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Brankovic M, Ivanovic V, Basta I, Khang R, Lee E, Stevic Z, Ralic B, Tubic R, Seo G, Markovic V, Bozovic I, Svetel M, Marjanovic A, Veselinovic N, Mesaros S, Jankovic M, Savic-Pavicevic D, Jovin Z, Novakovic I, Lee H, Peric S. Whole exome sequencing in Serbian patients with hereditary spastic paraplegia. Neurogenetics 2024; 25:165-177. [PMID: 38499745 DOI: 10.1007/s10048-024-00755-x] [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: 12/14/2023] [Accepted: 03/08/2024] [Indexed: 03/20/2024]
Abstract
Hereditary spastic paraplegia (HSP) is a group of neurodegenerative diseases with a high genetic and clinical heterogeneity. Numerous HSP patients remain genetically undiagnosed despite screening for known genetic causes of HSP. Therefore, identification of novel variants and genes is needed. Our previous study analyzed 74 adult Serbian HSP patients from 65 families using panel of the 13 most common HSP genes in combination with a copy number variation analysis. Conclusive genetic findings were established in 23 patients from 19 families (29%). In the present study, nine patients from nine families previously negative on the HSP gene panel were selected for the whole exome sequencing (WES). Further, 44 newly diagnosed adult HSP patients from 44 families were sent to WES directly, since many studies showed WES may be used as the first step in HSP diagnosis. WES analysis of cohort 1 revealed a likely genetic cause in five (56%) of nine HSP families, including variants in the ETHE1, ZFYVE26, RNF170, CAPN1, and WASHC5 genes. In cohort 2, possible causative variants were found in seven (16%) of 44 patients (later updated to 27% when other diagnosis were excluded), comprising six different genes: SPAST, SPG11, WASCH5, KIF1A, KIF5A, and ABCD1. These results expand the genetic spectrum of HSP patients in Serbia and the region with implications for molecular genetic diagnosis and future causative therapies. Wide HSP panel can be the first step in diagnosis, alongside with the copy number variation (CNV) analysis, while WES should be performed after.
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Affiliation(s)
- Marija Brankovic
- Faculty of Medicine, University of Belgrade, Dr Subotica 6, Belgrade, Serbia.
| | - Vukan Ivanovic
- Faculty of Medicine, University of Belgrade, Dr Subotica 6, Belgrade, Serbia
| | - Ivana Basta
- Faculty of Medicine, University of Belgrade, Dr Subotica 6, Belgrade, Serbia
- Neurology Clinic, University Clinical Center of Serbia, Belgrade, Serbia
| | | | | | - Zorica Stevic
- Faculty of Medicine, University of Belgrade, Dr Subotica 6, Belgrade, Serbia
- Neurology Clinic, University Clinical Center of Serbia, Belgrade, Serbia
| | | | - Radoje Tubic
- Institute for Oncology and Radiology of Serbia, Belgrade, Serbia
| | | | - Vladana Markovic
- Faculty of Medicine, University of Belgrade, Dr Subotica 6, Belgrade, Serbia
- Neurology Clinic, University Clinical Center of Serbia, Belgrade, Serbia
| | - Ivo Bozovic
- Faculty of Medicine, University of Belgrade, Dr Subotica 6, Belgrade, Serbia
| | - Marina Svetel
- Faculty of Medicine, University of Belgrade, Dr Subotica 6, Belgrade, Serbia
- Neurology Clinic, University Clinical Center of Serbia, Belgrade, Serbia
| | - Ana Marjanovic
- Faculty of Medicine, University of Belgrade, Dr Subotica 6, Belgrade, Serbia
| | - Nikola Veselinovic
- Faculty of Medicine, University of Belgrade, Dr Subotica 6, Belgrade, Serbia
- Neurology Clinic, University Clinical Center of Serbia, Belgrade, Serbia
| | - Sarlota Mesaros
- Faculty of Medicine, University of Belgrade, Dr Subotica 6, Belgrade, Serbia
- Neurology Clinic, University Clinical Center of Serbia, Belgrade, Serbia
| | - Milena Jankovic
- Neurology Clinic, University Clinical Center of Serbia, Belgrade, Serbia
| | - Dusanka Savic-Pavicevic
- Center for Human Molecular Genetics, Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | - Zita Jovin
- Neurology Clinic, University Clinical Center of Vojvodina, Novi Sad, Serbia
| | - Ivana Novakovic
- Faculty of Medicine, University of Belgrade, Dr Subotica 6, Belgrade, Serbia
| | - Hane Lee
- 3Billion, Inc., Seoul, South Korea
| | - Stojan Peric
- Faculty of Medicine, University of Belgrade, Dr Subotica 6, Belgrade, Serbia
- Neurology Clinic, University Clinical Center of Serbia, Belgrade, Serbia
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Fortin O, Mulkey SB, Fraser JL. Advancing fetal diagnosis and prognostication using comprehensive prenatal phenotyping and genetic testing. Pediatr Res 2024:10.1038/s41390-024-03343-9. [PMID: 38937640 DOI: 10.1038/s41390-024-03343-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 05/14/2024] [Accepted: 06/04/2024] [Indexed: 06/29/2024]
Abstract
Prenatal diagnoses of congenital malformations have increased significantly in recent years with use of high-resolution prenatal imaging. Despite more precise radiological diagnoses, discussions with expectant parents remain challenging because congenital malformations are associated with a wide spectrum of outcomes. Comprehensive prenatal genetic testing has become an essential tool that improves the accuracy of prognostication. Testing strategies include chromosomal microarray, exome sequencing, and genome sequencing. The diagnostic yield varies depending on the specific malformations, severity of the abnormalities, and multi-organ involvement. The utility of prenatal genetic diagnosis includes increased diagnostic clarity for clinicians and families, informed pregnancy decision-making, neonatal care planning, and reproductive planning. Turnaround time for results of comprehensive genetic testing remains a barrier, especially for parents that are decision-making, although this has improved over time. Uncertainty inherent to many genetic testing results is a challenge. Appropriate genetic counseling is essential for parents to understand the diagnosis and prognosis and to make informed decisions. Recent research has investigated the yield of exome or genome sequencing in structurally normal fetuses, both with non-invasive screening methods and invasive diagnostic testing; the prenatal diagnostic community must evaluate and analyze the significant ethical considerations associated with this practice prior to generalizing its use. IMPACT: Reviews available genetic testing options during the prenatal period in detail. Discusses the impact of prenatal genetic testing on care using case-based examples. Consolidates the current literature on the yield of genetic testing for prenatal diagnosis of congenital malformations.
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Affiliation(s)
- Olivier Fortin
- Zickler Family Prenatal Pediatrics Institute, Children's National Hospital, Washington, DC, USA
| | - Sarah B Mulkey
- Zickler Family Prenatal Pediatrics Institute, Children's National Hospital, Washington, DC, USA
- Department of Neurology and Rehabilitation Medicine, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Jamie L Fraser
- Zickler Family Prenatal Pediatrics Institute, Children's National Hospital, Washington, DC, USA.
- Rare Disease Institute, Children's National Hospital, Washington, DC, USA.
- Center for Genetic Medicine Research, Children's National Hospital, Washington, DC, USA.
- Department of Pediatrics, George Washington University School of Medicine and Health Sciences, Washington, DC, USA.
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Azuelos C, Marquis MA, Laberge AM. A systematic review of the assessment of the clinical utility of genomic sequencing: Implications of the lack of standard definitions and measures of clinical utility. Eur J Med Genet 2024; 68:104925. [PMID: 38432472 DOI: 10.1016/j.ejmg.2024.104925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 12/31/2023] [Accepted: 02/11/2024] [Indexed: 03/05/2024]
Abstract
PURPOSE Exome sequencing (ES) and genome sequencing (GS) are diagnostic tests for rare genetic diseases. Studies report clinical utility of ES/GS. The goal of this systematic review is to establish how clinical utility is defined and measured in studies evaluating the impacts of ES/GS results for pediatric patients. METHODS Relevant articles were identified in PubMed, Medline, Embase, and Web of Science. Eligible studies assessed clinical utility of ES/GS for pediatric patients published before 2021. Other relevant articles were added based on articles' references. Articles were coded to assess definitions and measures of clinical utility. RESULTS Of 1346 articles, 83 articles met eligibility criteria. Clinical utility was not clearly defined in 19% of studies and 92% did not use an explicit measure of clinical utility. When present, definitions of clinical utility diverged from recommended definitions and varied greatly, from narrow (diagnostic yield of ES/GS) to broad (including decisions about withdrawal of care/palliative care and/or impacts on other family members). CONCLUSION Clinical utility is used to guide policy and practice decisions about test use. The lack of a standard definition of clinical utility of ES/GS may lead to under- or overestimations of clinical utility, complicating policymaking and raising ethical issues.
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Affiliation(s)
- Claudia Azuelos
- Medical Genetics, Dept of Pediatrics, CHU Sainte-Justine and Université de Montréal, Canada.
| | - Marc-Antoine Marquis
- Palliative Care, Dept of Pediatrics, CHU Sainte-Justine and Université de Montréal, Canada
| | - Anne-Marie Laberge
- Medical Genetics, Dept of Pediatrics, CHU Sainte-Justine and Université de Montréal, Canada.
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Szalai R, Till A, Gyenesei A, Bene J, Hadzsiev K. Importance and application of WES in fetal genetic diagnostics: Identification of novel ASPM mutation in a fetus with microcephaly. Mol Genet Metab Rep 2024; 38:101056. [PMID: 38469100 PMCID: PMC10926227 DOI: 10.1016/j.ymgmr.2024.101056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 01/10/2024] [Accepted: 01/15/2024] [Indexed: 03/13/2024] Open
Abstract
Background Prenatal whole exome sequencing (WES) approaches can provide genetic diagnosis with rapid turnaround time and high diagnostic rate when conventional tests are negative. Here we report a family with multiple pregnancy loss and with repeated occurrence of fetal microcephaly. Methods and results Because of positive family history and recurrent structural abnormality during the pregnancies that may lead postnatal neurodevelopmental consequences, WES analysis was indicated. Umbilical cord blood sampling was carried out and WES was performed using Twist Human Core Exome Kit and Illumina sequencing technology. The presence of pathogenic variants was confirmed by Sanger sequencing. WES analysis revealed a known pathogenic c.8506_8507delCA (p.Gln2836Glufs*35, rs587783280) and a novel pathogenic c.3134_3135delTC (p.Leu1045Glnfs*17) ASPM mutations in the fetus in compound heterozygous state. The c.3134_3135delTC has never been reported in the literature. Conclusions Our findings serve additional evidence that WES can be an efficient and relevant tool to diagnose certain genetic disorders with appropriate indication and to assess the recurrence risk of a disease. With the application of WES in combination with pre-implantation genetic tests, we can avoid the transmission of pathogenic mutations and we can achieve a decreased abortion rate in obstetric care.
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Affiliation(s)
- Renata Szalai
- University of Pecs, Medical School, Department of Medical Genetics, Pecs, Hungary
| | - Agnes Till
- University of Pecs, Medical School, Department of Medical Genetics, Pecs, Hungary
| | - Attila Gyenesei
- Szentagothai Research Center, University of Pecs, Pecs, Hungary
| | - Judit Bene
- University of Pecs, Medical School, Department of Medical Genetics, Pecs, Hungary
| | - Kinga Hadzsiev
- University of Pecs, Medical School, Department of Medical Genetics, Pecs, Hungary
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Ferri-Rufete D, López-González A, Casas-Alba D, Cuadras D, Palau F, Martínez-Monseny A. Clinical Genetics Assessment Triangle (CGAT): A simple tool to identify patients with genetic conditions. Eur J Med Genet 2023; 66:104858. [PMID: 37758166 DOI: 10.1016/j.ejmg.2023.104858] [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: 07/03/2023] [Revised: 09/04/2023] [Accepted: 09/24/2023] [Indexed: 10/03/2023]
Abstract
OBJECTIVE The objective of this study was to develop a simple tool for general physicians to promptly identify and refer pediatric patients with a higher probability of having a genetic condition. STUDY DESIGN This retrospective, descriptive study was conducted at a tertiary pediatric hospital's Clinical Genetics Unit from June 2019 to January 2020. We included patients under 18 years of age who visited the unit, excluding those without genetic testing. Epidemiological, clinical, and genetic variables were collected from electronic medical records. The primary outcome was the diagnosis of a genetic condition based on genetic testing. RESULTS Among 445 patients, 304 were included; 163 (53.6%) were male, and mean age was 7.4 years (SD 5.1 years). A genetic condition was diagnosed in 139 patients (45.7%). Using a multiple logistic regression model, five variables significantly contributed to reaching a diagnosis: suspected diagnosis at referral (OR 3.45, P < 0.001), short stature (OR 3.11, P < 0.001), global developmental delay/intellectual disability (OR 2.65, P < 0.001), dysmorphic craniofacial features (OR 1.99, P = 0.035), and multiple congenital anomalies (OR 2.54, P = 0.033). The association strength (OR) increased when these variables were paired with each other. The study's findings are presented in the form of a triangle, known as the Clinical Genetics Assessment Triangle (CGAT), which summarizes the results. A decision tree model is applied to guide clinical department referrals based on the affected sides of the triangle. CONCLUSIONS The CGAT has the potential to enable general physicians to promptly identify pediatric patients with an increased probability of having a genetic condition.
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Affiliation(s)
- David Ferri-Rufete
- Pediatrics Department, Hospital Sant Joan de Déu, Esplugues de Llobregat, 08950, Spain.
| | - Aitor López-González
- Pediatrics Department, Hospital Sant Joan de Déu, Esplugues de Llobregat, 08950, Spain.
| | - Dídac Casas-Alba
- Department of Genetic Medicine, Pediatric Institute of Rare Diseases (IPER), Hospital Sant Joan de Déu, Esplugues de Llobregat, 08950, Spain.
| | - Daniel Cuadras
- Statistics Department, Fundació Sant Joan de Déu, Esplugues de Llobregat, 08950, Spain.
| | - Francesc Palau
- Department of Genetic Medicine, Pediatric Institute of Rare Diseases (IPER), Hospital Sant Joan de Déu, Esplugues de Llobregat, 08950, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, 28029, Spain.
| | - Antonio Martínez-Monseny
- Department of Genetic Medicine, Pediatric Institute of Rare Diseases (IPER), Hospital Sant Joan de Déu, Esplugues de Llobregat, 08950, Spain.
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Chung CCY, Hue SPY, Ng NYT, Doong PHL, Chu ATW, Chung BHY. Meta-analysis of the diagnostic and clinical utility of exome and genome sequencing in pediatric and adult patients with rare diseases across diverse populations. Genet Med 2023; 25:100896. [PMID: 37191093 DOI: 10.1016/j.gim.2023.100896] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 05/07/2023] [Accepted: 05/10/2023] [Indexed: 05/17/2023] Open
Abstract
PURPOSE This meta-analysis aims to compare the diagnostic and clinical utility of exome sequencing (ES) vs genome sequencing (GS) in pediatric and adult patients with rare diseases across diverse populations. METHODS A meta-analysis was conducted to identify studies from 2011 to 2021. RESULTS One hundred sixty-one studies across 31 countries/regions were eligible, featuring 50,417 probands of diverse populations. Diagnostic rates of ES (0.38, 95% CI 0.36-0.40) and GS (0.34, 95% CI 0.30-0.38) were similar (P = .1). Within-cohort comparison illustrated 1.2-times odds of diagnosis by GS over ES (95% CI 0.79-1.83, P = .38). GS studies discovered a higher range of novel genes than ES studies; yet, the rate of variant of unknown significance did not differ (P = .78). Among high-quality studies, clinical utility of GS (0.77, 95% CI 0.64-0.90) was higher than that of ES (0.44, 95% CI 0.30-0.58) (P < .01). CONCLUSION This meta-analysis provides an important update to demonstrate the similar diagnostic rates between ES and GS and the higher clinical utility of GS over ES. With the newly published recommendations for clinical interpretation of variants found in noncoding regions of the genome and the trend of decreasing variant of unknown significance and GS cost, it is expected that GS will be more widely used in clinical settings.
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Affiliation(s)
| | - Shirley P Y Hue
- Hong Kong Genome Institute, Hong Kong Special Administrative Region
| | - Nicole Y T Ng
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Phoenix H L Doong
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Annie T W Chu
- Hong Kong Genome Institute, Hong Kong Special Administrative Region.
| | - Brian H Y Chung
- Hong Kong Genome Institute, Hong Kong Special Administrative Region; Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region.
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Campaña C, Cabieses B, Obach A, Vezzani F. " Healthcare should be the same for everyone": perceived inequities in therapeutic trajectories of adult patients with lung cancer in Chile, a qualitative study. Front Public Health 2023; 11:1228304. [PMID: 37663832 PMCID: PMC10468573 DOI: 10.3389/fpubh.2023.1228304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 07/19/2023] [Indexed: 09/05/2023] Open
Abstract
Background Globally, it has been reported that different social determinants of health affect health outcomes in lung cancer (LC). Research on the therapeutic trajectories of patients (TTP) is a novel field for identifying barriers and facilitators in health. The objective of this study was to reveal perceived differences in TTP with LC in Chile according to selected social determinants of health (SDH) and the experiences of patients, health professionals, and civil society leaders. Methods This is a qualitative paradigm, one case-study design. Online semi-structured interviews were conducted with patients with LC, health professionals, and civil society leaders. The strategies for the recruitment process included social networks, civil society organizations, health professionals, and the snowball technique. A thematic analysis was carried out. Results Selected SDH impact LC's TTP in Chile, particularly concerning health system access, health services, information, and patient navigation experiences. The analysis of the experiences of the participants allowed us to identify barriers related to the selected SDH in three stages of the TTP: initiation, examinations, and diagnosis and treatment. Individuals with limited education, those residing outside the capital, women, and those in the public health system encountered more barriers throughout their TTP. Discussion Study findings suggest that being a woman with low education, from the public health system, and not from the capital might represent one of the most powerful intersections for experiencing barriers to effective healthcare in LC in Chile. It is necessary to monitor the TTP from an SDH perspective to guarantee the rights of access, opportunity, quality, and financial protection.
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Affiliation(s)
- Carla Campaña
- Centre of Global Intercultural Health (CeSGI) ICIM, Universidad del Desarrollo, Santiago, Chile
- Programa de Doctorado en Ciencias e Innovación en Medicina (DCIM), Universidad del Desarrollo, Santiago, Chile
| | - Báltica Cabieses
- Centre of Global Intercultural Health (CeSGI) ICIM, Universidad del Desarrollo, Santiago, Chile
- Center for Cancer Prevention and Control (CECAN), ANID FONDAP 152220002, Santiago, Chile
| | - Alexandra Obach
- Centre of Global Intercultural Health (CeSGI) ICIM, Universidad del Desarrollo, Santiago, Chile
- Center for Cancer Prevention and Control (CECAN), ANID FONDAP 152220002, Santiago, Chile
| | - Francisca Vezzani
- Centre of Global Intercultural Health (CeSGI) ICIM, Universidad del Desarrollo, Santiago, Chile
- Center for Cancer Prevention and Control (CECAN), ANID FONDAP 152220002, Santiago, Chile
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Squires JE, Miethke AG, Valencia CA, Hawthorne K, Henn L, Van Hove JL, Squires RH, Bove K, Horslen S, Kohli R, Molleston JP, Romero R, Alonso EM, Bezerra JA, Guthery SL, Hsu E, Karpen SJ, Loomes KM, Ng VL, Rosenthal P, Mysore K, Wang KS, Friederich MW, Magee JC, Sokol RJ. Clinical spectrum and genetic causes of mitochondrial hepatopathy phenotype in children. Hepatol Commun 2023; 7:e0139. [PMID: 37184518 PMCID: PMC10187840 DOI: 10.1097/hc9.0000000000000139] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 01/19/2023] [Indexed: 05/16/2023] Open
Abstract
BACKGROUND Alterations in both mitochondrial DNA (mtDNA) and nuclear DNA genes affect mitochondria function, causing a range of liver-based conditions termed mitochondrial hepatopathies (MH), which are subcategorized as mtDNA depletion, RNA translation, mtDNA deletion, and enzymatic disorders. We aim to enhance the understanding of pathogenesis and natural history of MH. METHODS We analyzed data from patients with MH phenotypes to identify genetic causes, characterize the spectrum of clinical presentation, and determine outcomes. RESULTS Three enrollment phenotypes, that is, acute liver failure (ALF, n = 37), chronic liver disease (Chronic, n = 40), and post-liver transplant (n = 9), were analyzed. Patients with ALF were younger [median 0.8 y (range, 0.0, 9.4) vs 3.4 y (0.2, 18.6), p < 0.001] with fewer neurodevelopmental delays (40.0% vs 81.3%, p < 0.001) versus Chronic. Comprehensive testing was performed more often in Chronic than ALF (90.0% vs 43.2%); however, etiology was identified more often in ALF (81.3% vs 61.1%) with mtDNA depletion being most common (ALF: 77% vs Chronic: 41%). Of the sequenced cohort (n = 60), 63% had an identified mitochondrial disorder. Cluster analysis identified a subset without an underlying genetic etiology, despite comprehensive testing. Liver transplant-free survival was 40% at 2 years (ALF vs Chronic, 16% vs 65%, p < 0.001). Eighteen (21%) underwent transplantation. With 33 patient-years of follow-up after the transplant, 3 deaths were reported. CONCLUSIONS Differences between ALF and Chronic MH phenotypes included age at diagnosis, systemic involvement, transplant-free survival, and genetic etiology, underscoring the need for ultra-rapid sequencing in the appropriate clinical setting. Cluster analysis revealed a group meeting enrollment criteria but without an identified genetic or enzymatic diagnosis, highlighting the need to identify other etiologies.
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Affiliation(s)
- James E. Squires
- UPMC Children’s Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | | | - C. Alexander Valencia
- Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, USA
- Interpath Laboratory, Pendleton, Oregon, USA
| | - Kieran Hawthorne
- Arbor Research Collaborative for Health, Ann Arbor, Michigan, USA
| | - Lisa Henn
- Arbor Research Collaborative for Health, Ann Arbor, Michigan, USA
| | - Johan L.K. Van Hove
- University of Colorado School of Medicine, Children’s Hospital Colorado, Aurora, Colorado, USA
| | - Robert H. Squires
- UPMC Children’s Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Kevin Bove
- Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, USA
| | - Simon Horslen
- UPMC Children’s Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Rohit Kohli
- Children’s Hospital Los Angeles, Los Angeles, California, USA
| | - Jean P. Molleston
- Indiana University-Riley Hospital for Children, Indianapolis, Indiana, USA
| | - Rene Romero
- Emory University School of Medicine, Atlanta, Georgia, USA
| | - Estella M. Alonso
- Ann and Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois, USA
| | - Jorge A. Bezerra
- Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, USA
| | - Stephen L. Guthery
- University of Utah School of Medicine, Primary Children’s Hospital, Salt Lake City, Utah, USA
| | - Evelyn Hsu
- University of Washington School of Medicine and Seattle Children’s Hospital, Seattle, Washington, USA
| | - Saul J. Karpen
- Emory University School of Medicine, Atlanta, Georgia, USA
| | - Kathleen M. Loomes
- The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Vicky L. Ng
- Hospital for Sick Children, University of Toronto, Toronto, Canada
| | | | - Krupa Mysore
- Texas Children’s Hospital, Baylor College of Medicine, Houston, Texas, USA
| | - Kasper S. Wang
- Children’s Hospital Los Angeles, Los Angeles, California, USA
| | - Marisa W. Friederich
- University of Colorado School of Medicine, Children’s Hospital Colorado, Aurora, Colorado, USA
| | - John C. Magee
- University of Michigan Hospitals and Health Centers, Ann Arbor, Michigan, USA
| | - Ronald J. Sokol
- University of Colorado School of Medicine, Children’s Hospital Colorado, Aurora, Colorado, USA
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Nurchis MC, Altamura G, Riccardi MT, Radio FC, Chillemi G, Bertini ES, Garlasco J, Tartaglia M, Dallapiccola B, Damiani G. Whole genome sequencing diagnostic yield for paediatric patients with suspected genetic disorders: systematic review, meta-analysis, and GRADE assessment. Arch Public Health 2023; 81:93. [PMID: 37231492 DOI: 10.1186/s13690-023-01112-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Accepted: 05/18/2023] [Indexed: 05/27/2023] Open
Abstract
BACKGROUND About 80% of the roughly 7,000 known rare diseases are single gene disorders, about 85% of which are ultra-rare, affecting less than one in one million individuals. NGS technologies, in particular whole genome sequencing (WGS) in paediatric patients suffering from severe disorders of likely genetic origin improve the diagnostic yield allowing targeted, effective care and management. The aim of this study is to perform a systematic review and meta-analysis to assess the effectiveness of WGS, with respect to whole exome sequencing (WES) and/or usual care, for the diagnosis of suspected genetic disorders among the paediatric population. METHODS A systematic review of the literature was conducted querying relevant electronic databases, including MEDLINE, EMBASE, ISI Web of Science, and Scopus from January 2010 to June 2022. A random-effect meta-analysis was run to inspect the diagnostic yield of different techniques. A network meta-analysis was also performed to directly assess the comparison between WGS and WES. RESULTS Of the 4,927 initially retrieved articles, thirty-nine met the inclusion criteria. Overall results highlighted a significantly higher pooled diagnostic yield for WGS, 38.6% (95% CI: [32.6 - 45.0]), in respect to WES, 37.8% (95% CI: [32.9 - 42.9]) and usual care, 7.8% (95% CI: [4.4 - 13.2]). The meta-regression output suggested a higher diagnostic yield of the WGS compared to WES after controlling for the type of disease (monogenic vs non-monogenic), with a tendency to better diagnostic performances for Mendelian diseases. The network meta-analysis showed a higher diagnostic yield for WGS compared to WES (OR = 1.54, 95%CI: [1.11 - 2.12]). CONCLUSIONS Although whole genome sequencing for the paediatric population with suspected genetic disorders provided an accurate and early genetic diagnosis in a high proportion of cases, further research is needed for evaluating costs, effectiveness, and cost-effectiveness of WGS and achieving an informed decision-making process. TRIAL REGISTRATION This systematic review has not been registered.
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Grants
- RF-2018-12,366,391, 2018 Ministero della Salute
- RF-2018-12,366,391, 2018 Ministero della Salute
- RF-2018-12,366,391, 2018 Ministero della Salute
- RF-2018-12,366,391, 2018 Ministero della Salute
- RF-2018-12,366,391, 2018 Ministero della Salute
- RF-2018-12,366,391, 2018 Ministero della Salute
- RF-2018-12,366,391, 2018 Ministero della Salute
- RF-2018-12,366,391, 2018 Ministero della Salute
- RF-2018-12,366,391, 2018 Ministero della Salute
- RF-2018-12,366,391, 2018 Ministero della Salute
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Affiliation(s)
- Mario Cesare Nurchis
- Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168, Rome, Italy
- School of Economics, Università Cattolica del Sacro Cuore, 00168, Rome, Italy
| | - Gerardo Altamura
- Department of Health Sciences and Public Health, Section of Hygiene, Università Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168, Rome, Italy.
| | - Maria Teresa Riccardi
- Department of Health Sciences and Public Health, Section of Hygiene, Università Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168, Rome, Italy
| | - Francesca Clementina Radio
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù IRCCS, 00146, Rome, Italy
| | - Giovanni Chillemi
- Department for Innovation in Biological Agro-Food and Forest Systems (DIBAF), University of Tuscia, 01100, Viterbo, Italy
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Centro Nazionale Delle Ricerche, 70126, Bari, Italy
| | - Enrico Silvio Bertini
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù IRCCS, 00146, Rome, Italy
| | - Jacopo Garlasco
- Department of Public Health Sciences and Paediatrics, University of Turin, 10126, Turin, Italy
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù IRCCS, 00146, Rome, Italy
| | - Bruno Dallapiccola
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù IRCCS, 00146, Rome, Italy
| | - Gianfranco Damiani
- Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168, Rome, Italy
- Department of Health Sciences and Public Health, Section of Hygiene, Università Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168, Rome, Italy
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10
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Stefka J, Streff H, Liu P, Towne M, Smith HS. Cascade testing after exome sequencing: Retrospective analysis of linked family data at 2 US laboratories. Genet Med 2023; 25:100818. [PMID: 36852743 DOI: 10.1016/j.gim.2023.100818] [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: 10/31/2022] [Revised: 02/16/2023] [Accepted: 02/22/2023] [Indexed: 02/26/2023] Open
Abstract
PURPOSE Cascade testing, the process of testing a proband's at-risk relatives, is integral to realizing the full value of genomic sequencing. However, there is little empirical evidence on the uptake of cascade testing after a positive exome sequencing (ES) result in a population of probands with diverse clinical indications. METHODS We retrospectively reviewed administrative data from 2 US clinical laboratories that perform ES. For each proband with a positive ES result, we used linked family data to describe the frequency of relatives' cascade testing performed at the same laboratory, variant detection yield of cascade tests, and characteristics of probands and relatives categorized on the basis of cascade testing completion. RESULTS Among the 3723 positive ES results across both laboratories, 426 relatives of 282 probands completed cascade testing (uptake = 7.6%). An average of 1.5 relatives (SD = 0.9) were tested per proband. Of the 426 relatives tested, 200 had a variant of interest detected (variant detection yield = 47.0%). CONCLUSION In our real-world data analysis, a small proportion of probands with a positive ES result subsequently had relatives complete cascade testing at the same laboratory. However, approximately half of the tested relatives received a clinically significant result that could have implications for clinical management or reproductive planning. Additional research on ways to increase cascade testing uptake is warranted.
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Affiliation(s)
- Julie Stefka
- Genetic Counseling Program, School of Health Professions, Baylor College of Medicine, Houston, TX; Clinical Diagnostics, Ambry Genetics, Aliso Viejo, CA.
| | - Haley Streff
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Baylor Genetics, Houston, TX
| | - Meghan Towne
- Medical Sciences, Ambry Genetics, Aliso Viejo, CA
| | - Hadley Stevens Smith
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX; Precision Medicine Translational Research Center (PROMoTeR), Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA
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11
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Wang J, Fang F, Ding C, Li J, Wu Y, Zhang W, Bao X, Lv J, Wang X, Ren X, Wang H. Clinical and genetic spectrum of hereditary spastic paraplegia in Chinese children. Dev Med Child Neurol 2023; 65:416-423. [PMID: 36109173 DOI: 10.1111/dmcn.15385] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 07/10/2022] [Accepted: 07/29/2022] [Indexed: 12/15/2022]
Abstract
AIM To explore the clinical and genetic spectrum of hereditary spastic paraplegia (HSP) in Chinese children. METHOD This retrospective study was conducted between January 2014 and October 2021 in children clinically diagnosed with either pure HSP (pHSP) or complex HSP (cHSP). RESULTS We investigated 45 children (32 males, 13 females; mean age [SD] at symptom onset 4 years [7 months]). clinically diagnosed with HSP and identified genetic causes in 35 patients. Most patients with autosomal dominant HSP had pHSP (16/18), whereas most patients with autosomal recessive HSP tended to have cHSP (14/16). SPG11 was the most common autosomal recessive subtype, followed by FA2H/SPG35, whereas SPAST/SPG4 was the most frequent cause of autosomal dominant HSP. Two patients with CPT1C mutations presented with a complex phenotype. Meanwhile, 10 patients were found to have likely pathogenic variants/variants of uncertain clinical significance in six genes related to HSP. INTERPRETATION SPG11 and SPG4 were the most frequent subtypes in Chinese children with autosomal recessive HSP and autosomal dominant HSP. However, the prevalence of SPG4 was much lower than that in adults, which might be explained by the late onset of the disease. On the other hand, FA2H/SPG35 was common in our cohort, while it contributed to only a small proportion of adult cases, which might be explained by its rapid progression and early death in some patients. We also expanded the genetic and clinical spectra of SPG73.
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Affiliation(s)
- Jiaping Wang
- Department of Neurology, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Fang Fang
- Department of Neurology, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Changhong Ding
- Department of Neurology, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Jiuwei Li
- Department of Neurology, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Yun Wu
- Department of Neurology, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Weihua Zhang
- Department of Neurology, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Xinhua Bao
- Department of Paediatric Neurology, Peking University First Hospital, Beijing, China
| | - Junlan Lv
- Department of Neurology, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Xiaohui Wang
- Department of Neurology, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Xiaotun Ren
- Department of Neurology, Beijing Children's Hospital, Capital Medical University, Beijing, China
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12
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13
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Venkat V, Abdelhalim H, DeGroat W, Zeeshan S, Ahmed Z. Investigating genes associated with heart failure, atrial fibrillation, and other cardiovascular diseases, and predicting disease using machine learning techniques for translational research and precision medicine. Genomics 2023; 115:110584. [PMID: 36813091 DOI: 10.1016/j.ygeno.2023.110584] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 02/06/2023] [Accepted: 02/11/2023] [Indexed: 02/22/2023]
Abstract
Cardiovascular disease (CVD) is the leading cause of mortality and loss of disability adjusted life years (DALYs) globally. CVDs like Heart Failure (HF) and Atrial Fibrillation (AF) are associated with physical effects on the heart muscles. As a result of the complex nature, progression, inherent genetic makeup, and heterogeneity of CVDs, personalized treatments are believed to be critical. Rightful application of artificial intelligence (AI) and machine learning (ML) approaches can lead to new insights into CVDs for providing better personalized treatments with predictive analysis and deep phenotyping. In this study we focused on implementing AI/ML techniques on RNA-seq driven gene-expression data to investigate genes associated with HF, AF, and other CVDs, and predict disease with high accuracy. The study involved generating RNA-seq data derived from the serum of consented CVD patients. Next, we processed the sequenced data using our RNA-seq pipeline and applied GVViZ for gene-disease data annotation and expression analysis. To achieve our research objectives, we developed a new Findable, Accessible, Intelligent, and Reproducible (FAIR) approach that includes a five-level biostatistical evaluation, primarily based on the Random Forest (RF) algorithm. During our AI/ML analysis, we have fitted, trained, and implemented our model to classify and distinguish high-risk CVD patients based on their age, gender, and race. With the successful execution of our model, we predicted the association of highly significant HF, AF, and other CVDs genes with demographic variables.
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Affiliation(s)
- Vignesh Venkat
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, 112 Paterson St, New Brunswick, NJ, USA
| | - Habiba Abdelhalim
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, 112 Paterson St, New Brunswick, NJ, USA
| | - William DeGroat
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, 112 Paterson St, New Brunswick, NJ, USA
| | - Saman Zeeshan
- Rutgers Cancer Institute of New Jersey, Rutgers University, 195 Little Albany St, New Brunswick, NJ, USA
| | - Zeeshan Ahmed
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, 112 Paterson St, New Brunswick, NJ, USA; Department of Medicine, Robert Wood Johnson Medical School, Rutgers Biomedical and Health Sciences, 125 Paterson St, New Brunswick, NJ, USA.
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14
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Pfrieger FW. The Niemann-Pick type diseases – A synopsis of inborn errors in sphingolipid and cholesterol metabolism. Prog Lipid Res 2023; 90:101225. [PMID: 37003582 DOI: 10.1016/j.plipres.2023.101225] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/27/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023]
Abstract
Disturbances of lipid homeostasis in cells provoke human diseases. The elucidation of the underlying mechanisms and the development of efficient therapies represent formidable challenges for biomedical research. Exemplary cases are two rare, autosomal recessive, and ultimately fatal lysosomal diseases historically named "Niemann-Pick" honoring the physicians, whose pioneering observations led to their discovery. Acid sphingomyelinase deficiency (ASMD) and Niemann-Pick type C disease (NPCD) are caused by specific variants of the sphingomyelin phosphodiesterase 1 (SMPD1) and NPC intracellular cholesterol transporter 1 (NPC1) or NPC intracellular cholesterol transporter 2 (NPC2) genes that perturb homeostasis of two key membrane components, sphingomyelin and cholesterol, respectively. Patients with severe forms of these diseases present visceral and neurologic symptoms and succumb to premature death. This synopsis traces the tortuous discovery of the Niemann-Pick diseases, highlights important advances with respect to genetic culprits and cellular mechanisms, and exposes efforts to improve diagnosis and to explore new therapeutic approaches.
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15
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Kagan M, Semo-Oz R, Ben Moshe Y, Atias-Varon D, Tirosh I, Stern-Zimmer M, Eliyahu A, Raas-Rothschild A, Bivas M, Shlomovitz O, Chorin O, Rock R, Tzadok M, Ben-Zeev B, Heimer G, Bolkier Y, Gruber N, Dagan A, Bar Aluma BE, Pessach IM, Rechavi G, Barel O, Pode-Shakked B, Anikster Y, Vivante A. Clinical impact of exome sequencing in the setting of a general pediatric ward for hospitalized children with suspected genetic disorders. Front Genet 2023; 13:1018062. [PMID: 36699461 PMCID: PMC9868164 DOI: 10.3389/fgene.2022.1018062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 12/13/2022] [Indexed: 01/11/2023] Open
Abstract
Background: Genetic conditions contribute a significant portion of disease etiologies in children admitted to general pediatric wards worldwide. While exome sequencing (ES) has improved clinical diagnosis and management over a variety of pediatric subspecialties, it is not yet routinely used by general pediatric hospitalists. We aim to investigate the impact of exome sequencing in sequencing-naive children suspected of having monogenic disorders while receiving inpatient care. Methods: We prospectively employed exome sequencing in children admitted to the general pediatric inpatient service at a large tertiary medical center in Israel. Genetic analysis was triggered by general and/or subspecialist pediatricians who were part of the primary inpatient team. We determined the diagnostic yield among children who were referred for exome sequencing and observed the effects of genetic diagnosis on medical care. Results: A total of fifty probands were evaluated and exome sequenced during the study period. The most common phenotypes included were neurodevelopmental (56%), gastrointestinal (34%), and congenital cardiac anomalies (24%). A molecular diagnosis was reached in 38% of patients. Among seven patients (37%), the molecular genetic diagnosis influenced subsequent clinical management already during admission or shortly following discharge. Conclusion: We identified a significant fraction of genetic etiologies among undiagnosed children admitted to the general pediatric ward. Our results support that early application of exome sequencing may be maximized by pediatric hospitalists' high index of suspicion for an underlying genetic etiology, prompting an in-house genetic evaluation. This framework should include a multidisciplinary co-management approach of the primary care team working alongside with subspecialties, geneticists and bioinformaticians.
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Affiliation(s)
- Maayan Kagan
- Department of Pediatrics B, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, Israel,Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel,Talpiot Medical Leadership Program, Sheba Medical Center, Tel-Hashomer, Israel
| | - Rotem Semo-Oz
- Department of Pediatrics B, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, Israel,Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel,Pediatric Rheumatology Unit, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, Israel
| | - Yishay Ben Moshe
- Department of Pediatrics B, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, Israel,Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Danit Atias-Varon
- Pediatric Nephrology Unit, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, Israel
| | - Irit Tirosh
- Department of Pediatrics B, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, Israel,Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel,Pediatric Rheumatology Unit, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, Israel
| | - Michal Stern-Zimmer
- Department of Pediatrics B, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, Israel,Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Aviva Eliyahu
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel,The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel-Hashomer, Israel
| | - Annick Raas-Rothschild
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel,The Institute of Rare Diseases, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, Israel
| | - Maayan Bivas
- Department of Pediatrics B, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, Israel,Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Omer Shlomovitz
- Department of Pediatrics B, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, Israel,Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Odelia Chorin
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel,The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel-Hashomer, Israel,The Institute of Rare Diseases, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, Israel
| | - Rachel Rock
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel,The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel-Hashomer, Israel,The Institute of Rare Diseases, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, Israel
| | - Michal Tzadok
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel,Pediatric Neurology Unit, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, Israel
| | - Bruria Ben-Zeev
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel,Pediatric Neurology Unit, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, Israel
| | - Gali Heimer
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel,Talpiot Medical Leadership Program, Sheba Medical Center, Tel-Hashomer, Israel,Pediatric Neurology Unit, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, Israel
| | - Yoav Bolkier
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel,Pediatric Heart Institute, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, Israel
| | - Noah Gruber
- Department of Pediatrics B, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, Israel,Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel,Pediatric Endocrinology and Diabetes Unit, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, Israel
| | - Adi Dagan
- Department of Pediatrics B, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, Israel,Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel,Pediatric Pulmonology and National CF Center, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, Israel
| | - Bat El Bar Aluma
- Department of Pediatrics B, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, Israel,Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel,Pediatric Pulmonology and National CF Center, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, Israel
| | - Itai M. Pessach
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel,Talpiot Medical Leadership Program, Sheba Medical Center, Tel-Hashomer, Israel,Department of Pediatric Intensive Care, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, Israel
| | - Gideon Rechavi
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel,The Wohl Institute for Translational Medicine, Sheba Medical Center, Tel-Hashomer, Israel,Sheba Cancer Research Center, Sheba Medical Center, Tel-Hashomer, Israel
| | - Ortal Barel
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel,The Wohl Institute for Translational Medicine, Sheba Medical Center, Tel-Hashomer, Israel,The Genomics Unit, Sheba Cancer Research Center, Sheba Medical Center, Tel-Hashomer, Israel
| | - Ben Pode-Shakked
- Department of Pediatrics B, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, Israel,Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel,Talpiot Medical Leadership Program, Sheba Medical Center, Tel-Hashomer, Israel,The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel-Hashomer, Israel
| | - Yair Anikster
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel,The Wohl Institute for Translational Medicine, Sheba Medical Center, Tel-Hashomer, Israel,Metabolic Disease Unit, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, Israel
| | - Asaf Vivante
- Department of Pediatrics B, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, Israel,Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel,Talpiot Medical Leadership Program, Sheba Medical Center, Tel-Hashomer, Israel,Pediatric Nephrology Unit, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, Israel,*Correspondence: Asaf Vivante,
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16
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Haviland I, Daniels CI, Greene CA, Drew J, Love-Nichols JA, Swanson LC, Smith L, Nie DA, Benke T, Sheidley BR, Zhang B, Poduri A, Olson HE. Genetic Diagnosis Impacts Medical Management for Pediatric Epilepsies. Pediatr Neurol 2023; 138:71-80. [PMID: 36403551 PMCID: PMC10099530 DOI: 10.1016/j.pediatrneurol.2022.10.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 10/05/2022] [Accepted: 10/19/2022] [Indexed: 11/18/2022]
Abstract
BACKGROUND Evidence of the impact of genetic diagnosis on medical management in individuals with previously unexplained epilepsy is lacking in the literature. Our goal was to determine the impact of genetic diagnosis on medical management in a cohort of individuals with early-onset epilepsy. METHODS We performed detailed phenotyping of individuals with epilepsy who underwent clinical genetic testing with an epilepsy panel and/or exome sequencing at Boston Children's Hospital between 2012 and 2019. We assessed the impact of genetic diagnosis on medical management. RESULTS We identified a genetic etiology in 152 of 602 (25%) individuals with infantile- or childhood-onset epilepsy who underwent next-generation sequencing. Diagnosis impacted medical management in at least one category for 72% of patients (110 of 152) and in more than one category in 34%. Treatment was impacted in 45% of individuals, including 36% with impact on antiseizure medication choice, 7% on use of disease-specific vitamin or metabolic treatments, 3% on pathway-driven off-label use of medications, and 10% on discussion of gene-specific clinical trials. Care coordination was impacted in 48% of individuals. Counseling on a change in prognosis was reported in 28% of individuals, and 1% of individuals had a correction of diagnosis. Impact was documented in 13 of 13 individuals with neurotypical development and in 55% of those with epilepsy onset after age two years. CONCLUSION We demonstrated meaningful impact of genetic diagnosis on medical care and prognosis in over 70% of individuals, including those with neurotypical development and age of epilepsy onset after age two years.
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Affiliation(s)
- Isabel Haviland
- Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Carolyn I Daniels
- Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Caitlin A Greene
- Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Jacqueline Drew
- Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts; Boston University Clinical Investigation Master's Program, Boston, Massachusetts
| | - Jamie A Love-Nichols
- Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts; Department of Genetics, Seattle Children's Hospital, Seattle, Washington
| | - Lindsay C Swanson
- Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Lacey Smith
- Division of Epilepsy and Clinical Neurophysiology and Epilepsy Genetics Program, Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Duyu A Nie
- Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts; Departments of Pediatrics, Neurology and Neurosurgery, Warren Alpert Medical School of Brown University, Providence, Rhode Island; Division of Pediatric Neurology and the Children's Neurodevelopment Center (CNDC), Hasbro Children's Hospital, Providence, Rhode Island
| | - Timothy Benke
- Departments of Pediatrics, Neurology, Pharmacology, and Otolaryngology, Children's Hospital Colorado, University of Colorado School of Medicine, Aurora, Colorado
| | - Beth R Sheidley
- Division of Epilepsy and Clinical Neurophysiology and Epilepsy Genetics Program, Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Bo Zhang
- Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts; Biostatistics and Research Design Center, Institutional Centers for Clinical and Translational Research, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Annapurna Poduri
- Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts; Division of Epilepsy and Clinical Neurophysiology and Epilepsy Genetics Program, Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Heather E Olson
- Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts; Division of Epilepsy and Clinical Neurophysiology and Epilepsy Genetics Program, Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts.
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17
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Terry LE, Arige V, Neumann J, Wahl AM, Knebel TR, Chaffer JW, Malik S, Liston A, Humblet-Baron S, Bultynck G, Yule DI. Missense mutations in inositol 1,4,5-trisphosphate receptor type 3 result in leaky Ca 2+ channels and activation of store-operated Ca 2+ entry. iScience 2022; 25:105523. [PMID: 36444295 PMCID: PMC9700043 DOI: 10.1016/j.isci.2022.105523] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 10/10/2022] [Accepted: 11/04/2022] [Indexed: 11/09/2022] Open
Abstract
Mutations in all subtypes of the inositol 1,4,5-trisphosphate receptor Ca2+ release channel are associated with human diseases. In this report, we investigated the functionality of three neuropathy-associated missense mutations in IP3R3 (V615M, T1424M, and R2524C). The mutants only exhibited function when highly over-expressed compared to endogenous hIP3R3. All variants resulted in elevated basal cytosolic Ca2+ levels, decreased endoplasmic reticulum Ca2+ store content, and constitutive store-operated Ca2+ entry in the absence of any stimuli, consistent with a leaky IP3R channel pore. These variants differed in channel function; when stably over-expressed the R2524C mutant was essentially dead, V615M was poorly functional, and T1424M exhibited activity greater than that of the corresponding wild-type following threshold stimulation. These results demonstrate that a common feature of these mutations is decreased IP3R3 function. In addition, these mutations exhibit a novel phenotype manifested as a constitutively open channel, which inappropriately gates SOCE in the absence of stimulation.
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Affiliation(s)
- Lara E. Terry
- Department of Pharmacology and Physiology, University of Rochester, Rochester, NY 14642, USA
| | - Vikas Arige
- Department of Pharmacology and Physiology, University of Rochester, Rochester, NY 14642, USA
| | - Julika Neumann
- KU Leuven, Department of Microbiology and Immunology, Leuven, Belgium
| | - Amanda M. Wahl
- Department of Pharmacology and Physiology, University of Rochester, Rochester, NY 14642, USA
| | - Taylor R. Knebel
- Department of Pharmacology and Physiology, University of Rochester, Rochester, NY 14642, USA
| | - James W. Chaffer
- Department of Pharmacology and Physiology, University of Rochester, Rochester, NY 14642, USA
| | - Sundeep Malik
- Department of Pharmacology and Physiology, University of Rochester, Rochester, NY 14642, USA
| | - Adrian Liston
- KU Leuven, Department of Microbiology and Immunology, Leuven, Belgium
| | | | - Geert Bultynck
- KU Leuven, Laboratory of Molecular and Cellular Signaling, Department of Cellular and Molecular Medicine, Leuven, Belgium
| | - David I. Yule
- Department of Pharmacology and Physiology, University of Rochester, Rochester, NY 14642, USA
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18
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Application of Prenatal Whole Exome Sequencing for Structural Congenital Anomalies-Experience from a Local Prenatal Diagnostic Laboratory. Healthcare (Basel) 2022; 10:healthcare10122521. [PMID: 36554045 PMCID: PMC9778831 DOI: 10.3390/healthcare10122521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/05/2022] [Accepted: 12/07/2022] [Indexed: 12/15/2022] Open
Abstract
Fetal structural congenital abnormalities (SCAs) complicate 2-3% of all pregnancies. Whole-exome sequencing (WES) has been increasingly adopted prenatally when karyotyping and chromosomal microarray do not yield a diagnosis. This is a retrospective cohort study of 104 fetuses with SCAs identified on antenatal ultrasound in Hong Kong, where whole exome sequencing is performed. Molecular diagnosis was obtained in 25 of the 104 fetuses (24%). The highest diagnostic rate was found in fetuses with multiple SCAs (29.2%), particularly those with involvement of the cardiac and musculoskeletal systems. Variants of uncertain significance were detected in 8 out of the 104 fetuses (7.7%). Our study shows the utility of WES in the prenatal setting, and the extended use of the technology would be recommended in addition to conventional genetic workup.
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Tosco-Herrera E, Muñoz-Barrera A, Jáspez D, Rubio-Rodríguez LA, Mendoza-Alvarez A, Rodriguez-Perez H, Jou J, Iñigo-Campos A, Corrales A, Ciuffreda L, Martinez-Bugallo F, Prieto-Morin C, García-Olivares V, González-Montelongo R, Lorenzo-Salazar JM, Marcelino-Rodriguez I, Flores C. Evaluation of a whole-exome sequencing pipeline and benchmarking of causal germline variant prioritizers. Hum Mutat 2022; 43:2010-2020. [PMID: 36054330 DOI: 10.1002/humu.24459] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 08/20/2022] [Accepted: 08/30/2022] [Indexed: 01/25/2023]
Abstract
Most causal variants of Mendelian diseases are exonic. Whole-exome sequencing (WES) has become the diagnostic gold standard, but causative variant prioritization constitutes a bottleneck. Here we assessed an in-house sample-to-sequence pipeline and benchmarked free prioritization tools for germline causal variants from WES data. WES of 61 unselected patients with a known genetic disease cause was obtained. Variant prioritizations were performed by diverse tools and recorded to obtain a diagnostic yield when the causal variant was present in the first, fifth, and 10th top rankings. A fraction of causal variants was not captured by WES (8.2%) or did not pass the quality control criteria (13.1%). Most of the applications inspected were unavailable or had technical limitations, leaving nine tools for complete evaluation. Exomiser performed best in the top first rankings, while LIRICAL led in the top fifth rankings. Based on the more conservative top 10th rankings, Xrare had the highest diagnostic yield, followed by a three-way tie among Exomiser, LIRICAL, and PhenIX, then followed by AMELIE, TAPES, Phen-Gen, AIVar, and VarNote-PAT. Xrare, Exomiser, LIRICAL, and PhenIX are the most efficient options for variant prioritization in real patient WES data.
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Affiliation(s)
- Eva Tosco-Herrera
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria (HUNSC), Santa Cruz de Tenerife, Spain.,Escuela de Doctorado y Estudios de Posgrado de la Universidad de La Laguna (EDEPULL), Universidad de La Laguna (ULL), San Cristóbal de La Laguna, Spain
| | - Adrián Muñoz-Barrera
- Escuela de Doctorado y Estudios de Posgrado de la Universidad de La Laguna (EDEPULL), Universidad de La Laguna (ULL), San Cristóbal de La Laguna, Spain.,Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Granadilla de Abona, Spain
| | - David Jáspez
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Granadilla de Abona, Spain
| | - Luis A Rubio-Rodríguez
- Escuela de Doctorado y Estudios de Posgrado de la Universidad de La Laguna (EDEPULL), Universidad de La Laguna (ULL), San Cristóbal de La Laguna, Spain.,Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Granadilla de Abona, Spain
| | - Alejandro Mendoza-Alvarez
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria (HUNSC), Santa Cruz de Tenerife, Spain.,Escuela de Doctorado y Estudios de Posgrado de la Universidad de La Laguna (EDEPULL), Universidad de La Laguna (ULL), San Cristóbal de La Laguna, Spain
| | - Hector Rodriguez-Perez
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria (HUNSC), Santa Cruz de Tenerife, Spain.,Escuela de Doctorado y Estudios de Posgrado de la Universidad de La Laguna (EDEPULL), Universidad de La Laguna (ULL), San Cristóbal de La Laguna, Spain
| | - Jonathan Jou
- Department of Surgery, University of Illinois College of Medicine, Peoria, Illinois, USA
| | - Antonio Iñigo-Campos
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Granadilla de Abona, Spain
| | - Almudena Corrales
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria (HUNSC), Santa Cruz de Tenerife, Spain.,CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Laura Ciuffreda
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria (HUNSC), Santa Cruz de Tenerife, Spain
| | - Francisco Martinez-Bugallo
- Clinical Analysis Service, Hospital Universitario Nuestra Señora de Candelaria (HUNSC), Santa Cruz de Tenerife, Spain
| | - Carol Prieto-Morin
- Clinical Analysis Service, Hospital Universitario Nuestra Señora de Candelaria (HUNSC), Santa Cruz de Tenerife, Spain
| | - Víctor García-Olivares
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Granadilla de Abona, Spain
| | | | - Jose Miguel Lorenzo-Salazar
- Escuela de Doctorado y Estudios de Posgrado de la Universidad de La Laguna (EDEPULL), Universidad de La Laguna (ULL), San Cristóbal de La Laguna, Spain.,Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Granadilla de Abona, Spain
| | | | - Carlos Flores
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria (HUNSC), Santa Cruz de Tenerife, Spain.,Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Granadilla de Abona, Spain.,CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain.,Facultad de Ciencias de la Salud, Universidad Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
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20
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Pitfalls of whole exome sequencing in undefined clinical conditions with a suspected genetic etiology. Genes Genomics 2022; 45:637-655. [PMID: 36454368 DOI: 10.1007/s13258-022-01341-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 10/26/2022] [Indexed: 12/03/2022]
Abstract
BACKGROUND Whole-Exome Sequencing (WES) is a valuable tool for the molecular diagnosis of patients with a suspected genetic condition. In complex and heterogeneous diseases, the interpretation of WES variants is more challenging given the absence of diagnostic handles and other reported cases with overlapping clinical presentations. OBJECTIVE To describe candidate variants emerging from trio-WES and possibly associated with the clinical phenotype in clinically heterogeneous conditions. METHODS We performed WES in ten patients from eight families, selected because of the lack of a clear clinical diagnosis or suspicion, the presence of multiple clinical signs, and the negative results of traditional genetic tests. RESULTS Although we identified ten candidate variants, reaching the diagnosis of these cases is challenging, given the complexity and the rarity of these syndromes and because affected genes are already associated with known genetic diseases only partially recapitulating patients' phenotypes. However, the identification of these variants could shed light into the definition of new genotype-phenotype correlations. Here, we describe the clinical and molecular data of these cases with the aim of favoring the match with other similar cases and, hopefully, confirm our diagnostic hypotheses. CONCLUSION This study emphasizes the major limitations associated with WES data interpretation, but also highlights its clinical utility in unraveling novel genotype-phenotype correlations in complex and heterogeneous undefined clinical conditions with a suspected genetic etiology.
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21
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Senaratne TN, Saitta SC. Evaluating Genetic Disorders in the Neonate: The Role of Exome Sequencing in the NICU. Neoreviews 2022; 23:e829-e840. [PMID: 36450644 DOI: 10.1542/neo.23-12-e829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
With recent advances in the technologies used for genetic diagnosis as well as our understanding of the genetic basis of disease, a growing list of options is available for providers when caring for a newborn with features suggesting an underlying genetic etiology. The choice of the most appropriate genetic test for a specific situation includes clinical considerations such as the phenotypic features and type of genetic abnormality suspected, as well as practical considerations such as cost and turnaround time. In this review, we discuss clinical exome sequencing in the context of genetic evaluation of newborns, including technical considerations, variant interpretation, and incidental/secondary findings. Strengths and limitations of exome sequencing are discussed and compared with those of other commonly known tests such as karyotype analysis, fluorescence in situ hybridization, chromosomal microarray, and sequencing panels, along with integration of results from prenatal testing if available. We also review future directions including genome sequencing and other emerging technologies that are starting to be used in clinical settings.
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Affiliation(s)
- T Niroshi Senaratne
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA
| | - Sulagna C Saitta
- Division of Clinical Genetics, Department of Pediatrics, Division of Reproductive Genetics, Department of Obstetrics and Gynecology, David Geffen School of Medicine at UCLA, Los Angeles, CA
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22
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Skryabin NA, Zhigalina DI, Stepanov VA. The Role of Splicing in the Pathogenesis of Monogenic Diseases. RUSS J GENET+ 2022. [DOI: 10.1134/s1022795422100088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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23
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Developing CIRdb as a catalog of natural genetic variation in the Canary Islanders. Sci Rep 2022; 12:16132. [PMID: 36168029 PMCID: PMC9514705 DOI: 10.1038/s41598-022-20442-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 09/13/2022] [Indexed: 11/29/2022] Open
Abstract
The current inhabitants of the Canary Islands have a unique genetic makeup in the European diversity landscape due to the existence of African footprints from recent admixture events, especially of North African components (> 20%). The underrepresentation of non-Europeans in genetic studies and the sizable North African ancestry, which is nearly absent from all existing catalogs of worldwide genetic diversity, justify the need to develop CIRdb, a population-specific reference catalog of natural genetic variation in the Canary Islanders. Based on array genotyping of the selected unrelated donors and comparisons against available datasets from European, sub-Saharan, and North African populations, we illustrate the intermediate genetic differentiation of Canary Islanders between Europeans and North Africans and the existence of within-population differences that are likely driven by genetic isolation. Here we describe the overall design and the methods that are being implemented to further develop CIRdb. This resource will help to strengthen the implementation of Precision Medicine in this population by contributing to increase the diversity in genetic studies. Among others, this will translate into improved ability to fine map disease genes and simplify the identification of causal variants and estimate the prevalence of unattended Mendelian diseases.
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24
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Rosenquist R, Cuppen E, Buettner R, Caldas C, Dreau H, Elemento O, Frederix G, Grimmond S, Haferlach T, Jobanputra V, Meggendorfer M, Mullighan CG, Wordsworth S, Schuh A. Clinical utility of whole-genome sequencing in precision oncology. Semin Cancer Biol 2022; 84:32-39. [PMID: 34175442 DOI: 10.1016/j.semcancer.2021.06.018] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 06/02/2021] [Accepted: 06/22/2021] [Indexed: 12/14/2022]
Abstract
Precision diagnostics is one of the two pillars of precision medicine. Sequencing efforts in the past decade have firmly established cancer as a primarily genetically driven disease. This concept is supported by therapeutic successes aimed at particular pathways that are perturbed by specific driver mutations in protein-coding domains and reflected in three recent FDA tissue agnostic cancer drug approvals. In addition, there is increasing evidence from studies that interrogate the entire genome by whole-genome sequencing that acquired global and complex genomic aberrations including those in non-coding regions of the genome might also reflect clinical outcome. After addressing technical, logistical, financial and ethical challenges, national initiatives now aim to introduce clinical whole-genome sequencing into real-world diagnostics as a rational and potentially cost-effective tool for response prediction in cancer and to identify patients who would benefit most from 'expensive' targeted therapies and recruitment into clinical trials. However, so far, this has not been accompanied by a systematic and prospective evaluation of the clinical utility of whole-genome sequencing within clinical trials of uniformly treated patients of defined clinical outcome. This approach would also greatly facilitate novel predictive biomarker discovery and validation, ultimately reducing size and duration of clinical trials and cost of drug development. This manuscript is the third in a series of three to review and critically appraise the potential and challenges of clinical whole-genome sequencing in solid tumors and hematological malignancies.
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Affiliation(s)
- Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden; Department of Clinical Genetics, Karolinska University Hospital, Solna, Sweden
| | - Edwin Cuppen
- Hartwig Medical Foundation, Amsterdam, The Netherlands; Center for Molecular Medicine and Oncode Institute, University Medical Center, Utrecht, The Netherlands
| | | | - Carlos Caldas
- Cancer Research UK Cambridge Institute and Department of Oncology, University of Cambridge, United Kingdom
| | - Helene Dreau
- NIHR Oxford Biomedical Research Centre and Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Olivier Elemento
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, United States; Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, United States
| | - Geert Frederix
- Julius Center for Health Sciences and Primary Care, University Medical Center, Utrecht, The Netherlands
| | - Sean Grimmond
- Centre for Cancer Research, University of Melbourne, Melbourne, Australia
| | | | - Vaidehi Jobanputra
- New York Genome Center, 101 Avenue of the Americas, New York, NY 100132, United States; Columbia University Medical Center, 650 W 168th St, New York, NY 10032, United States
| | | | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, United States
| | - Sarah Wordsworth
- Nuffield Department of Population Health and Oxford NIHR Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | - Anna Schuh
- NIHR Oxford Biomedical Research Centre and Department of Oncology, University of Oxford, Oxford, United Kingdom.
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25
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Van Der Merwe N, Ramesar R, De Vries J. Whole Exome Sequencing in South Africa: Stakeholder Views on Return of Individual Research Results and Incidental Findings. Front Genet 2022; 13:864822. [PMID: 35754817 PMCID: PMC9216214 DOI: 10.3389/fgene.2022.864822] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 03/30/2022] [Indexed: 11/17/2022] Open
Abstract
The use of whole exome sequencing (WES) in medical research is increasing in South Africa (SA), raising important questions about whether and which individual genetic research results, particularly incidental findings, should be returned to patients. Whilst some commentaries and opinions related to the topic have been published in SA, there is no qualitative data on the views of professional stakeholders on this topic. Seventeen participants including clinicians, genomics researchers, and genetic counsellors (GCs) were recruited from the Western Cape in SA. Semi-structured interviews were conducted, and the transcripts analysed using the framework approach for data analysis. Current roadblocks for the clinical adoption of WES in SA include a lack of standardised guidelines; complexities relating to variant interpretation due to lack of functional studies and underrepresentation of people of African ancestry in the reference genome, population and variant databases; lack of resources and skilled personnel for variant confirmation and follow-up. Suggestions to overcome these barriers include obtaining funding and buy-in from the private and public sectors and medical insurance companies; the generation of a locally relevant reference genome; training of health professionals in the field of genomics and bioinformatics; and multidisciplinary collaboration. Participants emphasised the importance of upscaling the accessibility to and training of GCs, as well as upskilling of clinicians and genetic nurses for return of genetic data in collaboration with GCs and medical geneticists. Future research could focus on exploring the development of stakeholder partnerships for increased access to trained specialists as well as community engagement and education, alongside the development of guidelines for result disclosure.
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Affiliation(s)
- Nicole Van Der Merwe
- UCT/MRC Genomic and Precision Medicine Research Unit, Division of Human Genetics, Institute for Infectious Diseases and Molecular Medicine, Department of Pathology, Faculty of Medicine and Health Sciences, University of Cape Town, Cape Town, South Africa.,Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Raj Ramesar
- UCT/MRC Genomic and Precision Medicine Research Unit, Division of Human Genetics, Institute for Infectious Diseases and Molecular Medicine, Department of Pathology, Faculty of Medicine and Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Jantina De Vries
- Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,Neuroscience Institute, Faculty of Health Sciences, University of Cape Town, Observatory, South Africa
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26
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Börklü E, Altunoğlu U, Eraslan S, Kayserili H. A New Family with a Novel OTUD6B Mutation: Practicing Whole Exome Sequencing for Antenatal Diagnosis of Tetralogy of Fallot. Mol Syndromol 2022; 13:206-211. [DOI: 10.1159/000519557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 09/09/2021] [Indexed: 11/19/2022] Open
Abstract
<i>OTUD6B,</i> which encodes a member of the ovarian tumor domain-containing deubiquitinating enzyme, has recently been associated with autosomal recessive intellectual disability syndrome with seizures and dysmorphic features. Here, we report one additional case with Tetralogy of Fallot (ToF), who has microcephaly and dysmorphic features along with renal parenchymal disease with simple cortical cysts. The family’s first pregnancy was medically terminated due to antenatal diagnosis of ToF. A novel homozygous variant in <i>OTUD6B</i> (c.815T>G; p.[Ile272Arg]) was revealed by whole exome sequencing (WES) along with a previously reported heterozygous <i>PKD1</i> variant, unraveling the blended phenotype observed in the proband. Our findings highlight the importance of WES for the prenatal diagnosis of ToF and expand the <i>OTUD6B</i> mutational spectrum.
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27
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McGinn RJ, Von Stein EL, Summers Stromberg JE, Li Y. Precision medicine in epilepsy. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2022; 190:147-188. [DOI: 10.1016/bs.pmbts.2022.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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28
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Stefka J, El-Khechen D, Cain T, Blanco K, Feldmann B, Towne MC, Hagman KDF. Misattributed parentage identified through diagnostic exome sequencing: Frequency of detection and reporting practices. J Genet Couns 2021; 31:631-640. [PMID: 34826357 DOI: 10.1002/jgc4.1530] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 03/26/2021] [Accepted: 10/16/2021] [Indexed: 11/08/2022]
Abstract
Access to genetic testing, namely, diagnostic exome sequencing (DES), has significantly improved, subsequently increasing the likelihood of discovering incidental findings, such as misattributed relationships and specifically misattributed parentage (MP). Until the recently published ACMG statement, there had been no consensus for laboratories and clinicians to follow when addressing such findings. Family-based genomic testing is valuable for accurate variant interpretation but has the potential to uncover misattributed familial relationships. Here, we present the first published data on the frequency of MP identified through DES at a clinical laboratory. We also investigated clinicians' decisions on how to proceed with analysis, reporting, and disclosure. A database of 6,752 families who underwent parent-proband ('trio') DES was retrospectively reviewed for molecular identification of MP and clinicians' MP disclosure decisions. Among 6,752 trios, 39 cases of MP were detected (0.58%). Non-paternity was detected in all cases, and in one instance, non-maternity was also identified. All clinicians decided to proceed by omitting the MP individual from the analysis. Clinicians chose to proceed with duo analysis (87.2%), modify information on the report (74.4%), and communicate MP results to the mother (71.8%), suggesting a trend toward not disclosing to the putative father or proband. The data show that trio DES involves a chance of detecting MP and that clinician disclosure practices do not appear to routinely include direct disclosure to the putative father. MP identified in our parent-proband trios sent in for DES is lower than the reported frequency of MP in the general population due in part to ascertainment bias as families with known or suspected MP are presumably less likely to pursue trio testing. These data may inform laboratory policies and clinician practices for addressing incidental findings such as MP.
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Affiliation(s)
| | | | - Taylor Cain
- Ambry Genetics, Aliso Viejo, California, USA
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29
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Finucane B, Oetjens MT, Johns A, Myers SM, Fisher C, Habegger L, Maxwell EK, Reid JG, Ledbetter DH, Kirchner HL, Martin CL. Medical manifestations and health care utilization among adult MyCode participants with neurodevelopmental psychiatric copy number variants. Genet Med 2021; 24:703-711. [PMID: 34906480 DOI: 10.1016/j.gim.2021.11.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 10/07/2021] [Accepted: 11/12/2021] [Indexed: 10/19/2022] Open
Abstract
PURPOSE Recurrent pathogenic copy number variants (pCNVs) have large-effect impacts on brain function and represent important etiologies of neurodevelopmental psychiatric disorders (NPDs), including autism and schizophrenia. Patterns of health care utilization in adults with pCNVs have gone largely unstudied and are likely to differ in significant ways from those of children. METHODS We compared the prevalence of NPDs and electronic health record-based medical conditions in 928 adults with 26 pCNVs to a demographically-matched cohort of pCNV-negative controls from >135,000 patient-participants in Geisinger's MyCode Community Health Initiative. We also evaluated 3 quantitative health care utilization measures (outpatient, inpatient, and emergency department visits) in both groups. RESULTS Adults with pCNVs (24.9%) were more likely than controls (16.0%) to have a documented NPD. They had significantly higher rates of several chronic diseases, including diabetes (29.3% in participants with pCNVs vs 20.4% in participants without pCNVs) and dementia (2.2% in participants with pCNVs vs 1.0% participants without pCNVs), and twice as many annual emergency department visits. CONCLUSION These findings highlight the potential for genetic information-specifically, pCNVs-to inform the study of health care outcomes and utilization in adults. If, as our findings suggest, adults with pCNVs have poorer health and require disproportionate health care resources, early genetic diagnosis paired with patient-centered interventions may help to anticipate problems, improve outcomes, and reduce the associated economic burden.
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Affiliation(s)
- Brenda Finucane
- Geisinger, Autism & Developmental Medicine Institute, Lewisburg, PA.
| | | | - Alicia Johns
- Geisinger, Department of Population Health Sciences, Danville, PA
| | - Scott M Myers
- Geisinger, Autism & Developmental Medicine Institute, Lewisburg, PA
| | - Ciaran Fisher
- Geisinger, Autism & Developmental Medicine Institute, Lewisburg, PA
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30
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Cost-effectiveness of genome sequencing for diagnosing patients with undiagnosed rare genetic diseases. Genet Med 2021; 24:109-118. [PMID: 34906478 DOI: 10.1016/j.gim.2021.08.015] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 06/26/2020] [Accepted: 08/25/2021] [Indexed: 12/28/2022] Open
Abstract
PURPOSE To estimate the cost-effectiveness of genome sequencing (GS) for diagnosing critically ill infants and noncritically ill pediatric patients (children) with suspected rare genetic diseases from a United States health sector perspective. METHODS A decision-analytic model was developed to simulate the diagnostic trajectory of patients. Parameter estimates were derived from a targeted literature review and meta-analysis. The model simulated clinical and economic outcomes associated with 3 diagnostic pathways: (1) standard diagnostic care, (2) GS, and (3) standard diagnostic care followed by GS. RESULTS For children, costs of GS ($7284) were similar to that of standard care ($7355) and lower than that of standard care followed by GS pathways ($12,030). In critically ill infants, when cost estimates were based on the length of stay in the neonatal intensive care unit, the lowest cost pathway was GS ($209,472). When only diagnostic test costs were included, the cost per diagnosis was $17,940 for standard, $17,019 for GS, and $20,255 for standard care followed by GS. CONCLUSION The results of this economic model suggest that GS may be cost neutral or possibly cost saving as a first line diagnostic tool for children and critically ill infants.
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31
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Olde Keizer RACM, Henneman L, Ploos van Amstel JK, Vissers LELM, Frederix GWJ. Economic evaluations of exome and genome sequencing in pediatric genetics: considerations towards a consensus strategy. J Med Econ 2021; 24:60-70. [PMID: 34915793 DOI: 10.1080/13696998.2021.2009725] [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: 10/19/2022]
Abstract
OBJECTIVE Next Generation Sequencing (NGS) is increasingly used for the diagnosis of rare genetic disorders. The aim of this study is to review the different approaches for economic evaluations of Next Generation Sequencing (NGS) in pediatric care used to date, to identify all costs, effects, and time horizons taken into account. METHODS A systematic literature review was conducted to identify published economic evaluations of NGS applications in pediatric diagnostics, i.e. exome sequencing (ES) and/or genome sequencing (GS). Information regarding methodological approach, costs, effects, and time horizon was abstracted from these publications. RESULTS Twenty-eight economic evaluations of ES/GS within pediatrics were identified. Costs included were mainly restricted to direct in-hospital healthcare costs and varied widely in inclusion of sort of costs and time-horizon. Nineteen studies included diagnostic yield and eight studies included cost-effectiveness as outcome measures. Studies varied greatly in terms of included sort of costs data, effects, and time horizon. CONCLUSION Large differences in inclusion of cost and effect parameters were identified between studies. Validity of outcomes can therefore be questioned, which hinders valid comparison and widespread generalization of conclusions. In addition to current health economic guidance, specific guidance for evaluations in pediatric care is therefore necessary to improve the validity of outcomes and furthermore facilitate comparable decision-making for implementing novel NGS-based diagnostic modalities in pediatric genetics and beyond.
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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
| | - Lidewij Henneman
- Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
| | | | - Lisenka E L M Vissers
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, 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
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32
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Ezekian JE, Rehder C, Kishnani PS, Landstrom AP. Interpretation of Incidental Genetic Findings Localizing to Genes Associated With Cardiac Channelopathies and Cardiomyopathies. CIRCULATION-GENOMIC AND PRECISION MEDICINE 2021; 14:e003200. [PMID: 34384235 DOI: 10.1161/circgen.120.003200] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Recent advances in next-genetic sequencing technology have facilitated an expansion in the use of exome and genome sequencing in the research and clinical settings. While this has aided in the genetic diagnosis of individuals with atypical clinical presentations, there has been a marked increase in the number of incidentally identified variants of uncertain diagnostic significance in genes identified as clinically actionable by the American College of Medical Genetics guidelines. Approximately 20 of these genes are associated with cardiac diseases, which carry a significant risk of sudden cardiac death. While identification of at-risk individuals is paramount, increased discovery of incidental variants of uncertain diagnostic significance has placed a burden on the clinician tasked with determining the diagnostic significance of these findings. Herein, we describe the scope of this emerging problem using cardiovascular genetics to illustrate the challenges associated with variants of uncertain diagnostic significance interpretation. We review the evidence for diagnostic weight of these variants, discuss the role of clinical genetics providers in patient care, and put forward general recommendations about the interpretation of incidentally identified variants found with clinical genetic testing.
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Affiliation(s)
- Jordan E Ezekian
- Division of Cardiology, Department of Pediatrics (J.E.E., A.P.L.), Duke University School of Medicine, Durham, NC
| | - Catherine Rehder
- Department of Pathology (C.R.), Duke University School of Medicine, Durham, NC
| | - Priya S Kishnani
- Division of Medical Genetics, Department of Pediatrics (P.S.K.), Duke University School of Medicine, Durham, NC
| | - Andrew P Landstrom
- Division of Cardiology, Department of Pediatrics (J.E.E., A.P.L.), Duke University School of Medicine, Durham, NC.,Department of Cell Biology (A.P.L.), Duke University School of Medicine, Durham, NC
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Bolkier Y, Barel O, Marek-Yagel D, Atias-Varon D, Kagan M, Vardi A, Mishali D, Katz U, Salem Y, Tirosh-Wagner T, Jacobson JM, Raas-Rothschild A, Chorin O, Eliyahu A, Sarouf Y, Shlomovitz O, Veber A, Shalva N, Javasky E, Ben Moshe Y, Staretz-Chacham O, Rechavi G, Mane S, Anikster Y, Vivante A, Pode-Shakked B. Whole-exome sequencing reveals a monogenic cause in 56% of individuals with laterality disorders and associated congenital heart defects. J Med Genet 2021; 59:691-696. [PMID: 34215651 DOI: 10.1136/jmedgenet-2021-107775] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 06/19/2021] [Indexed: 01/19/2023]
Abstract
BACKGROUND The molecular basis of heterotaxy and congenital heart malformations associated with disruption of left-right asymmetry is broad and heterogenous, with over 25 genes implicated in its pathogenesis thus far. OBJECTIVE We sought to elucidate the molecular basis of laterality disorders and associated congenital heart defects in a cohort of 30 unrelated probands of Arab-Muslim descent, using next-generation sequencing techniques. METHODS Detailed clinical phenotyping followed by whole-exome sequencing (WES) was pursued for each of the probands and their parents (when available). Sanger sequencing was used for segregation analysis of disease-causing mutations in the families. RESULTS Using WES, we reached a molecular diagnosis for 17 of the 30 probands (56.7%). Genes known to be associated with heterotaxy and/or primary ciliary dyskinesia, in which homozygous pathogenic or likely pathogenic variants were detected, included CFAP53 (CCDC11), CFAP298 (C21orf59), CFAP300, LRRC6, GDF1, DNAAF1, DNAH5, CCDC39, CCDC40, PKD1L1 and TTC25. Additionally, we detected a homozygous disease causing mutation in DAND5, as a novel recessive monogenic cause for heterotaxy in humans. Three additional probands were found to harbour variants of uncertain significance. These included variants in DNAH6, HYDIN, CELSR1 and CFAP46. CONCLUSIONS Our findings contribute to the current knowledge regarding monogenic causes of heterotaxy and its associated congenital heart defects and underscore the role of next-generation sequencing techniques in the diagnostic workup of such patients, and especially among consanguineous families.
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Affiliation(s)
- Yoav Bolkier
- Pediatric Heart Institute, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Metabolic Disease Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel
| | - Ortal Barel
- Genomic Unit, Sheba Cancer Research Center, Sheba Medical Center, Tel Hashomer, Israel.,The Wohl Institute for Translational Medicine, Sheba Medical Center, Tel Hashomer, Israel
| | - Dina Marek-Yagel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Metabolic Disease Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel
| | - Danit Atias-Varon
- Pediatric Nephrology Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel
| | - Maayan Kagan
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Pediatric Nephrology Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel
| | - Amir Vardi
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Department of Pediatric Cardiac Intensive Care, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel
| | - David Mishali
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Department of Pediatric Cardiac Intensive Care, Edmond Safra International Congenital Heart Center, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel
| | - Uriel Katz
- Pediatric Heart Institute, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Yishay Salem
- Pediatric Heart Institute, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Tal Tirosh-Wagner
- Pediatric Heart Institute, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Jeffrey M Jacobson
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Pediatric Imaging Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel
| | - Annick Raas-Rothschild
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,The Institute of Rare Diseases, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel
| | - Odelia Chorin
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,The Institute of Rare Diseases, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel
| | - Aviva Eliyahu
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Israel
| | - Yarden Sarouf
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Department of Pediatrics B, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel
| | - Omer Shlomovitz
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Department of Pediatrics B, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel
| | - Alvit Veber
- Metabolic Disease Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel
| | - Nechama Shalva
- Metabolic Disease Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel
| | - Elisheva Javasky
- Genomic Unit, Sheba Cancer Research Center, Sheba Medical Center, Tel Hashomer, Israel
| | - Yishay Ben Moshe
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Department of Pediatrics B, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel
| | - Orna Staretz-Chacham
- Metabolic Clinic, Division of Pediatrics, Soroka Medical Center, Ben-Gurion University, Beer Sheva, Israel
| | - Gideon Rechavi
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,The Wohl Institute for Translational Medicine, Sheba Medical Center, Tel Hashomer, Israel.,Sheba Cancer Research Center, Sheba Medical Center, Tel Hashomer, Israel
| | - Shrikant Mane
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Yair Anikster
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Metabolic Disease Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel.,The Wohl Institute for Translational Medicine, Sheba Medical Center, Tel Hashomer, Israel
| | - Asaf Vivante
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Department of Pediatrics B, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel.,Talpiot Medical Leadership Program, Sheba Medical Center, Tel Hashomer, Israel
| | - Ben Pode-Shakked
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel .,Metabolic Disease Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel.,Department of Pediatrics B, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel.,Talpiot Medical Leadership Program, Sheba Medical Center, Tel Hashomer, Israel
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Exome and genome sequencing for pediatric patients with congenital anomalies or intellectual disability: an evidence-based clinical guideline of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2021; 23:2029-2037. [PMID: 34211152 DOI: 10.1038/s41436-021-01242-6] [Citation(s) in RCA: 229] [Impact Index Per Article: 76.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 05/26/2021] [Accepted: 05/26/2021] [Indexed: 01/22/2023] Open
Abstract
PURPOSE To develop an evidence-based clinical practice guideline for the use of exome and genome sequencing (ES/GS) in the care of pediatric patients with one or more congenital anomalies (CA) with onset prior to age 1 year or developmental delay (DD) or intellectual disability (ID) with onset prior to age 18 years. METHODS The Pediatric Exome/Genome Sequencing Evidence-Based Guideline Work Group (n = 10) used the Grading of Recommendations Assessment, Development and Evaluation (GRADE) evidence to decision (EtD) framework based on the recent American College of Medical Genetics and Genomics (ACMG) systematic review, and an Ontario Health Technology Assessment to develop and present evidence summaries and health-care recommendations. The document underwent extensive internal and external peer review, and public comment, before approval by the ACMG Board of Directors. RESULTS The literature supports the clinical utility and desirable effects of ES/GS on active and long-term clinical management of patients with CA/DD/ID, and on family-focused and reproductive outcomes with relatively few harms. Compared with standard genetic testing, ES/GS has a higher diagnostic yield and may be more cost-effective when ordered early in the diagnostic evaluation. CONCLUSION We strongly recommend that ES/GS be considered as a first- or second-tier test for patients with CA/DD/ID.
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Marinakis NM, Svingou M, Veltra D, Kekou K, Sofocleous C, Tilemis FN, Kosma K, Tsoutsou E, Fryssira H, Traeger-Synodinos J. Phenotype-driven variant filtration strategy in exome sequencing toward a high diagnostic yield and identification of 85 novel variants in 400 patients with rare Mendelian disorders. Am J Med Genet A 2021; 185:2561-2571. [PMID: 34008892 DOI: 10.1002/ajmg.a.62338] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 04/26/2021] [Accepted: 04/27/2021] [Indexed: 11/10/2022]
Abstract
About 6000 to 7000 different rare disorders with suspected genetic etiologies have been described and almost 4500 causative gene(s) have been identified. The advent of next-generation sequencing (NGS) technologies has revolutionized genomic research and diagnostics, representing a major advance in the identification of pathogenic genetic variations. This study presents a 3-year experience from an academic genetics center, where 400 patients were referred for genetic analysis of disorders with unknown etiology. A phenotype-driven proband-only exome sequencing (ES) strategy was applied for the investigation of rare disorders, in the context of optimizing ES diagnostic yield and minimizing costs and time to definitive diagnosis. Overall molecular diagnostic yield reached 53% and characterized 243 pathogenic variants in 210 cases, 85 of which were novel and 148 known, contributing information to the community of disease and variant databases. ES provides an opportunity to resolve the genetic etiology of disorders and support appropriate medical management and genetic counseling. In cases with complex phenotypes, the identification of complex genotypes may contribute to more comprehensive clinical management. In the context of effective multidisciplinary collaboration between clinicians and laboratories, ES provides an efficient and appropriate tool for first-tier genomic analysis.
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Affiliation(s)
- Nikolaos M Marinakis
- Laboratory of Medical Genetics, St. Sophia's Children's Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Maria Svingou
- Laboratory of Medical Genetics, St. Sophia's Children's Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Danai Veltra
- Laboratory of Medical Genetics, St. Sophia's Children's Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Kyriaki Kekou
- Laboratory of Medical Genetics, St. Sophia's Children's Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Christalena Sofocleous
- Laboratory of Medical Genetics, St. Sophia's Children's Hospital, National and Kapodistrian University of Athens, Athens, Greece.,Research University Institute for the Study and Prevention of Genetic and Malignant Disease of Childhood, St. Sophia's Children's Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Faidon-Nikolaos Tilemis
- Laboratory of Medical Genetics, St. Sophia's Children's Hospital, National and Kapodistrian University of Athens, Athens, Greece.,Research University Institute for the Study and Prevention of Genetic and Malignant Disease of Childhood, St. Sophia's Children's Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Konstantina Kosma
- Laboratory of Medical Genetics, St. Sophia's Children's Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Eirini Tsoutsou
- Laboratory of Medical Genetics, St. Sophia's Children's Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Helen Fryssira
- Laboratory of Medical Genetics, St. Sophia's Children's Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Joanne Traeger-Synodinos
- Laboratory of Medical Genetics, St. Sophia's Children's Hospital, National and Kapodistrian University of Athens, Athens, Greece
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Novel compound heterozygous missense variants (c.G955A and c.A1822C) of CACNA2D4 likely causing autosomal recessive retinitis pigmentosa in a Chinese patient. 3 Biotech 2021; 11:208. [PMID: 33927996 DOI: 10.1007/s13205-021-02761-4] [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: 12/23/2020] [Accepted: 03/29/2021] [Indexed: 12/28/2022] Open
Abstract
Retinitis pigmentosa (RP) is a rare and heterogeneous group of inherited ocular diseases. However, the relationship between CACNA2D4 mutations and RP is not well understood. In this study, a Chinese autosomal recessive retinitis pigmentosa (arRP) pedigree was enrolled and targeted next-generation sequencing was employed for identifying the causative gene in the proband. These steps were followed by confirmatory Sanger sequencing and segregation analysis. RNA-sequencing (RNA-seq) data and semi-quantitative reverse transcription polymerase chain reaction analysis were then applied to examine the expressions in the human and mouse tissues. Novel compound heterozygous, deleterious missense variants of the CACNA2D4 gene, NM_172364.4: c.G955A (p.D319N) and c.A1822C (p.I608L), were identified in the arRP pedigree, co-segregating with the clinical phenotype in the patient. The CACNA2D4 protein is highly conserved among species. The CACNA2D4 mRNA expression showed the highest expression in the retina of humans and in the later four developmental stages/times of retinal tissues in mice, indicating its role in retina/eye functions and developments. This study is the first to identify novel compound heterozygous mutations c.G955A (p.D319N) and c.A1822C (p.I608L) in the CACNA2D4 gene. These might be disease-causing mutations, thereby extending the mutational spectra. The identification of pathogenic CACNA2D4 variants is expected to enhance our understanding of the genotype-phenotype correlations of arRP for disease diagnosis and genetic counseling. The relationship between the CACNA2D4 variants and diseases/phenotypes other than RP has also been reviewed and discussed in this paper.
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37
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Molina-Ramírez LP, Kyle C, Ellingford JM, Wright R, Taylor A, Bhaskar SS, Campbell C, Jackson H, Fairclough A, Rousseau A, Burghel GJ, Dutton L, Banka S, Briggs TA, Clayton-Smith J, Douzgou S, Jones EA, Kingston HM, Kerr B, Ealing J, Somarathi S, Chandler KE, Stuart HM, Burkitt-Wright EM, Newman WG, Bruce IA, Black GC, Gokhale D. Personalised virtual gene panels reduce interpretation workload and maintain diagnostic rates of proband-only clinical exome sequencing for rare disorders. J Med Genet 2021; 59:393-398. [PMID: 33879512 PMCID: PMC8961756 DOI: 10.1136/jmedgenet-2020-107303] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 01/17/2021] [Accepted: 02/14/2021] [Indexed: 01/20/2023]
Abstract
Purpose The increased adoption of genomic strategies in the clinic makes it imperative for diagnostic laboratories to improve the efficiency of variant interpretation. Clinical exome sequencing (CES) is becoming a valuable diagnostic tool, capable of meeting the diagnostic demand imposed by the vast array of different rare monogenic disorders. We have assessed a clinician-led and phenotype-based approach for virtual gene panel generation for analysis of targeted CES in patients with rare disease in a single institution. Methods Retrospective survey of 400 consecutive cases presumed by clinicians to have rare monogenic disorders, referred on singleton basis for targeted CES. We evaluated diagnostic yield and variant workload to characterise the usefulness of a clinician-led approach for generation of virtual gene panels that can incorporate up to three different phenotype-driven gene selection methods. Results Abnormalities of the nervous system (54.5%), including intellectual disability, head and neck (19%), skeletal system (16%), ear (15%) and eye (15%) were the most common clinical features reported in referrals. Combined phenotype-driven strategies for virtual gene panel generation were used in 57% of cases. On average, 7.3 variants (median=5) per case were retained for clinical interpretation. The overall diagnostic rate of proband-only CES using personalised phenotype-driven virtual gene panels was 24%. Conclusions Our results show that personalised virtual gene panels are a cost-effective approach for variant analysis of CES, maintaining diagnostic yield and optimising the use of resources for clinical genomic sequencing in the clinic.
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Affiliation(s)
- Leslie Patricia Molina-Ramírez
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK.,North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Claire Kyle
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Jamie M Ellingford
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK.,North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Ronnie Wright
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Algy Taylor
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Sanjeev S Bhaskar
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Christopher Campbell
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Harriet Jackson
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Adele Fairclough
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Abigail Rousseau
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - George J Burghel
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Laura Dutton
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Siddharth Banka
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK.,North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Tracy A Briggs
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK.,North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Jill Clayton-Smith
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK.,North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Sofia Douzgou
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK.,North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Elizabeth A Jones
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK.,Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, UK
| | - Helen M Kingston
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Bronwyn Kerr
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - John Ealing
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, UK.,Department of Neurology, Salford Royal NHS Foundation Trust, Salford, Salford, UK
| | - Suresh Somarathi
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Kate E Chandler
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK.,North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Helen M Stuart
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK.,North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Emma Mm Burkitt-Wright
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK.,North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - William G Newman
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK.,North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Iain A Bruce
- Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK.,Paediatric ENT Department, Royal Manchester Children's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Graeme C Black
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK .,North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - David Gokhale
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
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Abstract
Neurodevelopmental disorders are the most prevalent chronic medical conditions encountered in pediatric primary care. In addition to identifying appropriate descriptive diagnoses and guiding families to evidence-based treatments and supports, comprehensive care for individuals with neurodevelopmental disorders includes a search for an underlying etiologic diagnosis, primarily through a genetic evaluation. Identification of an underlying genetic etiology can inform prognosis, clarify recurrence risk, shape clinical management, and direct patients and families to condition-specific resources and supports. Here we review the utility of genetic testing in patients with neurodevelopmental disorders and describe the three major testing modalities and their yields - chromosomal microarray, exome sequencing (with/without copy number variant calling), and FMR1 CGG repeat analysis for fragile X syndrome. Given the diagnostic yield of genetic testing and the potential for clinical and personal utility, there is consensus that genetic testing should be offered to all patients with global developmental delay, intellectual disability, and/or autism spectrum disorder. Despite this recommendation, data suggest that a minority of children with autism spectrum disorder and intellectual disability have undergone genetic testing. To address this gap in care, we describe a structured but flexible approach to facilitate integration of genetic testing into clinical practice across pediatric specialties and discuss future considerations for genetic testing in neurodevelopmental disorders to prepare pediatric providers to care for patients with such diagnoses today and tomorrow.
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Affiliation(s)
- Juliann M. Savatt
- Autism & Developmental Medicine Institute, Geisinger, Danville, PA, United States
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Fontes Marx M, Ataguba JE, de Vries J, Wonkam A. Systematic Review of the Economic Evaluation of Returning Incidental Findings in Genomic Research. Front Public Health 2021; 9:697381. [PMID: 34277554 PMCID: PMC8281014 DOI: 10.3389/fpubh.2021.697381] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 06/03/2021] [Indexed: 12/18/2022] Open
Abstract
Objectives: Discussions regarding who and how incidental findings (IFs) should be returned and the ethics behind returning IFs have increased dramatically over the years. However, information on the cost and benefits of returning IFs to patients remains scanty. Design: This study systematically reviews the economic evaluation of returning IFs in genomic sequencing. We searched for published articles on the cost-effectiveness, cost-benefit, and cost-utility of IFs in Medline, Scopus, PubMed, and Google Scholar. Results: We found six published articles that met the eligibility criteria of this study. Two articles used cost analysis only, one used cost-benefit analysis only, two used both cost analysis and cost-effectiveness, and one used both cost-benefit analysis and cost-utility to describe the cost of returning IFs in genomic sequencing. Conclusion: While individuals value the IF results and are willing to pay for them, the cost of returning IFs depends on the primary health condition of the patient. Although patients were willing to pay, there was no clear evidence that returning IFs might be cost-effective. More rigorous economic evaluation studies of IFs are needed to determine whether or not the cost of returning IFs is beneficial to the patient.
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Affiliation(s)
- Mayara Fontes Marx
- Department of Pathology, Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - John E Ataguba
- Health Economics Unit, School of Public Health and Family Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Jantina de Vries
- Department of Pathology, Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Ambroise Wonkam
- Department of Pathology, Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,Institute to Infectious Disease and Molecular Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
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40
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Simpson BN, Khattar D, Saal H, Prada CE, Choo D, Marcheschi L, Wiley S, Hopkin RJ. CHARGE syndrome in the era of molecular diagnosis: Similar outcomes in those without coloboma or choanal atresia. Eur J Med Genet 2020; 64:104103. [PMID: 33189935 DOI: 10.1016/j.ejmg.2020.104103] [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: 06/11/2020] [Revised: 11/01/2020] [Accepted: 11/09/2020] [Indexed: 11/17/2022]
Abstract
CHARGE syndrome (OMIM 214800) is a condition characterized by multisystem involvement with CHD7 pathogenic mutations leading to disease in the majority of patients. Discovery of the molecular cause of CHARGE unmasked a larger phenotypic spectrum than was previously appreciated. Within our interdisciplinary CHARGE syndrome program, we sought to characterize our CHD7-positive CHARGE cohort without coloboma or choanal atresia, highlighting complications and outcomes. We describe 18 individuals with CHD7-confirmed diagnosis from 15 families. The most sensitive finding in the cohort was temporal bone malformations, present in 13/15 individuals. Individuals had an average of 1.6 major features and 3.3 minor features defined by the Blake et al. guidelines. Despite lack of major features or major malformations, the majority of individuals continued to have difficulties with pneumonia, aspiration, secretion management and motility issues that greatly impacted their lives. Our findings illustrate the need for molecular testing and timely recognition given that the major co-morbidities are frequently experienced by patients with the mildest clinical spectrum of CHARGE syndrome.
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Affiliation(s)
- Brittany N Simpson
- Cincinnati Children's Hospital Medical Center: Division of Human Genetics, United States; Cincinnati Children's Hospital Medical Center: Department of Pediatrics, University of Cincinnati College of Medicine, United States.
| | - Divya Khattar
- Cincinnati Children's Hospital Medical Center: Division of Human Genetics, United States; Cincinnati Children's Hospital Medical Center: Department of Pediatrics, University of Cincinnati College of Medicine, United States
| | - Howard Saal
- Cincinnati Children's Hospital Medical Center: Division of Human Genetics, United States; Cincinnati Children's Hospital Medical Center: Department of Pediatrics, University of Cincinnati College of Medicine, United States
| | - Carlos E Prada
- Cincinnati Children's Hospital Medical Center: Division of Human Genetics, United States; Cincinnati Children's Hospital Medical Center: Department of Pediatrics, University of Cincinnati College of Medicine, United States
| | - Daniel Choo
- Cincinnati Children's Hospital Medical Center, Division of Pediatric Otolaryngology, University of Cincinnati College of Medicine, Department of Otolaryngology Head and Neck Surgery, United States
| | - Lucy Marcheschi
- Cincinnati Children's Hospital Medical Center: Division of Pediatric Otolaryngology, United States
| | - Susan Wiley
- Cincinnati Children's Hospital Medical Center: Division of Developmental and Behavioral Pediatrics, United States
| | - Robert J Hopkin
- Cincinnati Children's Hospital Medical Center: Division of Human Genetics, United States; Cincinnati Children's Hospital Medical Center: Department of Pediatrics, University of Cincinnati College of Medicine, United States
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41
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Beyzaei Z, Geramizadeh B, Karimzadeh S. Diagnosis of hepatic glycogen storage disease patients with overlapping clinical symptoms by massively parallel sequencing: a systematic review of literature. Orphanet J Rare Dis 2020; 15:286. [PMID: 33054851 PMCID: PMC7557034 DOI: 10.1186/s13023-020-01573-8] [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: 02/01/2020] [Accepted: 10/05/2020] [Indexed: 12/17/2022] Open
Abstract
Background Glycogen storage diseases (GSDs) with liver involvement are complex disorders with similar manifestations. Currently, the main diagnostic methods such as tissue diagnosis, either histopathology or enzyme assay, are invasive. Meanwhile, GSDs are diseases with significant genetic heterogeneity, and gene-sequencing methods can be more useful. This systematic review aims to review the literature to assess the value of massively parallel sequencing in the diagnosis of GSDs on patients with previously undiagnosed hepatic involvement. Methods Relevant studies identified in the MEDLINE/PubMed, EMBASE, Cochrane Library, Scopus, and Web of Science Core Collection databases up to July 2019 with no time and language restrictions. Publications were included in the review if they analyzed GSDs with hepatic involvement (GSD I, GSD III, GSD IV, GSD VI, GSD IX), using targeted gene sequencing (TGS) or exome sequencing (ES). Results Eleven studies were included in this systematic review. ES demonstrated a 93% diagnostic yield. These methods correctly distinguished all types of pathogenic variants. The diagnostic yield of the TGS method was around 79.7%. Conclusions According to our results, TGS analysis can be considered as the first-line diagnostic method with valuable results and ES can be used to diagnose complex cases of GSD with liver involvement. Overall, these molecular methods are considered as accurate diagnostic tools, which expedite correct diagnosis and treatment with significant cost-effectiveness by reducing unnecessary and inaccurate tests. PROSPERO registration CRD42020139931. Registered 8 January 2020.
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Affiliation(s)
- Zahra Beyzaei
- Transplant Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Bita Geramizadeh
- Transplant Research Center, Shiraz University of Medical Sciences, Shiraz, Iran. .,Department of Pathology, Shiraz University of Medical Sciences, Zand St., Shiraz, Iran.
| | - Sara Karimzadeh
- Shiraz Medical School Library, Shiraz University of Medical Sciences, Shiraz, Iran
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Schiavoni S, Spagnoli C, Rizzi S, Salerno GG, Frattini D, Pisani F, Fusco C. Paediatric-onset hereditary spastic paraplegias: a retrospective cohort study. Dev Med Child Neurol 2020; 62:1068-1074. [PMID: 32277485 DOI: 10.1111/dmcn.14547] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/11/2020] [Indexed: 12/12/2022]
Abstract
AIM To describe the clinical and neurogenetic spectrum of paediatric-onset hereditary spastic paraplegias (HSPs) diagnosed in our unit. METHOD We report on 47 patients (30 males, 17 females; mean [SD] age 12y 7mo [6y 2mo], range 4-34y) clinically diagnosed with an HSP at the Child Neurology Unit, IRCCS-ASMN (Reggio Emilia, Italy) between 1990 and 2018, who were genetically investigated by means of single-gene direct sequencing and/or next-generation sequencing technologies (targeted panels, whole-exome sequencing [WES]). RESULTS Complex forms prevailed slightly (n=26), autosomal dominant being the main inheritance pattern (n=11), followed by recessive (n=5) and X-linked (n=1). A definite genetic diagnosis was achieved in 17 patients. Spastic paraplegia 3A (n=4) was the most frequent cause of autosomal dominant HSP in our cohort, while no genetic variant prevailed in autosomal recessive forms and pathogenic/likely pathogenic variants were disclosed in a wide range of different genes. INTERPRETATION We found wide phenotypic and genetic heterogeneity. With increasing accessibility to WES, a higher number of patients receive a diagnosis, allowing detection of variants in ultra-rare disease-causing genes and refining genotype-phenotype correlations. WHAT THIS PAPER ADDS A genetic diagnosis of paediatric-onset hereditary spastic paraplegia was achieved in one-third of patients. Pathogenic/likely pathogenic variants in rare genes were found. Genotypic and phenotypic heterogeneity favours targeted panel/whole-exome sequencing for diagnosis.
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Affiliation(s)
- Silvia Schiavoni
- Child Neurology Unit, Department of Paediatrics, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Carlotta Spagnoli
- Child Neurology Unit, Department of Paediatrics, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Susanna Rizzi
- Child Neurology Unit, Department of Paediatrics, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Grazia G Salerno
- Child Neurology Unit, Department of Paediatrics, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Daniele Frattini
- Child Neurology Unit, Department of Paediatrics, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Francesco Pisani
- Child Neuropsychiatry Unit, Neuroscience Division, Medicine & Surgery Department, University of Parma, Parma, Italy
| | - Carlo Fusco
- Child Neurology Unit, Department of Paediatrics, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy.,Paediatric Neurophysiology Laboratory, Department of Paediatrics, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
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43
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Melas M, Subbiah S, Saadat S, Rajurkar S, McDonnell KJ. The Community Oncology and Academic Medical Center Alliance in the Age of Precision Medicine: Cancer Genetics and Genomics Considerations. J Clin Med 2020; 9:E2125. [PMID: 32640668 PMCID: PMC7408957 DOI: 10.3390/jcm9072125] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 06/28/2020] [Accepted: 07/02/2020] [Indexed: 12/15/2022] Open
Abstract
Recent public policy, governmental regulatory and economic trends have motivated the establishment and deepening of community health and academic medical center alliances. Accordingly, community oncology practices now deliver a significant portion of their oncology care in association with academic cancer centers. In the age of precision medicine, this alliance has acquired critical importance; novel advances in nucleic acid sequencing, the generation and analysis of immense data sets, the changing clinical landscape of hereditary cancer predisposition and ongoing discovery of novel, targeted therapies challenge community-based oncologists to deliver molecularly-informed health care. The active engagement of community oncology practices with academic partners helps with meeting these challenges; community/academic alliances result in improved cancer patient care and provider efficacy. Here, we review the community oncology and academic medical center alliance. We examine how practitioners may leverage academic center precision medicine-based cancer genetics and genomics programs to advance their patients' needs. We highlight a number of project initiatives at the City of Hope Comprehensive Cancer Center that seek to optimize community oncology and academic cancer center precision medicine interactions.
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Affiliation(s)
- Marilena Melas
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43205, USA;
| | - Shanmuga Subbiah
- Department of Medical Oncology and Therapeutics Research, City of Hope Comprehensive Cancer Center, Glendora, CA 91741, USA;
| | - Siamak Saadat
- Department of Medical Oncology and Therapeutics Research, City of Hope Comprehensive Cancer Center, Colton, CA 92324, USA;
| | - Swapnil Rajurkar
- Department of Medical Oncology and Therapeutics Research, City of Hope Comprehensive Cancer Center, Upland, CA 91786, USA;
| | - Kevin J. McDonnell
- Department of Medical Oncology and Therapeutics Research, City of Hope Comprehensive Cancer Center and Beckman Research Institute, Duarte, CA 91010, USA
- Center for Precision Medicine, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
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Ross JP, Dion PA, Rouleau GA. Exome sequencing in genetic disease: recent advances and considerations. F1000Res 2020; 9:F1000 Faculty Rev-336. [PMID: 32431803 PMCID: PMC7205110 DOI: 10.12688/f1000research.19444.1] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/30/2020] [Indexed: 12/14/2022] Open
Abstract
Over the past decade, exome sequencing (ES) has allowed significant advancements to the field of disease research. By targeting the protein-coding regions of the genome, ES combines the depth of knowledge on protein-altering variants with high-throughput data generation and ease of analysis. New discoveries continue to be made using ES, and medical science has benefitted both theoretically and clinically from its continued use. In this review, we describe recent advances and successes of ES in disease research. Through selected examples of recent publications, we explore how ES continues to be a valuable tool to find variants that might explain disease etiology or provide insight into the biology underlying the disease. We then discuss shortcomings of ES in terms of variant discoveries made by other sequencing technologies that would be missed because of the scope and techniques of ES. We conclude with a brief outlook on the future of ES, suggesting that although newer and more thorough sequencing methods will soon supplant ES, its results will continue to be useful for disease research.
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Affiliation(s)
- Jay P. Ross
- Department of Human Genetics, McGill University, 3640 University, Montréal, QC, H3A 0C7, Canada
- Montreal Neurological Institute and Hospital, McGill University, 3801 University, Montréal, QC, H3A 2B4, Canada
| | - Patrick A. Dion
- Montreal Neurological Institute and Hospital, McGill University, 3801 University, Montréal, QC, H3A 2B4, Canada
- Department of Neurology and Neurosurgery, McGill University, 3801 University, Montréal, QC, H3A 2B4, Canada
| | - Guy A. Rouleau
- Department of Human Genetics, McGill University, 3640 University, Montréal, QC, H3A 0C7, Canada
- Montreal Neurological Institute and Hospital, McGill University, 3801 University, Montréal, QC, H3A 2B4, Canada
- Department of Neurology and Neurosurgery, McGill University, 3801 University, Montréal, QC, H3A 2B4, Canada
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Wang H, Qian Y, Lu Y, Qin Q, Lu G, Cheng G, Zhang P, Yang L, Wu B, Zhou W. Clinical utility of 24-h rapid trio-exome sequencing for critically ill infants. NPJ Genom Med 2020; 5:20. [PMID: 32411386 PMCID: PMC7200743 DOI: 10.1038/s41525-020-0129-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 03/26/2020] [Indexed: 12/15/2022] Open
Abstract
Genetic diseases are a leading cause of death in infants in the intensive care setting; therefore, rapid and accurate genetic diagnosis is desired. To validate 24-h trio-exome sequencing (TES), samples from probands and their parents were processed by the AmpliSeq /Ion S5XL platform in a hospital clinical laboratory. Infants from the intensive care unit (ICU) suspected of having a genetic disease were enrolled. Regular and 24-h TES using the Agilent SureSelect capture kit/Illumina platform were performed on all samples in parallel. Of 33 enrolled infants, 23 received positive results with rapid TES, and an additional two diagnoses were achieved with regular TES. Among the 23 diagnosed patients, 10 experienced changes in medical management, such as hematopoietic stem cell transplant. Ten diagnosed cases were discharged prior to receiving the regular TES results; six received timely symptom control, and four withdrew medical support. Rapid TES enabled faster time to diagnosis, which resulted in an overall decrease in length of hospital stay. The 24-h TES can serve as a rapid response tool for patients with suspected monogenic disorders and can guide clinical decision-making in urgent cases.
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Affiliation(s)
- Huijun Wang
- 1Center for Molecular Medicine, Children's Hospital of Fudan University, 201102 Shanghai, China
| | - Yanyan Qian
- 1Center for Molecular Medicine, Children's Hospital of Fudan University, 201102 Shanghai, China
| | - Yulan Lu
- 1Center for Molecular Medicine, Children's Hospital of Fudan University, 201102 Shanghai, China
| | - Qian Qin
- 1Center for Molecular Medicine, Children's Hospital of Fudan University, 201102 Shanghai, China
| | - Guoping Lu
- 2Pediatric intensive care unit, Children's Hospital of Fudan University, 201102 Shanghai, China
| | - Guoqiang Cheng
- 3Department of Neonates, Key Laboratory of Neonatal Diseases, Ministry of Health, Children's Hospital of Fudan University, 201102 Shanghai, China
| | - Ping Zhang
- 1Center for Molecular Medicine, Children's Hospital of Fudan University, 201102 Shanghai, China
| | - Lin Yang
- 1Center for Molecular Medicine, Children's Hospital of Fudan University, 201102 Shanghai, China
| | - Bingbing Wu
- 1Center for Molecular Medicine, Children's Hospital of Fudan University, 201102 Shanghai, China
| | - Wenhao Zhou
- 1Center for Molecular Medicine, Children's Hospital of Fudan University, 201102 Shanghai, China.,2Pediatric intensive care unit, Children's Hospital of Fudan University, 201102 Shanghai, China
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Luksic D, Sukhu R, Koval C, Cho MT, Espinal A, Rufino K, Loarte TV, Chung WK, Wynn J. A qualitative study of Latinx parents' experiences of clinical exome sequencing. J Genet Couns 2020; 29:574-586. [PMID: 32298033 DOI: 10.1002/jgc4.1276] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 02/25/2020] [Accepted: 02/26/2020] [Indexed: 01/29/2023]
Abstract
Clinical exome sequencing (CES) is an established method for genetic diagnosis and is used widely in clinical practice. Studies of the parental experience of CES, which inform guidelines for best practices for genetic counseling, have been predominately comprised of White, non-Latinx participants. The aim of this study was to explore the parental experiences of CES in a Latinx community and to understand how their experiences are influenced by culture and language. We conducted semi-structured interviews in English and Spanish with 38 Latinx parents of children who had CES. Some of the themes that emerged were common to those previously identified, including a sense of obligation to pursue testing and a mixed emotional response to their child's results. Parents who had lower education level and/or received care from a provider who did not share their language had more confusion about their child's CES results and greater dissatisfaction with care compared with parents who had higher education level and/or received care from a provider who spoke their language. We also found evidence of hampered shared decision making and/or disempowered patient decision making regarding CES testing. Our data suggest unique needs for Latinx families having CES, particularly those who are non-English speaking when an interpreter is used. Our data support the value in continuing to take steps to improve culturally competent care by improving interpretation services and recruiting and training a genetic workforce that is ethnically, linguistically, and culturally diverse.
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Affiliation(s)
- Daniel Luksic
- Graduate School of Genetic Counseling, Sarah Lawrence College, Bronxville, NY, USA
| | - Radha Sukhu
- Graduate School of Genetic Counseling, Sarah Lawrence College, Bronxville, NY, USA
| | - Carrie Koval
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Megan T Cho
- Graduate School of Genetic Counseling, Sarah Lawrence College, Bronxville, NY, USA
| | - Aileen Espinal
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Katiana Rufino
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Tania Vasquez Loarte
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Wendy K Chung
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA.,Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Julia Wynn
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
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Inositol 1,4,5-Trisphosphate Receptors in Human Disease: A Comprehensive Update. J Clin Med 2020; 9:jcm9041096. [PMID: 32290556 PMCID: PMC7231134 DOI: 10.3390/jcm9041096] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 03/30/2020] [Accepted: 04/10/2020] [Indexed: 12/22/2022] Open
Abstract
Inositol 1,4,5-trisphosphate receptors (ITPRs) are intracellular calcium release channels located on the endoplasmic reticulum of virtually every cell. Herein, we are reporting an updated systematic summary of the current knowledge on the functional role of ITPRs in human disorders. Specifically, we are describing the involvement of its loss-of-function and gain-of-function mutations in the pathogenesis of neurological, immunological, cardiovascular, and neoplastic human disease. Recent results from genome-wide association studies are also discussed.
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48
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Mollison L, O'Daniel JM, Henderson GE, Berg JS, Skinner D. Parents' perceptions of personal utility of exome sequencing results. Genet Med 2020; 22:752-757. [PMID: 31857707 PMCID: PMC7192542 DOI: 10.1038/s41436-019-0730-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 12/04/2019] [Indexed: 12/29/2022] Open
Abstract
PURPOSE Clinical genome or exome sequencing (GS/ES) provides a diagnosis for many individuals with suspected genetic disorders, but also yields negative or uncertain results for the majority. This study examines how parents of a child with an undiagnosed condition attribute personal utility to all types of ES results. METHODS Return of 31 exome sequencing results was observed during clinic sessions, followed by semistructured interviews with parents one month later. Observations and interviews were recorded and transcribed. Data display matrices were used for content analysis and systematic comparisons of parents' perceptions of utility. RESULTS ES results could not provide all the answers to parents' questions, especially in cases of clinically uninformative results, but parents nonetheless attributed utility to the knowledge gained. Parents across all results categories used the genomic information to rule out possible causes, end or postpone the diagnostic odyssey, and shift focus to treatment and management of symptoms. CONCLUSION This study suggests that parents value even uninformative ES results while expressing hope for future discoveries. As pediatric genetics moves toward GS/ES as a first-tier test, how parents perceive the personal utility of negative or uncertain results is an important topic for genetic counseling and further research.
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Affiliation(s)
- Lonna Mollison
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Julianne M O'Daniel
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Gail E Henderson
- Department of Social Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jonathan S Berg
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Debra Skinner
- FPG Child Development Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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Malinowski J, Miller DT, Demmer L, Gannon J, Pereira EM, Schroeder MC, Scheuner MT, Tsai ACH, Hickey SE, Shen J. Systematic evidence-based review: outcomes from exome and genome sequencing for pediatric patients with congenital anomalies or intellectual disability. Genet Med 2020; 22:986-1004. [PMID: 32203227 PMCID: PMC7222126 DOI: 10.1038/s41436-020-0771-z] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 02/24/2020] [Accepted: 02/25/2020] [Indexed: 12/31/2022] Open
Abstract
Purpose Exome and genome sequencing (ES/GS) are performed frequently in patients with congenital anomalies, developmental delay, or intellectual disability (CA/DD/ID), but the impact of results from ES/GS on clinical management and patient outcomes is not well characterized. A systematic evidence review (SER) can support future evidence-based guideline development for use of ES/GS in this patient population. Methods We undertook an SER to identify primary literature from January 2007 to March 2019 describing health, clinical, reproductive, and psychosocial outcomes resulting from ES/GS in patients with CA/DD/ID. A narrative synthesis of results was performed. Results We retrieved 2654 publications for full-text review from 7178 articles. Only 167 articles met our inclusion criteria, and these were primarily case reports or small case series of fewer than 20 patients. The most frequently reported outcomes from ES/GS were changes to clinical management or reproductive decision-making. Two studies reported on the reduction of mortality or morbidity or impact on quality of life following ES/GS. Conclusion There is evidence that ES/GS for patients with CA/DD/ID informs clinical and reproductive decision-making, which could lead to improved outcomes for patients and their family members. Further research is needed to generate evidence regarding health outcomes to inform robust guidelines regarding ES/GS in the care of patients with CA/DD/ID.
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Affiliation(s)
| | - David T Miller
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Laurie Demmer
- Atrium Health's Levine Children's Hospital, Charlotte, NC, USA
| | - Jennifer Gannon
- Division of Clinical Genetics, Children's Mercy Hospital, Kansas City, MO, USA.,Department of Pediatrics, University of Missouri, Kansas City, MO, USA
| | - Elaine Maria Pereira
- Division of Clinical Genetics, Department of Pediatrics, Columbia University Medical Center, New York, NY, USA
| | - Molly C Schroeder
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Maren T Scheuner
- Division of Medical Genetics, Department of Pediatrics and Division of Hematology-Oncology, Department of Medicine, University of California, San Francisco, CA, USA.,San Francisco VA Healthcare System, San Francisco, CA, USA
| | - Anne Chun-Hui Tsai
- Section of Clinical Genetics and Metabolism, Department of Pediatrics, University of Colorado, Aurora, CO, USA
| | - Scott E Hickey
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Jun Shen
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
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Genome-Wide Sequencing for Unexplained Developmental Disabilities or Multiple Congenital Anomalies: A Health Technology Assessment. ONTARIO HEALTH TECHNOLOGY ASSESSMENT SERIES 2020; 20:1-178. [PMID: 32194879 PMCID: PMC7080457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
BACKGROUND People with unexplained developmental disabilities or multiple congenital anomalies might have had many biochemical, metabolic, and genetic tests for a period of years without receiving a diagnosis. A genetic diagnosis can help these people and their families better understand their condition and may help them to connect with others who have the same condition. Ontario Health (Quality), in collaboration with the Canadian Agency for Drugs and Technologies in Health (CADTH) conducted a health technology assessment about the use of genome-wide sequencing for patients with unexplained developmental disabilities or multiple congenital anomalies. Ontario Health (Quality) evaluated the effectiveness, cost-effectiveness, and budget impact of publicly funding genome-wide sequencing. We also conducted interviews with patients and examined the quantitative evidence of preferences and values literature to better understand the patient preferences and values for these tests. METHODS Ontario Health (Quality) performed a systematic literature search of the clinical evidence. We assessed the risk of bias of each included study using the Risk of Bias Assessment tool for Non-randomized Studies (RoBANS) and the quality of the body of evidence according to the Grading of Recommendations Assessment, Development, and Evaluation (GRADE) Working Group criteria. We also performed a search of the quantitative evidence and undertook direct patient engagement to ascertain patient preferences for genetic testing for unexplained developmental disabilities or multiple congenital anomalies. CADTH performed a review of qualitative literature about patient perspectives and experiences, and a review of ethical issues.Ontario Health (Quality) performed an economic literature review of genome-wide sequencing in people with unexplained developmental disabilities or multiple congenital anomalies. Although we found eight published cost-effectiveness studies, none completely addressed our research question. Therefore, we conducted a primary economic evaluation using a discrete event simulation model. Owing to its high cost and early stage of clinical implementation, whole exome sequencing is primarily used for people who do not have a diagnosis from standard testing (referred to here as whole exome sequencing after standard testing; standard testing includes chromosomal microarray and targeted single-gene tests or gene panels). Therefore, in our first analysis, we evaluated the cost-effectiveness of whole exome sequencing after standard testing versus standard testing alone. In our second analysis, we explored the cost-effectiveness of whole exome and whole genome sequencing used at various times in the diagnostic pathway (e.g., first tier, second tier, after standard testing) versus standard testing. We also estimated the budget impact of publicly funding genome-wide sequencing in Ontario for the next 5 years. RESULTS Forty-four studies were included in the clinical evidence review. The overall diagnostic yield of genome-wide sequencing for people with unexplained development disability and multiple congenital anomalies was 37%, but we are very uncertain about this estimate (GRADE: Very Low). Compared with standard genetic testing of chromosomal microarray and targeted single-gene tests or gene panels, genome-wide sequencing could have a higher diagnostic yield (GRADE: Low). As well, for some who are tested, genome-wide sequencing prompts some changes to medications, treatments, and referrals to specialists (GRADE: Very Low).Whole exome sequencing after standard testing cost an additional $3,261 per patient but was more effective than standard testing alone. For every 1,000 persons tested, using whole exome sequencing after standard testing would lead to an additional 240 persons with a molecular diagnosis, 272 persons with any positive finding, and 46 persons with active treatment change (modifications to medications, procedures, or treatment). The resulting incremental cost-effectiveness ratios (ICERs) were $13,591 per additional molecular diagnosis. The use of genome-wide sequencing early in the diagnostic pathway (e.g., as a first- or second-tier test) can save on costs and improve diagnostic yields over those of standard testing. Results remained robust when parameters and assumptions were varied.Our budget impact analysis showed that, if whole exome sequencing after standard testing continues to be funded through Ontario's Out-of-Country Prior Approval Program, its budget impact would range from $4 to $5 million in years 1 to 5. If whole exome sequencing becomes publicly funded in Ontario (not through the Out-of-Country Prior Approval Program), the budget impact would be about $9 million yearly. We also found that using whole exome sequencing as a second-tier test would lead to cost savings ($3.4 million per 1,000 persons tested yearly).Participants demonstrated consistent motivations for and expectations of obtaining a diagnosis for unexplained developmental delay or congenital anomalies through genome-wide sequencing. Patients and families greatly value the support and information they receive through genetic counselling when considering genome-wide sequencing and learning of a diagnosis. CONCLUSIONS Genome-wide sequencing could have a higher diagnostic yield than standard testing for people with unexplained developmental disabilities or multiple congenital anomalies. Genome-wide sequencing can also prompt some changes to medications, treatments, and referrals to specialists for some people tested; however, we are very uncertain about this. Genome-wide sequencing could be a cost-effective strategy when used after standard testing to diagnose people with unexplained developmental disabilities or multiple congenital anomalies. It could also lead to cost savings when used earlier in the diagnostic pathway. Patients and families consistently noted a benefit from seeking a diagnosis through genetic testing.
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