myopathy. We thus wanted to identify genes and pathways targeted by prednisolone in skeletal muscle to discover clinically approved drugs that are predicted to emulate prednisolone's activities. Using an RNA-sequencing, bioinformatics, and drug repositioning pipeline on skeletal muscle from symptomatic prednisolone-treated and untreated Smn-/-; SMN2 SMA and Smn+/-; SMN2 healthy mice, we identified molecular targets linked to prednisolone's ameliorative effects and a list of 580 drug candidates with similar predicted activities. Two of these candidates, metformin and oxandrolone, were further investigated in SMA cellular and animal models, which highlighted that these compounds do not have the same ameliorative effects on SMA phenotypes as prednisolone; however, a number of other important drug targets remain. Overall, our work further supports the usefulness of prednisolone's potential as a second-generation therapy for SMA, identifies a list of potential SMA drug treatments and highlights improvements for future transcriptomic-based drug repositioning studies in SMA.
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Affiliation(s)
- Joseph M Hoolachan
- School of Medicine, David Weatherall Building, Keele University, Staffordshire, ST5 5BG, United Kingdom
| | - Eve McCallion
- School of Medicine, David Weatherall Building, Keele University, Staffordshire, ST5 5BG, United Kingdom
| | - Emma R Sutton
- School of Medicine, David Weatherall Building, Keele University, Staffordshire, ST5 5BG, United Kingdom
| | - Özge Çetin
- School of Medicine, David Weatherall Building, Keele University, Staffordshire, ST5 5BG, United Kingdom
| | - Paloma Pacheco-Torres
- School of Life and Medical Sciences, University of Hertfordshire, Hatfield, Hertfordshire, AL910 9AB, United Kingdom
| | - Maria Dimitriadi
- School of Life and Medical Sciences, University of Hertfordshire, Hatfield, Hertfordshire, AL910 9AB, United Kingdom
| | - Suat Sari
- Department of Pharmaceutical Chemistry, Hacettepe University, Ankara, 06100, Turkey
- School of Chemical and Physical Sciences, Lennard-Jones Building, Keele University, Staffordshire, ST5 5BG, United Kingdom
| | - Gavin J Miller
- School of Chemical and Physical Sciences, Lennard-Jones Building, Keele University, Staffordshire, ST5 5BG, United Kingdom
- Centre for Glycoscience, Keele University, Staffordshire, ST5 5BG, United Kingdom
| | - Magnus Okoh
- School of Medicine, David Weatherall Building, Keele University, Staffordshire, ST5 5BG, United Kingdom
| | - Lisa M Walter
- SMATHERIA gGmbH – Non-Profit Biomedical Research Institute, Feodor-Lynen-Straße 31, 30625, Hannover, Germany
- Centre of Systems Neuroscience (ZSN), Hannover Medical School, Bünteweg 2, 30559, Hannover, Germany
| | - Peter Claus
- SMATHERIA gGmbH – Non-Profit Biomedical Research Institute, Feodor-Lynen-Straße 31, 30625, Hannover, Germany
- Centre of Systems Neuroscience (ZSN), Hannover Medical School, Bünteweg 2, 30559, Hannover, Germany
| | - Matthew J A Wood
- Department of Paediatrics, University of Oxford, Level 2, Children's Hospital, John Radcliffe, Headington Oxford, OX3 9DU, United Kingdom
| | - Daniel P Tonge
- School of Life Sciences, Huxley Building, Keele University, Staffordshire ST5 5BG, United Kingdom
| | - Melissa Bowerman
- School of Medicine, David Weatherall Building, Keele University, Staffordshire, ST5 5BG, United Kingdom
- Wolfson Centre for Inherited Neuromuscular Disease, RJAH Orthopaedic Hospital, Oswestry, SY10 7AG, United Kingdom
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D'Gama AM, Hills S, Douglas J, Young V, Genetti CA, Wojcik MH, Feldman HA, Yu TW, G Parker M, Agrawal PB. Implementation of rapid genomic sequencing in safety-net neonatal intensive care units: protocol for the VIrtual GenOme CenteR (VIGOR) proof-of-concept study. BMJ Open 2024; 14:e080529. [PMID: 38320840 PMCID: PMC10859977 DOI: 10.1136/bmjopen-2023-080529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 01/17/2024] [Indexed: 02/15/2024] Open
Abstract
INTRODUCTION Rapid genomic sequencing (rGS) in critically ill infants with suspected genetic disorders has high diagnostic and clinical utility. However, rGS has primarily been available at large referral centres with the resources and expertise to offer state-of-the-art genomic care. Critically ill infants from racial and ethnic minority and/or low-income populations disproportionately receive care in safety-net and/or community settings lacking access to state-of-the-art genomic care, contributing to unacceptable health equity gaps. VIrtual GenOme CenteR is a 'proof-of-concept' implementation science study of an innovative delivery model for genomic care in safety-net neonatal intensive care units (NICUs). METHODS AND ANALYSIS We developed a virtual genome centre at a referral centre to remotely support safety-net NICU sites predominantly serving racial and ethnic minority and/or low-income populations and have limited to no access to rGS. Neonatal providers at each site receive basic education about genomic medicine from the study team and identify eligible infants. The study team enrols eligible infants (goal n of 250) and their parents and follows families for 12 months. Enrolled infants receive rGS, the study team creates clinical interpretive reports to guide neonatal providers on interpreting results, and neonatal providers return results to families. Data is collected via (1) medical record abstraction, (2) surveys, interviews and focus groups with neonatal providers and (3) surveys and interviews with families. We aim to examine comprehensive implementation outcomes based on the Proctor Implementation Framework using a mixed methods approach. ETHICS AND DISSEMINATION This study is approved by the institutional review board of Boston Children's Hospital (IRB-P00040496) and participating sites. Participating families are required to provide electronic written informed consent and neonatal provider consent is implied through the completion of surveys. The results will be disseminated via peer-reviewed publications and data will be made accessible per National Institutes of Health (NIH) policies. TRIAL REGISTRATION NUMBER NCT05205356/clinicaltrials.gov.
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Affiliation(s)
- Alissa M D'Gama
- Division of Newborn Medicine, Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts, USA
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Sonia Hills
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Jessica Douglas
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Vanessa Young
- Division of Newborn Medicine, Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Casie A Genetti
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts, USA
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Monica H Wojcik
- Division of Newborn Medicine, Department of Pediatrics, Harvard Medical School, Boston Children's Hospital, Boston, Massachusetts, USA
- Division of Genetics and Genomics, Department of Pediatrics, Harvard Medical School, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Henry A Feldman
- Division of Newborn Medicine, Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Timothy W Yu
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts, USA
| | | | - Pankaj B Agrawal
- Division of Neonatology, Department of Pediatrics, University of Miami Miller School of Medicine, Miami, Florida, USA
- Jackson Health System, Holtz Children's Hospital, Miami, Florida, USA
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Grabowska ME, Van Driest SL, Robinson JR, Patrick AE, Guardo C, Gangireddy S, Ong HH, Feng Q, Carroll R, Kannankeril PJ, Wei WQ. Developing and evaluating pediatric phecodes (Peds-Phecodes) for high-throughput phenotyping using electronic health records. J Am Med Inform Assoc 2024; 31:386-395. [PMID: 38041473 PMCID: PMC10797257 DOI: 10.1093/jamia/ocad233] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 10/04/2023] [Accepted: 11/20/2023] [Indexed: 12/03/2023] Open
Abstract
OBJECTIVE Pediatric patients have different diseases and outcomes than adults; however, existing phecodes do not capture the distinctive pediatric spectrum of disease. We aim to develop specialized pediatric phecodes (Peds-Phecodes) to enable efficient, large-scale phenotypic analyses of pediatric patients. MATERIALS AND METHODS We adopted a hybrid data- and knowledge-driven approach leveraging electronic health records (EHRs) and genetic data from Vanderbilt University Medical Center to modify the most recent version of phecodes to better capture pediatric phenotypes. First, we compared the prevalence of patient diagnoses in pediatric and adult populations to identify disease phenotypes differentially affecting children and adults. We then used clinical domain knowledge to remove phecodes representing phenotypes unlikely to affect pediatric patients and create new phecodes for phenotypes relevant to the pediatric population. We further compared phenome-wide association study (PheWAS) outcomes replicating known pediatric genotype-phenotype associations between Peds-Phecodes and phecodes. RESULTS The Peds-Phecodes aggregate 15 533 ICD-9-CM codes and 82 949 ICD-10-CM codes into 2051 distinct phecodes. Peds-Phecodes replicated more known pediatric genotype-phenotype associations than phecodes (248 vs 192 out of 687 SNPs, P < .001). DISCUSSION We introduce Peds-Phecodes, a high-throughput EHR phenotyping tool tailored for use in pediatric populations. We successfully validated the Peds-Phecodes using genetic replication studies. Our findings also reveal the potential use of Peds-Phecodes in detecting novel genotype-phenotype associations for pediatric conditions. We expect that Peds-Phecodes will facilitate large-scale phenomic and genomic analyses in pediatric populations. CONCLUSION Peds-Phecodes capture higher-quality pediatric phenotypes and deliver superior PheWAS outcomes compared to phecodes.
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Affiliation(s)
- Monika E Grabowska
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37203, United States
| | - Sara L Van Driest
- Department of Pediatrics and the Center for Pediatric Precision Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, United States
| | - Jamie R Robinson
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37203, United States
- Department of Pediatric Surgery, Vanderbilt University Medical Center, Nashville, TN 37232, United States
| | - Anna E Patrick
- Department of Pediatrics and the Center for Pediatric Precision Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, United States
| | - Chris Guardo
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37203, United States
| | - Srushti Gangireddy
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37203, United States
| | - Henry H Ong
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37203, United States
| | - QiPing Feng
- Department of Medicine, Division of Clinical Pharmacology, Vanderbilt University Medical Center, Nashville, TN 37232, United States
| | - Robert Carroll
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37203, United States
| | - Prince J Kannankeril
- Department of Pediatrics and the Center for Pediatric Precision Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, United States
| | - Wei-Qi Wei
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37203, United States
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Abstract
Rare diseases are a leading cause of infant mortality and lifelong disability. To improve outcomes, timely diagnosis and effective treatments are needed. Genomic sequencing has transformed the traditional diagnostic process, providing rapid, accurate and cost-effective genetic diagnoses to many. Incorporating genomic sequencing into newborn screening programmes at the population scale holds the promise of substantially expanding the early detection of treatable rare diseases, with stored genomic data potentially benefitting health over a lifetime and supporting further research. As several large-scale newborn genomic screening projects launch internationally, we review the challenges and opportunities presented, particularly the need to generate evidence of benefit and to address the ethical, legal and psychosocial issues that genomic newborn screening raises.
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Affiliation(s)
- Zornitza Stark
- Australian Genomics, Melbourne, Victoria, Australia.
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia.
| | - Richard H Scott
- Great Ormond Street Hospital for Children, London, UK
- UCL Great Ormond Street Institute of Child Health, London, UK
- Genomics England, London, UK
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10
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Wojcik MH, Callahan KP, Antoniou A, Del Rosario MC, Brunelli L, ElHassan NO, Gogcu S, Murthy K, Rumpel JA, Wambach JA, Suhrie K, Fishler K, Chaudhari BP. Provision and availability of genomic medicine services in Level IV neonatal intensive care units. Genet Med 2023; 25:100926. [PMID: 37422715 PMCID: PMC10592224 DOI: 10.1016/j.gim.2023.100926] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/30/2023] [Accepted: 07/02/2023] [Indexed: 07/10/2023] Open
Abstract
PURPOSE To describe variation in genomic medicine services across level IV neonatal intensive care units (NICUs) in the United States and Canada. METHODS We developed and distributed a novel survey to the 43 level IV NICUs belonging to the Children's Hospitals Neonatal Consortium, requesting a single response per site from a clinician with knowledge of the provision of genomic medicine services. RESULTS Overall response rate was 74% (32/43). Although chromosomal microarray and exome or genome sequencing (ES or GS) were universally available, access was restricted for 22% (7/32) and 81% (26/32) of centers, respectively. The most common restriction on ES or GS was requiring approval by a specialist (41%, 13/32). Rapid ES/GS was available in 69% of NICUs (22/32). Availability of same-day genetics consultative services was limited (41%, 13/32 sites), and pre- and post-test counseling practices varied widely. CONCLUSION We observed large inter-center variation in genomic medicine services across level IV NICUs: most notably, access to rapid, comprehensive genetic testing in time frames relevant to critical care decision making was limited at many level IV Children's Hospitals Neonatal Consortium NICUs despite a significant burden of genetic disease. Further efforts are needed to improve access to neonatal genomic medicine services.
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Affiliation(s)
- Monica H Wojcik
- Divisions of Newborn Medicine and Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, Boston, MA; Neonatal Genomics Program, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, Boston, MA.
| | - Katharine P Callahan
- Division of Neonatology, Children's Hospital of Philadelphia, Philadelphia, PA; Division of Medical Ethics and Health Policy, University of Pennsylvania, Philadelphia, PA
| | - Austin Antoniou
- Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH
| | - Maya C Del Rosario
- Neonatal Genomics Program, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, Boston, MA
| | - Luca Brunelli
- Division of Neonatology, University of Utah Health and Primary Children's Hospital, Salt Lake City, UT
| | - Nahed O ElHassan
- Division of Neonatology, Arkansas Children's Hospital, University of Arkansas for Medical Sciences, Little Rock, AR
| | - Semsa Gogcu
- Wake Forest School of Medicine, Department of Pediatrics, Winston-Salem, NC
| | - Karna Murthy
- Ann & Robert H Lurie Children's Hospital of Chicago and Northwestern University, Chicago, IL; Children's Hospitals Neonatal Consortium, Dover, DE
| | - Jennifer A Rumpel
- Division of Neonatology, Arkansas Children's Hospital, University of Arkansas for Medical Sciences, Little Rock, AR
| | - Jennifer A Wambach
- Washington University School of Medicine and St Louis Children's Hospital, St Louis, MO
| | - Kristen Suhrie
- Department of Pediatrics, Division of Neonatal-Perinatal Medicine, and Department of Medical and Molecular Genetics, Riley Hospital for Children and Indiana University School of Medicine, Indianapolis, IN
| | - Kristen Fishler
- Munroe-Meyer Institute for Genetics and Rehabilitation, University of Nebraska Medical Center, Omaha, NE
| | - Bimal P Chaudhari
- Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH; Divisions of Neonatology and Genetics and Genomic Medicine, Department of Pediatrics, Nationwide Children's Hospital and The Ohio State University College of Medicine, Columbus, OH
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11
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Suzuki R, Sakakibara N, Ichikawa Y, Kitakado H, Ueda C, Tanaka Y, Okada E, Kondo A, Ishiko S, Ishimori S, Nagano C, Yamamura T, Horinouchi T, Okamoto T, Nozu K. Systematic Review of Clinical Characteristics and Genotype-Phenotype Correlation in LAMB2-Associated Disease. Kidney Int Rep 2023; 8:1811-1821. [PMID: 37705905 PMCID: PMC10496080 DOI: 10.1016/j.ekir.2023.06.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 05/21/2023] [Accepted: 06/21/2023] [Indexed: 09/15/2023] Open
Abstract
Introduction Laminin subunit beta-2 (LAMB2)-associated disease, termed Pierson syndrome, presents with congenital nephrotic syndrome, ocular symptoms, and neuromuscular symptoms. In recent years, however, the widespread use of next-generation sequencing (NGS) has helped to discover a variety of phenotypes associated with this disease. Therefore, we conducted this systematic review. Methods A literature search of patients with LAMB2 variants was conducted, and 110 patients were investigated, including 12 of our patients. For genotype-phenotype correlation analyses, the extracted data were investigated for pathogenic variant types, the severity of nephropathy, and extrarenal symptoms. Survival analyses were also performed for the onset age of end-stage kidney disease (ESKD). Results Among all patients, 81 (78%) presented with congenital nephrotic syndrome, and 52 (55%) developed ESKD within 12 months. The median age at ESKD onset was 6.0 months. Kidney survival analysis showed that patients with biallelic truncating variants had a significantly earlier progression to ESKD than those with other variants (median age 1.2 months vs. 60.0 months, P < 0.05). Although the laminin N-terminal domain is functionally important in laminin proteins, and variants in the laminin N-terminal domain are said to result in a severe kidney phenotype such as earlier onset age and worse prognosis, there were no significant differences in onset age of nephropathy and progression to ESKD between patients with nontruncating variants located in the laminin N-terminal domain and those with variants located outside this domain. Conclusion This study revealed a diversity of LAMB2-associated diseases, characteristics of LAMB2 nephropathy, and genotype-phenotype correlations.
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Affiliation(s)
- Ryota Suzuki
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
- Department of Pediatrics, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Nana Sakakibara
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Yuta Ichikawa
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Hideaki Kitakado
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Chika Ueda
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Yu Tanaka
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Eri Okada
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Atsushi Kondo
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Shinya Ishiko
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Shingo Ishimori
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - China Nagano
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Tomohiko Yamamura
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Tomoko Horinouchi
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Takayuki Okamoto
- Department of Pediatrics, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Kandai Nozu
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
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12
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Grabowska ME, Van Driest SL, Robinson JR, Patrick AE, Guardo C, Gangireddy S, Ong H, Feng Q, Carroll R, Kannankeril PJ, Wei WQ. Developing and Evaluating Pediatric Phecodes (Peds-Phecodes) for High-Throughput Phenotyping Using Electronic Health Records. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.08.22.23294435. [PMID: 37662278 PMCID: PMC10473796 DOI: 10.1101/2023.08.22.23294435] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Objective Pediatric patients have different diseases and outcomes than adults; however, existing phecodes do not capture the distinctive pediatric spectrum of disease. We aim to develop specialized pediatric phecodes (Peds-Phecodes) to enable efficient, large-scale phenotypic analyses of pediatric patients. Materials and Methods We adopted a hybrid data- and knowledge-driven approach leveraging electronic health records (EHRs) and genetic data from Vanderbilt University Medical Center to modify the most recent version of phecodes to better capture pediatric phenotypes. First, we compared the prevalence of patient diagnoses in pediatric and adult populations to identify disease phenotypes differentially affecting children and adults. We then used clinical domain knowledge to remove phecodes representing phenotypes unlikely to affect pediatric patients and create new phecodes for phenotypes relevant to the pediatric population. We further compared phenome-wide association study (PheWAS) outcomes replicating known pediatric genotype-phenotype associations between Peds-Phecodes and phecodes. Results The Peds-Phecodes aggregate 15,533 ICD-9-CM codes and 82,949 ICD-10-CM codes into 2,051 distinct phecodes. Peds-Phecodes replicated more known pediatric genotype-phenotype associations than phecodes (248 versus 192 out of 687 SNPs, p<0.001). Discussion We introduce Peds-Phecodes, a high-throughput EHR phenotyping tool tailored for use in pediatric populations. We successfully validated the Peds-Phecodes using genetic replication studies. Our findings also reveal the potential use of Peds-Phecodes in detecting novel genotype-phenotype associations for pediatric conditions. We expect that Peds-Phecodes will facilitate large-scale phenomic and genomic analyses in pediatric populations. Conclusion Peds-Phecodes capture higher-quality pediatric phenotypes and deliver superior PheWAS outcomes compared to phecodes.
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13
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Gandhi A, Elsea SH. Editorial: Insights in neurogenomics: 2022. Front Genet 2023; 14:1252582. [PMID: 37609035 PMCID: PMC10442150 DOI: 10.3389/fgene.2023.1252582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 07/20/2023] [Indexed: 08/24/2023] Open
Affiliation(s)
| | - Sarah H. Elsea
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
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14
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Baldo MS, Nogueira C, Pereira C, Janeiro P, Ferreira S, Lourenço CM, Bandeira A, Martins E, Magalhães M, Rodrigues E, Santos H, Ferreira AC, Vilarinho L. Leigh Syndrome Spectrum: A Portuguese Population Cohort in an Evolutionary Genetic Era. Genes (Basel) 2023; 14:1536. [PMID: 37628588 PMCID: PMC10454233 DOI: 10.3390/genes14081536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/21/2023] [Accepted: 07/24/2023] [Indexed: 08/27/2023] Open
Abstract
Mitochondrial diseases are the most common inherited inborn error of metabolism resulting in deficient ATP generation, due to failure in homeostasis and proper bioenergetics. The most frequent mitochondrial disease manifestation in children is Leigh syndrome (LS), encompassing clinical, neuroradiological, biochemical, and molecular features. It typically affects infants but occurs anytime in life. Considering recent updates, LS clinical presentation has been stretched, and is now named LS spectrum (LSS), including classical LS and Leigh-like presentations. Apart from clinical diagnosis challenges, the molecular characterization also progressed from Sanger techniques to NGS (next-generation sequencing), encompassing analysis of nuclear (nDNA) and mitochondrial DNA (mtDNA). This upgrade resumed steps and favored diagnosis. Hereby, our paper presents molecular and clinical data on a Portuguese cohort of 40 positive cases of LSS. A total of 28 patients presented mutation in mtDNA and 12 in nDNA, with novel mutations identified in a heterogeneous group of genes. The present results contribute to the better knowledge of the molecular basis of LS and expand the clinical spectrum associated with this syndrome.
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Affiliation(s)
- Manuela Schubert Baldo
- Research and Development Unit, Human Genetics Department, National Institute of Health Doutor Ricardo Jorge, 4000-055 Porto, Portugal; (M.S.B.)
| | - Célia Nogueira
- Research and Development Unit, Human Genetics Department, National Institute of Health Doutor Ricardo Jorge, 4000-055 Porto, Portugal; (M.S.B.)
- Neonatal Screening, Metabolism and Genetics Unit, Human Genetics Department, National Institute of Health Doutor Ricardo Jorge, 4000-055 Porto, Portugal
| | - Cristina Pereira
- Research and Development Unit, Human Genetics Department, National Institute of Health Doutor Ricardo Jorge, 4000-055 Porto, Portugal; (M.S.B.)
- Neonatal Screening, Metabolism and Genetics Unit, Human Genetics Department, National Institute of Health Doutor Ricardo Jorge, 4000-055 Porto, Portugal
| | - Patrícia Janeiro
- Inherited Metabolic Disease Reference Center, Lisbon North University Hospital Center (CHULN), EPE, 1649-028 Lisbon, Portugal
| | - Sara Ferreira
- Inherited Metabolic Disease Reference Center, Pediatric Hospital, Hospital and University Center of Coimbra, 3004-561 Coimbra, Portugal
| | - Charles M. Lourenço
- Neurogenetics Department, Faculdade de Medicina de São Jose do Rio Preto, São Jose do Rio Preto 15090-000, Brazil
| | - Anabela Bandeira
- Oporto Hospital Centre, University of Porto, 4099-001 Porto, Portugal
| | - Esmeralda Martins
- Oporto Hospital Centre, University of Porto, 4099-001 Porto, Portugal
- Unit for Multidisciplinary Research in Biomedicine, Instituto de Ciências Biomédicas Abel Salazar, Porto University, 4050-313 Porto, Portugal
| | - Marina Magalhães
- Department of Neurology Porto Hospital and University Centre, EPE, 4050-011 Porto, Portugal
| | - Esmeralda Rodrigues
- Reference Center for Inherited Metabolic Disorders, University Hospital Centre S. João, 4200-319 Porto, Portugal
| | - Helena Santos
- Department of Pediatrics, Hospital Centre, EPE, 4434-502 Vila Nova de Gaia, Portugal
| | | | - Laura Vilarinho
- Research and Development Unit, Human Genetics Department, National Institute of Health Doutor Ricardo Jorge, 4000-055 Porto, Portugal; (M.S.B.)
- Neonatal Screening, Metabolism and Genetics Unit, Human Genetics Department, National Institute of Health Doutor Ricardo Jorge, 4000-055 Porto, Portugal
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15
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D'Gama AM, Agrawal PB. Role of genomic medicine and implementing equitable access for critically ill infants in neonatal intensive care units. J Perinatol 2023; 43:963-967. [PMID: 36774516 PMCID: PMC9918837 DOI: 10.1038/s41372-023-01630-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 01/27/2023] [Accepted: 01/31/2023] [Indexed: 02/13/2023]
Abstract
Genetic disorders are a leading cause of morbidity and mortality in infants admitted to neonatal intensive care units. This population has immense potential to benefit from genomic medicine, as early precision diagnosis is critical to early personalized management. However, the implementation of genomic medicine in neonatology thus far has arguably worsened health inequities, and strategies are urgently needed to achieve equitable access to genomics in neonatal care. In this perspective, we demonstrate the utility of genomic sequencing in critically ill infants and highlight three key recommendations to advance equitable access: recruitment of underrepresented populations, education of non-genetics providers to empower practice of genomic medicine, and development of innovative infrastructure to implement genomic medicine across diverse settings.
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Affiliation(s)
- Alissa M D'Gama
- Epilepsy Genetics Program, Division of Epilepsy and Neurophysiology, Department of Neurology, Boston Children's Hospital, Boston, MA, USA
- Neonatal Genomics Program, Division of Newborn Medicine, Boston Children's Hospital, Boston, MA, USA
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Pankaj B Agrawal
- Neonatal Genomics Program, Division of Newborn Medicine, Boston Children's Hospital, Boston, MA, USA.
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA.
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA.
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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16
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Wojcik MH, Poduri AH, Holm IA, MacRae CA, Goldstein RD. The fundamental need for unifying phenotypes in sudden unexpected pediatric deaths. Front Med (Lausanne) 2023; 10:1166188. [PMID: 37332751 PMCID: PMC10273404 DOI: 10.3389/fmed.2023.1166188] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 05/03/2023] [Indexed: 06/20/2023] Open
Abstract
A definitive, authoritative approach to evaluate the causes of unexpected, and ultimately unexplained, pediatric deaths remains elusive, relegating final conclusions to diagnoses of exclusion in the vast majority of cases. Research into unexplained pediatric deaths has focused primarily on sudden infant deaths (under 1 year of age) and led to the identification of several potential, albeit incompletely understood, contributory factors: nonspecific pathology findings, associations with sleep position and environment that may not be uniformly relevant, and the elucidation of a role for serotonin that is practically difficult to estimate in any individual case. Any assessment of progress in this field must also acknowledge the failure of current approaches to substantially decrease mortality rates in decades. Furthermore, potential commonalities with pediatric deaths across a broader age spectrum have not been widely considered. Recent epilepsy-related observations and genetic findings, identified post-mortem in both infants and children who died suddenly and unexpectedly, suggest a role for more intense and specific phenotyping efforts as well as an expanded role for genetic and genomic evaluation. We therefore present a new approach to reframe the phenotype in sudden unexplained deaths in the pediatric age range, collapsing many distinctions based on arbitrary factors (such as age) that have previously guided research in this area, and discuss its implications for the future of postmortem investigation.
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Affiliation(s)
- Monica H. Wojcik
- Robert’s Program for Sudden Unexpected Death in Pediatrics, Boston Children’s Hospital, Boston, MA, United States
- Division of Newborn Medicine, Department of Pediatrics, Boston Children’s Hospital, Boston, MA, United States
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
| | - Annapurna H. Poduri
- Robert’s Program for Sudden Unexpected Death in Pediatrics, Boston Children’s Hospital, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, United States
- Epilepsy Genetics Program, Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA, United States
| | - Ingrid A. Holm
- Robert’s Program for Sudden Unexpected Death in Pediatrics, Boston Children’s Hospital, Boston, MA, United States
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
| | - Calum A. MacRae
- Harvard Medical School, Boston, MA, United States
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, United States
| | - Richard D. Goldstein
- Robert’s Program for Sudden Unexpected Death in Pediatrics, Boston Children’s Hospital, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
- Division of General Pediatrics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, United States
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17
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da Silva-Buttkus P, Spielmann N, Klein-Rodewald T, Schütt C, Aguilar-Pimentel A, Amarie OV, Becker L, Calzada-Wack J, Garrett L, Gerlini R, Kraiger M, Leuchtenberger S, Östereicher MA, Rathkolb B, Sanz-Moreno A, Stöger C, Hölter SM, Seisenberger C, Marschall S, Fuchs H, Gailus-Durner V, Hrabě de Angelis M. Knockout mouse models as a resource for the study of rare diseases. Mamm Genome 2023; 34:244-261. [PMID: 37160609 PMCID: PMC10290595 DOI: 10.1007/s00335-023-09986-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 03/07/2023] [Indexed: 05/11/2023]
Abstract
Rare diseases (RDs) are a challenge for medicine due to their heterogeneous clinical manifestations and low prevalence. There is a lack of specific treatments and only a few hundred of the approximately 7,000 RDs have an approved regime. Rapid technological development in genome sequencing enables the mass identification of potential candidates that in their mutated form could trigger diseases but are often not confirmed to be causal. Knockout (KO) mouse models are essential to understand the causality of genes by allowing highly standardized research into the pathogenesis of diseases. The German Mouse Clinic (GMC) is one of the pioneers in mouse research and successfully uses (preclinical) data obtained from single-gene KO mutants for research into monogenic RDs. As part of the International Mouse Phenotyping Consortium (IMPC) and INFRAFRONTIER, the pan-European consortium for modeling human diseases, the GMC expands these preclinical data toward global collaborative approaches with researchers, clinicians, and patient groups.Here, we highlight proprietary genes that when deleted mimic clinical phenotypes associated with known RD targets (Nacc1, Bach2, Klotho alpha). We focus on recognized RD genes with no pre-existing KO mouse models (Kansl1l, Acsf3, Pcdhgb2, Rabgap1, Cox7a2) which highlight novel phenotypes capable of optimizing clinical diagnosis. In addition, we present genes with intriguing phenotypic data (Zdhhc5, Wsb2) that are not presently associated with known human RDs.This report provides comprehensive evidence for genes that when deleted cause differences in the KO mouse across multiple organs, providing a huge translational potential for further understanding monogenic RDs and their clinical spectrum. Genetic KO studies in mice are valuable to further explore the underlying physiological mechanisms and their overall therapeutic potential.
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Affiliation(s)
- Patricia da Silva-Buttkus
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, Neuherberg, Germany
| | - Nadine Spielmann
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, Neuherberg, Germany
| | - Tanja Klein-Rodewald
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, Neuherberg, Germany
| | - Christine Schütt
- Institute of Experimental Genetics, Applied Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, Neuherberg, Germany
| | - Antonio Aguilar-Pimentel
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, Neuherberg, Germany
| | - Oana V Amarie
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, Neuherberg, Germany
| | - Lore Becker
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, Neuherberg, Germany
| | - Julia Calzada-Wack
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, Neuherberg, Germany
| | - Lillian Garrett
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, Neuherberg, Germany
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, Neuherberg, Germany
| | - Raffaele Gerlini
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, Neuherberg, Germany
| | - Markus Kraiger
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, Neuherberg, Germany
| | - Stefanie Leuchtenberger
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, Neuherberg, Germany
| | - Manuela A Östereicher
- Institute of Experimental Genetics, Applied Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, Neuherberg, Germany
| | - Birgit Rathkolb
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Ingolstaedter Landstrasse 1, 85764, Neuherberg, Germany
- Institute of Molecular Animal Breeding and Biotechnology, Gene Center, Ludwig-Maximilians-Universität München, Feodor-Lynen Strasse 25, 81377, Munich, Germany
| | - Adrián Sanz-Moreno
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, Neuherberg, Germany
| | - Claudia Stöger
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, Neuherberg, Germany
| | - Sabine M Hölter
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, Neuherberg, Germany
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, Neuherberg, Germany
| | - Claudia Seisenberger
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, Neuherberg, Germany
| | - Susan Marschall
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, Neuherberg, Germany
| | - Helmut Fuchs
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, Neuherberg, Germany
| | - Valerie Gailus-Durner
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, Neuherberg, Germany
| | - Martin Hrabě de Angelis
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, Neuherberg, Germany.
- German Center for Diabetes Research (DZD), Ingolstaedter Landstrasse 1, 85764, Neuherberg, Germany.
- Chair of Experimental Genetics, TUM School of Life Sciences, Technische Universität München, Alte Akademie 8, 85354, Freising, Germany.
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18
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Callahan KP, Radack J, Wojcik MH, Jenkins SM, Nye RT, Skraban C, Wild KT, Feudtner C. Hospital-level variation in genetic testing in children's hospitals' neonatal intensive care units from 2016 to 2021. Genet Med 2023; 25:100357. [PMID: 36521640 PMCID: PMC9991964 DOI: 10.1016/j.gim.2022.12.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 12/07/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022] Open
Abstract
PURPOSE This study aimed to examine variation in genetic testing between neonatal intensive care units (NICUs) across hospitals over time. METHODS We performed a multicenter large-scale retrospective cohort study using NICU discharge data from the Pediatric Hospital Information System database between 2016 and 2021. We analyzed the variation in the percentage of NICU patients who had any genetic testing across hospitals and over time. We used a multivariable multilevel logistic regression model to investigate the potential association between patient characteristics and genetic testing. RESULTS The final analysis included 207,228 neonates from 38 hospitals. Overall, 13% of patients had at least 1 genetic test sent, although this varied from 4% to 50% across hospitals. Over the study period, the proportion of patients tested increased, with the increase disproportionately borne by hospitals already testing high proportions of patients. On average, patients who received genetic testing had higher illness severity. Controlling for severity, however, only minimally reduced the degree of hospital-level variation in genetic testing. CONCLUSION The percentage of NICU patients who undergo genetic testing varies among hospitals and increasingly so over time. Variation is largely unexplained by differences in severity between hospitals. The degree of variation suggests that clearer guidelines for NICU genetic testing are warranted.
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Affiliation(s)
- Katharine Press Callahan
- Division of Neonatology, Children's Hospital of Philadelphia Philadelphia, PA; Department of Medical Ethics and Health Policy, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA.
| | - Joshua Radack
- Division of Neonatology, Children's Hospital of Philadelphia Philadelphia, PA
| | - Monica H Wojcik
- Divisions of Newborn Medicine and Genetics and Genomics, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Sabrina Malone Jenkins
- Division of Neonatology, Department of Pediatrics, School of Medicine, Health University of Utah, Salt Lake City, UT
| | - Russell T Nye
- Division of Neonatology, Children's Hospital of Philadelphia Philadelphia, PA
| | - Cara Skraban
- Division of Neonatology, Children's Hospital of Philadelphia Philadelphia, PA
| | | | - Chris Feudtner
- Division of Neonatology, Children's Hospital of Philadelphia Philadelphia, PA; Department of Medical Ethics and Health Policy, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
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19
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Lumaka A, Fasquelle C, Debray FG, Alkan S, Jacquinet A, Harvengt J, Boemer F, Mulder A, Vaessen S, Viellevoye R, Palmeira L, Charloteaux B, Brysse A, Bulk S, Rigo V, Bours V. Rapid Whole Genome Sequencing Diagnoses and Guides Treatment in Critically Ill Children in Belgium in Less than 40 Hours. Int J Mol Sci 2023; 24:4003. [PMID: 36835410 PMCID: PMC9967120 DOI: 10.3390/ijms24044003] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/05/2023] [Accepted: 02/13/2023] [Indexed: 02/18/2023] Open
Abstract
Rapid Whole Genome Sequencing (rWGS) represents a valuable exploration in critically ill pediatric patients. Early diagnosis allows care to be adjusted. We evaluated the feasibility, turnaround time (TAT), yield, and utility of rWGS in Belgium. Twenty-one unrelated critically ill patients were recruited from the neonatal intensive care units, the pediatric intensive care unit, and the neuropediatric unit, and offered rWGS as a first tier test. Libraries were prepared in the laboratory of human genetics of the University of Liège using Illumina DNA PCR-free protocol. Sequencing was performed on a NovaSeq 6000 in trio for 19 and in duo for two probands. The TAT was calculated from the sample reception to the validation of results. Clinical utility data were provided by treating physicians. A definite diagnosis was reached in twelve (57.5%) patients in 39.80 h on average (range: 37.05-43.7). An unsuspected diagnosis was identified in seven patients. rWGS guided care adjustments in diagnosed patients, including a gene therapy, an off-label drug trial and two condition-specific treatments. We successfully implemented the fastest rWGS platform in Europe and obtained one of the highest rWGS yields. This study establishes the path for a nationwide semi-centered rWGS network in Belgium.
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Affiliation(s)
- Aimé Lumaka
- Human Genetic Laboratory, GIGA Institute, University of Liège, 4000 Liège, Belgium
- Center for Human Genetics, Centre Hospitalier Universitaire, 4032 Liège, Belgium
| | - Corinne Fasquelle
- Center for Human Genetics, Centre Hospitalier Universitaire, 4032 Liège, Belgium
| | | | - Serpil Alkan
- Center for Human Genetics, Centre Hospitalier Universitaire, 4032 Liège, Belgium
- Neuropediatric Division, CHU de Liège—CHR de la Citadelle, University of Liège, 4000 Liège, Belgium
| | - Adeline Jacquinet
- Center for Human Genetics, Centre Hospitalier Universitaire, 4032 Liège, Belgium
| | - Julie Harvengt
- Center for Human Genetics, Centre Hospitalier Universitaire, 4032 Liège, Belgium
| | - François Boemer
- Center for Human Genetics, Centre Hospitalier Universitaire, 4032 Liège, Belgium
| | - André Mulder
- Department of Pediatrics, Division of Pediatric Critical Care Medicine, CHC Mont-Légia, 4000 Liège, Belgium
| | - Sandrine Vaessen
- Neuropediatric Division, CHU de Liège—CHR de la Citadelle, University of Liège, 4000 Liège, Belgium
| | - Renaud Viellevoye
- Neonatology Division, CHU de Liège—CHR de la Citadelle, University of Liège, 4000 Liège, Belgium
| | - Leonor Palmeira
- Center for Human Genetics, Centre Hospitalier Universitaire, 4032 Liège, Belgium
| | - Benoit Charloteaux
- Center for Human Genetics, Centre Hospitalier Universitaire, 4032 Liège, Belgium
| | - Anne Brysse
- Center for Human Genetics, Centre Hospitalier Universitaire, 4032 Liège, Belgium
| | - Saskia Bulk
- Center for Human Genetics, Centre Hospitalier Universitaire, 4032 Liège, Belgium
| | - Vincent Rigo
- Neonatology Division, CHU de Liège—CHR de la Citadelle, University of Liège, 4000 Liège, Belgium
| | - Vincent Bours
- Human Genetic Laboratory, GIGA Institute, University of Liège, 4000 Liège, Belgium
- Center for Human Genetics, Centre Hospitalier Universitaire, 4032 Liège, Belgium
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20
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Owen MJ, Wright MS, Batalov S, Kwon Y, Ding Y, Chau KK, Chowdhury S, Sweeney NM, Kiernan E, Richardson A, Batton E, Baer RJ, Bandoli G, Gleeson JG, Bainbridge M, Chambers CD, Kingsmore SF. Reclassification of the Etiology of Infant Mortality With Whole-Genome Sequencing. JAMA Netw Open 2023; 6:e2254069. [PMID: 36757698 PMCID: PMC9912130 DOI: 10.1001/jamanetworkopen.2022.54069] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 11/27/2022] [Indexed: 02/10/2023] Open
Abstract
Importance Understanding the causes of infant mortality shapes public health, surveillance, and research investments. However, the association of single-locus (mendelian) genetic diseases with infant mortality is poorly understood. Objective To determine the association of genetic diseases with infant mortality. Design, Setting, and Participants This cohort study was conducted at a large pediatric hospital system in San Diego County (California) and included 546 infants (112 infant deaths [20.5%] and 434 infants [79.5%] with acute illness who survived; age, 0 to 1 year) who underwent diagnostic whole-genome sequencing (WGS) between January 2015 and December 2020. Data analysis was conducted between 2015 and 2022. Exposure Infants underwent WGS either premortem or postmortem with semiautomated phenotyping and diagnostic interpretation. Main Outcomes and Measures Proportion of infant deaths associated with single-locus genetic diseases. Results Among 112 infant deaths (54 girls [48.2%]; 8 [7.1%] African American or Black, 1 [0.9%] American Indian or Alaska Native, 8 [7.1%] Asian, 48 [42.9%] Hispanic, 1 [0.9%] Native Hawaiian or Pacific Islander, and 34 [30.4%] White infants) in San Diego County between 2015 and 2020, single-locus genetic diseases were the most common identifiable cause of infant mortality, with 47 genetic diseases identified in 46 infants (41%). Thirty-nine (83%) of these diseases had been previously reported to be associated with childhood mortality. Twenty-eight death certificates (62%) for 45 of the 46 infants did not mention a genetic etiology. Treatments that can improve outcomes were available for 14 (30%) of the genetic diseases. In 5 of 7 infants in whom genetic diseases were identified postmortem, death might have been avoided had rapid, diagnostic WGS been performed at time of symptom onset or regional intensive care unit admission. Conclusions and Relevance In this cohort study of 112 infant deaths, the association of genetic diseases with infant mortality was higher than previously recognized. Strategies to increase neonatal diagnosis of genetic diseases and immediately implement treatment may decrease infant mortality. Additional study is required to explore the generalizability of these findings and measure reduction in infant mortality.
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Affiliation(s)
- Mallory J. Owen
- Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, California
- Department of Pediatrics, University of California, San Diego, La Jolla
| | - Meredith S. Wright
- Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, California
| | - Sergey Batalov
- Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, California
| | - Yonghyun Kwon
- Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, California
| | - Yan Ding
- Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, California
| | - Kevin K. Chau
- Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, California
| | - Shimul Chowdhury
- Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, California
| | - Nathaly M. Sweeney
- Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, California
- Department of Pediatrics, University of California, San Diego, La Jolla
| | - Elizabeth Kiernan
- Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, California
| | - Andrew Richardson
- Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, California
| | - Emily Batton
- Department of Pediatrics, University of California, San Diego, La Jolla
| | - Rebecca J. Baer
- Department of Pediatrics, University of California, San Diego, La Jolla
- California Preterm Birth Initiative, University of California, San Francisco
| | - Gretchen Bandoli
- Department of Pediatrics, University of California, San Diego, La Jolla
| | - Joseph G. Gleeson
- Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, California
- Department of Pediatrics, University of California, San Diego, La Jolla
| | - Matthew Bainbridge
- Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, California
| | | | - Stephen F. Kingsmore
- Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, California
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21
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Wojcik MH, D'Gama AM, Agrawal PB. A model to implement genomic medicine in the neonatal intensive care unit. J Perinatol 2023; 43:248-252. [PMID: 35750755 PMCID: PMC9789202 DOI: 10.1038/s41372-022-01428-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 06/07/2022] [Accepted: 06/08/2022] [Indexed: 02/06/2023]
Abstract
Rapid genomic sequencing has been shown to have a high diagnostic yield for critically ill infants, with multiple research studies demonstrating both diagnostic and clinical utility. However, clinical implementation of rapid sequencing in the neonatal intensive care unit (NICU), as well as other aspects of genomic medicine such as precision therapy, may be challenging. We describe the Neonatal Genomics Program, developed at our institution as a multidisciplinary approach to improve clinical genetic diagnosis and outcomes for infants in our NICU through genomic medicine. The creation of a dedicated program implementing genomic medicine to improve care in the NICU allows not only for improved access to genomic sequencing for rapid diagnosis, but also advancement of rare disease research and precision therapeutics. Ongoing efforts will help to define an optimal approach to genomic medicine in the NICU context.
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Affiliation(s)
- Monica H Wojcik
- Division of Newborn Medicine, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA.
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA.
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA.
- The Broad Institute, Cambridge, MA, USA.
| | - Alissa M D'Gama
- Division of Newborn Medicine, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
- Epilepsy Genetics Program, Division of Epilepsy and Neurophysiology, Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Pankaj B Agrawal
- Division of Newborn Medicine, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA.
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA.
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA.
- The Broad Institute, Cambridge, MA, USA.
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22
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Tran Mau-Them F, Delanne J, Denommé-Pichon AS, Safraou H, Bruel AL, Vitobello A, Garde A, Nambot S, Bourgon N, Racine C, Sorlin A, Moutton S, Marle N, Rousseau T, Sagot P, Simon E, Vincent-Delorme C, Boute O, Colson C, Petit F, Legendre M, Naudion S, Rooryck C, Prouteau C, Colin E, Guichet A, Ziegler A, Bonneau D, Morel G, Fradin M, Lavillaureix A, Quelin C, Pasquier L, Odent S, Vera G, Goldenberg A, Guerrot AM, Brehin AC, Putoux A, Attia J, Abel C, Blanchet P, Wells CF, Deiller C, Nizon M, Mercier S, Vincent M, Isidor B, Amiel J, Dard R, Godin M, Gruchy N, Jeanne M, Schaeffer E, Maillard PY, Payet F, Jacquemont ML, Francannet C, Sigaudy S, Bergot M, Tisserant E, Ascencio ML, Binquet C, Duffourd Y, Philippe C, Faivre L, Thauvin-Robinet C. Prenatal diagnosis by trio exome sequencing in fetuses with ultrasound anomalies: A powerful diagnostic tool. Front Genet 2023; 14:1099995. [PMID: 37035737 PMCID: PMC10076577 DOI: 10.3389/fgene.2023.1099995] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 02/24/2023] [Indexed: 04/11/2023] Open
Abstract
Introduction: Prenatal ultrasound (US) anomalies are detected in around 5%-10% of pregnancies. In prenatal diagnosis, exome sequencing (ES) diagnostic yield ranges from 6% to 80% depending on the inclusion criteria. We describe the first French national multicenter pilot study aiming to implement ES in prenatal diagnosis following the detection of anomalies on US. Patients and methods: We prospectively performed prenatal trio-ES in 150 fetuses with at least two US anomalies or one US anomaly known to be frequently linked to a genetic disorder. Trio-ES was only performed if the results could influence pregnancy management. Chromosomal microarray (CMA) was performed before or in parallel. Results: A causal diagnosis was identified in 52/150 fetuses (34%) with a median time to diagnosis of 28 days, which rose to 56/150 fetuses (37%) after additional investigation. Sporadic occurrences were identified in 34/56 (60%) fetuses and unfavorable vital and/or neurodevelopmental prognosis was made in 13/56 (24%) fetuses. The overall diagnostic yield was 41% (37/89) with first-line trio-ES versus 31% (19/61) after normal CMA. Trio-ES and CMA were systematically concordant for identification of pathogenic CNV. Conclusion: Trio-ES provided a substantial prenatal diagnostic yield, similar to postnatal diagnosis with a median turnaround of approximately 1 month, supporting its routine implementation during the detection of prenatal US anomalies.
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Affiliation(s)
- Frédéric Tran Mau-Them
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, CHU Dijon Bourgogne, Dijon, France
- INSERM UMR1231 GAD, F-21000, Dijon, France
- *Correspondence: Frédéric Tran Mau-Them,
| | - Julian Delanne
- Centre de Référence Maladies Rares “Anomalies Du Développement et Syndromes Malformatifs”, Centre de Génétique, FHU TRANSLAD et Institut GIMI, CHU Dijon Bourgogne, Dijon, France
| | - Anne-Sophie Denommé-Pichon
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, CHU Dijon Bourgogne, Dijon, France
- INSERM UMR1231 GAD, F-21000, Dijon, France
| | - Hana Safraou
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, CHU Dijon Bourgogne, Dijon, France
- INSERM UMR1231 GAD, F-21000, Dijon, France
| | - Ange-Line Bruel
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, CHU Dijon Bourgogne, Dijon, France
- INSERM UMR1231 GAD, F-21000, Dijon, France
| | - Antonio Vitobello
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, CHU Dijon Bourgogne, Dijon, France
- INSERM UMR1231 GAD, F-21000, Dijon, France
| | - Aurore Garde
- Centre de Référence Maladies Rares “Anomalies Du Développement et Syndromes Malformatifs”, Centre de Génétique, FHU TRANSLAD et Institut GIMI, CHU Dijon Bourgogne, Dijon, France
| | - Sophie Nambot
- Centre de Référence Maladies Rares “Anomalies Du Développement et Syndromes Malformatifs”, Centre de Génétique, FHU TRANSLAD et Institut GIMI, CHU Dijon Bourgogne, Dijon, France
| | - Nicolas Bourgon
- Centre de Référence Maladies Rares “Anomalies Du Développement et Syndromes Malformatifs”, Centre de Génétique, FHU TRANSLAD et Institut GIMI, CHU Dijon Bourgogne, Dijon, France
| | - Caroline Racine
- Centre de Référence Maladies Rares “Anomalies Du Développement et Syndromes Malformatifs”, Centre de Génétique, FHU TRANSLAD et Institut GIMI, CHU Dijon Bourgogne, Dijon, France
| | - Arthur Sorlin
- INSERM UMR1231 GAD, F-21000, Dijon, France
- Centre de Référence Maladies Rares “Anomalies Du Développement et Syndromes Malformatifs”, Centre de Génétique, FHU TRANSLAD et Institut GIMI, CHU Dijon Bourgogne, Dijon, France
| | - Sébastien Moutton
- Centre de Référence Maladies Rares “Anomalies Du Développement et Syndromes Malformatifs”, Centre de Génétique, FHU TRANSLAD et Institut GIMI, CHU Dijon Bourgogne, Dijon, France
| | - Nathalie Marle
- Laboratoire Génétique Chromosomique et Moléculaire, CHU Dijon Bourgogne, Dijon, France
| | - Thierry Rousseau
- Service de Gynécologie Obstétrique, Médecine Fœtale et Stérilité Conjugale, Centre Hospitalier Universitaire Dijon Bourgogne, Dijon, France
| | - Paul Sagot
- Service de Gynécologie Obstétrique, Médecine Fœtale et Stérilité Conjugale, Centre Hospitalier Universitaire Dijon Bourgogne, Dijon, France
| | - Emmanuel Simon
- Service de Gynécologie Obstétrique, Médecine Fœtale et Stérilité Conjugale, Centre Hospitalier Universitaire Dijon Bourgogne, Dijon, France
| | - Catherine Vincent-Delorme
- CHU Lille, Clinique de Génétique Guy Fontaine, Centre de Référence Maladies Rares “Anomalies Du Développement et Syndromes Malformatifs” Nord-Ouest, FLille, France
| | - Odile Boute
- CHU Lille, Clinique de Génétique Guy Fontaine, Centre de Référence Maladies Rares “Anomalies Du Développement et Syndromes Malformatifs” Nord-Ouest, FLille, France
| | - Cindy Colson
- CHU Lille, Clinique de Génétique Guy Fontaine, Centre de Référence Maladies Rares “Anomalies Du Développement et Syndromes Malformatifs” Nord-Ouest, FLille, France
| | - Florence Petit
- CHU Lille, Clinique de Génétique Guy Fontaine, Centre de Référence Maladies Rares “Anomalies Du Développement et Syndromes Malformatifs” Nord-Ouest, FLille, France
| | - Marine Legendre
- CHU de Bordeaux, Service de Génétique Médicale, Bordeaux, France
| | - Sophie Naudion
- CHU de Bordeaux, Service de Génétique Médicale, Bordeaux, France
| | - Caroline Rooryck
- CHU de Bordeaux, Service de Génétique Médicale, Bordeaux, France
| | - Clément Prouteau
- Biochemistry and Genetics Department, University Hospital of Angers, Angers, France
| | - Estelle Colin
- Biochemistry and Genetics Department, University Hospital of Angers, Angers, France
| | - Agnès Guichet
- Biochemistry and Genetics Department, University Hospital of Angers, Angers, France
| | - Alban Ziegler
- Biochemistry and Genetics Department, University Hospital of Angers, Angers, France
| | - Dominique Bonneau
- Biochemistry and Genetics Department, University Hospital of Angers, Angers, France
| | - Godelieve Morel
- Service de Génétique Clinique, Centre de Référence Maladies Rares CLAD-Ouest, CHU Hôpital Sud, Rennes, France
| | - Mélanie Fradin
- Service de Génétique Clinique, Centre de Référence Maladies Rares CLAD-Ouest, CHU Hôpital Sud, Rennes, France
| | - Alinoé Lavillaureix
- Service de Génétique Clinique, Centre de Référence Maladies Rares CLAD-Ouest, CHU Hôpital Sud, Rennes, France
| | - Chloé Quelin
- Service de Génétique Clinique, Centre de Référence Maladies Rares CLAD-Ouest, CHU Hôpital Sud, Rennes, France
| | - Laurent Pasquier
- Service de Génétique Clinique, Centre de Référence Maladies Rares CLAD-Ouest, CHU Hôpital Sud, Rennes, France
| | - Sylvie Odent
- Service de Génétique Clinique, Centre de Référence Maladies Rares CLAD-Ouest, CHU Hôpital Sud, Rennes, France
| | - Gabriella Vera
- Service de Génétique—Unité de Génétique Clinique, Rouen, France
| | | | | | | | - Audrey Putoux
- Service de Génétique—GH Est-Hôpital Femme Mère Enfant, Lyon, France
| | | | - Carine Abel
- Service de Génétique et Centre de Diagnostic Anténatal, CHU de Lyon HCL—GH Nord-Hôpital de La Croix Rousse, Lyon, France
| | - Patricia Blanchet
- Equipe Maladies Génétiques de L’Enfant et de L’Adulte, Département Génétique Médicale, Maladies Rares et Médecine Personnalisée, CHU de Montpellier, University Montpellier, Montpellier, France
| | - Constance F. Wells
- Equipe Maladies Génétiques de L’Enfant et de L’Adulte, Département Génétique Médicale, Maladies Rares et Médecine Personnalisée, CHU de Montpellier, University Montpellier, Montpellier, France
| | - Caroline Deiller
- Equipe Maladies Génétiques de L’Enfant et de L’Adulte, Département Génétique Médicale, Maladies Rares et Médecine Personnalisée, CHU de Montpellier, University Montpellier, Montpellier, France
| | - Mathilde Nizon
- CHU Nantes, Service de Génétique Médicale, Nantes, France
- Institut Du Thorax, INSERM, CNRS, UNIV Nantes, Nantes, France
| | - Sandra Mercier
- CHU Nantes, Service de Génétique Médicale, Nantes, France
- Institut Du Thorax, INSERM, CNRS, UNIV Nantes, Nantes, France
| | - Marie Vincent
- CHU Nantes, Service de Génétique Médicale, Nantes, France
- Institut Du Thorax, INSERM, CNRS, UNIV Nantes, Nantes, France
| | - Bertrand Isidor
- CHU Nantes, Service de Génétique Médicale, Nantes, France
- Institut Du Thorax, INSERM, CNRS, UNIV Nantes, Nantes, France
| | - Jeanne Amiel
- Equipe “Embryologie et Génétiques des Malformations Congénitales", Institut Imagine—INSERM U1163, Institut des Maladies Génétiques, Paris, France
- Service de Génétique Médicale et Clinique, Hôpital Necker-Enfants Malades, Paris, France
| | - Rodolphe Dard
- Unité Fonctionnelle de Génétique Médicale, Cytogénétique, Génétique Médicale et Biologie de La Reproduction, Centre Hospitalier Intercommunal Poissy-Saint-Germain-en-Laye, Poissy, France
| | - Manon Godin
- Service de Génétique, CHU Caen Clemenceau, EA 7450 Biotargen, University Caen, Caen, France
| | - Nicolas Gruchy
- Service de Génétique, CHU Caen Clemenceau, EA 7450 Biotargen, University Caen, Caen, France
| | - Médéric Jeanne
- Service de Génétique, CHU de Tours, Tours, France
- UMR 1253, IBrain, Université de Tours, Inserm, Tours, France
| | - Elise Schaeffer
- Service de Génétique Médicale, CHU de Strasbourg—Hôpital de Hautepierre, Strasbourg, France
| | - Pierre-Yves Maillard
- Service de Génétique Médicale, CHU de Strasbourg—Hôpital de Hautepierre, Strasbourg, France
| | - Frédérique Payet
- Service de Génétique Médicale, Pôle Femme, Mère, Enfants CHU de La Réunion—GH Sud Réunion—Saint-Pierre, Saint-Pierre, France
| | - Marie-Line Jacquemont
- Service de Génétique Médicale, Pôle Femme, Mère, Enfants CHU de La Réunion—GH Sud Réunion—Saint-Pierre, Saint-Pierre, France
| | - Christine Francannet
- Service de Génétique Médicale, Pôle Femme et Enfant, CHU de Clermont-Ferrand—Hôpital D'Estaing, Clermont-Ferrand, France
| | - Sabine Sigaudy
- Unité de Génétique Clinique Prénatale, Département de Génétique Médicale, CHU de Marseille—Hôpital de La Timone, Marseille, France
| | - Marine Bergot
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, CHU Dijon Bourgogne, Dijon, France
- INSERM UMR1231 GAD, F-21000, Dijon, France
| | | | - Marie-Laure Ascencio
- Centre D'Investigation Clinique CIC-EC Inserm CIC1432, UFR des Sciences de Santé, Université de Bourgogne-Franche-Comté, Dijon, France
| | - Christine Binquet
- Centre D'Investigation Clinique CIC-EC Inserm CIC1432, UFR des Sciences de Santé, Université de Bourgogne-Franche-Comté, Dijon, France
| | - Yannis Duffourd
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, CHU Dijon Bourgogne, Dijon, France
- INSERM UMR1231 GAD, F-21000, Dijon, France
| | - Christophe Philippe
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, CHU Dijon Bourgogne, Dijon, France
- INSERM UMR1231 GAD, F-21000, Dijon, France
| | - Laurence Faivre
- INSERM UMR1231 GAD, F-21000, Dijon, France
- Centre de Référence Maladies Rares “Anomalies Du Développement et Syndromes Malformatifs”, Centre de Génétique, FHU TRANSLAD et Institut GIMI, CHU Dijon Bourgogne, Dijon, France
| | - Christel Thauvin-Robinet
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, CHU Dijon Bourgogne, Dijon, France
- INSERM UMR1231 GAD, F-21000, Dijon, France
- Centre de Référence Maladies Rares “Anomalies Du Développement et Syndromes Malformatifs”, Centre de Génétique, FHU TRANSLAD et Institut GIMI, CHU Dijon Bourgogne, Dijon, France
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Wojcik MH, Bresnahan M, del Rosario MC, Ojeda MM, Kritzer A, Fraiman YS. Rare diseases, common barriers: disparities in pediatric clinical genetics outcomes. Pediatr Res 2023; 93:110-117. [PMID: 35963884 PMCID: PMC9892172 DOI: 10.1038/s41390-022-02240-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 07/14/2022] [Accepted: 07/24/2022] [Indexed: 02/04/2023]
Abstract
BACKGROUND Identifying a precise genetic diagnosis can improve outcomes for individuals with rare disease, though the resources required to do so may impede access and exacerbate healthcare disparities leading to inequitable care. Our objective was therefore to determine the effect of multiple sociodemographic factors on the yield of the diagnostic evaluation for genetics outpatients. METHODS This is a retrospective cohort study from 2017 to 2019 of outpatient genetics referrals at a pediatric academic tertiary care center. Exposures included: primary language, insurance type, and neighborhood resources (via the Childhood Opportunity Index, COI). The primary outcome was identification of a genetic diagnosis within 2 years of the initial clinic visit. RESULTS COI quintile was not significantly associated with the odds of diagnosis but was significantly associated with clinic attendance, with lower neighborhood resources leading to incomplete referrals. Limited English proficiency was associated with a higher odds of diagnosis, though at an older age. Public insurance was associated with increased access to genetic testing. CONCLUSIONS Lower neighborhood resources are negatively associated with clinic attendance. Our findings further suggest delays in care and a referral bias for more severe phenotypes among families with limited English proficiency. Improved access to clinical genetics is needed to improve diagnostic equity. IMPACT The resources required to identify a genetic diagnosis may impede access and exacerbate healthcare disparities leading to inequitable care. In an analysis of pediatric outpatient genetics referrals, we observed a significant association between neighborhood resources and clinic attendance but not diagnostic yield for those attending, and a higher diagnostic yield for families with limited English proficiency, suggesting referral bias for more severe phenotypes. Thus, the primary barrier to finding a genetic diagnosis was initiation of care, not the ensuing diagnostic odyssey. Further research efforts should be directed at increasing access to clinical genetics evaluations for children with rare disease.
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Affiliation(s)
- Monica H Wojcik
- Division of Newborn Medicine, Department of Medicine, Boston Children's Hospital, Boston, MA, 02115, USA. .,Division of Genetics and Genomics, Department of Medicine, Boston Children's Hospital, Boston, MA, 02115, USA. .,Harvard Medical School, Boston, MA, USA.
| | - Mairead Bresnahan
- Genetics and Genomics, Department of Medicine, Boston Children’s Hospital, Boston, MA, 02115
| | - Maya C del Rosario
- Genetics and Genomics, Department of Medicine, Boston Children’s Hospital, Boston, MA, 02115
| | - Mayra Martinez Ojeda
- Genetics and Genomics, Department of Medicine, Boston Children’s Hospital, Boston, MA, 02115
| | - Amy Kritzer
- Genetics and Genomics, Department of Medicine, Boston Children’s Hospital, Boston, MA, 02115
| | - Yarden S. Fraiman
- Divisions of Newborn Medicine, Boston Children’s Hospital, Boston, MA, 02115.,Harvard Medical School, Boston, MA.,Department of Neonatology, Beth Israel Deaconess Medical Center, Boston, MA
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24
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Li MJ, Chien TW, Liao KW, Lai FJ. Using the Sankey diagram to visualize article features on the topics of whole-exome sequencing (WES) and whole-genome sequencing (WGS) since 2012: Bibliometric analysis. Medicine (Baltimore) 2022; 101:e30682. [PMID: 36197161 PMCID: PMC9509026 DOI: 10.1097/md.0000000000030682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Sequencing technologies, such as whole-exome sequencing (WES) and whole-genome sequencing (WGS), have been increasingly applied to medical research in recent years. Which countries, journals, and institutes (called entities) contributed most to the fields (WES/WGS) remains unknown. Temporal bar graphs (TBGs) are frequently used in trend analysis of publications. However, how to draw the TBG on the Sankey diagram is not well understood in bibliometrics. We thus aimed to investigate the evolution of article entities in the WES/WGS fields using publication-based TBGs and compare the individual research achievements (IRAs) among entities. METHODS A total of 3599 abstracts downloaded from icite analysis were matched to entities, including article identity numbers, citations, publication years, journals, affiliated countries/regions of origin, and medical subject headings (MeSH terms) in PubMed on March 12, 2022. The relative citation ratio (RCR) was extracted from icite analysis to compute the hT index (denoting the IRA, taking both publications and citations into account) for each entity in the years between 2012 and 2021. Three types of visualizations were applied to display the trends of publications (e.g., choropleth maps and the enhanced TBGs) and IRAs (e.g., the flowchart on the Sankey diagram) for article entities in WES/WGS. RESULTS We observed that the 3 countries (the US, China, and the UK) occupied most articles in the WES/WGS fields since 2012, the 3 entities (i.e., top 5 journals, research institutes, and MeSH terms) were demonstrated on the enhanced TBGs, the top 2 MeSH terms were genetics and methods in WES and WGS, and the IRAs of 6 article entities with their hT-indices were succinctly and simultaneously displayed on a single Sankey diagram that was never launched in bibliographical studies. CONCLUSION The number of WES/WGS-related articles has dramatically increased since 2017. TBGs, particularly with hTs on the Sankey, are recommended for research on a topic (or in a discipline) to compare trends of publications and IRAs for entities in future bibliographical studies.
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Affiliation(s)
- Meng-Ju Li
- Department of Pediatrics, National Taiwan University Hsin-Chu Hospital, Hsinchu, Taiwan
- Department of Biological Science and Technology, College of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Tsair-Wei Chien
- Department of Medical Research, Chi-Mei Medical Center, Tainan, Taiwan
| | - Kuang-Wen Liao
- Department of Biological Science and Technology, College of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Feng-Jie Lai
- Department of Dermatology, Chi Mei Medical Center, Tainan, Taiwan
- Center for General Education, Southern Taiwan University of Science and Technology, Tainan, Taiwan
- *Correspondence: Feng-Jie Lai, Chi-Mei Medical Center, 901 Chung Hwa Road, Yung Kung Dist., Tainan 710, Taiwan (e-mail: )
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25
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Abstract
Genetic diseases disrupt the functionality of an infant's genome during fetal-neonatal adaptation and represent a leading cause of neonatal and infant mortality in the United States. Due to disease acuity, gene locus and allelic heterogeneity, and overlapping and diverse clinical phenotypes, diagnostic genome sequencing in neonatal intensive care units has required the development of methods to shorten turnaround times and improve genomic interpretation. From 2012 to 2021, 31 clinical studies documented the diagnostic and clinical utility of first-tier rapid or ultrarapid whole-genome sequencing through cost-effective identification of pathogenic genomic variants that change medical management, suggest new therapeutic strategies, and refine prognoses. Genomic diagnosis also permits prediction of reproductive recurrence risk for parents and surviving probands. Using implementation science and quality improvement, deployment of a genomic learning healthcare system will contribute to a reduction of neonatal and infant mortality through the integration of genome sequencing into best-practice neonatal intensive care.
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Affiliation(s)
- Stephen F. Kingsmore
- Rady Children’s Hospital Institute for Genomic Medicine, Rady Children’s Hospital-San Diego
| | - F. Sessions Cole
- Division of Newborn Medicine, Edward Mallinckrodt Department of Pediatrics, Washington University School of Medicine in St. Louis
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26
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Sanford Kobayashi EF, Dimmock DP. Better and faster is cheaper. Hum Mutat 2022; 43:1495-1506. [PMID: 35723630 DOI: 10.1002/humu.24422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 05/23/2022] [Accepted: 06/08/2022] [Indexed: 11/09/2022]
Abstract
The rapid pace of advancement in genomic sequencing technology has recently reached a new milestone, with a record-setting time to molecular diagnosis of a mere 8 h. The catalyst behind this achievement is the accumulation of evidence indicating that quicker results more often make an impact on patient care and lead to healthcare cost savings. Herein, we review the diagnostic and clinical utility of rapid whole genome and rapid whole exome sequencing, the associated reduction in healthcare costs, and the relationship between these outcome measures and time-to-diagnosis.
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Affiliation(s)
- Erica F Sanford Kobayashi
- Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, California, USA.,Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, California, USA
| | - David P Dimmock
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, California, USA
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27
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Wojcik MH, Del Rosario MC, Agrawal PB. Perspectives of United States neonatologists on genetic testing practices. Genet Med 2022; 24:1372-1377. [PMID: 35304021 DOI: 10.1016/j.gim.2022.02.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 02/11/2022] [Accepted: 02/14/2022] [Indexed: 01/22/2023] Open
Abstract
PURPOSE Genetic disorders often present in the neonatal intensive care unit (NICU), and detecting or confirming these diagnoses has been shown to impact care. However, the availability and use of genetic testing, particularly exome or genome sequencing, among NICUs varies widely. We therefore sought to investigate practice patterns related to genetic testing in NICUs around the country to identify and quantify potential discrepancies. METHODS We designed a survey that was distributed to neonatologists via email. The survey contained questions related to test availability and desirability, the process of test ordering in NICU, and general comfort with ordering and interpreting genetic testing. Demographic data related to the survey participants and characteristics of their NICU were also obtained. RESULTS In total, 162 neonatologists completed the survey, representing 40 states and 112 distinct NICUs. Although nearly all (93.2%) neonatologists attributed a high level of importance to identifying a genetic diagnosis for their patients, genetic consultations were only available at 78% of NICUs and exome or genome sequencing was not available on a regular basis (69% of NICUs). CONCLUSION Although, among US neonatologists surveyed, most feel that genetic tests are indicated for their patients, these are not always clinically available. Further research into implementation barriers is warranted.
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Affiliation(s)
- Monica H Wojcik
- Division of Newborn Medicine, Department of Pediatrics, Boston Children' Hospital and Harvard Medical School, Boston, MA; Division of Genetics & Genomics, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, Boston, MA; The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA.
| | - Maya C Del Rosario
- Division of Newborn Medicine, Department of Pediatrics, Boston Children' Hospital and Harvard Medical School, Boston, MA; Division of Genetics & Genomics, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, Boston, MA
| | - Pankaj B Agrawal
- Division of Newborn Medicine, Department of Pediatrics, Boston Children' Hospital and Harvard Medical School, Boston, MA; Division of Genetics & Genomics, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, Boston, MA; The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA.
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28
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Mortality in the neonatal intensive care unit: improving the accuracy of death reporting. J Perinatol 2022; 42:671-676. [PMID: 34584196 PMCID: PMC9126052 DOI: 10.1038/s41372-021-01214-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 08/09/2021] [Accepted: 09/10/2021] [Indexed: 11/09/2022]
Abstract
OBJECTIVE Death certificates commonly contain errors, which hinders understanding of infant mortality. We, therefore, undertook a quality improvement (QI) initiative to improve death reporting in our neonatal intensive care unit (NICU). STUDY DESIGN After our baseline assessment (January 1, 2015 to June 30, 2017), we implemented our QI initiatives using Plan, Do, Study, Act (PDSA) tests of change. We prospectively reviewed death certificates (July 1, 2017 to December 31, 2019) to evaluate the impact of our interventions. RESULTS The overall proportion of incorrect death certificates significantly decreased from 71 to 22% with special cause variation noted after the second PDSA cycle. The most common errors involved inaccurate or incomplete reporting of prematurity and errors in the sequence of events. CONCLUSION Through a series of PDSA cycles focused on formal provider education and ongoing review, we significantly reduced inaccurate death reporting. These interventions are generalizable across NICUs and important to improve public health reporting accuracy.
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29
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Abstract
The XPG/ERCC5 endonuclease was originally identified as the causative gene for Xeroderma Pigmentosum complementation group G. Ever since its discovery, in depth biochemical, structural and cell biological studies have provided detailed mechanistic insight into its function in excising DNA damage in nucleotide excision repair, together with the ERCC1–XPF endonuclease. In recent years, it has become evident that XPG has additional important roles in genome maintenance that are independent of its function in NER, as XPG has been implicated in protecting replication forks by promoting homologous recombination as well as in resolving R-loops. Here, we provide an overview of the multitasking of XPG in genome maintenance, by describing in detail how its activity in NER is regulated and the evidence that points to important functions outside of NER. Furthermore, we present the various disease phenotypes associated with inherited XPG deficiency and discuss current ideas on how XPG deficiency leads to these different types of disease.
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30
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Kotecha UH, Mistri M, Rayabarapu P, Shah P, Shah N. The diagnostic utility of exome-based carrier screening in families with a positive family history. Am J Med Genet A 2022; 188:1323-1333. [PMID: 34997808 DOI: 10.1002/ajmg.a.62633] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 10/15/2021] [Accepted: 12/26/2021] [Indexed: 11/09/2022]
Abstract
Identification of disease-causing variants in families with a history of a suspected recessive disorder is essential for appropriate counseling and reproductive decision making. The present case series depicts the utility of whole exome-based phenotypes-driven carrier analysis in 14 families with a positive family history. A phenotype-based analysis revealed a putative diagnostic yield of 71.4%. Proband sample, though insufficient, was available in only one family, which allowed the diagnosis to be confirmed. In the remaining nine families, despite the detection of heterozygous pathogenic/likely pathogenic variants, only a putative diagnosis was possible due to incomplete proband phenotyping as well as nonavailability of proband samples. We describe the youngest known patient homozygous for a likely pathogenic variant in PPP1R21. He is currently asymptomatic at 7 days of life and has a simplified gyral pattern on neuroimaging. The case series, though small, captures the challenges in the diagnosis of genetic disorders in low to middle income countries with in-equitable health care access. It reinforces the significance of detailed phenotyping in the proband as well as the importance of DNA storage for a conclusive diagnosis. A recurring post-test counseling challenge was risk ascertainment and reproductive decision making in subsequent pregnancies if the detected pathogenic/likely pathogenic variants are co-inherited, in families with a putative diagnosis. When opted for, prenatal testing in such a scenario would be limited in its ability to comment on the fetal status with respect to the disorder in the proband.
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Affiliation(s)
| | - Mehul Mistri
- Neuberg Centre for Genomic Medicine, Ahmedabad, India
| | | | - Parth Shah
- Neuberg Centre for Genomic Medicine, Ahmedabad, India
| | - Nidhi Shah
- Neuberg Centre for Genomic Medicine, Ahmedabad, India
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31
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Kelly CJ, Brown APY, Taylor JA. Artificial Intelligence in Pediatrics. Artif Intell Med 2022. [DOI: 10.1007/978-3-030-64573-1_316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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32
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McKenzie-Sampson S, Baer RJ, Blebu BE, Karasek D, Oltman SP, Pantell MS, Rand L, Rogers EE, Torres JM, Jelliffe-Pawlowski LL, Scott KA, Chambers BD. Maternal nativity and risk of adverse perinatal outcomes among Black women residing in California, 2011-2017. J Perinatol 2021; 41:2736-2741. [PMID: 34282261 PMCID: PMC8939260 DOI: 10.1038/s41372-021-01149-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 06/23/2021] [Accepted: 07/06/2021] [Indexed: 11/09/2022]
Abstract
OBJECTIVE Examine the risk of adverse perinatal outcomes among the United States (US)-born and foreign-born Black women in California. STUDY DESIGN The study comprised all singleton live births to Black women in California between 2011 and 2017. We defined maternal nativity as US-born or foreign-born. Using Poisson regression, we computed risk ratios (RR) and 95% confidence intervals (CI) for three adverse perinatal outcomes: preterm birth, small for gestational age deliveries, and infant mortality. RESULTS Rates of adverse perinatal outcomes were significantly higher among US-born Black women. In adjusted models, US-born Black women experienced an increased risk of preterm birth (RR 1.51, 95% CI 1.39, 1.65) and small for gestational age deliveries (RR 1.52, 95% CI 1.41, 1.64), compared to foreign-born Black women. CONCLUSIONS Future studies should consider experiences of racism across the life course when exploring heterogeneity in the risk of adverse perinatal outcomes by nativity among Black women in the US.
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Affiliation(s)
- Safyer McKenzie-Sampson
- Department of Epidemiology & Biostatistics, University of California San Francisco School of Medicine, San Francisco, CA, USA.
- UCSF California Preterm Birth Initiative, University of California San Francisco School of Medicine, San Francisco, CA, USA.
| | - Rebecca J Baer
- UCSF California Preterm Birth Initiative, University of California San Francisco School of Medicine, San Francisco, CA, USA
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California San Francisco School of Medicine, San Francisco, CA, USA
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Bridgette E Blebu
- UCSF California Preterm Birth Initiative, University of California San Francisco School of Medicine, San Francisco, CA, USA
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California San Francisco School of Medicine, San Francisco, CA, USA
| | - Deborah Karasek
- UCSF California Preterm Birth Initiative, University of California San Francisco School of Medicine, San Francisco, CA, USA
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California San Francisco School of Medicine, San Francisco, CA, USA
| | - Scott P Oltman
- Department of Epidemiology & Biostatistics, University of California San Francisco School of Medicine, San Francisco, CA, USA
- UCSF California Preterm Birth Initiative, University of California San Francisco School of Medicine, San Francisco, CA, USA
| | - Matthew S Pantell
- Department of Pediatrics, University of California San Francisco School of Medicine, San Francisco, CA, USA
| | - Larry Rand
- UCSF California Preterm Birth Initiative, University of California San Francisco School of Medicine, San Francisco, CA, USA
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California San Francisco School of Medicine, San Francisco, CA, USA
| | - Elizabeth E Rogers
- UCSF California Preterm Birth Initiative, University of California San Francisco School of Medicine, San Francisco, CA, USA
- Department of Pediatrics, University of California San Francisco School of Medicine, San Francisco, CA, USA
| | - Jacqueline M Torres
- Department of Epidemiology & Biostatistics, University of California San Francisco School of Medicine, San Francisco, CA, USA
- UCSF California Preterm Birth Initiative, University of California San Francisco School of Medicine, San Francisco, CA, USA
| | - Laura L Jelliffe-Pawlowski
- Department of Epidemiology & Biostatistics, University of California San Francisco School of Medicine, San Francisco, CA, USA
- UCSF California Preterm Birth Initiative, University of California San Francisco School of Medicine, San Francisco, CA, USA
| | - Karen A Scott
- UCSF California Preterm Birth Initiative, University of California San Francisco School of Medicine, San Francisco, CA, USA
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California San Francisco School of Medicine, San Francisco, CA, USA
- Department of Humanities and Social Sciences, University of California San Francisco School of Medicine, San Francisco, CA, USA
| | - Brittany D Chambers
- Department of Epidemiology & Biostatistics, University of California San Francisco School of Medicine, San Francisco, CA, USA
- UCSF California Preterm Birth Initiative, University of California San Francisco School of Medicine, San Francisco, CA, USA
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Al-Hamed MH, Kurdi W, Khan R, Tulbah M, AlNemer M, AlSahan N, AlMugbel M, Rafiullah R, Assoum M, Monies D, Shah Z, Rahbeeni Z, Derar N, Hakami F, Almutairi G, AlOtaibi A, Ali W, AlShammasi A, AlMubarak W, AlDawoud S, AlAmri S, Saeed B, Bukhari H, Ali M, Akili R, Alquayt L, Hagos S, Elbardisy H, Akilan A, Almuhana N, AlKhalifah A, Abouelhoda M, Ramzan K, Sayer JA, Imtiaz F. Prenatal exome sequencing and chromosomal microarray analysis in fetal structural anomalies in a highly consanguineous population reveals a propensity of ciliopathy genes causing multisystem phenotypes. Hum Genet 2021; 141:101-126. [PMID: 34853893 DOI: 10.1007/s00439-021-02406-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 11/26/2021] [Indexed: 12/25/2022]
Abstract
Fetal abnormalities are detected in 3% of all pregnancies and are responsible for approximately 20% of all perinatal deaths. Chromosomal microarray analysis (CMA) and exome sequencing (ES) are widely used in prenatal settings for molecular genetic diagnostics with variable diagnostic yields. In this study, we aimed to determine the diagnostic yield of trio-ES in detecting the cause of fetal abnormalities within a highly consanguineous population. In families with a history of congenital anomalies, a total of 119 fetuses with structural anomalies were recruited and DNA from invasive samples were used together with parental DNA samples for trio-ES and CMA. Data were analysed to determine possible underlying genetic disorders associated with observed fetal phenotypes. The cohort had a known consanguinity of 81%. Trio-ES led to diagnostic molecular genetic findings in 59 fetuses (with pathogenic/likely pathogenic variants) most with multisystem or renal abnormalities. CMA detected chromosomal abnormalities compatible with the fetal phenotype in another 7 cases. Monogenic ciliopathy disorders with an autosomal recessive inheritance were the predominant cause of multisystem fetal anomalies (24/59 cases, 40.7%) with loss of function variants representing the vast majority of molecular genetic abnormalities. Heterozygous de novo pathogenic variants were found in four fetuses. A total of 23 novel variants predicted to be associated with the phenotype were detected. Prenatal trio-ES and CMA detected likely causative molecular genetic defects in a total of 55% of families with fetal anomalies confirming the diagnostic utility of trio-ES and CMA as first-line genetic test in the prenatal diagnosis of multisystem fetal anomalies including ciliopathy syndromes.
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Affiliation(s)
- Mohamed H Al-Hamed
- Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, MBC# 26, P. O. Box 3354, Riyadh, Saudi Arabia.
- Saudi Diagnostics Laboratory, KFSHI, P.O.BOX 6802, Riyadh, 12311, Saudi Arabia.
| | - Wesam Kurdi
- Department of Obstetrics and Genecology, King Faisal Specialist Hospital and Research Centre, P. O. Box 3354, Riyadh, 11211, Saudi Arabia
| | - Rubina Khan
- Department of Obstetrics and Genecology, King Faisal Specialist Hospital and Research Centre, P. O. Box 3354, Riyadh, 11211, Saudi Arabia
| | - Maha Tulbah
- Department of Obstetrics and Genecology, King Faisal Specialist Hospital and Research Centre, P. O. Box 3354, Riyadh, 11211, Saudi Arabia
| | - Maha AlNemer
- Department of Obstetrics and Genecology, King Faisal Specialist Hospital and Research Centre, P. O. Box 3354, Riyadh, 11211, Saudi Arabia
| | - Nada AlSahan
- Department of Obstetrics and Genecology, King Faisal Specialist Hospital and Research Centre, P. O. Box 3354, Riyadh, 11211, Saudi Arabia
| | - Maisoon AlMugbel
- Department of Obstetrics and Genecology, King Faisal Specialist Hospital and Research Centre, P. O. Box 3354, Riyadh, 11211, Saudi Arabia
| | - Rafiullah Rafiullah
- Saudi Diagnostics Laboratory, KFSHI, P.O.BOX 6802, Riyadh, 12311, Saudi Arabia
| | - Mirna Assoum
- Saudi Diagnostics Laboratory, KFSHI, P.O.BOX 6802, Riyadh, 12311, Saudi Arabia
| | - Dorota Monies
- Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, MBC# 26, P. O. Box 3354, Riyadh, Saudi Arabia
| | - Zeeshan Shah
- Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, MBC# 26, P. O. Box 3354, Riyadh, Saudi Arabia
| | - Zuhair Rahbeeni
- Medical Genetics Department, King Faisal Specialist Hospital and Research Centre, P. O. Box 3354, Riyadh, Saudi Arabia
| | - Nada Derar
- Medical Genetics Department, King Faisal Specialist Hospital and Research Centre, P. O. Box 3354, Riyadh, Saudi Arabia
| | - Fahad Hakami
- King Abdulaziz Medical City/King Saud bin Abdulaziz University for Health Science, Jeddah, Saudi Arabia
| | - Gawaher Almutairi
- Department of Obstetrics and Genecology, King Faisal Specialist Hospital and Research Centre, P. O. Box 3354, Riyadh, 11211, Saudi Arabia
| | - Afaf AlOtaibi
- Saudi Diagnostics Laboratory, KFSHI, P.O.BOX 6802, Riyadh, 12311, Saudi Arabia
| | - Wafaa Ali
- Saudi Diagnostics Laboratory, KFSHI, P.O.BOX 6802, Riyadh, 12311, Saudi Arabia
| | - Amal AlShammasi
- Saudi Diagnostics Laboratory, KFSHI, P.O.BOX 6802, Riyadh, 12311, Saudi Arabia
| | - Wardah AlMubarak
- Department of Obstetrics and Genecology, King Faisal Specialist Hospital and Research Centre, P. O. Box 3354, Riyadh, 11211, Saudi Arabia
| | - Samia AlDawoud
- Department of Obstetrics and Genecology, King Faisal Specialist Hospital and Research Centre, P. O. Box 3354, Riyadh, 11211, Saudi Arabia
| | - Saja AlAmri
- Department of Obstetrics and Genecology, King Faisal Specialist Hospital and Research Centre, P. O. Box 3354, Riyadh, 11211, Saudi Arabia
| | - Bashayer Saeed
- Department of Obstetrics and Genecology, King Faisal Specialist Hospital and Research Centre, P. O. Box 3354, Riyadh, 11211, Saudi Arabia
| | - Hanifa Bukhari
- Department of Obstetrics and Genecology, King Faisal Specialist Hospital and Research Centre, P. O. Box 3354, Riyadh, 11211, Saudi Arabia
| | - Mohannad Ali
- Department of Obstetrics and Genecology, King Faisal Specialist Hospital and Research Centre, P. O. Box 3354, Riyadh, 11211, Saudi Arabia
| | - Rana Akili
- Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, MBC# 26, P. O. Box 3354, Riyadh, Saudi Arabia
| | - Laila Alquayt
- Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, MBC# 26, P. O. Box 3354, Riyadh, Saudi Arabia
| | - Samia Hagos
- Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, MBC# 26, P. O. Box 3354, Riyadh, Saudi Arabia
| | - Hadeel Elbardisy
- Saudi Diagnostics Laboratory, KFSHI, P.O.BOX 6802, Riyadh, 12311, Saudi Arabia
| | - Asma Akilan
- Saudi Diagnostics Laboratory, KFSHI, P.O.BOX 6802, Riyadh, 12311, Saudi Arabia
| | - Nora Almuhana
- Saudi Diagnostics Laboratory, KFSHI, P.O.BOX 6802, Riyadh, 12311, Saudi Arabia
| | - Abrar AlKhalifah
- Saudi Diagnostics Laboratory, KFSHI, P.O.BOX 6802, Riyadh, 12311, Saudi Arabia
| | - Mohamed Abouelhoda
- Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, MBC# 26, P. O. Box 3354, Riyadh, Saudi Arabia
| | - Khushnooda Ramzan
- Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, MBC# 26, P. O. Box 3354, Riyadh, Saudi Arabia
| | - John A Sayer
- Faculty of Medical Sciences, Translational and Clinical Research Institute, Newcastle University, Central Parkway, Newcastle upon Tyne, NE1 3BZ, UK
- Renal Services, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, NE7 7DN, UK
- NIHR Newcastle Biomedical Research Centre, Newcastle University, Tyne and Wear, Newcastle upon Tyne, NE4 5PL, UK
| | - Faiqa Imtiaz
- Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, MBC# 26, P. O. Box 3354, Riyadh, Saudi Arabia.
- Saudi Diagnostics Laboratory, KFSHI, P.O.BOX 6802, Riyadh, 12311, Saudi Arabia.
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Ali Alghamdi M, Alrasheedi A, Alghamdi E, Adly N, AlAali WY, Alhashem A, Alshahrani A, Shamseldin H, Alkuraya FS, Alfadhel M. Molecular autopsy by proxy in preconception counseling. Clin Genet 2021; 100:678-691. [PMID: 34406647 PMCID: PMC9290025 DOI: 10.1111/cge.14049] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 08/15/2021] [Accepted: 08/17/2021] [Indexed: 01/06/2023]
Abstract
Monogenic diseases that result in early pregnancy loss or neonatal death are genetically and phenotypically highly variable. This often poses significant challenges in arriving at a molecular diagnosis for reproductive planning. Molecular autopsy by proxy (MABP) refers to the genetic testing of relatives of deceased individuals to deduce the cause of death. Here, we specifically tested couples who lost one or more children/pregnancies with no available DNA. We developed our testing strategy using whole exome sequencing data from 83 consanguineous Saudi couples. We detected the shared carrier state of 50 pathogenic variants/likely pathogenic variants in 43 families and of 28 variants of uncertain significance in 24 families. Negative results were seen in 16 couples after variant reclassification. In 10 families, the risk of more than one genetic disease was documented. Secondary findings were seen in 10 families: either genetic variants with potential clinical consequences for the tested individual or a female carrier for X‐linked conditions. This couple‐based approach has enabled molecularly informed genetic counseling for 52% (43/83 families). Given the predominance of autosomal recessive causes of pregnancy and child death in consanguineous populations, MABP can be a helpful approach to consanguineous couples who seek counseling but lack molecular data on their deceased offspring.
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Affiliation(s)
- Malak Ali Alghamdi
- Medical Genetic Division, Pediatric Department, College of Medicine, King Saud University, Riyadh, Saudi Arabia.,Medical Genetics Division, Department of Pediatrics, King Saud University Medical City, Riyadh, Saudi Arabia
| | - Ameinah Alrasheedi
- Department of Pediatrics, College of Medicine and Medical Sciences, Qassim University, Al Qassim, Saudi Arabia
| | - Esra Alghamdi
- College of Medicine, Imam Mohammed Ibn Saud Islamic University, Riyadh, Saudi Arabia
| | - Nouran Adly
- College of Medicine Research Center, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Wajeih Y AlAali
- Dr. Sulaiman Al Habib Medical Group, Riyadh, Saudi Arabia.,Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia.,College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Amal Alhashem
- Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia.,College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | | | - Hanan Shamseldin
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Majid Alfadhel
- King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard-Health Affairs, Riyadh, Saudi Arabia.,Genetics and Precision Medicine department, King Abdullah Specialized Children Hospital, King Abdulaziz Medical City, Ministry of National Guard-Health Affairs, Riyadh, Saudi Arabia
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35
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Wojcik MH, Stadelmaier R, Heinke D, Holm IA, Tan WH, Agrawal PB. The Unrecognized Mortality Burden of Genetic Disorders in Infancy. Am J Public Health 2021; 111:S156-S162. [PMID: 34314210 PMCID: PMC8495634 DOI: 10.2105/ajph.2021.306275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/11/2021] [Indexed: 11/04/2022]
Abstract
Objectives. To determine how deaths of infants with genetic diagnoses are described in national mortality statistics. Methods. We present a retrospective cohort study of mortality data, obtained from the National Death Index (NDI), and clinical data for 517 infants born from 2011 to 2017 who died before 1 year of age in the United States. Results. Although 115 of 517 deceased infants (22%) had a confirmed diagnosis of a genetic disorder, only 61 of 115 deaths (53%) were attributed to International Classification of Diseases, 10th Revision codes representing congenital anomalies or genetic disorders (Q00-Q99) as the underlying cause of death because of inconsistencies in death reporting. Infants with genetic diagnoses whose underlying causes of death were coded as Q00-Q99 were more likely to have chromosomal disorders than monogenic conditions (43/61 [70%] vs 18/61 [30%]; P < .001), which reflects the need for improved accounting for monogenic disorders in mortality statistics. Conclusions. Genetic disorders, although a leading cause of infant mortality, are not accurately captured by vital statistics. Public Health Implications. Expanded access to genetic testing and further clarity in death reporting are needed to describe properly the contribution of genetic disorders to infant mortality.
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Affiliation(s)
- Monica H Wojcik
- Monica H. Wojcik and Pankaj B. Agrawal are with the Division of Newborn Medicine and Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, Boston, MA. Rachel Stadelmaier is with the Department of Pediatrics, Boston Children's Hospital and Harvard Medical School. Dominique Heinke is with the Center for Birth Defects Research and Prevention, Massachusetts Department of Public Health and Harvard T. H. Chan School of Public Health, Harvard University, Boston. Ingrid A. Holm and Wen-Hann Tan are with the Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School
| | - Rachel Stadelmaier
- Monica H. Wojcik and Pankaj B. Agrawal are with the Division of Newborn Medicine and Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, Boston, MA. Rachel Stadelmaier is with the Department of Pediatrics, Boston Children's Hospital and Harvard Medical School. Dominique Heinke is with the Center for Birth Defects Research and Prevention, Massachusetts Department of Public Health and Harvard T. H. Chan School of Public Health, Harvard University, Boston. Ingrid A. Holm and Wen-Hann Tan are with the Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School
| | - Dominique Heinke
- Monica H. Wojcik and Pankaj B. Agrawal are with the Division of Newborn Medicine and Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, Boston, MA. Rachel Stadelmaier is with the Department of Pediatrics, Boston Children's Hospital and Harvard Medical School. Dominique Heinke is with the Center for Birth Defects Research and Prevention, Massachusetts Department of Public Health and Harvard T. H. Chan School of Public Health, Harvard University, Boston. Ingrid A. Holm and Wen-Hann Tan are with the Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School
| | - Ingrid A Holm
- Monica H. Wojcik and Pankaj B. Agrawal are with the Division of Newborn Medicine and Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, Boston, MA. Rachel Stadelmaier is with the Department of Pediatrics, Boston Children's Hospital and Harvard Medical School. Dominique Heinke is with the Center for Birth Defects Research and Prevention, Massachusetts Department of Public Health and Harvard T. H. Chan School of Public Health, Harvard University, Boston. Ingrid A. Holm and Wen-Hann Tan are with the Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School
| | - Wen-Hann Tan
- Monica H. Wojcik and Pankaj B. Agrawal are with the Division of Newborn Medicine and Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, Boston, MA. Rachel Stadelmaier is with the Department of Pediatrics, Boston Children's Hospital and Harvard Medical School. Dominique Heinke is with the Center for Birth Defects Research and Prevention, Massachusetts Department of Public Health and Harvard T. H. Chan School of Public Health, Harvard University, Boston. Ingrid A. Holm and Wen-Hann Tan are with the Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School
| | - Pankaj B Agrawal
- Monica H. Wojcik and Pankaj B. Agrawal are with the Division of Newborn Medicine and Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, Boston, MA. Rachel Stadelmaier is with the Department of Pediatrics, Boston Children's Hospital and Harvard Medical School. Dominique Heinke is with the Center for Birth Defects Research and Prevention, Massachusetts Department of Public Health and Harvard T. H. Chan School of Public Health, Harvard University, Boston. Ingrid A. Holm and Wen-Hann Tan are with the Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School
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36
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Owen MJ, Lenberg J, Feigenbaum A, Gold J, Chau K, Bezares-Orin Z, Ding Y, Chowdhury S, Kingsmore SF. Postmortem whole-genome sequencing on a dried blood spot identifies a novel homozygous SUOX variant causing isolated sulfite oxidase deficiency. Cold Spring Harb Mol Case Stud 2021; 7:mcs.a006091. [PMID: 34117075 PMCID: PMC8208044 DOI: 10.1101/mcs.a006091] [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: 02/26/2021] [Accepted: 03/26/2021] [Indexed: 12/03/2022] Open
Abstract
Rapid whole-genome sequencing (rWGS) has shown that genetic diseases are a common cause of infant mortality in neonatal intensive care units. Dried blood spots collected for newborn screening allow investigation of causes of infant mortality that were not diagnosed during life. Here, we present a neonate who developed seizures and encephalopathy on the third day of life that was refractory to antiepileptic medications. The patient died on day of life 16 after progressive respiratory failure and sepsis. The parents had lost two prior children after similar presentations, neither of whom had a definitive diagnosis. Postmortem rWGS of a dried blood spot identified a pathogenic homozygous frameshift variant in the SUOX gene associated with isolated sulfite oxidase deficiency (c.1390_1391del, p.Leu464GlyfsTer10). This case highlights that early, accurate molecular diagnosis has the potential to influence prenatal counseling and guide management in rare, genetic disorders and has added importance in cases of a strong family history and risk factors such as consanguinity.
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Affiliation(s)
- Mallory J Owen
- Rady Children's Institute for Genomic Medicine, San Diego, California 92123, USA.,Rady Children's Hospital, San Diego, California 92123, USA
| | - Jerica Lenberg
- Rady Children's Institute for Genomic Medicine, San Diego, California 92123, USA.,Rady Children's Hospital, San Diego, California 92123, USA
| | - Annette Feigenbaum
- Rady Children's Hospital, San Diego, California 92123, USA.,Department of Pediatrics, University of California San Diego, San Diego, California 92093, USA
| | - Jeffrey Gold
- Rady Children's Hospital, San Diego, California 92123, USA
| | - Kevin Chau
- Rady Children's Institute for Genomic Medicine, San Diego, California 92123, USA.,Rady Children's Hospital, San Diego, California 92123, USA
| | - Zaira Bezares-Orin
- Rady Children's Institute for Genomic Medicine, San Diego, California 92123, USA
| | - Yan Ding
- Rady Children's Institute for Genomic Medicine, San Diego, California 92123, USA.,Rady Children's Hospital, San Diego, California 92123, USA
| | - Shimul Chowdhury
- Rady Children's Institute for Genomic Medicine, San Diego, California 92123, USA.,Rady Children's Hospital, San Diego, California 92123, USA
| | - Stephen F Kingsmore
- Rady Children's Institute for Genomic Medicine, San Diego, California 92123, USA.,Rady Children's Hospital, San Diego, California 92123, USA
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37
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Beyond diagnostic yield: prenatal exome sequencing results in maternal, neonatal, and familial clinical management changes. Genet Med 2021; 23:909-917. [PMID: 33442022 PMCID: PMC7804210 DOI: 10.1038/s41436-020-01067-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 12/02/2020] [Accepted: 12/03/2020] [Indexed: 12/30/2022] Open
Abstract
Purpose Previous studies have reported that prenatal exome sequencing (pES) can detect monogenic diseases in fetuses with congenital anomalies with diagnostic yields ranging from 6% to 81%, but there are few reports of its clinical utility. Methods We conducted a retrospective chart review of patients who had pES to determine whether results led to clinical management changes. Results Of 20 patients, 8 (40%) received a definitive diagnosis. Seven patients (35%) had medical management changes based on the pES results, including alterations to their delivery plan and neonatal management (such as use of targeted medications, subspecialty referrals, additional imaging and/or procedures). All patients who received a definitive diagnosis and one who received a likely pathogenic variant (n = 9; 45%) received specific counseling about recurrence risk and the medical/developmental prognosis for the baby. In five (25%) cases, the result facilitated a diagnosis in parents and/or siblings. Conclusion pES results can have significant impacts on clinical management, some of which would not be possible if testing is deferred until after birth. To maximize the clinical utility, pES should be prioritized in cases where multiple care options are available and the imaging findings alone are not sufficient to guide parental decision-making, or where postnatal testing will not be feasible.
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38
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Artificial Intelligence in Pediatrics. Artif Intell Med 2021. [DOI: 10.1007/978-3-030-58080-3_316-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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39
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Dimmock DP, Clark MM, Gaughran M, Cakici JA, Caylor SA, Clarke C, Feddock M, Chowdhury S, Salz L, Cheung C, Bird LM, Hobbs C, Wigby K, Farnaes L, Bloss CS, Kingsmore SF. An RCT of Rapid Genomic Sequencing among Seriously Ill Infants Results in High Clinical Utility, Changes in Management, and Low Perceived Harm. Am J Hum Genet 2020; 107:942-952. [PMID: 33157007 PMCID: PMC7675004 DOI: 10.1016/j.ajhg.2020.10.003] [Citation(s) in RCA: 111] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 10/12/2020] [Indexed: 12/20/2022] Open
Abstract
The second Newborn Sequencing in Genomic Medicine and Public Health (NSIGHT2) study was a randomized, controlled trial of rapid whole-genome sequencing (rWGS) or rapid whole-exome sequencing (rWES) in infants with diseases of unknown etiology in intensive care units (ICUs). Gravely ill infants were not randomized and received ultra-rapid whole-genome sequencing (urWGS). Herein we report results of clinician surveys of the clinical utility of rapid genomic sequencing (RGS). The primary end-point-clinician perception that RGS was useful- was met for 154 (77%) of 201 infants. Both positive and negative tests were rated as having clinical utility (42 of 45 [93%] and 112 of 156 [72%], respectively). Physicians reported that RGS changed clinical management in 57 (28%) infants, particularly in those receiving urWGS (p = 0.0001) and positive tests (p < 0.00001). Outcomes of 32 (15%) infants were perceived to be changed by RGS. Positive tests changed outcomes more frequently than negative tests (p < 0.00001). In logistic regression models, the likelihood that RGS was perceived as useful increased 6.7-fold when associated with changes in management (95% CI 1.8-43.3). Changes in management were 10.1-fold more likely when results were positive (95% CI 4.7-22.4) and turnaround time was shorter (odds ratio 0.92, 95% CI 0.85-0.99). RGS seldom led to clinician-perceived confusion or distress among families (6 of 207 [3%]). In summary, clinicians perceived high clinical utility and low likelihood of harm with first-tier RGS of infants in ICUs with diseases of unknown etiology. RGS was perceived as beneficial irrespective of whether results were positive or negative.
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Affiliation(s)
- David P Dimmock
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA.
| | - Michelle M Clark
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | - Mary Gaughran
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | - Julie A Cakici
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA; Department of Family Medicine and Public Health, University of California San Diego, San Diego, CA 92093, USA
| | - Sara A Caylor
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | - Christina Clarke
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | - Michele Feddock
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | - Shimul Chowdhury
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | - Lisa Salz
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | - Cynthia Cheung
- Department of Family Medicine and Public Health, University of California San Diego, San Diego, CA 92093, USA; Department of Psychiatry, University of California San Diego, San Diego, CA 92093, USA
| | - Lynne M Bird
- Rady Children's Hospital, San Diego, CA 92123, USA; Department of Pediatrics, University of California San Diego, San Diego, CA 92093, USA
| | - Charlotte Hobbs
- 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
| | - Lauge Farnaes
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | - Cinnamon S Bloss
- Department of Family Medicine and Public Health, University of California San Diego, San Diego, CA 92093, USA; Department of Psychiatry, University of California San Diego, San Diego, CA 92093, USA
| | - Stephen F Kingsmore
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
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40
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Kingsmore SF, Henderson A, Owen MJ, Clark MM, Hansen C, Dimmock D, Chambers CD, Jeliffe-Pawlowski LL, Hobbs C. Measurement of genetic diseases as a cause of mortality in infants receiving whole genome sequencing. NPJ Genom Med 2020; 5:49. [PMID: 33154820 PMCID: PMC7608690 DOI: 10.1038/s41525-020-00155-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 10/02/2020] [Indexed: 12/19/2022] Open
Abstract
Understanding causes of infant mortality shapes public health policy and prioritizes diseases for investments in surveillance, intervention and medical research. Rapid genomic sequencing has created a novel opportunity to decrease infant mortality associated with treatable genetic diseases. Herein, we sought to measure the contribution of genetic diseases to mortality among infants by secondary analysis of babies enrolled in two clinical studies and a systematic literature review. Among 312 infants who had been admitted to an ICU at Rady Children's Hospital between November 2015 and September 2018 and received rapid genomic sequencing, 30 (10%) died in infancy. Ten (33%) of the infants who died were diagnosed with 11 genetic diseases. The San Diego Study of Outcomes in Mothers and Infants platform identified differences between in-hospital and out-of-hospital causes of infant death. Similarly, in six published studies, 195 (21%) of 918 infant deaths were associated with genetic diseases by genomic sequencing. In 195 infant deaths associated with genetic diseases, locus heterogeneity was 70%. Treatment guidelines existed for 70% of the genetic diseases diagnosed, suggesting that rapid genomic sequencing has substantial potential to decrease infant mortality among infants in ICUs. Further studies are needed in larger, comprehensive, unbiased patient sets to determine the generalizability of these findings.
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Affiliation(s)
| | - Audrey Henderson
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA
| | - Mallory J. Owen
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA
| | - Michelle M. Clark
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA
| | - Christian Hansen
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA
| | - David Dimmock
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA
| | | | - Laura L. Jeliffe-Pawlowski
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA USA
| | - Charlotte Hobbs
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA
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41
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Dempsey E, Pryce J, Thilaganathan B, Mansour S, Homfray T, Drury S. Diagnosis of fetal abnormalities using exome sequencing: translating research into practice. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2020; 56:779. [PMID: 31875334 DOI: 10.1002/uog.21959] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 12/06/2019] [Accepted: 12/13/2019] [Indexed: 06/10/2023]
Affiliation(s)
- E Dempsey
- South West Thames Regional Genetics, St George's Hospital, London, UK
| | - J Pryce
- Pathology, St George's Hospital, London, UK
| | - B Thilaganathan
- Fetal Medicine Unit, St George's University Hospitals NHS Foundation Trust, University of London, London, UK
- Vascular Biology Research Centre, Molecular and Clinical Sciences Research Institute, St George's University of London, London, UK
| | - S Mansour
- South West Thames Regional Genetics, St George's Hospital, London, UK
| | - T Homfray
- South West Thames Regional Genetics, St George's Hospital, London, UK
| | - S Drury
- Congenica Ltd, Biodata Innovation Centre, Wellcome Trust Genome Campus, Hinxton, UK
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Wojcik MH, Agrawal PB. Deciphering congenital anomalies for the next generation. Cold Spring Harb Mol Case Stud 2020; 6:mcs.a005504. [PMID: 32826208 PMCID: PMC7552931 DOI: 10.1101/mcs.a005504] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Congenital anomalies are common, with 2%-3% of infants estimated to have at least one major congenital malformation and countless others with minor malformations of lesser cosmetic or medical importance. As congenital malformations are major drivers of morbidity and mortality, representing the leading cause of infant mortality in the United States, there is substantial interest in understanding the underlying etiologies-particularly if modifiable causes may be identified or pre- or postnatal treatments can be offered. Recent research has begun to reveal the spectrum of monogenic disorders that commonly result in birth defects, and newer approaches have revealed non-Mendelian genetic contributions including gene-environment interactions. Our experience suggests that increased efforts to sequence and analyze cases of perinatal death, as well as continued global collaboration, will be essential in understanding the genomic landscape of structural anomalies.
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Affiliation(s)
- Monica H Wojcik
- Divisions of Newborn Medicine and Genetics and Genomics, Department of Pediatrics, The Manton Center for Orphan Disease Research, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Pankaj B Agrawal
- Divisions of Newborn Medicine and Genetics and Genomics, Department of Pediatrics, The Manton Center for Orphan Disease Research, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
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43
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Rapid Phenotype-Driven Gene Sequencing with the NeoSeq Panel: A Diagnostic Tool for Critically Ill Newborns with Suspected Genetic Disease. J Clin Med 2020; 9:jcm9082362. [PMID: 32718099 PMCID: PMC7464859 DOI: 10.3390/jcm9082362] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 07/20/2020] [Accepted: 07/21/2020] [Indexed: 12/17/2022] Open
Abstract
New genomic sequencing techniques have shown considerable promise in the field of neonatology, increasing the diagnostic rate and reducing time to diagnosis. However, several obstacles have hindered the incorporation of this technology into routine clinical practice. We prospectively evaluated the diagnostic rate and diagnostic turnaround time achieved in newborns with suspected genetic diseases using a rapid phenotype-driven gene panel (NeoSeq) containing 1870 genes implicated in congenital malformations and neurological and metabolic disorders of early onset (<2 months of age). Of the 33 newborns recruited, a genomic diagnosis was established for 13 (39.4%) patients (median diagnostic turnaround time, 7.5 days), resulting in clinical management changes in 10 (76.9%) patients. An analysis of 12 previous prospective massive sequencing studies (whole genome (WGS), whole exome (WES), and clinical exome (CES) sequencing) in newborns admitted to neonatal intensive care units (NICUs) with suspected genetic disorders revealed a comparable median diagnostic rate (37.2%), but a higher median diagnostic turnaround time (22.3 days) than that obtained with NeoSeq. Our phenotype-driven gene panel, which is specific for genetic diseases in critically ill newborns is an affordable alternative to WGS and WES that offers comparable diagnostic efficacy, supporting its implementation as a first-tier genetic test in NICUs.
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