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Weymann D, Buckell J, Fahr P, Loewen R, Ehman M, Pollard S, Friedman JM, Stockler-Ipsiroglu S, Elliott AM, Wordsworth S, Buchanan J, Regier DA. Health Care Costs After Genome-Wide Sequencing for Children With Rare Diseases in England and Canada. JAMA Netw Open 2024; 7:e2420842. [PMID: 38985473 PMCID: PMC11238031 DOI: 10.1001/jamanetworkopen.2024.20842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 05/07/2024] [Indexed: 07/11/2024] Open
Abstract
Importance Etiologic diagnoses for rare diseases can involve a diagnostic odyssey, with repeated health care interactions and inconclusive diagnostics. Prior studies reported cost savings associated with genome-wide sequencing (GWS) compared with cytogenetic or molecular testing through rapid genetic diagnosis, but there is limited evidence on whether diagnosis from GWS is associated with reduced health care costs. Objective To measure changes in health care costs after diagnosis from GWS for Canadian and English children with suspected rare diseases. Design, Setting, and Participants This cohort study was a quasiexperimental retrospective analysis across 3 distinct English and Canadian cohorts, completed in 2023. Mixed-effects generalized linear regression was used to estimate associations between GWS and costs in the 2 years before and after GWS. Difference-in-differences regression was used to estimate associations of genetic diagnosis and costs. Costs are in 2019 US dollars. GWS was conducted in a research setting (Genomics England 100 000 Genomes Project [100KGP] and Clinical Assessment of the Utility of Sequencing and Evaluation as a Service [CAUSES] Research Clinic) or clinical outpatient setting (publicly reimbursed GWS in British Columbia [BC], Canada). Participants were children with developmental disorders, seizure disorders, or both undergoing GWS between 2014 and 2019. Data were analyzed from April 2021 to September 2023. Exposures GWS and genetic diagnosis. Main Outcomes and Measures Annual health care costs and diagnostic costs per child. Results Study cohorts included 7775 patients in 100KGP, among whom 788 children had epilepsy (mean [SD] age at GWS, 11.6 [11.1] years; 400 female [50.8%]) and 6987 children had an intellectual disability (mean [SD] age at GWS, 8.2 [8.4] years; 2750 female [39.4%]); 77 patients in CAUSES (mean [SD] age at GWS, 8.5 [4.4] years; 33 female [42.9%]); and 118 publicly reimbursed GWS recipients from BC (mean [SD] age at GWS, 5.5 [5.2] years; 58 female [49.2%]). GWS diagnostic yield was 143 children (18.1%) for those with epilepsy and 1323 children (18.9%) for those with an intellectual disability in 100KGP, 47 children (39.8%) in the BC publicly reimbursed setting, and 42 children (54.5%) in CAUSES. Mean annual per-patient spending over the study period was $5283 (95% CI, $5121-$5427) for epilepsy and $3373 (95% CI, $3322-$3424) for intellectual disability in the 100KGP, $724 (95% CI, $563-$886) in CAUSES, and $1573 (95% CI, $1372-$1773) in the BC reimbursed setting. Receiving a genetic diagnosis from GWS was not associated with changed costs in any cohort. Conclusions and Relevance In this study, receiving a genetic diagnosis was not associated with cost savings. This finding suggests that patient benefit and cost-effectiveness should instead drive GWS implementation.
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Affiliation(s)
- Deirdre Weymann
- Cancer Control Research, BC Cancer Research Institute, Vancouver, British Columbia, Canada
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - John Buckell
- Health Economics Research Centre, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
- Nuffield Department of Primary Health Care Sciences, University of Oxford, Oxford, United Kingdom
- National Institute for Health Research Biomedical Research Centre, Oxford, United Kingdom
| | - Patrick Fahr
- Health Economics Research Centre, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | - Rosalie Loewen
- Cancer Control Research, BC Cancer Research Institute, Vancouver, British Columbia, Canada
| | - Morgan Ehman
- Cancer Control Research, BC Cancer Research Institute, Vancouver, British Columbia, Canada
| | - Samantha Pollard
- Cancer Control Research, BC Cancer Research Institute, Vancouver, British Columbia, Canada
| | - Jan M. Friedman
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- BC Children’s Hospital Research Institute, Vancouver, British Columbia, Canada
| | - Sylvia Stockler-Ipsiroglu
- BC Children’s Hospital Research Institute, Vancouver, British Columbia, Canada
- Department of Pediatrics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Division of Biochemical Genetics, BC Children’s Hospital, Vancouver, British Columbia, Canada
| | - Alison M. Elliott
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- BC Children’s Hospital Research Institute, Vancouver, British Columbia, Canada
| | - Sarah Wordsworth
- Health Economics Research Centre, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
- National Institute for Health Research Biomedical Research Centre, Oxford, United Kingdom
| | - James Buchanan
- Health Economics Research Centre, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
- National Institute for Health Research Biomedical Research Centre, Oxford, United Kingdom
| | - Dean A. Regier
- Cancer Control Research, BC Cancer Research Institute, Vancouver, British Columbia, Canada
- School of Population and Public Health, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
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Sandal S, Verma IC, Mahay SB, Dubey S, Sabharwal RK, Kulshrestha S, Saxena R, Suman P, Kumar P, Puri RD. Next-Generation Sequencing in Unexplained Intellectual Disability. Indian J Pediatr 2024; 91:682-695. [PMID: 37804371 DOI: 10.1007/s12098-023-04820-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 06/23/2023] [Indexed: 10/09/2023]
Abstract
OBJECTIVES To determine the diagnostic yield of next generation sequencing (NGS) in patients with moderate/severe/profound intellectual disability (ID) unexplained by conventional tests and to assess the impact of definitive diagnosis on the clinical management and genetic counselling of these families. METHODS This was a ambi-directional study conducted at Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi. The study comprised 227 patients (prospective cohort - 126, retrospective cohort - 101) in whom NGS based tests were performed. RESULTS The mean age of study cohort was 4.5 ± 4.4 y (2.5 mo to 37.3 y). The male: female ratio was 1.6:1. The overall diagnostic yield of NGS was 53.3% (121/227) with causative variants identified in 84 known ID genes. Autosomal recessive intellectual disability (ARID) (23.3%, 53/227) was the most common followed by autosomal dominant intellectual disability (ADID) (20.7%, 47/227) and X-linked intellectual disability (XLID) (9.2%, 21/227). The diagnostic yield was notably higher for ID plus associated condition group (55.6% vs. 20%) (p = 0.0075, Fisher's exact test) compared to isolated ID group. The impact of diagnosis on active or long-term management was observed in 17/121 (14%) and on reproductive outcomes in 26/121 (21.4%) families. CONCLUSIONS There is paucity of data on molecular genetic spectrum of ID from India. The current study identifies extensive genetic heterogeneity and the impact of NGS in patients with ID unexplained by standard genetic tests. The study identified ARID as the most common cause of ID with additional implications for reproductive outcomes. It reiterates the importance of phenotype in genetic testing.
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Affiliation(s)
- Sapna Sandal
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Ishwar Chander Verma
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Sunita Bijarnia Mahay
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Sudhisha Dubey
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - R K Sabharwal
- Department of Pediatric Neurology, Sir Ganga Ram Hospital, New Delhi, India
| | - Samarth Kulshrestha
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Renu Saxena
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Praveen Suman
- Department of Developmental Pediatrics, Sir Ganga Ram Hospital, New Delhi, India
| | - Praveen Kumar
- Department of Pediatric Neurology, Sir Ganga Ram Hospital, New Delhi, India
| | - Ratna Dua Puri
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India.
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Ilic N, Maric N, Maver A, Armengol L, Kravljanac R, Cirkovic J, Krstic J, Radivojevic D, Cirkovic S, Ostojic S, Krasic S, Paripovic A, Vukomanovic V, Peterlin B, Maric G, Sarajlija A. Reverse Phenotyping after Whole-Exome Sequencing in Children with Developmental Delay/Intellectual Disability-An Exception or a Necessity? Genes (Basel) 2024; 15:789. [PMID: 38927725 PMCID: PMC11203244 DOI: 10.3390/genes15060789] [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: 05/02/2024] [Revised: 06/11/2024] [Accepted: 06/12/2024] [Indexed: 06/28/2024] Open
Abstract
This study delves into the diagnostic yield of whole-exome sequencing (WES) in pediatric patients presenting with developmental delay/intellectual disability (DD/ID), while also exploring the utility of Reverse Phenotyping (RP) in refining diagnoses. A cohort of 100 pediatric patients underwent WES, yielding a diagnosis in 66% of cases. Notably, RP played a significant role in cases with negative prior genetic testing, underscoring its significance in complex diagnostic scenarios. The study revealed a spectrum of genetic conditions contributing to DD/ID, illustrating the heterogeneity of etiological factors. Despite challenges, WES demonstrated effectiveness, particularly in cases with metabolic abnormalities. Reverse phenotyping was indicated in half of the patients with positive WES findings. Neural network models exhibited moderate-to-exceptional predictive abilities for aiding in patient selection for WES and RP. These findings emphasize the importance of employing comprehensive genetic approaches and RP in unraveling the genetic underpinnings of DD/ID, thereby facilitating personalized management and genetic counseling for affected individuals and families. This research contributes insights into the genetic landscape of DD/ID, enhancing our understanding and guiding clinical practice in this particular field of clinical genetics.
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Affiliation(s)
- Nikola Ilic
- Clinical Genetics Outpatient Clinic, Mother and Child Health Care Institute of Serbia “Dr Vukan Cupic”, 11070 Belgrade, Serbia; (N.I.); (J.C.); (J.K.)
| | - Nina Maric
- Clinic for Children Diseases, University Clinical Center of the Republic of Srpska, Banja Luka 78000, Bosnia and Herzegovina;
| | - Ales Maver
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia; (A.M.); (B.P.)
| | - Lluis Armengol
- CIBER en Epidemiología y Salud Pública (CIBERESP), Genes and Disease Program, Center for Genomic Regulation (CRG-UPF), 08003 Barcelona, Spain;
| | - Ruzica Kravljanac
- Department of Neurology, Mother and Child Health Care Institute of Serbia “Dr Vukan Cupic”, 11070 Belgrade, Serbia; (R.K.); (S.O.)
- Department of Pediatrics, Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia; (A.P.); (V.V.)
| | - Jana Cirkovic
- Clinical Genetics Outpatient Clinic, Mother and Child Health Care Institute of Serbia “Dr Vukan Cupic”, 11070 Belgrade, Serbia; (N.I.); (J.C.); (J.K.)
| | - Jovana Krstic
- Clinical Genetics Outpatient Clinic, Mother and Child Health Care Institute of Serbia “Dr Vukan Cupic”, 11070 Belgrade, Serbia; (N.I.); (J.C.); (J.K.)
| | - Danijela Radivojevic
- Laboratory of Medical Genetics, Mother and Child Health Care Institute of Serbia “Dr Vukan Cupic”, 11070 Belgrade, Serbia; (D.R.); (S.C.)
| | - Sanja Cirkovic
- Laboratory of Medical Genetics, Mother and Child Health Care Institute of Serbia “Dr Vukan Cupic”, 11070 Belgrade, Serbia; (D.R.); (S.C.)
| | - Slavica Ostojic
- Department of Neurology, Mother and Child Health Care Institute of Serbia “Dr Vukan Cupic”, 11070 Belgrade, Serbia; (R.K.); (S.O.)
- Department of Pediatrics, Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia; (A.P.); (V.V.)
| | - Stasa Krasic
- Department of Cardiology, Mother and Child Health Care Institute of Serbia “Dr Vukan Cupic”, 11070 Belgrade, Serbia;
| | - Aleksandra Paripovic
- Department of Pediatrics, Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia; (A.P.); (V.V.)
- Department of Nephrology, Mother and Child Health Care Institute of Serbia “Dr Vukan Cupic”, 11070 Belgrade, Serbia
| | - Vladislav Vukomanovic
- Department of Pediatrics, Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia; (A.P.); (V.V.)
- Department of Cardiology, Mother and Child Health Care Institute of Serbia “Dr Vukan Cupic”, 11070 Belgrade, Serbia;
| | - Borut Peterlin
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia; (A.M.); (B.P.)
| | - Gorica Maric
- Institute of Epidemiology, Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia;
| | - Adrijan Sarajlija
- Clinical Genetics Outpatient Clinic, Mother and Child Health Care Institute of Serbia “Dr Vukan Cupic”, 11070 Belgrade, Serbia; (N.I.); (J.C.); (J.K.)
- Department of Pediatrics, Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia; (A.P.); (V.V.)
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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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Kim J, Lee J, Jang DH. Combining chromosomal microarray and clinical exome sequencing for genetic diagnosis of intellectual disability. Sci Rep 2023; 13:22807. [PMID: 38129582 PMCID: PMC10739828 DOI: 10.1038/s41598-023-50285-z] [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: 06/21/2023] [Accepted: 12/18/2023] [Indexed: 12/23/2023] Open
Abstract
Despite the current widespread use of chromosomal microarray analysis (CMA) and exome/genome sequencing for the genetic diagnosis of unexplained intellectual disability (ID) in children, gaining improved diagnostic yields and defined guidelines remains a significant challenge. This is a cohort study of children with unexplained ID. We analyzed the diagnostic yield and its correlation to clinical phenotypes in children with ID who underwent concurrent CMA and clinical exome sequencing (CES). A total of 154 children were included (110 [71.4%] male; mean [SD] age, 51.9 [23.1] months). The overall diagnosis yield was 26.0-33.8%, with CMA contributing 12.3-14.3% and CES contributing 13.6-19.4%, showing no significant difference. The diagnostic rate was significantly higher when gross motor delay (odds ratio, 6.69; 95% CI, 3.20-14.00; P < 0.001), facial dysmorphism (odds ratio, 9.34; 95% CI 4.29-20.30; P < 0.001), congenital structural anomaly (odds ratio 3.62; 95% CI 1.63-8.04; P = 0.001), and microcephaly or macrocephaly (odds ratio 4.87; 95% CI 2.05-11.60; P < 0.001) were presented. Patients with only ID without any other concomitant phenotype (63/154, 40.9%) exhibited a 6.3-11.1% diagnostic rate.
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Affiliation(s)
- Jaewon Kim
- Department of Physical Medicine and Rehabilitation, Incheon St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- Medical Genetics and Rare Disease Center, Incheon St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Jaewoong Lee
- Department of Laboratory Medicine, Incheon St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- Medical Genetics and Rare Disease Center, Incheon St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Dae-Hyun Jang
- Department of Physical Medicine and Rehabilitation, Incheon St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.
- Medical Genetics and Rare Disease Center, Incheon St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.
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Cuppens T, Kaur M, Kumar AA, Shatto J, Ng ACH, Leclercq M, Reformat MZ, Droit A, Dunham I, Bolduc FV. Developing a cluster-based approach for deciphering complexity in individuals with neurodevelopmental differences. Front Pediatr 2023; 11:1171920. [PMID: 37790694 PMCID: PMC10543689 DOI: 10.3389/fped.2023.1171920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 09/01/2023] [Indexed: 10/05/2023] Open
Abstract
Objective Individuals with neurodevelopmental disorders such as global developmental delay (GDD) present both genotypic and phenotypic heterogeneity. This diversity has hampered developing of targeted interventions given the relative rarity of each individual genetic etiology. Novel approaches to clinical trials where distinct, but related diseases can be treated by a common drug, known as basket trials, which have shown benefits in oncology but have yet to be used in GDD. Nonetheless, it remains unclear how individuals with GDD could be clustered. Here, we assess two different approaches: agglomerative and divisive clustering. Methods Using the largest cohort of individuals with GDD, which is the Deciphering Developmental Disorders (DDD), characterized using a systematic approach, we extracted genotypic and phenotypic information from 6,588 individuals with GDD. We then used a k-means clustering (divisive) and hierarchical agglomerative clustering (HAC) to identify subgroups of individuals. Next, we extracted gene network and molecular function information with regard to the clusters identified by each approach. Results HAC based on phenotypes identified in individuals with GDD revealed 16 clusters, each presenting with one dominant phenotype displayed by most individuals in the cluster, along with other minor phenotypes. Among the most common phenotypes reported were delayed speech, absent speech, and seizure. Interestingly, each phenotypic cluster molecularly included several (3-12) gene sub-networks of more closely related genes with diverse molecular function. k-means clustering also segregated individuals harboring those phenotypes, but the genetic pathways identified were different from the ones identified from HAC. Conclusion Our study illustrates how divisive (k-means) and agglomerative clustering can be used in order to group individuals with GDD for future basket trials. Moreover, the result of our analysis suggests that phenotypic clusters should be subdivided into molecular sub-networks for an increased likelihood of successful treatment. Finally, a combination of both agglomerative and divisive clustering may be required for developing of a comprehensive treatment.
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Affiliation(s)
- Tania Cuppens
- Département de Médecine Moléculaire de L'Université Laval, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC, Canada
| | - Manpreet Kaur
- Department of Pediatric Neurology, University of Alberta, Edmonton, AB, Canada
| | - Ajay A. Kumar
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, United Kingdom
| | - Julie Shatto
- Department of Pediatric Neurology, University of Alberta, Edmonton, AB, Canada
| | - Andy Cheuk-Him Ng
- Department of Pediatric Neurology, University of Alberta, Edmonton, AB, Canada
| | - Mickael Leclercq
- Département de Médecine Moléculaire de L'Université Laval, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC, Canada
| | - Marek Z. Reformat
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, AB, Canada
| | - Arnaud Droit
- Département de Médecine Moléculaire de L'Université Laval, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC, Canada
| | - Ian Dunham
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, United Kingdom
| | - François V. Bolduc
- Department of Pediatric Neurology, University of Alberta, Edmonton, AB, Canada
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada
- Neuroscience and Mental Health Institute, University of Alberta, Edmonton, AB, Canada
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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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8
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Wang J, Li S, Jiang Y, Wang Y, Ouyang J, Yi Z, Sun W, Jia X, Xiao X, Wang P, Zhang Q. Pathogenic Variants in CEP290 or IQCB1 Cause Earlier-Onset Retinopathy in Senior-Loken Syndrome Compared to Those in INVS, NPHP3, or NPHP4. Am J Ophthalmol 2023; 252:188-204. [PMID: 36990420 DOI: 10.1016/j.ajo.2023.03.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 03/20/2023] [Accepted: 03/20/2023] [Indexed: 03/29/2023]
Abstract
PURPOSE Senior-Loken syndrome (SLSN) is an autosomal recessive disorder characterized by retinopathy and nephronophthisis. This study aimed to evaluate whether different phenotypes are associated with different variants or subsets of 10 SLSN-associated genes based on an in-house data set and a literature review. DESIGN Retrospective case series. METHODS Patients with biallelic variants in SLSN-associated genes, including NPHP1, INVS, NPHP3, NPHP4, IQCB1, CEP290, SDCCAG8, WDR19, CEP164, and TRAF3IP1, were recruited. Ocular phenotypes and nephrology medical records were collected for comprehensive analysis. RESULTS Variants in 5 genes were identified in 74 patients from 70 unrelated families, including CEP290 (61.4%), IQCB1 (28.6%), NPHP1 (4.2%), NPHP4 (2.9%), and WDR19 (2.9%). The median age at the onset of retinopathy was approximately 1 month (since birth). Nystagmus was the most common initial sign in patients with CEP290 (28 of 44, 63.6%) or IQCB1 (19 of 22, 86.4%) variants. Cone and rod responses were extinguished in 53 of 55 patients (96.4%). Characteristic fundus changes were observed in CEP290- and IQCB1-associated patients. During follow-up, 70 of the 74 patients were referred to nephrology, among whom nephronophthisis was not detected in 62 patients (88.6%) at a median age of 6 years but presented in 8 patients (11.4%) aged approximately 9 years. CONCLUSIONS Patients with pathogenic variants in CEP290 or IQCB1 presented early with retinopathy, whereas other patients with INVS, NPHP3, or NPHP4 variants first developed nephropathy. Therefore, awareness of the genetic and clinical features may facilitate the clinical management of SLSN, especially early intervention of kidney problems for patients with eyes affected first.
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Affiliation(s)
- Junwen Wang
- From the The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Shiqiang Li
- From the The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Yi Jiang
- From the The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Yingwei Wang
- From the The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Jiamin Ouyang
- From the The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Zhen Yi
- From the The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Wenmin Sun
- From the The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Xiaoyun Jia
- From the The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Xueshan Xiao
- From the The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Panfeng Wang
- From the The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Qingjiong Zhang
- From the The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China.
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Schuermans N, Verdin H, Ghijsels J, Hellemans M, Debackere E, Bogaert E, Symoens S, Naesens L, Lecomte E, Crosiers D, Bergmans B, Verhoeven K, Poppe B, Laureys G, Herdewyn S, Van Langenhove T, Santens P, De Bleecker JL, Hemelsoet D, Dermaut B. Exome Sequencing and Multigene Panel Testing in 1,411 Patients With Adult-Onset Neurologic Disorders. Neurol Genet 2023; 9:e200071. [PMID: 37152446 PMCID: PMC10160959 DOI: 10.1212/nxg.0000000000200071] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 02/21/2023] [Indexed: 05/09/2023]
Abstract
Background and Objectives Owing to their extensive clinical and molecular heterogeneity, hereditary neurologic diseases in adults are difficult to diagnose. The current knowledge about the diagnostic yield and clinical utility of exome sequencing (ES) for neurologic diseases in adults is limited. This observational study assesses the diagnostic value of ES and multigene panel analysis in adult-onset neurologic disorders. Methods From January 2019 through April 2022, ES-based multigene panel testing was conducted in 1,411 patients with molecularly unexplained neurologic phenotypes at the Ghent University Hospital. Gene panels were developed for ataxia and spasticity, leukoencephalopathy, movement disorders, paroxysmal episodic disorders, neurodegeneration with brain iron accumulation, progressive myoclonic epilepsy, and amyotrophic lateral sclerosis. Single nucleotide variants, small indels, and copy number variants were analyzed. Across all panels, our analysis covered a total of 725 genes associated with Mendelian inheritance. Results A molecular diagnosis was established in 10% of the cases (144 of 1,411) representing 71 different monogenic disorders. The diagnostic yield depended significantly on the presenting phenotype with the highest yield seen in patients with ataxia or spastic paraparesis (19%). Most of the established diagnoses comprised disorders with an autosomal dominant inheritance (62%), and the most frequently mutated genes were NOTCH3 (13 patients), SPG7 (11 patients), and RFC1 (8 patients). 34% of the disease-causing variants were novel, including a unique likely pathogenic variant in APP (Ghent mutation, p.[Asn698Asp]) in a family presenting with stroke and severe cerebral white matter disease. 7% of the pathogenic variants comprised copy number variants detected in the ES data and confirmed by an independent technique. Discussion ES and multigene panel testing is a powerful and efficient tool to diagnose patients with unexplained, adult-onset neurologic disorders.
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Affiliation(s)
- Nika Schuermans
- Center for Medical Genetics (N.S., H.V., J.G., E.D., E.B., S.S., B.P., B.D.), Ghent University Hospital; Department of Biomolecular Medicine (N.S., H.V., J.G., M.H., E.D., E.B., S.S., B.P., B.D.), Faculty of Medicine and Health Sciences, Ghent University; Department of Internal Medicine and Pediatrics (L.N.), Ghent University; Primary Immunodeficiency Research Lab (L.N.), Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital; Department of Neurology (E.L.), O.L.V. Lourdes Hospital, Waregem; Department of Neurology (D.C.), Antwerp University Hospital UZA; Translational Neurosciences (D.C.), Faculty of Medicine and Health Sciences, University of Antwerp; Department of Neurology (B.B., K.V.), AZ Sint-Jan, Bruges; and Department of Neurology (B.B., G.L., S.H., T.V.L., P.S., J.L.D.B., D.H.), Ghent University Hospital, Belgium
| | - Hannah Verdin
- Center for Medical Genetics (N.S., H.V., J.G., E.D., E.B., S.S., B.P., B.D.), Ghent University Hospital; Department of Biomolecular Medicine (N.S., H.V., J.G., M.H., E.D., E.B., S.S., B.P., B.D.), Faculty of Medicine and Health Sciences, Ghent University; Department of Internal Medicine and Pediatrics (L.N.), Ghent University; Primary Immunodeficiency Research Lab (L.N.), Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital; Department of Neurology (E.L.), O.L.V. Lourdes Hospital, Waregem; Department of Neurology (D.C.), Antwerp University Hospital UZA; Translational Neurosciences (D.C.), Faculty of Medicine and Health Sciences, University of Antwerp; Department of Neurology (B.B., K.V.), AZ Sint-Jan, Bruges; and Department of Neurology (B.B., G.L., S.H., T.V.L., P.S., J.L.D.B., D.H.), Ghent University Hospital, Belgium
| | - Jody Ghijsels
- Center for Medical Genetics (N.S., H.V., J.G., E.D., E.B., S.S., B.P., B.D.), Ghent University Hospital; Department of Biomolecular Medicine (N.S., H.V., J.G., M.H., E.D., E.B., S.S., B.P., B.D.), Faculty of Medicine and Health Sciences, Ghent University; Department of Internal Medicine and Pediatrics (L.N.), Ghent University; Primary Immunodeficiency Research Lab (L.N.), Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital; Department of Neurology (E.L.), O.L.V. Lourdes Hospital, Waregem; Department of Neurology (D.C.), Antwerp University Hospital UZA; Translational Neurosciences (D.C.), Faculty of Medicine and Health Sciences, University of Antwerp; Department of Neurology (B.B., K.V.), AZ Sint-Jan, Bruges; and Department of Neurology (B.B., G.L., S.H., T.V.L., P.S., J.L.D.B., D.H.), Ghent University Hospital, Belgium
| | - Madeleine Hellemans
- Center for Medical Genetics (N.S., H.V., J.G., E.D., E.B., S.S., B.P., B.D.), Ghent University Hospital; Department of Biomolecular Medicine (N.S., H.V., J.G., M.H., E.D., E.B., S.S., B.P., B.D.), Faculty of Medicine and Health Sciences, Ghent University; Department of Internal Medicine and Pediatrics (L.N.), Ghent University; Primary Immunodeficiency Research Lab (L.N.), Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital; Department of Neurology (E.L.), O.L.V. Lourdes Hospital, Waregem; Department of Neurology (D.C.), Antwerp University Hospital UZA; Translational Neurosciences (D.C.), Faculty of Medicine and Health Sciences, University of Antwerp; Department of Neurology (B.B., K.V.), AZ Sint-Jan, Bruges; and Department of Neurology (B.B., G.L., S.H., T.V.L., P.S., J.L.D.B., D.H.), Ghent University Hospital, Belgium
| | - Elke Debackere
- Center for Medical Genetics (N.S., H.V., J.G., E.D., E.B., S.S., B.P., B.D.), Ghent University Hospital; Department of Biomolecular Medicine (N.S., H.V., J.G., M.H., E.D., E.B., S.S., B.P., B.D.), Faculty of Medicine and Health Sciences, Ghent University; Department of Internal Medicine and Pediatrics (L.N.), Ghent University; Primary Immunodeficiency Research Lab (L.N.), Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital; Department of Neurology (E.L.), O.L.V. Lourdes Hospital, Waregem; Department of Neurology (D.C.), Antwerp University Hospital UZA; Translational Neurosciences (D.C.), Faculty of Medicine and Health Sciences, University of Antwerp; Department of Neurology (B.B., K.V.), AZ Sint-Jan, Bruges; and Department of Neurology (B.B., G.L., S.H., T.V.L., P.S., J.L.D.B., D.H.), Ghent University Hospital, Belgium
| | - Elke Bogaert
- Center for Medical Genetics (N.S., H.V., J.G., E.D., E.B., S.S., B.P., B.D.), Ghent University Hospital; Department of Biomolecular Medicine (N.S., H.V., J.G., M.H., E.D., E.B., S.S., B.P., B.D.), Faculty of Medicine and Health Sciences, Ghent University; Department of Internal Medicine and Pediatrics (L.N.), Ghent University; Primary Immunodeficiency Research Lab (L.N.), Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital; Department of Neurology (E.L.), O.L.V. Lourdes Hospital, Waregem; Department of Neurology (D.C.), Antwerp University Hospital UZA; Translational Neurosciences (D.C.), Faculty of Medicine and Health Sciences, University of Antwerp; Department of Neurology (B.B., K.V.), AZ Sint-Jan, Bruges; and Department of Neurology (B.B., G.L., S.H., T.V.L., P.S., J.L.D.B., D.H.), Ghent University Hospital, Belgium
| | - Sofie Symoens
- Center for Medical Genetics (N.S., H.V., J.G., E.D., E.B., S.S., B.P., B.D.), Ghent University Hospital; Department of Biomolecular Medicine (N.S., H.V., J.G., M.H., E.D., E.B., S.S., B.P., B.D.), Faculty of Medicine and Health Sciences, Ghent University; Department of Internal Medicine and Pediatrics (L.N.), Ghent University; Primary Immunodeficiency Research Lab (L.N.), Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital; Department of Neurology (E.L.), O.L.V. Lourdes Hospital, Waregem; Department of Neurology (D.C.), Antwerp University Hospital UZA; Translational Neurosciences (D.C.), Faculty of Medicine and Health Sciences, University of Antwerp; Department of Neurology (B.B., K.V.), AZ Sint-Jan, Bruges; and Department of Neurology (B.B., G.L., S.H., T.V.L., P.S., J.L.D.B., D.H.), Ghent University Hospital, Belgium
| | - Leslie Naesens
- Center for Medical Genetics (N.S., H.V., J.G., E.D., E.B., S.S., B.P., B.D.), Ghent University Hospital; Department of Biomolecular Medicine (N.S., H.V., J.G., M.H., E.D., E.B., S.S., B.P., B.D.), Faculty of Medicine and Health Sciences, Ghent University; Department of Internal Medicine and Pediatrics (L.N.), Ghent University; Primary Immunodeficiency Research Lab (L.N.), Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital; Department of Neurology (E.L.), O.L.V. Lourdes Hospital, Waregem; Department of Neurology (D.C.), Antwerp University Hospital UZA; Translational Neurosciences (D.C.), Faculty of Medicine and Health Sciences, University of Antwerp; Department of Neurology (B.B., K.V.), AZ Sint-Jan, Bruges; and Department of Neurology (B.B., G.L., S.H., T.V.L., P.S., J.L.D.B., D.H.), Ghent University Hospital, Belgium
| | - Elien Lecomte
- Center for Medical Genetics (N.S., H.V., J.G., E.D., E.B., S.S., B.P., B.D.), Ghent University Hospital; Department of Biomolecular Medicine (N.S., H.V., J.G., M.H., E.D., E.B., S.S., B.P., B.D.), Faculty of Medicine and Health Sciences, Ghent University; Department of Internal Medicine and Pediatrics (L.N.), Ghent University; Primary Immunodeficiency Research Lab (L.N.), Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital; Department of Neurology (E.L.), O.L.V. Lourdes Hospital, Waregem; Department of Neurology (D.C.), Antwerp University Hospital UZA; Translational Neurosciences (D.C.), Faculty of Medicine and Health Sciences, University of Antwerp; Department of Neurology (B.B., K.V.), AZ Sint-Jan, Bruges; and Department of Neurology (B.B., G.L., S.H., T.V.L., P.S., J.L.D.B., D.H.), Ghent University Hospital, Belgium
| | - David Crosiers
- Center for Medical Genetics (N.S., H.V., J.G., E.D., E.B., S.S., B.P., B.D.), Ghent University Hospital; Department of Biomolecular Medicine (N.S., H.V., J.G., M.H., E.D., E.B., S.S., B.P., B.D.), Faculty of Medicine and Health Sciences, Ghent University; Department of Internal Medicine and Pediatrics (L.N.), Ghent University; Primary Immunodeficiency Research Lab (L.N.), Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital; Department of Neurology (E.L.), O.L.V. Lourdes Hospital, Waregem; Department of Neurology (D.C.), Antwerp University Hospital UZA; Translational Neurosciences (D.C.), Faculty of Medicine and Health Sciences, University of Antwerp; Department of Neurology (B.B., K.V.), AZ Sint-Jan, Bruges; and Department of Neurology (B.B., G.L., S.H., T.V.L., P.S., J.L.D.B., D.H.), Ghent University Hospital, Belgium
| | - Bruno Bergmans
- Center for Medical Genetics (N.S., H.V., J.G., E.D., E.B., S.S., B.P., B.D.), Ghent University Hospital; Department of Biomolecular Medicine (N.S., H.V., J.G., M.H., E.D., E.B., S.S., B.P., B.D.), Faculty of Medicine and Health Sciences, Ghent University; Department of Internal Medicine and Pediatrics (L.N.), Ghent University; Primary Immunodeficiency Research Lab (L.N.), Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital; Department of Neurology (E.L.), O.L.V. Lourdes Hospital, Waregem; Department of Neurology (D.C.), Antwerp University Hospital UZA; Translational Neurosciences (D.C.), Faculty of Medicine and Health Sciences, University of Antwerp; Department of Neurology (B.B., K.V.), AZ Sint-Jan, Bruges; and Department of Neurology (B.B., G.L., S.H., T.V.L., P.S., J.L.D.B., D.H.), Ghent University Hospital, Belgium
| | - Kristof Verhoeven
- Center for Medical Genetics (N.S., H.V., J.G., E.D., E.B., S.S., B.P., B.D.), Ghent University Hospital; Department of Biomolecular Medicine (N.S., H.V., J.G., M.H., E.D., E.B., S.S., B.P., B.D.), Faculty of Medicine and Health Sciences, Ghent University; Department of Internal Medicine and Pediatrics (L.N.), Ghent University; Primary Immunodeficiency Research Lab (L.N.), Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital; Department of Neurology (E.L.), O.L.V. Lourdes Hospital, Waregem; Department of Neurology (D.C.), Antwerp University Hospital UZA; Translational Neurosciences (D.C.), Faculty of Medicine and Health Sciences, University of Antwerp; Department of Neurology (B.B., K.V.), AZ Sint-Jan, Bruges; and Department of Neurology (B.B., G.L., S.H., T.V.L., P.S., J.L.D.B., D.H.), Ghent University Hospital, Belgium
| | - Bruce Poppe
- Center for Medical Genetics (N.S., H.V., J.G., E.D., E.B., S.S., B.P., B.D.), Ghent University Hospital; Department of Biomolecular Medicine (N.S., H.V., J.G., M.H., E.D., E.B., S.S., B.P., B.D.), Faculty of Medicine and Health Sciences, Ghent University; Department of Internal Medicine and Pediatrics (L.N.), Ghent University; Primary Immunodeficiency Research Lab (L.N.), Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital; Department of Neurology (E.L.), O.L.V. Lourdes Hospital, Waregem; Department of Neurology (D.C.), Antwerp University Hospital UZA; Translational Neurosciences (D.C.), Faculty of Medicine and Health Sciences, University of Antwerp; Department of Neurology (B.B., K.V.), AZ Sint-Jan, Bruges; and Department of Neurology (B.B., G.L., S.H., T.V.L., P.S., J.L.D.B., D.H.), Ghent University Hospital, Belgium
| | - Guy Laureys
- Center for Medical Genetics (N.S., H.V., J.G., E.D., E.B., S.S., B.P., B.D.), Ghent University Hospital; Department of Biomolecular Medicine (N.S., H.V., J.G., M.H., E.D., E.B., S.S., B.P., B.D.), Faculty of Medicine and Health Sciences, Ghent University; Department of Internal Medicine and Pediatrics (L.N.), Ghent University; Primary Immunodeficiency Research Lab (L.N.), Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital; Department of Neurology (E.L.), O.L.V. Lourdes Hospital, Waregem; Department of Neurology (D.C.), Antwerp University Hospital UZA; Translational Neurosciences (D.C.), Faculty of Medicine and Health Sciences, University of Antwerp; Department of Neurology (B.B., K.V.), AZ Sint-Jan, Bruges; and Department of Neurology (B.B., G.L., S.H., T.V.L., P.S., J.L.D.B., D.H.), Ghent University Hospital, Belgium
| | - Sarah Herdewyn
- Center for Medical Genetics (N.S., H.V., J.G., E.D., E.B., S.S., B.P., B.D.), Ghent University Hospital; Department of Biomolecular Medicine (N.S., H.V., J.G., M.H., E.D., E.B., S.S., B.P., B.D.), Faculty of Medicine and Health Sciences, Ghent University; Department of Internal Medicine and Pediatrics (L.N.), Ghent University; Primary Immunodeficiency Research Lab (L.N.), Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital; Department of Neurology (E.L.), O.L.V. Lourdes Hospital, Waregem; Department of Neurology (D.C.), Antwerp University Hospital UZA; Translational Neurosciences (D.C.), Faculty of Medicine and Health Sciences, University of Antwerp; Department of Neurology (B.B., K.V.), AZ Sint-Jan, Bruges; and Department of Neurology (B.B., G.L., S.H., T.V.L., P.S., J.L.D.B., D.H.), Ghent University Hospital, Belgium
| | - Tim Van Langenhove
- Center for Medical Genetics (N.S., H.V., J.G., E.D., E.B., S.S., B.P., B.D.), Ghent University Hospital; Department of Biomolecular Medicine (N.S., H.V., J.G., M.H., E.D., E.B., S.S., B.P., B.D.), Faculty of Medicine and Health Sciences, Ghent University; Department of Internal Medicine and Pediatrics (L.N.), Ghent University; Primary Immunodeficiency Research Lab (L.N.), Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital; Department of Neurology (E.L.), O.L.V. Lourdes Hospital, Waregem; Department of Neurology (D.C.), Antwerp University Hospital UZA; Translational Neurosciences (D.C.), Faculty of Medicine and Health Sciences, University of Antwerp; Department of Neurology (B.B., K.V.), AZ Sint-Jan, Bruges; and Department of Neurology (B.B., G.L., S.H., T.V.L., P.S., J.L.D.B., D.H.), Ghent University Hospital, Belgium
| | - Patrick Santens
- Center for Medical Genetics (N.S., H.V., J.G., E.D., E.B., S.S., B.P., B.D.), Ghent University Hospital; Department of Biomolecular Medicine (N.S., H.V., J.G., M.H., E.D., E.B., S.S., B.P., B.D.), Faculty of Medicine and Health Sciences, Ghent University; Department of Internal Medicine and Pediatrics (L.N.), Ghent University; Primary Immunodeficiency Research Lab (L.N.), Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital; Department of Neurology (E.L.), O.L.V. Lourdes Hospital, Waregem; Department of Neurology (D.C.), Antwerp University Hospital UZA; Translational Neurosciences (D.C.), Faculty of Medicine and Health Sciences, University of Antwerp; Department of Neurology (B.B., K.V.), AZ Sint-Jan, Bruges; and Department of Neurology (B.B., G.L., S.H., T.V.L., P.S., J.L.D.B., D.H.), Ghent University Hospital, Belgium
| | - Jan L De Bleecker
- Center for Medical Genetics (N.S., H.V., J.G., E.D., E.B., S.S., B.P., B.D.), Ghent University Hospital; Department of Biomolecular Medicine (N.S., H.V., J.G., M.H., E.D., E.B., S.S., B.P., B.D.), Faculty of Medicine and Health Sciences, Ghent University; Department of Internal Medicine and Pediatrics (L.N.), Ghent University; Primary Immunodeficiency Research Lab (L.N.), Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital; Department of Neurology (E.L.), O.L.V. Lourdes Hospital, Waregem; Department of Neurology (D.C.), Antwerp University Hospital UZA; Translational Neurosciences (D.C.), Faculty of Medicine and Health Sciences, University of Antwerp; Department of Neurology (B.B., K.V.), AZ Sint-Jan, Bruges; and Department of Neurology (B.B., G.L., S.H., T.V.L., P.S., J.L.D.B., D.H.), Ghent University Hospital, Belgium
| | - Dimitri Hemelsoet
- Center for Medical Genetics (N.S., H.V., J.G., E.D., E.B., S.S., B.P., B.D.), Ghent University Hospital; Department of Biomolecular Medicine (N.S., H.V., J.G., M.H., E.D., E.B., S.S., B.P., B.D.), Faculty of Medicine and Health Sciences, Ghent University; Department of Internal Medicine and Pediatrics (L.N.), Ghent University; Primary Immunodeficiency Research Lab (L.N.), Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital; Department of Neurology (E.L.), O.L.V. Lourdes Hospital, Waregem; Department of Neurology (D.C.), Antwerp University Hospital UZA; Translational Neurosciences (D.C.), Faculty of Medicine and Health Sciences, University of Antwerp; Department of Neurology (B.B., K.V.), AZ Sint-Jan, Bruges; and Department of Neurology (B.B., G.L., S.H., T.V.L., P.S., J.L.D.B., D.H.), Ghent University Hospital, Belgium
| | - Bart Dermaut
- Center for Medical Genetics (N.S., H.V., J.G., E.D., E.B., S.S., B.P., B.D.), Ghent University Hospital; Department of Biomolecular Medicine (N.S., H.V., J.G., M.H., E.D., E.B., S.S., B.P., B.D.), Faculty of Medicine and Health Sciences, Ghent University; Department of Internal Medicine and Pediatrics (L.N.), Ghent University; Primary Immunodeficiency Research Lab (L.N.), Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital; Department of Neurology (E.L.), O.L.V. Lourdes Hospital, Waregem; Department of Neurology (D.C.), Antwerp University Hospital UZA; Translational Neurosciences (D.C.), Faculty of Medicine and Health Sciences, University of Antwerp; Department of Neurology (B.B., K.V.), AZ Sint-Jan, Bruges; and Department of Neurology (B.B., G.L., S.H., T.V.L., P.S., J.L.D.B., D.H.), Ghent University Hospital, Belgium
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Diagnostic yield of patients with undiagnosed intellectual disability, global developmental delay and multiples congenital anomalies using karyotype, microarray analysis, whole exome sequencing from Central Brazil. PLoS One 2022; 17:e0266493. [PMID: 35390071 PMCID: PMC8989190 DOI: 10.1371/journal.pone.0266493] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 03/21/2022] [Indexed: 11/19/2022] Open
Abstract
Intellectual Disability (ID) is a neurodevelopmental disorder that affects approximately 3% of children and adolescents worldwide. It is a heterogeneous and multifactorial clinical condition. Several methodologies have been used to identify the genetic causes of ID and in recent years new generation sequencing techniques, such as exome sequencing, have enabled an increase in the detection of new pathogenic variants and new genes associated with ID. The aim of this study was to evaluate exome sequencing with analysis of the ID gene panel as a tool to increase the diagnostic yield of patients with ID/GDD/MCA in Central Brazil, together with karyotype and CMA tests. A retrospective cohort study was carried out with 369 patients encompassing both sexes. Karyotype analysis was performed for all patients. CMA was performed for patients who did not present structural and or numerical alterations in the karyotype. Cases that were not diagnosed after performing karyotyping and CMA were referred for exome sequencing using a gene panel for ID that included 1,252 genes. The karyotype identified chromosomal alterations in 34.7% (128/369). CMA was performed in 83 patients who had normal karyotype results resulting in a diagnostic yield of 21.7% (18/83). Exome sequencing with analysis of the ID gene panel was performed in 19 trios of families that had negative results with previous methodologies. With the ID gene panel analysis, we identified mutations in 63.1% (12/19) of the cases of which 75% (9/12) were pathogenic variants,8.3% (1/12) likely pathogenic and in 16.7% (2/12) it concerned a Variant of Uncertain Significance. With the three methodologies applied, it was possible to identify the genetic cause of ID in 42.3% (156/369) of the patients. In conclusion, our studies show the different methodologies that can be useful in diagnosing ID/GDD/MCA and that whole exome sequencing followed by gene panel analysis, when combined with clinical and laboratory screening, is an efficient diagnostic strategy.
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Brea-Fernández AJ, Álvarez-Barona M, Amigo J, Tubío-Fungueiriño M, Caamaño P, Fernández-Prieto M, Barros F, De Rubeis S, Buxbaum J, Carracedo Á. Trio-based exome sequencing reveals a high rate of the de novo variants in intellectual disability. Eur J Hum Genet 2022; 30:938-945. [PMID: 35322241 PMCID: PMC9349217 DOI: 10.1038/s41431-022-01087-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 02/15/2022] [Accepted: 03/08/2022] [Indexed: 12/16/2022] Open
Abstract
Intellectual disability (ID), a neurodevelopmental disorder affecting 1-3% of the general population, is characterized by limitations in both intellectual function and adaptive skills. The high number of conditions associated with ID underlines its heterogeneous origin and reveals the difficulty of obtaining a rapid and accurate genetic diagnosis. However, the Next Generation Sequencing, and the whole exome sequencing (WES) in particular, has boosted the diagnosis rate associated with ID. In this study, WES performed on 244 trios of patients clinically diagnosed with isolated or syndromic ID and their respective unaffected parents has allowed the identification of the underlying genetic basis of ID in 64 patients, yielding a diagnosis rate of 25.2%. Our results suggest that trio-based WES facilitates ID's genetic diagnosis, particularly in patients who have been extensively waiting for a definitive molecular diagnosis. Moreover, genotypic information from parents provided by trio-based WES enabled the detection of a high percentage (61.5%) of de novo variants inside our cohort. Establishing a quick genetic diagnosis of ID would allow early intervention and better clinical management, thus improving the quality of life of these patients and their families.
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Affiliation(s)
- Alejandro J Brea-Fernández
- Grupo de Medicina Xenómica, Universidade de Santiago de Compostela, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Santiago de Compostela, Spain.
| | - Miriam Álvarez-Barona
- Grupo de Medicina Xenómica, Fundación Instituto de Investigación Sanitaria de Santiago de Compostela (FIDIS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Jorge Amigo
- Grupo de Medicina Xenómica, Universidade de Santiago de Compostela, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Santiago de Compostela, Spain.,Fundación Pública Galega de Medicina Xenómica (FPGMX), Santiago de Compostela, Spain
| | - María Tubío-Fungueiriño
- Grupo de Medicina Xenómica, Fundación Instituto de Investigación Sanitaria de Santiago de Compostela (FIDIS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain.,Genomics and Bioinformatics Group, Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Pilar Caamaño
- Fundación Pública Galega de Medicina Xenómica (FPGMX), Santiago de Compostela, Spain
| | - Montserrat Fernández-Prieto
- Genetics Group, GC05, Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain.,Grupo de Medicina Xenómica, Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Santiago de Compostela, Spain
| | - Francisco Barros
- Grupo de Medicina Xenómica, Universidade de Santiago de Compostela, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Santiago de Compostela, Spain.,Grupo de Medicina Xenómica, Fundación Instituto de Investigación Sanitaria de Santiago de Compostela (FIDIS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain.,Fundación Pública Galega de Medicina Xenómica (FPGMX), Santiago de Compostela, Spain
| | | | - Joseph Buxbaum
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ángel Carracedo
- Grupo de Medicina Xenómica, Universidade de Santiago de Compostela, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Santiago de Compostela, Spain.,Grupo de Medicina Xenómica, Fundación Instituto de Investigación Sanitaria de Santiago de Compostela (FIDIS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain.,Fundación Pública Galega de Medicina Xenómica (FPGMX), Santiago de Compostela, Spain.,Genomics and Bioinformatics Group, Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
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12
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Bruel AL, Vitobello A, Thiffault I, Manwaring L, Willing M, Agrawal PB, Bayat A, Kitzler TM, Brownstein CA, Genetti CA, Gonzalez-Heydrich J, Jayakar P, Zyskind JW, Zhu Z, Vachet C, Wilson GR, Pruniski B, Goyette AM, Duffourd Y, Thauvin-Robinet C, Philippe C, Faivre L. ITSN1: a novel candidate gene involved in autosomal dominant neurodevelopmental disorder spectrum. Eur J Hum Genet 2022; 30:111-116. [PMID: 34707297 PMCID: PMC8738743 DOI: 10.1038/s41431-021-00985-9] [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: 04/28/2021] [Revised: 09/21/2021] [Accepted: 10/05/2021] [Indexed: 01/03/2023] Open
Abstract
ITSN1 plays an important role in brain development. Recent studies in large cohorts of subjects with neurodevelopmental disorders have identified de novo variants in ITSN1 gene thereby suggesting that this gene is involved in the development of such disorders. The aim of this study is to provide further proof of such a link. We performed trio exome sequencing in a patient presenting autism, intellectual disability, and severe behavioral difficulties. Additional affected patients with a neurodevelopmental disorder harboring a heterozygous variant in ITSN1 (NM_003024.2) were collected through a worldwide collaboration. All patients underwent detailed phenotypic and genetic assessment and data was collected and shared by healthcare givers. We identified ten novel patients from eight families with heterozygous truncating or missense variants in ITSN1 gene. In addition, four previously published patients from large meta-analysis studies were included. In total, 7/14 patients presented a de novo variant in ITSN1. All patients showed neurodevelopmental disorders from autism spectrum disorders (90%), intellectual disability (86%), and epilepsy (30%). We demonstrated that truncating variants are in the first half of ITSN1 whereas missense variants are clustered in C-terminal region. We suggest ITSN1 gene is involved in development of an autism spectrum disorder with variable additional neurodevelopmental deficiency, thus confirming the hypothesis that ITSN1 is important for brain development.
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Affiliation(s)
- Ange-Line Bruel
- grid.493090.70000 0004 4910 6615UMR1231 GAD, Inserm - Université Bourgogne-Franche Comté, Dijon, France ,grid.31151.37Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Antonio Vitobello
- grid.493090.70000 0004 4910 6615UMR1231 GAD, Inserm - Université Bourgogne-Franche Comté, Dijon, France ,grid.31151.37Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Isabelle Thiffault
- grid.239559.10000 0004 0415 5050Center for Pediatric Genomic Medicine, Children’s Mercy Hospital, Kansas City, MO USA
| | - Linda Manwaring
- grid.4367.60000 0001 2355 7002Department of Pediatrics, Division of Genetics and Genomic Medicine, Washington University School of Medicine, St. Louis, MO USA
| | - Marcia Willing
- grid.4367.60000 0001 2355 7002Department of Pediatrics, Division of Genetics and Genomic Medicine, Washington University School of Medicine, St. Louis, MO USA
| | - Pankaj B. Agrawal
- grid.2515.30000 0004 0378 8438Divisions of Newborn Medicine, Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, MA USA ,grid.38142.3c000000041936754XDepartment of Pediatrics, Harvard Medical School, Boston, MA USA
| | - Allan Bayat
- grid.452376.1Department of Genetics and Precision Medicine, Danish Epilepsy Centre, Dianalund, Denmark
| | - Thomas M. Kitzler
- grid.63984.300000 0000 9064 4811Research Institute, McGill University Health Centre, Montreal, QC Canada ,grid.63984.300000 0000 9064 4811Division of Medical Genetics, Department of Medicine, McGill University Health Centre, Montreal, QC Canada ,grid.14709.3b0000 0004 1936 8649Department of Human Genetics, McGill University, Montreal, QC Canada
| | - Catherine A. Brownstein
- grid.2515.30000 0004 0378 8438Divisions of Newborn Medicine, Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, MA USA
| | - Casie A. Genetti
- grid.2515.30000 0004 0378 8438Divisions of Newborn Medicine, Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, MA USA
| | - Joseph Gonzalez-Heydrich
- grid.2515.30000 0004 0378 8438Department of Psychiatry, Boston Children’s Hospital, Manton Center for Orphan Disease Research, Division of Genetics and Genomics, Boston Children’s Hospital, Department of Pediatrics, Harvard Medical School, Boston, MA USA
| | - Parul Jayakar
- grid.415486.a0000 0000 9682 6720Division of Genetics and Metabolism, Nicklaus Children’s Hospital, Miami, FL USA
| | | | - Zehua Zhu
- grid.428467.b0000 0004 0409 2707GeneDX, Gaitherburg, MD USA
| | - Clemence Vachet
- grid.411158.80000 0004 0638 9213Service de néphrologie pédiatrique, Centre Hospitalier Régional Universitaire Besançon, Besançon, France
| | - Gena R. Wilson
- Division of Genetics and Metabolism, Phoenix Children’s Medical Group, Phoenix, AZ USA
| | - Brianna Pruniski
- Division of Genetics and Metabolism, Phoenix Children’s Medical Group, Phoenix, AZ USA
| | - Anne-Marie Goyette
- FRCPC, Developmental Pediatrician, Montreal Children’s Hospital, McGill University Health Center, Montreal, QC Canada
| | - Yannis Duffourd
- grid.493090.70000 0004 4910 6615UMR1231 GAD, Inserm - Université Bourgogne-Franche Comté, Dijon, France ,grid.31151.37Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Christel Thauvin-Robinet
- grid.493090.70000 0004 4910 6615UMR1231 GAD, Inserm - Université Bourgogne-Franche Comté, Dijon, France ,grid.31151.37Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France ,grid.31151.37Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Centre Hospitalier Universitaire Dijon, Dijon, France
| | - Christophe Philippe
- grid.493090.70000 0004 4910 6615UMR1231 GAD, Inserm - Université Bourgogne-Franche Comté, Dijon, France ,grid.31151.37Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France ,grid.31151.37Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Centre Hospitalier Universitaire Dijon, Dijon, France
| | - Laurence Faivre
- grid.493090.70000 0004 4910 6615UMR1231 GAD, Inserm - Université Bourgogne-Franche Comté, Dijon, France ,grid.31151.37Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France ,grid.31151.37Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Centre Hospitalier Universitaire Dijon, Dijon, France
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13
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Miletic A, Stojanovic JR, Parezanovic V, Rsovac S, Drakulic D, Soldatovic I, Mijovic M, Bosankic B, Petrovic H, Borlja N, Milivojevic M, Marjanovic A, Brankovic M, Cuturilo G. Genetic evaluation of newborns with critical congenital heart defects admitted to the intensive care unit. Eur J Pediatr 2021; 180:3219-3227. [PMID: 33963417 DOI: 10.1007/s00431-021-04097-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 04/28/2021] [Accepted: 04/30/2021] [Indexed: 11/30/2022]
Abstract
Rapid and efficient diagnostics is crucial for newborns with congenital heart defects (CHD) in intensive care unit (ICU) but is often challenging. Given that genetic factors play a role in 20-30% cases of CHD, it is likely that genetic tests could improve both its speed and efficiency. We aimed to analyze the utility of rapid and cost-effective multiplex ligation dependent probe amplification analysis (MLPA) for chromosomal analysis in newborns with critical CHD. One hundred consecutive newborns admitted with critical CHD to the ICU were included in the study. Those with normal MLPA findings were further tested by chromosomal microarray and clinical exome sequencing. Overall, pathogenic/likely pathogenic variants were determined in ten (10%) newborns by MLPA, three (3%) by chromosomal microarray, and three (3%) by clinical exome sequencing. The most common variant detected was deletion of 22q11.2 region.Conclusion: MLPA is fast and cost-effective analysis that could be used as the first-tier test in newborns with critical CHD admitted to the ICU. What is Known: • MLPA is an established method for chromosome analysis in patients with CHD, but detection rate in newborns with critical CHD is unknown. What is New: • Study suggests that detection rate of casual variants using MLPA in newborns with critical CHD is 10%.
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Affiliation(s)
- Aleksandra Miletic
- Department of Clinical Genetics, University Children's Hospital, Belgrade, Serbia
| | | | - Vojislav Parezanovic
- Faculty of Medicine, University of Belgrade, Belgrade, Serbia.,Department of Cardiology, University Children's Hospital, Belgrade, Serbia
| | - Snezana Rsovac
- Department of Pediatric and Neonatal Intensive Care, University Children's Hospital, Belgrade, Serbia
| | - Danijela Drakulic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Ivan Soldatovic
- Institute for Medical Statistics and Informatics, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Marija Mijovic
- Department of Clinical Genetics, University Children's Hospital, Belgrade, Serbia
| | - Brankica Bosankic
- Department of Clinical Genetics, University Children's Hospital, Belgrade, Serbia
| | - Hristina Petrovic
- Department of Clinical Genetics, University Children's Hospital, Belgrade, Serbia
| | | | - Milena Milivojevic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Ana Marjanovic
- Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | | | - Goran Cuturilo
- Department of Clinical Genetics, University Children's Hospital, Belgrade, Serbia. .,Faculty of Medicine, University of Belgrade, Belgrade, Serbia.
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14
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Sanchez-Jimeno C, Blanco-Kelly F, López-Grondona F, Losada-Del Pozo R, Moreno B, Rodrigo-Moreno M, Martinez-Cayuelas E, Riveiro-Alvarez R, Fenollar-Cortés M, Ayuso C, Rodríguez de Alba M, Lorda-Sanchez I, Almoguera B. Attention Deficit Hyperactivity and Autism Spectrum Disorders as the Core Symptoms of AUTS2 Syndrome: Description of Five New Patients and Update of the Frequency of Manifestations and Genotype-Phenotype Correlation. Genes (Basel) 2021; 12:genes12091360. [PMID: 34573342 PMCID: PMC8471078 DOI: 10.3390/genes12091360] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/23/2021] [Accepted: 08/27/2021] [Indexed: 12/14/2022] Open
Abstract
Haploinsufficiency of AUTS2 has been associated with a syndromic form of neurodevelopmental delay characterized by intellectual disability, autistic features, and microcephaly, also known as AUTS2 syndrome. While the phenotype associated with large deletions and duplications of AUTS2 is well established, clinical features of patients harboring AUTS2 sequence variants have not been extensively described. In this study, we describe the phenotype of five new patients with AUTS2 pathogenic variants, three of them harboring loss-of-function sequence variants. The phenotype of the patients was characterized by attention deficit/hyperactivity disorder (ADHD) and autism spectrum disorder (ASD) or autistic features and mild global developmental delay (GDD) or intellectual disability (ID), all in 4/5 patients (80%), a frequency higher than previously reported for ADHD and autistic features. Microcephaly and short stature were found in 60% of the patients; and feeding difficulties, generalized hypotonia, and ptosis, were each found in 40%. We also provide the aggregated frequency of the 32 items included in the AUTS2 syndrome severity score (ASSS) in patients currently reported in the literature. The main characteristics of the syndrome are GDD/ID in 98% of patients, microcephaly in 65%, feeding difficulties in 62%, ADHD or hyperactivity in 54%, and autistic traits in 52%. Finally, using the location of 31 variants from the literature together with variants from the five patients, we found significantly higher ASSS values in patients with pathogenic variants affecting the 3′ end of the gene, confirming the genotype-phenotype correlation initially described.
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Affiliation(s)
- Carolina Sanchez-Jimeno
- Department of Genetics and Genomics, IIS–Fundación Jiménez Díaz University Hospital, 28040 Madrid, Spain; (C.S.-J.); (F.B.-K.); (F.L.-G.); (R.R.-A.); (C.A.); (M.R.d.A.); (I.L.-S.)
- Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, 28040 Madrid, Spain
| | - Fiona Blanco-Kelly
- Department of Genetics and Genomics, IIS–Fundación Jiménez Díaz University Hospital, 28040 Madrid, Spain; (C.S.-J.); (F.B.-K.); (F.L.-G.); (R.R.-A.); (C.A.); (M.R.d.A.); (I.L.-S.)
- Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, 28040 Madrid, Spain
| | - Fermina López-Grondona
- Department of Genetics and Genomics, IIS–Fundación Jiménez Díaz University Hospital, 28040 Madrid, Spain; (C.S.-J.); (F.B.-K.); (F.L.-G.); (R.R.-A.); (C.A.); (M.R.d.A.); (I.L.-S.)
- Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, 28040 Madrid, Spain
| | - Rebeca Losada-Del Pozo
- Department of Pediatrics, IIS–Fundación Jiménez Díaz University Hospital, 28040 Madrid, Spain; (R.L.-D.P.); (B.M.); (M.R.-M.); (E.M.-C.)
| | - Beatriz Moreno
- Department of Pediatrics, IIS–Fundación Jiménez Díaz University Hospital, 28040 Madrid, Spain; (R.L.-D.P.); (B.M.); (M.R.-M.); (E.M.-C.)
| | - María Rodrigo-Moreno
- Department of Pediatrics, IIS–Fundación Jiménez Díaz University Hospital, 28040 Madrid, Spain; (R.L.-D.P.); (B.M.); (M.R.-M.); (E.M.-C.)
| | - Elena Martinez-Cayuelas
- Department of Pediatrics, IIS–Fundación Jiménez Díaz University Hospital, 28040 Madrid, Spain; (R.L.-D.P.); (B.M.); (M.R.-M.); (E.M.-C.)
| | - Rosa Riveiro-Alvarez
- Department of Genetics and Genomics, IIS–Fundación Jiménez Díaz University Hospital, 28040 Madrid, Spain; (C.S.-J.); (F.B.-K.); (F.L.-G.); (R.R.-A.); (C.A.); (M.R.d.A.); (I.L.-S.)
- Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, 28040 Madrid, Spain
| | - María Fenollar-Cortés
- Clinical Genetics Unit, Department of Clinical Analysis, Clínico San Carlos University Hospital, 28040 Madrid, Spain;
- IIS-Clínico San Carlos University Hospital (IsISSC), 28040 Madrid, Spain
| | - Carmen Ayuso
- Department of Genetics and Genomics, IIS–Fundación Jiménez Díaz University Hospital, 28040 Madrid, Spain; (C.S.-J.); (F.B.-K.); (F.L.-G.); (R.R.-A.); (C.A.); (M.R.d.A.); (I.L.-S.)
- Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, 28040 Madrid, Spain
| | - Marta Rodríguez de Alba
- Department of Genetics and Genomics, IIS–Fundación Jiménez Díaz University Hospital, 28040 Madrid, Spain; (C.S.-J.); (F.B.-K.); (F.L.-G.); (R.R.-A.); (C.A.); (M.R.d.A.); (I.L.-S.)
- Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, 28040 Madrid, Spain
| | - Isabel Lorda-Sanchez
- Department of Genetics and Genomics, IIS–Fundación Jiménez Díaz University Hospital, 28040 Madrid, Spain; (C.S.-J.); (F.B.-K.); (F.L.-G.); (R.R.-A.); (C.A.); (M.R.d.A.); (I.L.-S.)
- Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, 28040 Madrid, Spain
| | - Berta Almoguera
- Department of Genetics and Genomics, IIS–Fundación Jiménez Díaz University Hospital, 28040 Madrid, Spain; (C.S.-J.); (F.B.-K.); (F.L.-G.); (R.R.-A.); (C.A.); (M.R.d.A.); (I.L.-S.)
- Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, 28040 Madrid, Spain
- Correspondence:
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15
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Shickh S, Mighton C, Uleryk E, Pechlivanoglou P, Bombard Y. The clinical utility of exome and genome sequencing across clinical indications: a systematic review. Hum Genet 2021; 140:1403-1416. [PMID: 34368901 DOI: 10.1007/s00439-021-02331-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 07/31/2021] [Indexed: 12/15/2022]
Abstract
Exome sequencing and genome sequencing have the potential to improve clinical utility for patients undergoing genetic investigations. However, evidence of clinical utility is limited to pediatric populations; we aimed to fill this gap by conducting a systematic review of the literature on the clinical utility of exome/genome sequencing across disease indications in pediatric and adult populations. MEDLINE, EMBASE and Cochrane Library were searched between 2016 and 2020. Quantitative studies evaluating diagnostic yield were included; other measures of clinical utility such as changes to clinical management were documented if reported. Two reviewers screened, extracted data, and appraised risk of bias. Fifty studies met our inclusion criteria. All studies reported diagnostic yield, which ranged from 3 to 70%, with higher range of yields reported for neurological indications and acute illness ranging from 22 to 68% and 37-70%, respectively. Diagnoses triggered a range of clinical management changes including surveillance, reproductive-risk counseling, and identifying at-risk relatives in 4-100% of patients, with higher frequencies reported for acute illness ranging from 67 to 95%. The frequency of variants of uncertain significance ranged from 5 to 85% across studies with a potential trend of decreasing frequency over time and higher rates identified in patients of non-European ancestry. This review provides evidence for a higher range of diagnostic yield of exome/genome sequencing compared to standard genetic tests, particularly in neurological and acute indications. However, we identified significant heterogeneity in study procedures and outcomes, precluding a meaningful meta-analysis and certainty in the evidence available for decision-making. Future research that incorporates a comprehensive and consistent approach in capturing clinical utility of exome/genome sequencing across broader ancestral groups is necessary to improve diagnostic accuracy and yield and allow for analysis of trends over time.Prospero registration CRD42019094101.
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Affiliation(s)
- Salma Shickh
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada.,Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, Unity Health Toronto, Toronto, ON, Canada
| | - Chloe Mighton
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada.,Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, Unity Health Toronto, Toronto, ON, Canada
| | | | - Petros Pechlivanoglou
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada.,The Hospital for Sick Children, Toronto, ON, Canada
| | - Yvonne Bombard
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada. .,Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, Unity Health Toronto, Toronto, ON, Canada. .,Li Ka Shing Knowledge Institute of St. Michael's Hospital, University of Toronto, 30 Bond Street, Toronto, ON, M5B 1W8, Canada.
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16
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Trakadis Y, Accogli A, Qi B, Bloom D, Joober R, Levy E, Tabbane K. Next-generation gene panel testing in adolescents and adults in a medical neuropsychiatric genetics clinic. Neurogenetics 2021; 22:313-322. [PMID: 34363551 DOI: 10.1007/s10048-021-00664-3] [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: 02/24/2021] [Accepted: 07/21/2021] [Indexed: 01/04/2023]
Abstract
Intellectual disability (ID) encompasses a clinically and genetically heterogeneous group of neurodevelopmental disorders that may present with psychiatric illness in up to 40% of cases. Despite the evidence for clinical utility of genetic panels in pediatrics, there are no published studies in adolescents/adults with ID or autism spectrum disorder (ASD). This study was approved by our institutional research ethics board. We retrospectively reviewed the medical charts of all patients evaluated between January 2017 and December 2019 in our adult neuropsychiatric genetics clinic at the McGill University Health Centre (MUHC), who had undergone a comprehensive ID/ASD gene panel. Thirty-four patients aged > 16 years, affected by ID/ASD and/or other neuropsychiatric/behavioral disorders, were identified. Pathogenic or likely pathogenic variants were identified in one-third of our cohort (32%): 8 single-nucleotide variants in 8 genes (CASK, SHANK3, IQSEC2, CHD2, ZBTB20, TREX1, SON, and TUBB2A) and 3 copy number variants (17p13.3, 16p13.12p13.11, and 9p24.3p24.1). The presence of psychiatric/behavioral disorders, regardless of the co-occurrence of ID, and, at a borderline level, the presence of ID alone were associated with positive genetic findings (p = 0.024 and p = 0.054, respectively). Moreover, seizures were associated with positive genetic results (p = 0.024). One-third of individuals presenting with psychiatric illness who met our red flags for Mendelian diseases have pathogenic or likely pathogenic variants which can be identified using a comprehensive ID/ASD gene panel (~ 2500 genes) performed on an exome backbone.
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Affiliation(s)
- Y Trakadis
- Division of Medical Genetics, Department of Specialized Medicine, Montreal Children's Hospital, McGill University Health Centre (MUHC), Room A04.3140, 1001 Boul. Décarie, Montreal, QC, H4A 3J1, Canada. .,Department of Human Genetics, McGill University, Montreal, QC, Canada. .,Douglas Mental Health Institute/Hospital, Montreal, Canada. .,Department of Psychiatry, McGill University, Montreal, Canada.
| | - A Accogli
- Division of Medical Genetics, Department of Specialized Medicine, Montreal Children's Hospital, McGill University Health Centre (MUHC), Room A04.3140, 1001 Boul. Décarie, Montreal, QC, H4A 3J1, Canada
| | - B Qi
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - D Bloom
- Douglas Mental Health Institute/Hospital, Montreal, Canada.,Department of Psychiatry, McGill University, Montreal, Canada
| | - R Joober
- Department of Human Genetics, McGill University, Montreal, QC, Canada.,Douglas Mental Health Institute/Hospital, Montreal, Canada.,Department of Psychiatry, McGill University, Montreal, Canada
| | - E Levy
- Douglas Mental Health Institute/Hospital, Montreal, Canada.,Department of Psychiatry, McGill University, Montreal, Canada
| | - K Tabbane
- Douglas Mental Health Institute/Hospital, Montreal, Canada.,Department of Psychiatry, McGill University, Montreal, Canada
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17
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Kritioti E, Theodosiou A, Parpaite T, Alexandrou A, Nicolaou N, Papaevripidou I, Séjourné N, Coste B, Christophidou-Anastasiadou V, Tanteles GA, Sismani C. Unravelling the genetic causes of multiple malformation syndromes: A whole exome sequencing study of the Cypriot population. PLoS One 2021; 16:e0253562. [PMID: 34324503 PMCID: PMC8320927 DOI: 10.1371/journal.pone.0253562] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 06/08/2021] [Indexed: 11/19/2022] Open
Abstract
Multiple malformation syndromes (MMS) belong to a group of genetic disorders characterised by neurodevelopmental anomalies and congenital malformations. Here we explore for the first time the genetic aetiology of MMS using whole-exome sequencing (WES) in undiagnosed patients from the Greek-Cypriot population after prior extensive diagnostics workup including karyotype and array-CGH. A total of 100 individuals (37 affected), from 32 families were recruited and family-based WES was applied to detect causative single-nucleotide variants (SNVs) and indels. A genetic diagnosis was reported for 16 MMS patients (43.2%), with 10/17 (58.8%) of the findings being novel. All autosomal dominant findings occurred de novo. Functional studies were also performed to elucidate the molecular mechanism relevant to the abnormal phenotypes, in cases where the clinical significance of the findings was unclear. The 17 variants identified in our cohort were located in 14 genes (PCNT, UBE3A, KAT6A, SPR, POMGNT1, PIEZO2, PXDN, KDM6A, PHIP, HECW2, TFAP2A, CNOT3, AGTPBP1 and GAMT). This study has highlighted the efficacy of WES through the high detection rate (43.2%) achieved for a challenging category of undiagnosed patients with MMS compared to other conventional diagnostic testing methods (10-20% for array-CGH and ~3% for G-banding karyotype analysis). As a result, family-based WES could potentially be considered as a first-tier cost effective diagnostic test for patients with MMS that facilitates better patient management, prognosis and offer accurate recurrence risks to the families.
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Affiliation(s)
- Evie Kritioti
- Department of Cytogenetics and Genomics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Clinical Genetics Clinic, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Athina Theodosiou
- Department of Cytogenetics and Genomics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | | | - Angelos Alexandrou
- Department of Cytogenetics and Genomics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Nayia Nicolaou
- Clinical Genetics Clinic, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Ioannis Papaevripidou
- Department of Cytogenetics and Genomics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Nina Séjourné
- Aix Marseille Université, CNRS, LNC-UMR 7291, Marseille, France
| | - Bertrand Coste
- Aix Marseille Université, CNRS, LNC-UMR 7291, Marseille, France
| | | | - George A. Tanteles
- Clinical Genetics Clinic, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Carolina Sismani
- Department of Cytogenetics and Genomics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
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18
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Bartoshesky LE, Wright C. Intellectual Developmental Disabilities:: Definitions, Diagnosis, and Delivery of Care. Dela J Public Health 2021; 7:6-8. [PMID: 34467189 PMCID: PMC8352486 DOI: 10.32481/djph.2021.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Affiliation(s)
- Louis E Bartoshesky
- Professor of Pediatrics, Sydney Kimmel Medical College, Thomas Jefferson University
- Medical Director, Center for Special Health Care Needs, ChristianaCare; Adjunct Assistant Professor of Medicine and Pediatrics, University of Pennsylvania
| | - Charmaine Wright
- Medical Director, Center for Special Health Care Needs, ChristianaCare; Adjunct Assistant Professor of Medicine and Pediatrics, University of Pennsylvania
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19
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Dingemans AJM, Stremmelaar DE, Vissers LELM, Jansen S, Nabais Sá MJ, van Remortele A, Jonis N, Truijen K, van de Ven S, Ewals J, Verbruggen M, Koolen DA, Brunner HG, Eichler EE, Gecz J, de Vries BBA. Human disease genes website series: An international, open and dynamic library for up-to-date clinical information. Am J Med Genet A 2021; 185:1039-1046. [PMID: 33439542 PMCID: PMC7986414 DOI: 10.1002/ajmg.a.62057] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 12/11/2020] [Accepted: 12/12/2020] [Indexed: 12/11/2022]
Abstract
Since the introduction of next‐generation sequencing, an increasing number of disorders have been discovered to have genetic etiology. To address diverse clinical questions and coordinate research activities that arise with the identification of these rare disorders, we developed the Human Disease Genes website series (HDG website series): an international digital library that records detailed information on the clinical phenotype of novel genetic variants in the human genome (https://humandiseasegenes.info/). Each gene website is moderated by a dedicated team of clinicians and researchers, focused on specific genes, and provides up‐to‐date—including unpublished—clinical information. The HDG website series is expanding rapidly with 424 genes currently adopted by 325 moderators from across the globe. On average, a gene website has detailed phenotypic information of 14.4 patients. There are multiple examples of added value, one being the ARID1B gene website, which was recently utilized in research to collect clinical information of 81 new patients. Additionally, several gene websites have more data available than currently published in the literature. In conclusion, the HDG website series provides an easily accessible, open and up‐to‐date clinical data resource for patients with pathogenic variants of individual genes. This is a valuable resource not only for clinicians dealing with rare genetic disorders such as developmental delay and autism, but other professionals working in diagnostics and basic research. Since the HDG website series is a dynamic platform, its data also include the phenotype of yet unpublished patients curated by professionals providing higher quality clinical detail to improve management of these rare disorders.
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Affiliation(s)
- Alexander J M Dingemans
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, Nijmegen, The Netherlands
| | - Diante E Stremmelaar
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, Nijmegen, The Netherlands
| | - Lisenka E L M Vissers
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, Nijmegen, The Netherlands
| | - Sandra Jansen
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, Nijmegen, The Netherlands
| | - Maria J Nabais Sá
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, Nijmegen, The Netherlands
| | - Angela van Remortele
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, Nijmegen, The Netherlands
| | - Noraly Jonis
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, Nijmegen, The Netherlands
| | - Kim Truijen
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, Nijmegen, The Netherlands
| | - Sam van de Ven
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, Nijmegen, The Netherlands
| | - Jeroen Ewals
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, Nijmegen, The Netherlands
| | - Michel Verbruggen
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, Nijmegen, The Netherlands
| | - David A Koolen
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, Nijmegen, The Netherlands
| | - Han G Brunner
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, Nijmegen, The Netherlands
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA.,Howard Hughes Medical Institute, University of Washington, Seattle, Washington, USA
| | - Jozef Gecz
- Adelaide Medical School and the Robinson Research Institute, University of Adelaide, Adelaide, South Australia, Australia
| | - Bert B A de Vries
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, Nijmegen, The Netherlands
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20
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Qi Q, Jiang Y, Zhou X, Meng H, Hao N, Chang J, Bai J, Wang C, Wang M, Guo J, Ouyang Y, Xu Z, Xiao M, Zhang VW, Liu J. Simultaneous Detection of CNVs and SNVs Improves the Diagnostic Yield of Fetuses with Ultrasound Anomalies and Normal Karyotypes. Genes (Basel) 2020; 11:genes11121397. [PMID: 33255631 PMCID: PMC7759943 DOI: 10.3390/genes11121397] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 11/09/2020] [Accepted: 11/16/2020] [Indexed: 12/17/2022] Open
Abstract
The routine assessment to determine the genetic etiology for fetal ultrasound anomalies follows a sequential approach, which usually takes about 6–8 weeks turnaround time (TAT). We evaluated the clinical utility of simultaneous detection of copy number variations (CNVs) and single nucleotide variants (SNVs)/small insertion-deletions (indels) in fetuses with a normal karyotype with ultrasound anomalies. We performed CNV detection by chromosomal microarray analysis (CMA) or low pass CNV-sequencing (CNV-seq), and in parallel SNVs/indels detection by trio-based clinical exome sequencing (CES) or whole exome sequencing (WES). Eight-three singleton pregnancies with a normal fetal karyotype were enrolled in this prospective observational study. Pathogenic or likely pathogenic variations were identified in 30 cases (CNVs in 3 cases, SNVs/indels in 27 cases), indicating an overall molecular diagnostic rate of 36.1% (30/83). Two cases had both a CNV of uncertain significance (VOUS) and likely pathogenic SNV, and one case carried both a VOUS CNV and an SNV. We demonstrated that simultaneous analysis of CNVs and SNVs/indels can improve the diagnostic yield of prenatal diagnosis with shortened reporting time, namely, 2–3 weeks. Due to the relatively long TAT for sequential procedure for prenatal genetic diagnosis, as well as recent sequencing technology advancements, it is clinically necessary to consider the simultaneous evaluation of CNVs and SNVs/indels to enhance the diagnostic yield and timely TAT, especially for cases in the late second trimester or third trimester.
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Affiliation(s)
- Qingwei Qi
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, China; (Y.J.); (X.Z.); (N.H.); (J.L.)
- Correspondence: ; Tel.: +86-1851-066-6066
| | - Yulin Jiang
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, China; (Y.J.); (X.Z.); (N.H.); (J.L.)
| | - Xiya Zhou
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, China; (Y.J.); (X.Z.); (N.H.); (J.L.)
| | - Hua Meng
- Department of Ultrasound, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, China; (H.M.); (Y.O.); (Z.X.); (M.X.)
| | - Na Hao
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, China; (Y.J.); (X.Z.); (N.H.); (J.L.)
| | - Jiazhen Chang
- Department of Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, China;
| | - Junjie Bai
- Be Creative Lab Co., Ltd. Beijing 101111, China; (J.B.); (M.W.); (J.G.)
| | - Chunli Wang
- AmCare Genomics Lab, Guangzhou 510335, China; (C.W.); (V.W.Z.)
| | - Mingming Wang
- Be Creative Lab Co., Ltd. Beijing 101111, China; (J.B.); (M.W.); (J.G.)
| | - Jiangshan Guo
- Be Creative Lab Co., Ltd. Beijing 101111, China; (J.B.); (M.W.); (J.G.)
| | - Yunshu Ouyang
- Department of Ultrasound, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, China; (H.M.); (Y.O.); (Z.X.); (M.X.)
| | - Zhonghui Xu
- Department of Ultrasound, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, China; (H.M.); (Y.O.); (Z.X.); (M.X.)
| | - Mengsu Xiao
- Department of Ultrasound, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, China; (H.M.); (Y.O.); (Z.X.); (M.X.)
| | | | - Juntao Liu
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, China; (Y.J.); (X.Z.); (N.H.); (J.L.)
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21
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Dai Y, Wei Y, Chen Y, Guo H, Zhong M. Intellectual disability in two Chinese sisters caused by a 3p26.3p25.3 microdeletion and a 14q32.13q32.33 microduplication inherited from the mother with 46, XX, t (3, 14) (p25; q32). Mol Genet Genomic Med 2020; 8:e1335. [PMID: 32489010 PMCID: PMC7434598 DOI: 10.1002/mgg3.1335] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 05/09/2020] [Accepted: 05/12/2020] [Indexed: 11/20/2022] Open
Abstract
Background Genetic factors associated with intellectual disability (ID) include chromosomal aberrations, copy number variations (CNVs), and pathogenic variants. Identifying the genetic etiologies is beneficial for patient classification, therapy, management, and prognostic evaluation. Emerging genetic tests are helpful in identifying these genetic causes. Methods We enrolled two girl siblings with ID. Trio whole‐exome sequencing (WES) and Copy number variation sequencing (CNV‐Seq) were performed for genetic molecular analysis in these probands and their parents. The parents also accepted high‐resolution G‐banded karyotype studies. Results No significant homozygous or heterozygous variants were identified through WES. By CNV‐seq, we identified an abnormal 3p26.3p25.3 microdeletion and 14q32.13q32.33 microduplication in the two girl siblings but not in their parents. A balanced translocation 46, XX, t (3, 14) (p25; q32) was found in their mother. Conclusion The affected siblings have similar phenotype, including ID, short stature, and microcephaly. Their mother had a history of seven first‐trimester miscarriages and one elective termination because of multiple malformations. This abnormal karyotype was also thought to be responsible for the mother's recurrent miscarriage. WES in combination with CNV‐seq analysis is very helpful for identification of the genetic causes of ID without positive karyotype findings.
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Affiliation(s)
- Ying Dai
- Department of Primary Child Health Care, Children's Hospital of Chongqing Medical University, Chongqing, China.,Pediatric Research Institute, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing Engineering Research Center of Stem Cell Therapy, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, China.,National Clinical Research Center for Child Health and Disorders, Chongqing, China
| | - Yongjuan Wei
- Pediatric Research Institute, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing Engineering Research Center of Stem Cell Therapy, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, China.,National Clinical Research Center for Child Health and Disorders, Chongqing, China.,Department of Neurology, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Yuanyuan Chen
- Pediatric Research Institute, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing Engineering Research Center of Stem Cell Therapy, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, China.,National Clinical Research Center for Child Health and Disorders, Chongqing, China.,Center for Clinical Molecular Medicine, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Hui Guo
- Department of Pediatric, Qianjiang Central Hospital of Chongqing, Chongqing, China
| | - Min Zhong
- Pediatric Research Institute, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing Engineering Research Center of Stem Cell Therapy, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, China.,National Clinical Research Center for Child Health and Disorders, Chongqing, China.,Department of Neurology, Children's Hospital of Chongqing Medical University, Chongqing, China.,Department of Pediatric, Qianjiang Central Hospital of Chongqing, Chongqing, China
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22
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Tripon F, Bogliș A, Micheu C, Streață I, Bănescu C. Pitt-Hopkins Syndrome: Clinical and Molecular Findings of a 5-Year-Old Patient. Genes (Basel) 2020; 11:genes11060596. [PMID: 32481733 PMCID: PMC7349262 DOI: 10.3390/genes11060596] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/20/2020] [Accepted: 05/27/2020] [Indexed: 11/23/2022] Open
Abstract
Pitt Hopkins syndrome (PTHS) is a very rare condition and until now, approximately 500 patients were reported worldwide, of which not all are genetically confirmed. Usually, individuals with variants affecting exons 1 to 5 in the TCF4 gene associate mild intellectual disability (ID), between exons 5 to 8, moderate to severe ID and sometimes have some of the characteristics of PTHS, and variants starting from exon 9 to exon 20 associate a typical PTHS phenotype. In this report, we describe the clinical and molecular findings of a Caucasian boy diagnosed with PTHS. PTHS phenotype is described including craniofacial dysmorphism with brachycephaly, biparietal narrowing, wide nasal bridge, thin and linear lateral eyebrows, palpebral edema, full cheeks, short philtrum, wide mouth with prominent and everted lips, prominent Cupid’s bow, downturned corners of the mouth, microdontia and also the clinical management of the patient. The previously and the current diagnosis scores are described in this report and also the challenges and their benefits for an accurate and early diagnosis.
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Affiliation(s)
- Florin Tripon
- Laboratory of Medical Genetics, Emergency Clinical County Hospital Târgu Mureș, 540136 Târgu Mureș, Romania; (F.T.); (C.B.)
- Department of Genetics, George Emil Palade University of Medicine, Pharmacy, Science, and Technology of Târgu Mureș, 540142 Târgu Mureș, Romania
- Laboratory of Molecular Biology/Genetics, Center for Advanced Medical and Pharmaceutical Research, George Emil Palade University of Medicine, Pharmacy, Science, and Technology of Târgu Mureș, 540142 Târgu Mureș, Romania
| | - Alina Bogliș
- Laboratory of Medical Genetics, Emergency Clinical County Hospital Târgu Mureș, 540136 Târgu Mureș, Romania; (F.T.); (C.B.)
- Department of Genetics, George Emil Palade University of Medicine, Pharmacy, Science, and Technology of Târgu Mureș, 540142 Târgu Mureș, Romania
- Laboratory of Molecular Biology/Genetics, Center for Advanced Medical and Pharmaceutical Research, George Emil Palade University of Medicine, Pharmacy, Science, and Technology of Târgu Mureș, 540142 Târgu Mureș, Romania
- Correspondence: ; Tel.: +40-265-21-55-51
| | - Cristian Micheu
- Child Neurology Psychiatry Clinic, Clinical County Hospital Mureș, 540072 Târgu Mureş, Romania;
| | - Ioana Streață
- Regional Center for Medical Genetics Dolj—Clinical County Emergency Hospital Craiova, University of Medicine and Pharmacy Craiova, 200642 Craiova, Romania;
| | - Claudia Bănescu
- Laboratory of Medical Genetics, Emergency Clinical County Hospital Târgu Mureș, 540136 Târgu Mureș, Romania; (F.T.); (C.B.)
- Department of Genetics, George Emil Palade University of Medicine, Pharmacy, Science, and Technology of Târgu Mureș, 540142 Târgu Mureș, Romania
- Laboratory of Molecular Biology/Genetics, Center for Advanced Medical and Pharmaceutical Research, George Emil Palade University of Medicine, Pharmacy, Science, and Technology of Târgu Mureș, 540142 Târgu Mureș, Romania
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