1
|
Sloper E, Jezkova J, Thomas J, Dawson K, Halstead J, Gardner J, Burke K, Oruganti S, Calvert J, Evans J, Anderson S, Corrin S, Pottinger C, Murch O. Wales Infants' and childreN's Genome Service (WINGS): providing rapid genetic diagnoses for unwell children. Arch Dis Child 2024; 109:409-413. [PMID: 38320813 DOI: 10.1136/archdischild-2023-326579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 01/24/2024] [Indexed: 04/20/2024]
Abstract
INTRODUCTION This study reviews the first 3 years of delivery of the first National Health Service (NHS)-commissioned trio rapid whole genome sequencing (rWGS) service for acutely unwell infants and children in Wales. METHODS Demographic and phenotypic data were prospectively collected as patients and their families were enrolled in the Wales Infants' and childreN's Genome Service (WINGS). These data were reviewed alongside trio rWGS results. RESULTS From April 2020 to March 2023, 82 families underwent WINGS, with a diagnostic yield of 34.1%. The highest diagnostic yields were noted in skeletal dysplasias, neurological or metabolic phenotypes. Mean time to reporting was 9 days. CONCLUSION This study demonstrates that trio rWGS is having a positive impact on the care of acutely unwell infants and children in an NHS setting. In particular, the study shows that rWGS can be applied in an NHS setting, achieving a diagnostic yield comparable with the previously published diagnostic yields achieved in research settings, while also helping to improve patient care and management.
Collapse
Affiliation(s)
- Emily Sloper
- All Wales Medical Genomics Service, University Hospital of Wales Healthcare NHS Trust, Cardiff, UK
| | - Jana Jezkova
- All Wales Medical Genomics Service, University Hospital of Wales Healthcare NHS Trust, Cardiff, UK
| | - Joanne Thomas
- Faculty of Life Science and Education, University of South Wales, Pontypridd, UK
| | | | - Joseph Halstead
- All Wales Medical Genomics Service, University Hospital of Wales Healthcare NHS Trust, Cardiff, UK
| | - Jennifer Gardner
- All Wales Medical Genomics Service, University Hospital of Wales Healthcare NHS Trust, Cardiff, UK
| | - Katherine Burke
- Neonatal Intensive Care Unit, Singleton Hospital, Swansea, UK
| | - Sivakumar Oruganti
- Paediatric Critical Care Unit, Noah's Ark Children's Hospital for Wales, Cardiff, UK
- College of Biomedical and Life Sciences, Cardiff University, Cardiff, UK
| | - Jennifer Calvert
- Neonatal Intensive Care Unit, University Hospital of Wales Healthcare NHS Trust, Cardiff, UK
| | - Jennifer Evans
- Child Health, Children's Hospital for Wales, Cardiff, UK
| | - Sarah Anderson
- All Wales Medical Genomics Service, University Hospital of Wales Healthcare NHS Trust, Cardiff, UK
| | - Sian Corrin
- All Wales Medical Genomics Service, University Hospital of Wales Healthcare NHS Trust, Cardiff, UK
| | - Caroline Pottinger
- All Wales Medical Genomics Service, University Hospital of Wales Healthcare NHS Trust, Cardiff, UK
| | - Oliver Murch
- All Wales Medical Genomics Service, University Hospital of Wales Healthcare NHS Trust, Cardiff, UK
| |
Collapse
|
2
|
Tinker RJ, Fisher M, Gimeno AF, Gill K, Ivey C, Peterson JF, Bastarache L. Diagnostic delay in monogenic disease: A scoping review. Genet Med 2024; 26:101074. [PMID: 38243783 PMCID: PMC11140588 DOI: 10.1016/j.gim.2024.101074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 01/09/2024] [Accepted: 01/11/2024] [Indexed: 01/21/2024] Open
Abstract
PURPOSE Diagnostic delay in monogenic disease is reportedly common. We conducted a scoping review investigating variability in study design, results, and conclusions. METHODS We searched the academic literature on January 17, 2023, for original peer reviewed journals and conference articles that quantified diagnostic delay in monogenic disease. We abstracted the reported diagnostic delay, relevant study design features, and definitions. RESULTS Our search identified 259 articles quantifying diagnostic delay in 111 distinct monogenetic diseases. Median reported diagnostic delay for all studies collectively in monogenetic diseases was 5.0 years (IQR 2-10). There was major variation in the reported delay within individual monogenetic diseases. Shorter delay was associated with disorders of childhood metabolism, immunity, and development. The majority (67.6%) of articles that studied delay reported an improvement with calendar time. Study design and definitions of delay were highly heterogenous. Three gaps were identified: (1) no studies were conducted in the least developed countries, (2) delay has not been studied for the majority of known, or (3) most prevalent genetic diseases. CONCLUSION Heterogenous study design and definitions of diagnostic delay inhibit comparison across studies. Future efforts should focus on standardizing delay measurements, while expanding the research to low-income countries.
Collapse
Affiliation(s)
- Rory J Tinker
- Division of Medical Genetics and Genomic Medicine, Vanderbilt University Medical Center, Nashville, TN.
| | - Miles Fisher
- Vanderbilt University Medical Center, Department of Child Neurology, Nashville, TN
| | - Alex F Gimeno
- Vanderbilt University School of Medicine, Nashville, TN
| | - Kayce Gill
- Annette and Irwin Eskind Family Biomedical Library and Learning Center, Vanderbilt University, Nashville, TN
| | - Camille Ivey
- Annette and Irwin Eskind Family Biomedical Library and Learning Center, Vanderbilt University, Nashville, TN
| | - Josh F Peterson
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN; Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Lisa Bastarache
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Kim S, Pistawka C, Langlois S, Osiovich H, Virani A, Kitchin V, Elliott AM. Genetic counselling considerations with genetic/genomic testing in Neonatal and Pediatric Intensive Care Units: A scoping review. Clin Genet 2024; 105:13-33. [PMID: 37927209 DOI: 10.1111/cge.14446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/23/2023] [Accepted: 10/15/2023] [Indexed: 11/07/2023]
Abstract
Genetic and genomic technologies can effectively diagnose numerous genetic disorders. Patients benefit when genetic counselling accompanies genetic testing and international guidelines recommend pre- and post-test genetic counselling with genome-wide sequencing. However, there is a gap in knowledge regarding the unique genetic counselling considerations with different types of genetic testing in the Neonatal Intensive Care Unit (NICU) and the Pediatric Intensive Care Unit (PICU). This scoping review was conducted to identify the gaps in care with respect to genetic counselling for infants/pediatric patients undergoing genetic and genomic testing in NICUs and PICUs and understand areas in need of improvement in order to optimize clinical care for patients, caregivers, and healthcare providers. Five databases (MEDLINE [Ovid], Embase [Ovid], PsycINFO [Ebsco], CENTRAL [Ovid], and CINHAL [Ebsco]) and grey literature were searched. A total of 170 studies were included and used for data extraction and analysis. This scoping review includes descriptive analysis, followed by a narrative account of the extracted data. Results were divided into three groups: pre-test, post-test, and comprehensive (both pre- and post-test) genetic counselling considerations based on indication for testing. More studies were conducted in the NICU than the PICU. Comprehensive genetic counselling was discussed in only 31% of all the included studies demonstrating the need for both pre-test and post-test genetic counselling for different clinical indications in addition to the need to account for different cultural aspects based on ethnicity and geographic factors.
Collapse
Affiliation(s)
- Sunu Kim
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Carly Pistawka
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sylvie Langlois
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada
- Women's Health Research Institute, Vancouver, British Columbia, Canada
| | - Horacio Osiovich
- BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada
- Women's Health Research Institute, Vancouver, British Columbia, Canada
- Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Alice Virani
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- Ethics Service, Provincial Health Services Authority, Vancouver, British Columbia, Canada
| | - Vanessa Kitchin
- Woodward Library, University of British Columbia, Vancouver, British Columbia, Canada
| | - Alison M Elliott
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada
- Women's Health Research Institute, Vancouver, British Columbia, Canada
| |
Collapse
|
6
|
Tesi B, Boileau C, Boycott KM, Canaud G, Caulfield M, Choukair D, Hill S, Spielmann M, Wedell A, Wirta V, Nordgren A, Lindstrand A. Precision medicine in rare diseases: What is next? J Intern Med 2023; 294:397-412. [PMID: 37211972 DOI: 10.1111/joim.13655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Molecular diagnostics is a cornerstone of modern precision medicine, broadly understood as tailoring an individual's treatment, follow-up, and care based on molecular data. In rare diseases (RDs), molecular diagnoses reveal valuable information about the cause of symptoms, disease progression, familial risk, and in certain cases, unlock access to targeted therapies. Due to decreasing DNA sequencing costs, genome sequencing (GS) is emerging as the primary method for precision diagnostics in RDs. Several ongoing European initiatives for precision medicine have chosen GS as their method of choice. Recent research supports the role for GS as first-line genetic investigation in individuals with suspected RD, due to its improved diagnostic yield compared to other methods. Moreover, GS can detect a broad range of genetic aberrations including those in noncoding regions, producing comprehensive data that can be periodically reanalyzed for years to come when further evidence emerges. Indeed, targeted drug development and repurposing of medicines can be accelerated as more individuals with RDs receive a molecular diagnosis. Multidisciplinary teams in which clinical specialists collaborate with geneticists, genomics education of professionals and the public, and dialogue with patient advocacy groups are essential elements for the integration of precision medicine into clinical practice worldwide. It is also paramount that large research projects share genetic data and leverage novel technologies to fully diagnose individuals with RDs. In conclusion, GS increases diagnostic yields and is a crucial step toward precision medicine for RDs. Its clinical implementation will enable better patient management, unlock targeted therapies, and guide the development of innovative treatments.
Collapse
Affiliation(s)
- Bianca Tesi
- Department of Molecular Medicine and Surgery and Centre of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
- Center for Hematology and Regenerative Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Catherine Boileau
- Département de Génétique, APHP, Hôpital Bichat-Claude Bernard, Université Paris Cité, Paris, France
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Guillaume Canaud
- INSERM U1151, Unité de médecine translationnelle et thérapies ciblées, Hôpital Necker-Enfants Malades, Université Paris Cité, AP-HP, Paris, France
| | - Mark Caulfield
- William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Daniela Choukair
- Division of Pediatric Endocrinology and Diabetes, Center for Pediatrics and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany and Center for Rare Diseases, University Hospital Heidelberg, Heidelberg, Germany
| | - Sue Hill
- Chief Scientific Officer, NHS England, London, UK
| | - Malte Spielmann
- Institute of Human Genetics, University Hospitals Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck, Kiel, Germany
| | - Anna Wedell
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Valtteri Wirta
- Science for Life Laboratory, Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institutet of Technology, Stockholm, Sweden
| | - Ann Nordgren
- Department of Molecular Medicine and Surgery and Centre of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
- Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Anna Lindstrand
- Department of Molecular Medicine and Surgery and Centre of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| |
Collapse
|
7
|
Ormond KE, Blasimme A, Vayena E. Ethical Aspects of Pediatric Genetic Care: Testing and Treatment. Pediatr Clin North Am 2023; 70:1029-1046. [PMID: 37704345 DOI: 10.1016/j.pcl.2023.05.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 09/15/2023]
Abstract
Pediatric health care providers caring for patients and families with genetic disease will encounter a range of ethical issues. These include traditional pediatric health care issues, such as surrogate decision making and end-of-life care. Genetic testing raises the importance of informed consent for potential risks that move beyond the oft discussed physical risks and into longer term concepts such as psychological impact, privacy and potential discrimination. Predictive testing in childhood also raises questions of whether the child has an autonomy interest in delaying testing until they have decision making capacity to do so on their own. And finally, treatments including gene therapies and gene editing, may raise issues of identity for families dealing with genetic disease.
Collapse
Affiliation(s)
- Kelly E Ormond
- Department of Health Sciences and Technology, Health Ethics & Policy Lab, ETH Zurich. Hottingerstrasse 10, Zurich 8092, Switzerland; Department of Genetics and Stanford Center for Biomedical Ethics, Stanford University School of Medicine.
| | - Alessandro Blasimme
- Department of Health Sciences and Technology, Health Ethics & Policy Lab, ETH Zurich. Hottingerstrasse 10, Zurich 8092, Switzerland
| | - Effy Vayena
- Department of Health Sciences and Technology, Health Ethics & Policy Lab, ETH Zurich. Hottingerstrasse 10, Zurich 8092, Switzerland
| |
Collapse
|
8
|
Adams S, Llorin H, Dobson LJ, Studwell C, Wilkins-Haug L, Guseh S, Gray KJ. Postnatal genetic testing on cord blood for prenatally identified high-probability cases. Prenat Diagn 2023; 43:1120-1131. [PMID: 37036331 DOI: 10.1002/pd.6352] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 03/20/2023] [Accepted: 03/27/2023] [Indexed: 04/11/2023]
Abstract
OBJECTIVE To evaluate the utility of postnatal genetic testing on umbilical cord blood (CB) for prenatally identified high-probability fetuses. METHOD CB for genetic testing was offered to individuals who met one of the following criteria: (i) fetal anomaly, (ii) positive non-invasive prenatal screening by cfDNA or biochemical analysis, or (iii) family history. Individuals with diagnostic testing, but not microarray, were also included when recommended by society guidelines. CB was collected at Brigham and Women's and Emerson Hospitals between 2016 and 2021. RESULTS 448 individuals consented for cord blood testing (370 (82.6%) for fetal anomalies, 51 (11.4%) for high-probability cfDNA, and 27 (6.0%) for family history) and a total of 393 (87.7%) samples were analyzed. Genetic testing yielded a diagnosis in 92 (23.4%) neonates by karyotype (n = 37), chromosomal microarray (CMA) (n = 32), and other molecular analysis (n = 23). Testing averaged 10.3 days (range 1-118 days). 68 (73.9%) diagnoses potentially impacted neonatal management. MCC could not be definitively excluded in only 1.4% (6/418) of samples. CONCLUSION Prenatal identification of high-probability fetuses and genetic testing on CB facilitates timely genetic diagnoses and neonatal management. Testing provides reassurance and reduces a postnatal diagnostic odyssey for high-probability neonates.
Collapse
Affiliation(s)
- Sophie Adams
- Center for Fetal Medicine and Reproductive Genetics, Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Hannah Llorin
- Center for Fetal Medicine and Reproductive Genetics, Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Lori J Dobson
- Center for Fetal Medicine and Reproductive Genetics, Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Courtney Studwell
- Center for Fetal Medicine and Reproductive Genetics, Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Louise Wilkins-Haug
- Center for Fetal Medicine and Reproductive Genetics, Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Division of Maternal-Fetal Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Stephanie Guseh
- Center for Fetal Medicine and Reproductive Genetics, Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Division of Maternal-Fetal Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Kathryn J Gray
- Center for Fetal Medicine and Reproductive Genetics, Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Division of Maternal-Fetal Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| |
Collapse
|
9
|
Bomback M, Everett S, Lyford A, Sahni R, Kim F, Baptiste C, Motelow JE, Tolia V, Clark R, Hays T. The Contribution of Commonly Diagnosed Genetic Disorders to Small for Gestational Age Birth and Subsequent Morbidity and Mortality in Preterm Infants. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.07.14.23292682. [PMID: 37503041 PMCID: PMC10371189 DOI: 10.1101/2023.07.14.23292682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Objective Preterm infants born small, vs. appropriate for gestational age (SGA, AGA) are at greater risk for morbidity and mortality. The contribution of genetic disorders to preterm SGA birth, morbidity, and mortality is unknown. We sought to determine the association between genetic disorders and preterm SGA birth, and the association between genetic disorders and morbidity or mortality within preterm SGA infants. We hypothesized that genetic disorders were significantly associated with both. Study Design This was a retrospective multicenter cohort study of 409 339 infants, born 23-33 weeks' gestation between 2000 and 2020. The odds of preterm SGA (vs AGA) birth, and the odds of severe morbidity or mortality within SGA preterm infants were determined for infants with genetic disorders, after adjusting for known risk factors. Results Genetic disorders were present in 3.0 and 1.3% of SGA and AGA preterm infants respectively; genetic disorders conferred an aOR (95% CI) of 2.06 (1.92, 2.21) of SGA birth. Genetic disorders were present in 4.3 of preterm SGA infants with morbidity or mortality and 2.1% of preterm SGA infants that did not experience morbidity or mortality. Genetic disorders conferred an aOR (95% CI) of 2.12 (2.66, 3.08) of morbidity or mortality. Conclusions Genetic disorders are strongly associated with preterm SGA birth, morbidity, and mortality. Clinicians should consider genetic testing of preterm SGA infants, particularly in the setting of other comorbidities or anomalies. Prospective, genomic research is needed to clarify the contribution of genetic disorders to disease in this population.
Collapse
|
10
|
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.
Collapse
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.
| |
Collapse
|
11
|
Laufer VA, Glover TW, Wilson TE. Applications of advanced technologies for detecting genomic structural variation. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2023; 792:108475. [PMID: 37931775 PMCID: PMC10792551 DOI: 10.1016/j.mrrev.2023.108475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 09/07/2023] [Accepted: 11/02/2023] [Indexed: 11/08/2023]
Abstract
Chromosomal structural variation (SV) encompasses a heterogenous class of genetic variants that exerts strong influences on human health and disease. Despite their importance, many structural variants (SVs) have remained poorly characterized at even a basic level, a discrepancy predicated upon the technical limitations of prior genomic assays. However, recent advances in genomic technology can identify and localize SVs accurately, opening new questions regarding SV risk factors and their impacts in humans. Here, we first define and classify human SVs and their generative mechanisms, highlighting characteristics leveraged by various SV assays. We next examine the first-ever gapless assembly of the human genome and the technical process of assembling it, which required third-generation sequencing technologies to resolve structurally complex loci. The new portions of that "telomere-to-telomere" and subsequent pangenome assemblies highlight aspects of SV biology likely to develop in the near-term. We consider the strengths and limitations of the most promising new SV technologies and when they or longstanding approaches are best suited to meeting salient goals in the study of human SV in population-scale genomics research, clinical, and public health contexts. It is a watershed time in our understanding of human SV when new approaches are expected to fundamentally change genomic applications.
Collapse
Affiliation(s)
- Vincent A Laufer
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
| | - Thomas W Glover
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
| | - Thomas E Wilson
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
| |
Collapse
|
12
|
Lemke AA, Thompson ML, Gimpel EC, McNamara KC, Rich CA, Finnila CR, Cochran ME, Lawlor JMJ, East KM, Bowling KM, Latner DR, Hiatt SM, Amaral MD, Kelley WV, Greve V, Gray DE, Felker SA, Meddaugh H, Cannon A, Luedecke A, Jackson KE, Hendon LG, Janani HM, Johnston M, Merin LA, Deans SL, Tuura C, Hughes T, Williams H, Laborde K, Neu MB, Patrick-Esteve J, Hurst ACE, Kirmse BM, Savich R, Spedale SB, Knight SJ, Barsh GS, Korf BR, Cooper GM, Brothers KB. Parents' Perspectives on the Utility of Genomic Sequencing in the Neonatal Intensive Care Unit. J Pers Med 2023; 13:1026. [PMID: 37511639 PMCID: PMC10382030 DOI: 10.3390/jpm13071026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/08/2023] [Accepted: 06/16/2023] [Indexed: 07/30/2023] Open
Abstract
BACKGROUND It is critical to understand the wide-ranging clinical and non-clinical effects of genome sequencing (GS) for parents in the NICU context. We assessed parents' experiences with GS as a first-line diagnostic tool for infants with suspected genetic conditions in the NICU. METHODS Parents of newborns (N = 62) suspected of having a genetic condition were recruited across five hospitals in the southeast United States as part of the SouthSeq study. Semi-structured interviews (N = 78) were conducted after parents received their child's sequencing result (positive, negative, or variants of unknown significance). Thematic analysis was performed on all interviews. RESULTS Key themes included that (1) GS in infancy is important for reproductive decision making, preparing for the child's future care, ending the diagnostic odyssey, and sharing results with care providers; (2) the timing of disclosure was acceptable for most parents, although many reported the NICU environment was overwhelming; and (3) parents deny that receiving GS results during infancy exacerbated parent-infant bonding, and reported variable impact on their feelings of guilt. CONCLUSION Parents reported that GS during the neonatal period was useful because it provided a "backbone" for their child's care. Parents did not consistently endorse negative impacts like interference with parent-infant bonding.
Collapse
Affiliation(s)
- Amy A Lemke
- Department of Pediatrics, Norton Children's Research Institute, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | | | - Emily C Gimpel
- Department of Pediatrics, Norton Children's Research Institute, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Katelyn C McNamara
- Department of Pediatrics, Norton Children's Research Institute, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Carla A Rich
- Department of Pediatrics, Norton Children's Research Institute, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | | | - Meagan E Cochran
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - James M J Lawlor
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Kelly M East
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Kevin M Bowling
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Donald R Latner
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Susan M Hiatt
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | | | - Whitley V Kelley
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Veronica Greve
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - David E Gray
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Stephanie A Felker
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
- Department of Biological Sciences, University of Alabama in Huntsville, Huntsville, AL 35899, USA
| | - Hannah Meddaugh
- Department of Genetics, Ochsner Health System, New Orleans, LA 70121, USA
| | - Ashley Cannon
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Amanda Luedecke
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Kelly E Jackson
- Division of Genetics, Norton Children's Genetics Center, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Laura G Hendon
- Department of Pediatrics, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Hillary M Janani
- Neonatal Intensive Care Unit, Woman's Hospital, Baton Rouge, LA 70817, USA
| | - Marla Johnston
- Department of Pediatrics, Children's Hospital New Orleans, New Orleans, LA 70118, USA
| | - Lee Ann Merin
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Sarah L Deans
- Department of Pediatrics, Norton Children's Research Institute, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Carly Tuura
- Department of Pediatrics, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Trent Hughes
- Department of Pediatrics, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Heather Williams
- Department of Pediatrics, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Kelly Laborde
- Neonatal Intensive Care Unit, Woman's Hospital, Baton Rouge, LA 70817, USA
| | - Matthew B Neu
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | | | - Anna C E Hurst
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Brian M Kirmse
- Department of Pediatrics, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Renate Savich
- Pediatrics Neonatology Division, University of New Mexico Health Sciences Center, Albuquerque, NM 87106, USA
| | - Steven B Spedale
- Neonatal Intensive Care Unit, Woman's Hospital, Baton Rouge, LA 70817, USA
| | - Sara J Knight
- Department of Internal Medicine, University of Utah, Salt Lake City, UT 84112, USA
| | - Gregory S Barsh
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Bruce R Korf
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Gregory M Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Kyle B Brothers
- Department of Pediatrics, Norton Children's Research Institute, University of Louisville School of Medicine, Louisville, KY 40202, USA
| |
Collapse
|
13
|
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.
Collapse
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
| |
Collapse
|
14
|
Olde Keizer RACM, Marouane A, Kerstjens-Frederikse WS, Deden AC, Lichtenbelt KD, Jonckers T, Vervoorn M, Vreeburg M, Henneman L, de Vries LS, Sinke RJ, Pfundt R, Stevens SJC, Andriessen P, van Lingen RA, Nelen M, Scheffer H, Stemkens D, Oosterwijk C, van Amstel HKP, de Boode WP, van Zelst-Stams WAG, Frederix GWJ, Vissers LELM. Rapid exome sequencing as a first-tier test in neonates with suspected genetic disorder: results of a prospective multicenter clinical utility study in the Netherlands. Eur J Pediatr 2023:10.1007/s00431-023-04909-1. [PMID: 36997769 PMCID: PMC10257607 DOI: 10.1007/s00431-023-04909-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 02/21/2023] [Accepted: 02/26/2023] [Indexed: 04/01/2023]
Abstract
The introduction of rapid exome sequencing (rES) for critically ill neonates admitted to the neonatal intensive care unit has made it possible to impact clinical decision-making. Unbiased prospective studies to quantify the impact of rES over routine genetic testing are, however, scarce. We performed a clinical utility study to compare rES to conventional genetic diagnostic workup for critically ill neonates with suspected genetic disorders. In a multicenter prospective parallel cohort study involving five Dutch NICUs, we performed rES in parallel to routine genetic testing for 60 neonates with a suspected genetic disorder and monitored diagnostic yield and the time to diagnosis. To assess the economic impact of rES, healthcare resource use was collected for all neonates. rES detected more conclusive genetic diagnoses than routine genetic testing (20% vs. 10%, respectively), in a significantly shorter time to diagnosis (15 days (95% CI 10-20) vs. 59 days (95% CI 23-98, p < 0.001)). Moreover, rES reduced genetic diagnostic costs by 1.5% (€85 per neonate). CONCLUSION Our findings demonstrate the clinical utility of rES for critically ill neonates based on increased diagnostic yield, shorter time to diagnosis, and net healthcare savings. Our observations warrant the widespread implementation of rES as first-tier genetic test in critically ill neonates with disorders of suspected genetic origin. WHAT IS KNOWN • Rapid exome sequencing (rES) enables diagnosing rare genetic disorders in a fast and reliable manner, but retrospective studies with neonates admitted to the neonatal intensive care unit (NICU) indicated that genetic disorders are likely underdiagnosed as rES is not routinely used. • Scenario modeling for implementation of rES for neonates with presumed genetic disorders indicated an expected increase in costs associated with genetic testing. WHAT IS NEW • This unique prospective national clinical utility study of rES in a NICU setting shows that rES obtained more and faster diagnoses than conventional genetic tests. • Implementation of rES as replacement for all other genetic tests does not increase healthcare costs but in fact leads to a reduction in healthcare costs.
Collapse
Grants
- 843002608, 846002003 ZonMw
- 843002608, 846002003 ZonMw
- 843002608, 846002003 ZonMw
- 843002608, 846002003 ZonMw
- 843002608, 846002003 ZonMw
- 843002608, 846002003 ZonMw
- 843002608, 846002003 ZonMw
- 843002608, 846002003 ZonMw
- 843002608, 846002003 ZonMw
- 843002608, 846002003 ZonMw
- 843002608, 846002003 ZonMw
- 843002608, 846002003 ZonMw
- 779257 Horizon 2020 Framework Programme
- 779257 Horizon 2020 Framework Programme
Collapse
Affiliation(s)
- Richelle A C M Olde Keizer
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Abderrahim Marouane
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, Netherlands
| | | | - A Chantal Deden
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, Netherlands
| | | | - Tinneke Jonckers
- Department of Pediatrics and Neonatology, Máxima Medical Center, Veldhoven, Netherlands
| | - Marieke Vervoorn
- Department of Pediatrics and Neonatology, Máxima Medical Center, Veldhoven, Netherlands
| | - Maaike Vreeburg
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, Netherlands
| | - Lidewij Henneman
- Department of Human Genetics and Amsterdam Reproduction and Development Research Institute, Amsterdam UMC, Vrije Universiteit, Amsterdam, Netherlands
| | - Linda S de Vries
- Department of Neonatology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Richard J Sinke
- Department of Genetics, University Medical Center, University of Groningen, Groningen, Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, Netherlands
| | - Servi J C Stevens
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, Netherlands
| | - Peter Andriessen
- Department of Pediatrics, Máxima Medical Center, Veldhoven, Netherlands
- Department of Applied Physics, Eindhoven University of Technology, Eindhoven, Netherlands
| | | | - Marcel Nelen
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, Netherlands
| | - Hans Scheffer
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, Netherlands
| | - Daphne Stemkens
- VSOP - National Patient Alliance for Rare and Genetic Diseases, Soest, Netherlands
| | - Cor Oosterwijk
- VSOP - National Patient Alliance for Rare and Genetic Diseases, Soest, Netherlands
| | | | - Willem P de Boode
- Department of Neonatology, Radboud University Medical Center, Radboud Institute for Health Sciences, Amalia Children's Hospital, Nijmegen, Netherlands
| | - Wendy A G van Zelst-Stams
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, Netherlands.
| | - Geert W J Frederix
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
- Department of Genetics, Utrecht University Medical Center, Utrecht, Netherlands
| | - Lisenka E L M Vissers
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, Netherlands.
| |
Collapse
|
15
|
Serrano JG, O'Leary M, VanNoy G, Holm IA, Fraiman YS, Rehm HL, O'Donnell-Luria A, Wojcik MH. Advancing Understanding of Inequities in Rare Disease Genomics. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.03.28.23286936. [PMID: 37034593 PMCID: PMC10081425 DOI: 10.1101/2023.03.28.23286936] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Purpose Advances in genomic research have led to the diagnosis of rare, early-onset diseases for thousands of individuals. Unfortunately, the benefits of advanced genetic diagnostic technology are not distributed equitably among the population, as has been seen in many other healthcare contexts. Even quantifying and describing inequities in genetic diagnostic yield is challenging due to variation in referrals to clinical genetics practices and other barriers to clinical genetic testing. Methods The Rare Genomes Project (RGP) at the Broad Institute of MIT and Harvard offers research genome sequencing to individuals with rare disease who remain genetically undiagnosed through direct interaction with the individual or family. This presents an opportunity for diagnosis beyond the clinical context, thus eliminating many barriers to access. Findings An initial goal of RGP was to equalize access to genomic sequencing by decoupling testing access from proximity to a major medical center and physician referral. However, our study participants are overwhelmingly non-disadvantaged, as evidenced by their access to specialist care and genetic testing prior to RGP enrollment, and are also predominantly white. Implications We therefore describe our novel initiative to diversify RGP enrollment in order to advance equity in rare disease genetic diagnosis and research. In addition to the moral imperative of medical equity, this is also critical in order to fully understand the genomic underpinnings of rare disease. We utilize a mixed methods approach to understand the priorities and values of underrepresented communities, existing disparities, and the obstacles to addressing them: all of which is necessary to promote equity in future genomic medicine initiatives.
Collapse
|
16
|
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: 16] [Impact Index Per Article: 16.0] [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.
Collapse
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
| |
Collapse
|
17
|
Shields K, Czerwinski J, Dauwe T, Hashmi S, Hillman P, Mowrey K, Gunther K. Genetics in the NICU: Nurses' Perceived Knowledge and Desired Education. J Contin Educ Nurs 2023; 54:16-24. [PMID: 36595722 DOI: 10.3928/00220124-20221207-06] [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: 01/04/2023]
Abstract
Background Many infants admitted to the neonatal intensive care unit (NICU) have genetic conditions. Previous research has shown that gaps exist in the genetics knowledge of nurses and that they lack comfort applying genetics information to clinical practice. Studies assessing the knowledge or comfort of NICU nurses with genetics have not previously been completed. Method A total of 122 NICU nurses completed a survey assessing perceived knowledge of genetics, comfort with clinical scenarios involving genetics, and desired genetics education. Results Perceived knowledge and overall comfort were correlated with highest degree received, how prepared a nurse felt by the genetics education received in their training, and having a close relationship with someone with a genetic condition. Almost all respondents (96%, n = 117) desired additional genetics education. Conclusion Gaps exist in the genetics knowledge of neonatal nurses in our cohort, and their overall comfort working with clinical scenarios involving genetics was low. There is significant interest in additional genetics education. [J Contin Educ Nurs. 2023;54(1):16-24.].
Collapse
|
18
|
Zhang T, Briere JM, Leeman KT, Wojcik MH, Agrawal PB. Ethical implications of early genetic diagnosis in an infant with Lesch-Nyhan syndrome. J Genet Couns 2022; 31:1434-1437. [PMID: 35916015 PMCID: PMC9722620 DOI: 10.1002/jgc4.1616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 06/22/2022] [Accepted: 06/23/2022] [Indexed: 12/14/2022]
Abstract
Pathogenic variants in HPRT1 lead to deficiency in hypoxanthine-guanine phosphoribosyltransferase and are responsible for a spectrum of disorders. The severe phenotype is termed Lesch-Nyhan syndrome (LNS) and is inherited in an X-linked recessive manner. Most individuals with LNS have profound intellectual and physical disabilities throughout life including self-mutilating behaviors. Here, we present the case of a male infant who was diagnosed with LNS at 3 weeks of age via rapid exome sequencing (ES), which revealed a hemizygous maternally inherited deletion of at least 1.3 Mb of Xq26.3, including exons 2 to 9 of HPRT1. We discuss the critical time points leading to this diagnosis while highlighting his parents' values that guided the decision-making. Genetic testing provided an early diagnosis for this infant that led to important considerations regarding goals of care in addition to raising new ethical concerns. This highlights the important role that early and rapid diagnostic genetic testing can play in helping families make difficult decisions. Additionally, this case highlights the complexity of discussing rare genetic diagnoses with families and facilitating critical discussions to empower the family toward making an informed decision.
Collapse
Affiliation(s)
- Tian Zhang
- Division of Newborn Medicine, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Julie M. Briere
- Division of Newborn Medicine, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Kristen T. Leeman
- Division of Newborn Medicine, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Monica H. Wojcik
- Division of Newborn Medicine, Department of Pediatrics, Boston Children's Hospital, 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
| | - Pankaj B. Agrawal
- Division of Newborn Medicine, Department of Pediatrics, Boston Children's Hospital, 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
| |
Collapse
|
19
|
Afifi HH, Gaber KR, Thomas MM, Taher MB, Tosson AMS. Genetic Implications in High-Risk Pregnancy and Its Outcome: A 2-Year Study. Am J Perinatol 2022; 39:1659-1667. [PMID: 33636738 DOI: 10.1055/s-0041-1724002] [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] [Indexed: 10/22/2022]
Abstract
OBJECTIVE The aim of this study is to evaluate high-risk pregnant females' offspring as regard the presence of any medical condition, hereditary disorder, or major anomaly as well as to document parental sociodemographic characteristics and compliance with follow-up schedules of fetal medicine and clinical genetic clinics. STUDY DESIGN This prospective 2-year cohort study of neonates and infants reported the referral indications, investigations, and diagnoses obtained through prenatal and postnatal examinations. It also reported their parental follow-up vigilance. RESULTS Of the 811 infants of high risk females referred 460 (56.7%) came for assessment. Mean parental consanguinity and endogamy were 67 and 71.3%, respectively. All pregnant mothers underwent first-trimester biochemical testing (plasma protein-A, α-fetoprotein [AFP], human chorionic gonadotropin [hCG]) and serial ultrasound examinations. Seventy mothers needed second-trimester biochemical testing (AFP, hCG, and estriol). Sixty-two mothers underwent amniocentesis where G-banding karyotype, fluorescence in situ hybridization and targeted molecular testing for the specific gene mutation of single gene disorders were conducted according to suspected disorders. High quality fetal ultrasound was performed when brain malformations were suspected, while 16 fetuses required brain MRI examination. Mean age of newborns at first examination was 26.5 days. They were grouped according to the maternal indication for referral. Upon examination, 18 neonates had confirmed congenital malformations/genetic disorders. Five of them were diagnosed prenatally. In four other fetuses with single gene disorder, the molecular diagnosis of their affected siblings was not established prior to this pregnancy; thus, prenatal diagnosis was not possible. The remaining nine cases were diagnosed postnatally. CONCLUSION Parental consanguinity and endogamy were increased among high-risk pregnancies. Public awareness about potential adverse effects of consanguineous marriages and the importance of genetic testing are imperative. A structured multidisciplinary team of specialists in fetal medicine, clinical genetics, and neonatology provides good genetic services. Expansion and financial support of these services are urgently required. KEY POINTS · A multidisciplinary team provides good genetic services in high-risk pregnancies.. · Parental consanguinity and endogamy are increased among high-risk pregnancies.. · Increased public awareness about genetic testing importance and financial support are imperative..
Collapse
Affiliation(s)
- Hanan H Afifi
- Division of Human Genetics and Genome Research, Department of Clinical Genetics, Developmental Assessment and Genetic Disorders Clinic, National Research Centre, Cairo, Egypt
| | - Khaled R Gaber
- Division of Human Genetics and Genome Research, Department of Prenatal Diagnosis and Fetal Medicine, National Research Centre, Cairo, Egypt
| | - Manal M Thomas
- Division of Human Genetics and Genome Research, Department of Clinical Genetics, Developmental Assessment and Genetic Disorders Clinic, National Research Centre, Cairo, Egypt
| | - Mohamed B Taher
- Division of Human Genetics and Genome Research, Department of Clinical Genetics, Developmental Assessment and Genetic Disorders Clinic, National Research Centre, Cairo, Egypt
| | - Angie M S Tosson
- Department of Pediatrics, Faculty of Medicine, Cairo University, Cairo, Egypt
| |
Collapse
|
20
|
Chad L, Anderson J, Cagliero D, Hayeems RZ, Ly LG, Szuto A. Rapid Genetic Testing in Pediatric and Neonatal Critical Care: A Scoping Review of Emerging Ethical Issues. Hosp Pediatr 2022; 12:e347-e359. [PMID: 36161483 DOI: 10.1542/hpeds.2022-006654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
BACKGROUND Rapid genome-wide sequencing (rGWS) is being increasingly used to aid in prognostication and decision-making for critically ill newborns and children. Although its feasibility in this fast-paced setting has been described, this new paradigm of inpatient genetic care raises new ethical challenges. OBJECTIVE A scoping review was performed to (1) identify salient ethical issues in this area of practice; and (2) bring attention to gaps and ethical tensions that warrant more deliberate exploration. METHODS Data sources, Ovid Medline and Cochrane Central Register of Controlled Trials, were searched up to November 2021. Articles included were those in English relating to rGWS deployed rapidly in a critical care setting. Publications were examined for ethical themes and were further characterized as including a superficial or in-depth discussion of that theme. New themes were inductively identified as they emerged. RESULTS Ninety-nine studies, published in 2012 or thereafter, met inclusion criteria. Themes identified elaborated upon established ethical principles related to beneficence and nonmaleficence (ie, clinical utility, medical uncertainty, impact on family, and data security) autonomy (ie, informed consent), and justice (ie, resource allocation and disability rights). Many themes were only narrowly discussed. CONCLUSIONS The application of rGWS in neonatal and pediatric acute care is inherently tied to ethically charged issues, some of which are reported here. Attention to the ethical costs and benefits of rGWS is not always discussed, with important gaps and unanswered questions that call for ongoing focus on these ethical considerations in this next application of acute care genomics.
Collapse
Affiliation(s)
- Lauren Chad
- Divisions of Clinical and Metabolic Genetics.,Departments of Bioethics.,Departments of Paediatrics
| | | | | | - Robin Z Hayeems
- Child Health Evaluative Sciences, Hospital for Sick Children Research Institute,Toronto, Ontario, Canada.,Institute of Health Policy, Management, and Evaluation, University of Toronto,Toronto, Ontario, Canada
| | - Linh G Ly
- Neonatology.,Departments of Paediatrics
| | - Anna Szuto
- Genetic Counselling, Hospital for Sick Children,Toronto, Ontario, Canada.,Molecular Genetics
| |
Collapse
|
21
|
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.
Collapse
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: )
| |
Collapse
|
22
|
Integrating rapid exome sequencing into NICU clinical care after a pilot research study. NPJ Genom Med 2022; 7:51. [PMID: 36064943 PMCID: PMC9441819 DOI: 10.1038/s41525-022-00326-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 08/22/2022] [Indexed: 11/29/2022] Open
Abstract
Genomic sequencing is a powerful diagnostic tool in critically ill infants, but performing exome or genome sequencing (ES/GS) in the context of a research study is different from implementing these tests clinically. We investigated the integration of rapid ES into routine clinical care after a pilot research study in a Level IV Neonatal Intensive Care Unit (NICU). We performed a retrospective cohort analysis of infants admitted with suspected genetic disorders to the NICU from December 1, 2018 to March 31, 2021 and compared results to those obtained from a previous research study cohort (March 1, 2017 to November 30, 2018). Clinical rapid ES was performed in 80/230 infants (35%) with a suspected genetic disorder and identified a genetic diagnosis in 22/80 infants (28%). The majority of diagnoses acutely impacted clinical management (14/22 (64%)). Compared to the previous research study, clinically integrated rapid ES had a significantly lower diagnostic yield and increased time from NICU admission and genetics consult to ES report, but identified four genetic diagnoses that may have been missed by the research study selection criteria. Compared to other genetic tests, rapid ES had similar or higher diagnostic yield and similar or decreased time to result. Overall, rapid ES was utilized in the NICU after the pilot research study, often as the first-tier sequencing test, and could identify the majority of disease-causing variants, shorten the diagnostic odyssey, and impact clinical care. Based on our experience, we have identified strategies to optimize the clinical implementation of rapid ES in the NICU.
Collapse
|
23
|
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.
Collapse
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
| |
Collapse
|
24
|
Abstract
The role of genomic sequencing (exome and whole genome) in the neonatal intensive care unit (NICU) has changed with advances in technology and bioinformatics in the last decade. Evidence from 18 retrospective and prospective studies of exome and whole genome sequencing in pediatric intensive care settings has demonstrated an average diagnostic yield of close to 40% and an immediate impact on clinical management in more than 20% of patients tested, and the highest clinical utility was in the perinatal setting. Genomic sequencing, when indicated, should be the standard of care for patients in the NICU.
Collapse
Affiliation(s)
- Michael Muriello
- Division of Genetics, Medical College of Wisconsin, 9000 W Wisconsin Avenue, MS 716, Milwaukee, WI 53226, USA.
| |
Collapse
|
25
|
Olde Keizer RACM, Marouane A, Deden AC, van Zelst-Stams WAG, de Boode WP, Keusters WR, Henneman L, van Amstel JKP, Frederix GWJ, Vissers LELM. Medical costs of children admitted to the neonatal intensive care unit: The role and possible economic impact of WES in early diagnosis. Eur J Med Genet 2022; 65:104467. [PMID: 35240323 DOI: 10.1016/j.ejmg.2022.104467] [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: 08/23/2021] [Revised: 12/29/2021] [Accepted: 02/25/2022] [Indexed: 11/18/2022]
Abstract
It has been estimated that at least 6.0% of neonates admitted to the Neonatal Intensive Care Unit remains genetically undiagnosed because genetic testing is not routinely performed. The objective of this study is to provide an overview of average healthcare costs for patients admitted to the Neonatal Intensive Care Unit and to assess possible impact of implementing Whole Exome Sequencing (WES) on these total healthcare costs. Hereto, we retrospectively collected postnatal healthcare data of all patients admitted to the level IV Neonatal Intensive Care Unit at the Radboudumc (October 2013-October 2015) and linked unit costs to these healthcare consumptions. Average healthcare costs were calculated and a distinction between patients was made based on performance of genetic tests and the presence of congenital anomalies. Overall, on average €26,627 was spent per patient. Genetic costs accounted for 2.3% of all costs. Healthcare costs were higher for patients with congenital anomalies compared to patients without congenital anomalies. Patients with genetic diagnostics were also more expensive than patients without genetic diagnostics. We next modelled four scenarios based on clinical preselection. First, when performing trio-WES for all patients instead of current diagnostics, overall healthcare costs will increase with 22.2%. Second, performing trio-WES only for patients with multiple congenital anomalies will not result in any cost changes, but this would leave patients with an isolated congenital anomalies untested. We therefore next modelled a scenario performing trio-WES for all patients with congenital anomalies, increasing the average per patient healthcare costs by 5.3%. This will rise to a maximum of 5.5% when also modelling for an extra genetic test for clinically selected patients to establish genetic diagnoses that are undetectable by WES. In conclusion, genetic diagnostic testing accounted for a small fraction of total costs. Implementation of trio-WES as first-tier test for all patients with congenital anomalies will lead to a limited increase in overall healthcare budget, but will facilitate personalized treatments options guided by the diagnoses made.
Collapse
Affiliation(s)
- Richelle A C M Olde Keizer
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands; Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, the Netherlands
| | - Abderrahim Marouane
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, the Netherlands
| | - A Chantal Deden
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, the Netherlands
| | - Wendy A G van Zelst-Stams
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, the Netherlands
| | - Willem P de Boode
- Department of Neonatology, Radboud University Medical Center, Radboud Institute for Health Sciences, Amalia Children's Hospital, Nijmegen, the Netherlands
| | - Willem R Keusters
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Lidewij Henneman
- Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit, Amsterdam, the Netherlands
| | | | - Gerardus W J Frederix
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands; Department of Genetics, Utrecht University Medical Center, Utrecht, the Netherlands.
| | - Lisenka E L M Vissers
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, the Netherlands
| |
Collapse
|
26
|
Marouane A, Olde Keizer RACM, Frederix GWJ, Vissers LELM, de Boode WP, van Zelst-Stams WAG. Congenital anomalies and genetic disorders in neonates and infants: a single-center observational cohort study. Eur J Pediatr 2022; 181:359-367. [PMID: 34347148 PMCID: PMC8760213 DOI: 10.1007/s00431-021-04213-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 06/21/2021] [Accepted: 07/15/2021] [Indexed: 11/28/2022]
Abstract
Neonates with genetic disorders or congenital anomalies (CA) contribute considerably to morbidity and mortality in neonatal intensive care units (NICUs). The objective of this study is to study the prevalence of genetic disorders in an academic level IV NICU. We retrospective collected and analyzed both clinical and genetic data of all 1444 infants admitted to the NICU of the Radboudumc (October 2013 to October 2015). Data were collected until infants reached at least 2 years of age. A total of 13% (194/1444) of the patients were genetically tested, and 32% (461/1444) had a CA. A total of 37% (72/194) had a laboratory-confirmed genetic diagnosis. In 53%, the diagnosis was made post-neonatally (median age = 209 days) using assays including exome sequencing. Exactly 63% (291/461) of the patients with CA, however, never received genetic testing, despite being clinically similar those who did.Conclusions: Genetic disorders were suspected in 13% of the cohort, but only confirmed in 5%. Most received their genetic diagnosis in the post-neonatal period. Extrapolation of the diagnostic yield suggests that up to 6% of our cohort may have remained genetically undiagnosed. Our data show the need to improve genetic care in the NICU for more inclusive, earlier, and faster genetic diagnosis to enable tailored management. What is Known: • Genetic disorders are suspected in many neonates but only genetically confirmed in a minority. • The presence of a genetic disorder can be easily missed and will often lead to a diagnostic odyssey requiring extensive evaluations, both clinically and genetically. What is New: • Different aspects of the clinical features and uptake of genetic test in a NICU cohort. • The need to improve genetic care in the NICU for more inclusive, earlier, and faster genetic diagnosis to enable tailored management.
Collapse
Affiliation(s)
- A. Marouane
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute of Health Sciences, Nijmegen, The Netherlands
| | - R. A. C. M. Olde Keizer
- Department of Health Sciences and Primary Care, University Medical Center, Utrecht, The Netherlands
| | - G. W. J. Frederix
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute of Health Sciences, Nijmegen, The Netherlands ,Department of Health Sciences and Primary Care, University Medical Center, Utrecht, The Netherlands
| | - L. E. L. M. Vissers
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - W. P. de Boode
- Department of Neonatology, Radboudumc Amalia Children’s Hospital, Radboud Institute of Health Sciences, Nijmegen, the Netherlands
| | - W. A. G. van Zelst-Stams
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute of Health Sciences, Nijmegen, The Netherlands
| |
Collapse
|
27
|
Ece Solmaz A, Pariltay E, Talim B, Onay H. A novel bi-allelic variant in the SDHB gene causes a severe mitochondrial complex II deficiency: a case report. Clin Neurol Neurosurg 2021; 212:107039. [PMID: 34839152 DOI: 10.1016/j.clineuro.2021.107039] [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: 08/13/2021] [Revised: 11/06/2021] [Accepted: 11/13/2021] [Indexed: 11/17/2022]
Abstract
Isolated deficiency of complex II is a rare inborn error of metabolism, accounting for approximately 2% of mitochondrial diseases. Mitochondrial complex II deficiency is predominantly seen in cases with bi-allelic SDHA mutations. To our knowledge, only 11 patients and five pathogenic variants have been reported for the SDHB gene. Our patient had a severe clinical presentation with seizures and sepsis, and died at the age of 2 months. Muscle biopsy analysis was compatible with mitochondrial myopathy with complex II deficiency. The family was given a molecular diagnosis for their child 2 years after his death via a clinical exome test of a frozen muscle biopsy specimen and a novel homozygous missense variant c.592 A>G (p.Ser198Gly) in SDHB gene was detected by next-generation sequencing. Here, we present another patient with a novel homozygous SDHB variant causing severe complex II deficiency and early death.
Collapse
Affiliation(s)
- Asli Ece Solmaz
- Department of Medical Genetics, Ege University Faculty of Medicine, Izmir, Turkey.
| | - Erhan Pariltay
- Department of Medical Genetics, Ege University Faculty of Medicine, Izmir, Turkey
| | - Beril Talim
- Pediatric Pathology Unit, Department of Pediatrics, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Huseyin Onay
- Department of Medical Genetics, Ege University Faculty of Medicine, Izmir, Turkey
| |
Collapse
|
28
|
Yang J, Shu L, Duan H, Li H. A Visual Phenotype-Based Differential Diagnosis Process for Rare Diseases. Interdiscip Sci 2021; 14:331-348. [PMID: 34751921 DOI: 10.1007/s12539-021-00490-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 10/23/2021] [Accepted: 10/28/2021] [Indexed: 02/01/2023]
Abstract
PURPOSE Phenotype-based rapid diagnosis can make up for the time-consuming genetic sequencing diagnosis of rare diseases. However, the collected phenotypes of patients can sometimes be inaccurate or incomplete, which limits the accuracy of diagnostic results. To solve this problem, we try to design a phenotype-based differential diagnosis process for rare diseases to achieve rapid and accurate diagnosis of rare diseases. METHODS The core of the differential diagnosis of rare diseases is to optimize the phenotype information of a specific patient and the visualized comparative analysis of diseases. To recommend additional phenotypes, replace the fuzzy phenotypes and filter the unexplained phenotypes for patients, we constructed a phenotype hierarchical network and a disease-phenotype differential network and calculated the phenotype co-occurrence relationship. In addition, we designed a visual comparative analysis method to explore the correlation and difference of disease phenotypes. RESULTS The evaluation based on the published 10 rare disease cases demonstrated that after the optimization of patient phenotype information through our differential diagnosis, the target disease often got a better ranking and recommendation score than before. We have deployed this scheme on the RDmap project ( http://rdmap.nbscn.org ). CONCLUSION Compared to genetic and molecular analysis, phenotype-based diagnosis is faster, cheaper, and easier. The differential diagnosis process we designed can optimize the phenotype information of patients and better locate the target disease. It can also help to make screening decisions before genetic testing.
Collapse
Affiliation(s)
- Jian Yang
- The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Binsheng Road 3333#, Hangzhou, 310052, Zhejiang, China.,The College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou, Zhejiang, China
| | - Liqi Shu
- Rhode Island Hospital, Warren Alpert Medical School of Brown University, Rhode Island, USA
| | - Huilong Duan
- The College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou, Zhejiang, China
| | - Haomin Li
- The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Binsheng Road 3333#, Hangzhou, 310052, Zhejiang, China.
| |
Collapse
|
29
|
Yang L, Wei Z, Chen X, Hu L, Peng X, Wang J, Lu C, Kong Y, Dong X, Ni Q, Lu Y, Wu B, Wang H, Meirelles K, Tian X, Zhang J, Chang F, Liu L, Li C, You W, Cheng G, Wang L, Cao Y, Chen C, Fang P, Tang S, Zhou W. Use of medical exome sequencing for identification of underlying genetic defects in NICU: Experience in a cohort of 2303 neonates in China. Clin Genet 2021; 101:101-109. [PMID: 34671977 DOI: 10.1111/cge.14075] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 09/27/2021] [Accepted: 10/15/2021] [Indexed: 12/17/2022]
Abstract
Emerging evidence demonstrates the clinical utility of genomic applications in newborn intensive care unit (NICU) patients with strong indications of Mendelian etiology. However, such applications' diagnostic yield and utility remain unclear for NICU cohorts with minimal phenotype selection. In this study, focused medical exome sequencing was used as a first-tier, singleton-focused diagnostic tool for 2303 unrelated sick neonates. Integrated analysis of single nucleotide variants (SNVs), small insertions and deletions (Indels), and large copy number variants (CNVs) was performed. The diagnostic rate in this NICU cohort is 12.3% (284/2303), with 190 probands with molecular diagnoses made from SNV/Indel analyses (66.9%), 93 patients with diagnostic aneuploidy/CNVs findings (32.8%), and 1 patient with both SNV and CNV (0.4%). In addition, 54 (2.3%) of patients had a reportable incidental finding. Multiple organ involvements, craniofacial abnormalities, and dermatologic abnormalities were the strongest positive predictors for a molecular diagnosis. Among the 190 cases with SNV/Indel defects, direct impacts on medical management were observed in 46.8% of patients after the results were reported. In this study, we demonstrate that focused medical exome sequencing is a powerful first-line diagnostic tool for NICU patients. Significant number of diagnosed NICU patients can benefit from more focused medical management and long-term care.
Collapse
Affiliation(s)
- Lin Yang
- Clinical Genetic Center, Children's Hospital of Fudan University, Shanghai, China.,Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai, China
| | - Zejun Wei
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai, China
| | - Xiang Chen
- Division of Neonatology, Children's Hospital of Fudan University, Shanghai, China
| | - Liyuan Hu
- Division of Neonatology, Children's Hospital of Fudan University, Shanghai, China
| | - Xiaomin Peng
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai, China
| | - Jin Wang
- Division of Neonatology, Children's Hospital of Fudan University, Shanghai, China
| | - Chunmei Lu
- Division of Neonatology, Children's Hospital of Fudan University, Shanghai, China
| | - Yanting Kong
- Division of Neonatology, Children's Hospital of Fudan University, Shanghai, China
| | - Xinran Dong
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai, China
| | - Qi Ni
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai, China
| | - Yulan Lu
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai, China
| | - Bingbing Wu
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai, China.,Key Laboratory of Neonatal Diseases, Ministry of Health, Children's Hospital of Fudan University, Shanghai, China
| | - Huijun Wang
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai, China.,Key Laboratory of Neonatal Diseases, Ministry of Health, Children's Hospital of Fudan University, Shanghai, China
| | | | - Xia Tian
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | | | | | - Liu Liu
- Sema4, Branford, Connecticut, USA
| | | | - Wesley You
- Google LLC, Mountain View, California, USA
| | - Guoqiang Cheng
- Division of Neonatology, Children's Hospital of Fudan University, Shanghai, China
| | - Laishuan Wang
- Division of Neonatology, Children's Hospital of Fudan University, Shanghai, China
| | - Yun Cao
- Division of Neonatology, Children's Hospital of Fudan University, Shanghai, China
| | - Chao Chen
- Division of Neonatology, Children's Hospital of Fudan University, Shanghai, China
| | - Ping Fang
- KingMed Diagnostics, Guangzhou, China
| | - Sha Tang
- KingMed Diagnostics, Guangzhou, China
| | - Wenhao Zhou
- Clinical Genetic Center, Children's Hospital of Fudan University, Shanghai, China.,Division of Neonatology, Children's Hospital of Fudan University, Shanghai, China.,CAS Center for Excellence in Brain Science and Intelligence Technology (CEBSIT), Shanghai, China
| |
Collapse
|
30
|
Whole Genome Sequencing as a First-Line Clinical Test: Almost Ready for Prime Time. Crit Care Med 2021; 49:1815-1817. [PMID: 34529612 DOI: 10.1097/ccm.0000000000005077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
|
31
|
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.
Collapse
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
| |
Collapse
|
32
|
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.
Collapse
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
| |
Collapse
|
33
|
Clarke JL. Impact of Pan-Ethnic Expanded Carrier Screening in Improving Population Health Outcomes: Proceedings from a Multi-Stakeholder Virtual Roundtable Summit, June 25, 2020. Popul Health Manag 2021; 24:622-630. [PMID: 34142856 DOI: 10.1089/pop.2021.0073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Janice L Clarke
- Jefferson College of Population Health, Philadelphia, Pennsylvania, USA
| |
Collapse
|
34
|
Application of Full-Spectrum Rapid Clinical Genome Sequencing Improves Diagnostic Rate and Clinical Outcomes in Critically Ill Infants in the China Neonatal Genomes Project. Crit Care Med 2021; 49:1674-1683. [PMID: 33935161 DOI: 10.1097/ccm.0000000000005052] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVES To determine the diagnostic and clinical utility of trio-rapid genome sequencing in critically ill infants. DESIGN In this prospective study, samples from critically ill infants were analyzed using both proband-only clinical exome sequencing and trio-rapid genome sequencing (proband and biological parents). The study occurred between April 2019 and December 2019. SETTING Thirteen member hospitals of the China Neonatal Genomes Project spanning 10 provinces were involved. PARTICIPANTS Critically ill infants (n = 202), from birth up until 13 months of life were enrolled based on eligibility criteria (e.g., CNS anomaly, complex congenital heart disease, evidence of metabolic disease, recurrent severe infection, suspected immune deficiency, and multiple malformations). INTERVENTIONS None. MEASUREMENTS AND MAIN RESULTS Of the 202 participants, neuromuscular (45%), respiratory (22%), and immunologic/infectious (18%) were the most commonly observed phenotypes. The diagnostic yield of trio-rapid genome sequencing was higher than that of proband-only clinical exome sequencing (36.6% [95% CI, 30.1-43.7%] vs 20.3% [95% CI, 15.1-26.6%], respectively; p = 0.0004), and the average turnaround time for trio-rapid genome sequencing (median: 7 d) was faster than that of proband-only clinical exome sequencing (median: 20 d) (p < 2.2 × 10-16). The metagenomic analysis identified pathogenic or likely pathogenic microbes in six infants with symptoms of sepsis, and these results guided the antibiotic treatment strategy. Sixteen infants (21.6%) experienced a change in clinical management following trio-rapid genome sequencing diagnosis, and 24 infants (32.4%) were referred to a new subspecialist. CONCLUSIONS Trio-rapid genome sequencing provided higher diagnostic yield in a shorter period of time in this cohort of critically ill infants compared with proband-only clinical exome sequencing. Precise and fast molecular diagnosis can alter medical management and positively impact patient outcomes.
Collapse
|
35
|
Abstract
PURPOSE OF REVIEW Perinatal disorders include stillbirth, congenital structural anomalies, and critical illnesses in neonates. The cause of these is often unknown despite a thorough clinical workup. Genetic diseases cause a significant portion of perinatal disorders. The purpose of this review is to describe recent advances in genetic testing of perinatal disorders of unknown cause and to provide a potential diagnostic strategy. RECENT FINDINGS Exome and genome sequencing (ES and GS) have demonstrated that significant portions of perinatal disorders are caused by genetic disease. However, estimates of the exact proportion have varied widely across fetal and neonatal cohorts and most of the genetic diagnoses found in recent studies have been unique to individual cases. Having a specific genetic diagnosis provides significant clinical utility, including improved prognostication of the outcome, tailored therapy, directed testing for associated syndromic manifestations, referral to appropriate subspecialists, family planning, and redirection of care. SUMMARY Perinatal disorders of unknown cause, with nonspecific presentations, are often caused by genetic diseases best diagnosed by ES or GS. Prompt diagnosis facilitates improved clinical care. Improvements in noninvasive sampling, variant interpretation, and population-level research will further enhance the clinical utility of genetic testing. VIDEO ABSTRACT http://links.lww.com/MOP/A61.
Collapse
Affiliation(s)
- Thomas Hays
- Division of Neonatology, Department of Pediatrics, Columbia University Irving Medical Center, New York, New York, USA
| | - Ronald J. Wapner
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, New York, USA
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, New York, USA
| |
Collapse
|
36
|
Altamimi E, Khanfar M, Rabab'h O, Dardas Z, Srour L, Mustafa L, Azab B. Effect of Genetic Testing on Diagnosing Gastrointestinal Pediatric Patients with Previously Undiagnosed Diseases. APPLICATION OF CLINICAL GENETICS 2020; 13:221-231. [PMID: 33364809 PMCID: PMC7751587 DOI: 10.2147/tacg.s275992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Accepted: 11/10/2020] [Indexed: 11/23/2022]
Abstract
Purpose Four consanguineous Jordanian families with affected members of unknown gastrointestinal related diseases were recruited to assess the utility and efficiency of whole exome sequencing (WES) in reaching the definitive diagnosis. Patients and Methods Members from four consanguineous Jordanian families were recruited in this study. Laboratory and imaging tests were used for initial diagnosis, followed by performing WES to test all affected members for the detection of causative variants. Sanger sequencing was used for validation. Results We had a 100% success rate identifying each case presented in this study. Conclusion This is the first study applying a WES testing approach in the diagnosis of pediatric diseases in Jordan. Our results strongly suggest the need to implement WES as an evident diagnostic tool in the clinical setting, as it will subsequently allow for proper disease management and genetic counseling.
Collapse
Affiliation(s)
- Eyad Altamimi
- Department of Pediatrics and Neonatology, Jordan University of Science and Technology, Irbid, Jordan
| | - Mariam Khanfar
- Department of Medical Laboratory Sciences, Jordan University of Science and Technology, Irbid, Jordan
| | - Omar Rabab'h
- Center of Cognition and Neuroethics, University of Michigan-Flint, Flint, MI, USA
| | - Zain Dardas
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, University of Jordan, Amman, Jordan.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Luma Srour
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, University of Jordan, Amman, Jordan
| | - Lina Mustafa
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, University of Jordan, Amman, Jordan
| | - Bilal Azab
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, University of Jordan, Amman, Jordan.,Human and Molecular Genetics, Medical College of Virginia, Virginia Commonwealth University, Richmond, VA, USA
| |
Collapse
|
37
|
Cao J, O'Day DR, Pliner HA, Kingsley PD, Deng M, Daza RM, Zager MA, Aldinger KA, Blecher-Gonen R, Zhang F, Spielmann M, Palis J, Doherty D, Steemers FJ, Glass IA, Trapnell C, Shendure J. A human cell atlas of fetal gene expression. Science 2020; 370:370/6518/eaba7721. [PMID: 33184181 DOI: 10.1126/science.aba7721] [Citation(s) in RCA: 348] [Impact Index Per Article: 87.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 09/10/2020] [Indexed: 12/14/2022]
Abstract
The gene expression program underlying the specification of human cell types is of fundamental interest. We generated human cell atlases of gene expression and chromatin accessibility in fetal tissues. For gene expression, we applied three-level combinatorial indexing to >110 samples representing 15 organs, ultimately profiling ~4 million single cells. We leveraged the literature and other atlases to identify and annotate hundreds of cell types and subtypes, both within and across tissues. Our analyses focused on organ-specific specializations of broadly distributed cell types (such as blood, endothelial, and epithelial), sites of fetal erythropoiesis (which notably included the adrenal gland), and integration with mouse developmental atlases (such as conserved specification of blood cells). These data represent a rich resource for the exploration of in vivo human gene expression in diverse tissues and cell types.
Collapse
Affiliation(s)
- Junyue Cao
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Diana R O'Day
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA
| | - Hannah A Pliner
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Paul D Kingsley
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY, USA
| | - Mei Deng
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA
| | - Riza M Daza
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Michael A Zager
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.,Center for Data Visualization, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Kimberly A Aldinger
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA.,Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Ronnie Blecher-Gonen
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | | | - Malte Spielmann
- Human Molecular Genomics Group, Max Planck Institute for Molecular Genetics, Berlin, Germany.,Institute of Human Genetics, University of Lübeck, Lübeck, Germany
| | - James Palis
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY, USA
| | - Dan Doherty
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA.,Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.,Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | | | - Ian A Glass
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA.,Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.,Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Cole Trapnell
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA. .,Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.,Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA. .,Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.,Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA.,Howard Hughes Medical Institute, Seattle, WA, USA
| |
Collapse
|
38
|
Zhu T, Gong X, Bei F, Ma L, Chen Y, Zhang Y, Wang X, Sun J, Wang J, Qiu G, Sun J, Sun Y, Zhang Y. Application of Next-Generation Sequencing for Genetic Diagnosis in Neonatal Intensive Care Units: Results of a Multicenter Study in China. Front Genet 2020; 11:565078. [PMID: 33240318 PMCID: PMC7677510 DOI: 10.3389/fgene.2020.565078] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 09/29/2020] [Indexed: 12/01/2022] Open
Abstract
To identify next-generation-sequencing (NGS) clinical usability and to propose a standard diagnostic routine for critically ill infants, aged less than 100 days and suspected of having a genetically heterogeneous condition, a retrospective study was conducted between January 2016 and December 2018 at neonatal intensive care units (NICUs) of three tertiary hospitals in Shanghai, China. Whole-exome sequencing (WES) or panel sequencing was performed on 307 patients. Trio-WES, trio-panel, proband-WES, and proband-panel diagnostic yields were 39.71% (83/209), 68.75% (22/32), 59.09% (26/44), and 33.33% (4/12), respectively. Definitive molecular diagnoses of 142 infants (46.25%) uncovered 99 disorders; 21 disorders displayed on 44.37% of the diagnosed patients. Genetic etiologies were identified for 61.73% (50/81) of the deceased infants. One in three (29.58%) diagnosed infants exhibited one of the following four clinical traits which had a higher odds of diagnostic rate: integument abnormality (adjusted odds ratio [aOR], 19.7; 95% confidence interval [CI], 2.5–156.3), complex immune-related phenotypes (aOR, 9.2; 95% CI, 1.4–83.5), mixed nervous system phenotypes and congenital anomalies (aOR, 5.0; 95% CI, 1.3–19.1), or mixed metabolism and nervous system phenotypes (aOR, 4.5; 95% CI, 1.0–21.5). Our results demonstrated that NGS was an effective diagnostic tool. Infants exhibiting integument, complex immune-related conditions, metabolism, and nervous signs have higher chances of carrying variants in known disease-causing genes. The number of specific phenotypes could be used as an independent predictor of a positive molecular diagnosis, rather than an isolated abnormality. We developed a molecular diagnostic procedure for the use of NGS for diagnosis in Chinese NICU population based on individual characteristics.
Collapse
Affiliation(s)
- Tianwen Zhu
- Department of Neonatology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaohui Gong
- Department of Neonatology, Shanghai Children's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Fei Bei
- Department of Neonatology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Li Ma
- Department of Neonatology, Shanghai Children's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yan Chen
- Department of Neonatology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yonghong Zhang
- Department of Neonatology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xia Wang
- Department of Neonatology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jingjing Sun
- Department of Neonatology, Shanghai Children's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jian Wang
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Gang Qiu
- Department of Neonatology, Shanghai Children's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jianhua Sun
- Department of Neonatology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yu Sun
- Department of Pediatric Endocrinology/Genetics, Xinhua Hospital, Shanghai Institute for Pediatric Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yongjun Zhang
- Department of Neonatology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| |
Collapse
|
39
|
Domcke S, Hill AJ, Daza RM, Cao J, O'Day DR, Pliner HA, Aldinger KA, Pokholok D, Zhang F, Milbank JH, Zager MA, Glass IA, Steemers FJ, Doherty D, Trapnell C, Cusanovich DA, Shendure J. A human cell atlas of fetal chromatin accessibility. Science 2020; 370:eaba7612. [PMID: 33184180 PMCID: PMC7785298 DOI: 10.1126/science.aba7612] [Citation(s) in RCA: 209] [Impact Index Per Article: 52.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 09/10/2020] [Indexed: 12/12/2022]
Abstract
The chromatin landscape underlying the specification of human cell types is of fundamental interest. We generated human cell atlases of chromatin accessibility and gene expression in fetal tissues. For chromatin accessibility, we devised a three-level combinatorial indexing assay and applied it to 53 samples representing 15 organs, profiling ~800,000 single cells. We leveraged cell types defined by gene expression to annotate these data and cataloged hundreds of thousands of candidate regulatory elements that exhibit cell type-specific chromatin accessibility. We investigated the properties of lineage-specific transcription factors (such as POU2F1 in neurons), organ-specific specializations of broadly distributed cell types (such as blood and endothelial), and cell type-specific enrichments of complex trait heritability. These data represent a rich resource for the exploration of in vivo human gene regulation in diverse tissues and cell types.
Collapse
Affiliation(s)
- Silvia Domcke
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Andrew J Hill
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Riza M Daza
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Junyue Cao
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Diana R O'Day
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA
| | - Hannah A Pliner
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Kimberly A Aldinger
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | | | | | - Jennifer H Milbank
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Michael A Zager
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Center for Data Visualization, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Ian A Glass
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | | | - Dan Doherty
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Cole Trapnell
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA
| | - Darren A Cusanovich
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ, USA
- Asthma and Airway Disease Research Center, University of Arizona, Tucson, AZ, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
| |
Collapse
|
40
|
Aldridge CE, Osiovich H, Hal Siden H, Elliott AM. Rapid genome-wide sequencing in a neonatal intensive care unit: A retrospective qualitative exploration of parental experiences. J Genet Couns 2020; 30:616-629. [PMID: 33131147 DOI: 10.1002/jgc4.1353] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 09/26/2020] [Accepted: 10/01/2020] [Indexed: 12/11/2022]
Abstract
Genome-wide sequencing (GWS) is increasingly being used in neonatal intensive care units. While studies have explored its clinical utility, little is known about parental experiences with this testing post-return of results. We conducted a qualitative study, using an interpretive description framework and thematic analysis, to gain further insight into parents' perceptions of the value and utility of GWS for their infant. We sought to explore whether parents' perceptions differ if their child received a diagnosis or not, and whether their child is living or deceased. Semi-structured, telephone interviews were conducted with parents of infants who had rapid exome sequencing while in the neonatal intensive care unit at BC Women's Hospital in Vancouver, Canada. Interviews addressed perceived benefits and harms of GWS and included an evaluation of decisional regret. Parents of 27 probands were approached and 14 (52%; 13 mothers and 1 father) participated in interviews. On average, 26 months had elapsed from the time of results to the interview. Six themes were identified. Firstly, parents had a positive regard for GWS. The results of GWS helped provide context for their child's admission to the NICU, and all parents experienced relief following receiving the results. A diagnosis by GWS enabled parents to picture the future, form connections with other parents, and coordinate their child's care. Lastly, some parents experienced discomfort with the concept of a genetic diagnosis, and interestingly felt lack of a genomic diagnosis indicated a reduced severity of their infant's condition. Decisional regret post-results was found to be low. Our results highlight how parents cope with the results of GWS and suggest that a genetic counselor can have an important role in helping families understand and adjust to these results in the neonatal intensive care unit.
Collapse
Affiliation(s)
- Caitlin E Aldridge
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Horacio Osiovich
- Department of Pediatrics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada.,BC Children's Hospital Research Institute, Vancouver, BC, Canada.,Women's Health Research Institute, Vancouver, BC, Canada
| | - Harold Hal Siden
- Department of Pediatrics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada.,BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | | | | | - Alison M Elliott
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada.,BC Children's Hospital Research Institute, Vancouver, BC, Canada.,Women's Health Research Institute, Vancouver, BC, Canada
| |
Collapse
|
41
|
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.
Collapse
|
42
|
Genetics and pediatric hospital admissions, 1985 to 2017. Genet Med 2020; 22:1777-1785. [PMID: 32555541 DOI: 10.1038/s41436-020-0871-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 06/05/2020] [Accepted: 06/07/2020] [Indexed: 11/08/2022] Open
Abstract
PURPOSE To determine the prevalence and sociodemographic and hospitalization history of genetic conditions in a sample of inpatients in a pediatric hospital in 2017, and to compare results with unpublished studies from 1985, 1995, and 2007. METHODS Two weeks of admissions were classified according to a pre-existing categorization, based on genetic etiology, encompassing chromosomal and monogenic conditions, multifactorial (MF) conditions, and no known genetic cause. RESULTS In 2017, 299 (16%) patients had chromosomal or monogenic conditions, 6-7% more than 2007 and 1995, but similar to 1985. Autosomal dominant (AD) conditions increased from <2% previously to 6% in 2017 (p < 0.001). MF conditions comprised the majority throughout, increasing from 45% to 54%. Age at admission was highest in autosomal recessive (AR) and X-linked categories in 1995, 2007, and 2017, reflected in their high number of previous admissions, while the AD, MF, and nongenetic categories were the youngest with similar lengths of stay and previous admissions. CONCLUSION Conditions with a genetic contribution account for over half of pediatric inpatients. Since 1985, there have been many changes in age at admission and length of stay, but it is the increasing prevalence of AR, AD, and MF conditions that is important when considering future service provision.
Collapse
|
43
|
Wojcik MH, Stewart JE, Waisbren SE, Litt JS. Developmental Support for Infants With Genetic Disorders. Pediatrics 2020; 145:peds.2019-0629. [PMID: 32327449 PMCID: PMC7193975 DOI: 10.1542/peds.2019-0629] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/15/2019] [Indexed: 01/03/2023] Open
Abstract
As the technical ability for genetic diagnosis continues to improve, an increasing number of diagnoses are made in infancy or as early as the neonatal period. Many of these diagnoses are known to be associated with developmental delay and intellectual disability, features that would not be clinically detectable at the time of diagnosis. Others may be associated with cognitive impairment, but the incidence and severity are yet to be fully described. These neonates and infants with genetic diagnoses therefore represent an emerging group of patients who are at high risk for neurodevelopmental disabilities. Although there are well-established developmental supports for high-risk infants, particularly preterm infants, after discharge from the NICU, programs specifically for infants with genetic diagnoses are rare. And although previous research has demonstrated the positive effect of early developmental interventions on outcomes among preterm infants, the impact of such supports for infants with genetic disorders who may be born term, remains to be understood. We therefore review the literature regarding existing developmental assessment and intervention approaches for children with genetic disorders, evaluating these in the context of current developmental supports postdischarge for preterm infants. Further research into the role of developmental support programs for early assessment and intervention in high-risk neonates diagnosed with rare genetic disorders is needed.
Collapse
Affiliation(s)
- Monica H. Wojcik
- Divisions of Newborn Medicine and,Genetics and Genomics, Department of Medicine, Boston Children’s Hospital, Boston, Massachusetts; and
| | - Jane E. Stewart
- Divisions of Newborn Medicine and,Department of Neonatology, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Susan E. Waisbren
- Genetics and Genomics, Department of Medicine, Boston Children’s Hospital, Boston, Massachusetts; and
| | - Jonathan S. Litt
- Divisions of Newborn Medicine and,Department of Neonatology, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| |
Collapse
|
44
|
Smith HS, Swint JM, Lalani SR, de Oliveira Otto MC, Yamal JM, Russell HV, Lee BH. Exome sequencing compared with standard genetic tests for critically ill infants with suspected genetic conditions. Genet Med 2020; 22:1303-1310. [PMID: 32336750 DOI: 10.1038/s41436-020-0798-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Revised: 03/26/2020] [Accepted: 03/27/2020] [Indexed: 02/04/2023] Open
Abstract
PURPOSE As exome sequencing (ES) is increasingly used as a diagnostic tool, we aimed to compare ES with status quo genetic diagnostic workup for infants with suspected genetic disorders in terms of identifying diagnoses, survival, and cost of care. METHODS We studied newborns and infants admitted to intensive care with a suspected genetic etiology within the first year of life at a US quaternary-referral children's hospital over 5 years. In this propensity-matched cohort study using electronic medical record data, we compared patients who received ES as part of a diagnostic workup (ES cohort, n = 368) with clinically similar patients who did not receive ES (No-ES cohort, n = 368). RESULTS Diagnostic yield (27.4% ES, 25.8% No-ES; p = 0.62) and 1-year survival (80.2% ES, 84.8% No-ES; p = 0.10) were no different between cohorts. ES cohort patients had higher cost of admission, diagnostic investigation, and genetic testing (all p < 0.01). CONCLUSION ES did not differ from status quo genetic testing collectively in terms of diagnostic yield or patient survival; however, it had high yield as a single test, led to complementary classes of diagnoses, and was associated with higher costs. Further work is needed to define the most efficient use of diagnostic ES for critically ill newborns and infants.
Collapse
Affiliation(s)
- Hadley Stevens Smith
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX, USA.
| | - John M Swint
- The University of Texas Health Science Center at Houston, School of Public Health, Houston, TX, USA
| | - Seema R Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Texas Children's Hospital, Houston, TX, USA
| | | | - Jose-Miguel Yamal
- The University of Texas Health Science Center at Houston, School of Public Health, Houston, TX, USA
| | - Heidi V Russell
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Brendan H Lee
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| |
Collapse
|
45
|
Lipid Nanoarchitectonics for Natural Products Delivery in Cancer Therapy. SUSTAINABLE AGRICULTURE REVIEWS 2020. [DOI: 10.1007/978-3-030-41842-7_5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
|
46
|
Wojcik MH, Schwartz TS, Thiele KE, Paterson H, Stadelmaier R, Mullen TE, VanNoy GE, Genetti CA, Madden JA, Gubbels CS, Yu TW, Tan WH, Agrawal PB. Infant mortality: the contribution of genetic disorders. J Perinatol 2019; 39:1611-1619. [PMID: 31395954 PMCID: PMC6879816 DOI: 10.1038/s41372-019-0451-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 06/10/2019] [Accepted: 06/11/2019] [Indexed: 11/09/2022]
Abstract
OBJECTIVE To determine the proportion of infant deaths occurring in the setting of a confirmed genetic disorder. STUDY DESIGN A retrospective analysis of the electronic medical records of infants born from 1 January, 2011 to 1 June, 2017, who died prior to 1 year of age. RESULTS Five hundred and seventy three deceased infants were identified. One hundred and seventeen were confirmed to have a molecular or cytogenetic diagnosis in a clinical diagnostic laboratory and an additional seven were diagnosed by research testing for a total of 124/573 (22%) diagnosed infants. A total of 67/124 (54%) had chromosomal disorders and 58/124 (47%) had single gene disorders (one infant had both). The proportion of diagnoses made by sequencing technologies, such as exome sequencing, increased over the years. CONCLUSIONS The prevalence of confirmed genetic disorders within our cohort of infant deaths is higher than that previously reported. Increased efforts are needed to further understand the mortality burden of genetic disorders in infancy.
Collapse
Affiliation(s)
- Monica H. Wojcik
- Division of Newborn Medicine, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA, 02115,Division of Genetics and Genomics, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA, 02115,The Manton Center for Orphan Disease Research, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA, 02115,The Neonatal Genomics Program, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA, 02115.,The Broad Institute of MIT and Harvard, Cambridge, MA, USA, 02142
| | - Talia S. Schwartz
- Division of Genetics and Genomics, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA, 02115,The Manton Center for Orphan Disease Research, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA, 02115
| | - Katri E. Thiele
- Division of Newborn Medicine, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA, 02115,The Manton Center for Orphan Disease Research, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA, 02115,The Brody School of Medicine at East Carolina University, Greenville, NC, USA, 27834
| | - Heather Paterson
- Division of Genetics and Genomics, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA, 02115,The Manton Center for Orphan Disease Research, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA, 02115
| | - Rachel Stadelmaier
- Division of Genetics and Genomics, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA, 02115
| | - Thomas E. Mullen
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA, 02142
| | - Grace E. VanNoy
- Division of Genetics and Genomics, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA, 02115,The Manton Center for Orphan Disease Research, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA, 02115,The Broad Institute of MIT and Harvard, Cambridge, MA, USA, 02142
| | - Casie A. Genetti
- Division of Genetics and Genomics, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA, 02115,The Manton Center for Orphan Disease Research, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA, 02115
| | - Jill A. Madden
- Division of Genetics and Genomics, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA, 02115,The Manton Center for Orphan Disease Research, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA, 02115
| | - Cynthia S. Gubbels
- Division of Genetics and Genomics, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA, 02115,The Manton Center for Orphan Disease Research, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA, 02115,The Broad Institute of MIT and Harvard, Cambridge, MA, USA, 02142
| | - Timothy W. Yu
- Division of Genetics and Genomics, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA, 02115,The Manton Center for Orphan Disease Research, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA, 02115,The Broad Institute of MIT and Harvard, Cambridge, MA, USA, 02142
| | - Wen-Hann Tan
- Division of Genetics and Genomics, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA, 02115
| | - Pankaj B. Agrawal
- Division of Newborn Medicine, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA, 02115,Division of Genetics and Genomics, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA, 02115,The Manton Center for Orphan Disease Research, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA, 02115,The Neonatal Genomics Program, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA, 02115.,The Broad Institute of MIT and Harvard, Cambridge, MA, USA, 02142
| |
Collapse
|
47
|
Prospective, phenotype-driven selection of critically ill neonates for rapid exome sequencing is associated with high diagnostic yield. Genet Med 2019; 22:736-744. [PMID: 31780822 DOI: 10.1038/s41436-019-0708-6] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 11/12/2019] [Indexed: 12/18/2022] Open
Abstract
PURPOSE To investigate the impact of rapid-turnaround exome sequencing in critically ill neonates using phenotype-based subject selection criteria. METHODS Intensive care unit babies aged <6 months with hypotonia, seizures, a complex metabolic phenotype, and/or multiple congenital malformations were prospectively enrolled for rapid (<7 day) trio-based exome sequencing. Genomic variants relevant to the presenting phenotype were returned to the medical team. RESULTS A genetic diagnosis was attained in 29 of 50 (58%) sequenced cases. Twenty-seven (54%) patients received a molecular diagnosis involving known disease genes; two additional cases (4%) were solved with pathogenic variants found in novel disease genes. In 24 of the solved cases, diagnosis had impact on patient management and/or family members. Management changes included shift to palliative care, medication changes, involvement of additional specialties, and the consideration of new experimental therapies. CONCLUSION Phenotype-based patient selection is effective at identifying critically ill neonates with a high likelihood of receiving a molecular diagnosis via rapid-turnaround exome sequencing, leading to faster and more accurate diagnoses, reducing unnecessary testing and procedures, and informing medical care.
Collapse
|
48
|
Tan NB, Tan TY, Martyn MM, Savarirayan R, Amor DJ, Moody A, White SM, Stark Z. Diagnostic and service impact of genomic testing technologies in a neonatal intensive care unit. J Paediatr Child Health 2019; 55:1309-1314. [PMID: 30756437 DOI: 10.1111/jpc.14398] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 12/28/2018] [Accepted: 01/16/2019] [Indexed: 12/18/2022]
Abstract
AIM To investigate the diagnostic and service impact of chromosomal microarray and whole exome sequencing (WES) in a neonatal intensive care unit (NICU). METHODS This was a retrospective medical record review of NICU patients referred for genetics consultation at three time points over a 9-year period at a single centre to determine referral indications, genetic consultation outcomes and time to diagnosis. RESULTS The number of NICU patients referred for genetics consultation increased from 44 in 2007 to 95 in 2015. The proportion of NICU patients suspected of having a genetic condition following clinical geneticist assessment remained stable, averaging 5.3% of all admissions. The proportion of patients receiving a confirmed diagnosis rose from 21% in 2007 to 53% in 2015, with a shift from primarily chromosomal abnormalities to a broad range of monogenic disorders, increasingly diagnosed by WES as a first-tier test. The average age at diagnosis in 2015 was 19 days (range 12-38 days) for chromosomal abnormalities and 138 days (range 10-309 days) for monogenic conditions. CONCLUSIONS The adoption of new genetic technologies at our centre has increased the proportion of patients receiving a confirmed genetic diagnosis. This study provides important benchmark data to measure further improvements as turn-around times for genomic testing decrease.
Collapse
Affiliation(s)
- Natalie B Tan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Tiong Yang Tan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Melissa M Martyn
- Melbourne Genomics Health Alliance, Melbourne, Victoria, Australia
| | - Ravi Savarirayan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - David J Amor
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Amanda Moody
- Department of Neonatal Medicine, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Susan M White
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Zornitza Stark
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia.,Melbourne Genomics Health Alliance, Melbourne, Victoria, Australia
| |
Collapse
|
49
|
Ferreira CR. The burden of rare diseases. Am J Med Genet A 2019; 179:885-892. [PMID: 30883013 DOI: 10.1002/ajmg.a.61124] [Citation(s) in RCA: 197] [Impact Index Per Article: 39.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 02/27/2019] [Accepted: 03/05/2019] [Indexed: 01/06/2023]
Abstract
The subject of rare disease numbers is rife with misconceptions, not just in websites and other layman's literature, but also in the medical literature. Various websites mention numbers that are not validated by any solid data, while in turn the medical literature cites the aforementioned websites as sources, thus perpetuating a number of myths about rare diseases and their burden. We review the existing literature on rare disease numbers, in an attempt to demystify the subject. Specifically, we summarize data pertaining to: (a) known number and cumulative prevalence of rare diseases; (b) rare disease-associated mortality; (c) rare disease-associated morbidity, including numbers on health care services related to rare diseases; and (d) orphan drug numbers.
Collapse
Affiliation(s)
- Carlos R Ferreira
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| |
Collapse
|
50
|
Peri-mortem evaluation of infants who die without a diagnosis: focus on advances in genomic technology. J Perinatol 2018; 38:1125-1134. [PMID: 30076402 PMCID: PMC6419510 DOI: 10.1038/s41372-018-0187-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 06/01/2018] [Accepted: 07/09/2018] [Indexed: 12/16/2022]
Abstract
Infants who die within the first weeks to months of life may have genetic disorders, though many die without a confirmed diagnosis. Non-genetic conditions may also be responsible for unexplained infant deaths, and the diagnosis may be reliant upon studies performed in the peri-mortem period. Neonatologists, obstetricians, or pediatricians caring for these children and their families may be unsure of which investigations can and should be performed in the setting of a newborn or infant who is dying or has died. Recent advances in genomic sequencing technology may provide additional diagnostic options, though the interpretation of genetic variants discovered by this technique may be contingent upon clinical phenotype information that is obtained peri-mortem or upon autopsy. We have reviewed the current literature concerning the evaluation of an unexplained neonatal or infantile demise and synthesized a diagnostic approach, with a focus on the contribution of new and emerging genomic technologies.
Collapse
|