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Biswas P, Villanueva A, Krajacich BJ, Moreno J, Zhao J, Berry AM, Lazaro D, Lajoie BR, Kruglyak S, Ayyagari R. Avidity sequencing of whole genomes from retinal degeneration pedigrees identifies causal variants. PLoS One 2024; 19:e0307266. [PMID: 39365799 DOI: 10.1371/journal.pone.0307266] [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: 01/19/2023] [Accepted: 07/01/2024] [Indexed: 10/06/2024] Open
Abstract
Whole genome sequencing has been an effective tool in the discovery of variants that cause rare diseases. In this study, we determined the suitability of a novel avidity sequencing approach for rare disease applications. We built a sample to results workflow, combining this sequencing technology with standard library preparation kits, analysis workflows, and interpretation tools. We applied the workflow to ten pedigrees with inherited retinal degeneration (IRD) phenotype. Candidate variants of interest identified through whole genome sequencing were further evaluated using segregation analysis in the additional family members. Potentially causal variants in known IRD genes were detected in five of the ten cases. These high confidence variants were found in ABCA4, CERKL, MAK, PEX6 and RDH12 genes associated with retinal degeneration, that could be sufficient to cause pathology. Pending confirmatory clinical evaluation, we observed a 50% diagnostic yield, consistent with previously reported outcomes of IRD patient analysis. The study confirms that avidity sequencing is effective in detection of causal variants when used for whole genome sequencing in rare disease applications.
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Affiliation(s)
- Pooja Biswas
- Department of Ophthalmology, Shiley Eye Institute, University of California at San Diego, San Diego, California, United States of America
| | - Adda Villanueva
- Department of Ophthalmology, Mejora Vision MD, Merida, Yucatan, Mexico
| | | | - Juan Moreno
- Element Biosciences, San Diego, California, United States of America
| | - Junhua Zhao
- Element Biosciences, San Diego, California, United States of America
| | - Anne Marie Berry
- Department of Ophthalmology, Shiley Eye Institute, University of California at San Diego, San Diego, California, United States of America
| | - Danielle Lazaro
- Department of Ophthalmology, Shiley Eye Institute, University of California at San Diego, San Diego, California, United States of America
| | - Bryan R Lajoie
- Element Biosciences, San Diego, California, United States of America
| | - Semyon Kruglyak
- Element Biosciences, San Diego, California, United States of America
| | - Radha Ayyagari
- Department of Ophthalmology, Shiley Eye Institute, University of California at San Diego, San Diego, California, United States of America
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Goh ESY, Chad L, Richer J, Bombard Y, Mighton C, Agatep R, Lacaria M, Penny B, Thomas MA, Zawati MH, MacFarlane J, Laberge AM, Nelson TN. Canadian College of Medical Geneticists: clinical practice advisory document - responsibility to recontact for reinterpretation of clinical genetic testing. J Med Genet 2024:jmg-2024-110330. [PMID: 39362754 DOI: 10.1136/jmg-2024-110330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2024] [Accepted: 09/26/2024] [Indexed: 10/05/2024]
Abstract
BACKGROUND Advances in technology and knowledge have facilitated both an increase in the number of patient variants reported and variants reclassified. While there is currently no duty to recontact for reclassified genetic variants, there may be a responsibility. The purpose of this clinical practice advisory document is to provide healthcare practitioners guidance for recontact of previously identified and classified variants, suggest methods for recontact, and principles to consider, taking account patient safety, feasibility, ethical considerations, health service capacity and resource constraints. The target audience are practitioners who order genetic testing, follow patients who have undergone genetic testing and those analysing and reporting genetic testing. METHODS A multidisciplinary group of laboratory and ordering clinicians, patient representatives, ethics and legal researchers and a genetic counsellor from the Canadian Association of Genetic Counsellors reviewed the existing literature and guidelines on responsibility to recontact in a clinical context to make recommendations. Comments were collected from the Canadian College of Medical Geneticists (CCMG) Education, Ethics, and Public Policy, Clinical Practice and Laboratory Practice committees, and the membership at large. RESULTS Following incorporation of feedback, and external review by the Canadian Association of Genetic Counsellors and patient groups, the document was approved by the CCMG Board of Directors. The CCMG is the Canadian organisation responsible for certifying laboratory and medical geneticists who provide medical genetics services, and for establishing professional and ethical standards for clinical genetics services in Canada. CONCLUSION The document describes the ethical and practical factors and suggests a shared responsibility between patients, ordering clinician and laboratory practitioners.
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Affiliation(s)
- Elaine Suk-Ying Goh
- Laboratory Medicine and Genetics, Trillium Health Partners, Mississauga, Ontario, Canada
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Lauren Chad
- The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Julie Richer
- Medical Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Yvonne Bombard
- Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Chloe Mighton
- Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Ron Agatep
- Genomics, Shared Health Diagnostic Services, Winnipeg, Manitoba, Canada
| | - Melanie Lacaria
- Newborn Screening Ontario, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | | | - Mary Ann Thomas
- Departments of Medical Genetics and Pediatrics, University of Calgary, Calgary, Alberta, Canada
| | - Ma'n H Zawati
- Human Genetics, Centre of Genomics and Policy - McGill University, Montreal, Quebec, Canada
| | - Julie MacFarlane
- Screening Programs, Perinatal Services BC, Vancouver, British Columbia, Canada
| | - Anne-Marie Laberge
- Department of Pediatrics, University of Montreal, Montreal, Quebec, Canada
- Medical Genetics, Department of Pediatrics, CHU Sainte-Justine, Montreal, Quebec, Canada
| | - Tanya N Nelson
- Genome Diagnostics, Pathology and Laboratory Medicine, BC Children's Hospital, Vancouver, British Columbia, Canada
- Genome Diagnostics, Pathology and Laboratory Medicine, BC Women's Hospital and Health Centre, Vancouver, British Columbia, Canada
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Lin H, Chu S, Tang C, Wang S, Cai Y, Sun L. A CD3G homozygous pathogenic variant in a Chinese child with lupus-like disease, autoimmune thyroiditis and immunodeficiency. Clin Chim Acta 2024; 563:119898. [PMID: 39094808 DOI: 10.1016/j.cca.2024.119898] [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: 05/14/2024] [Revised: 07/19/2024] [Accepted: 07/31/2024] [Indexed: 08/04/2024]
Abstract
BACKGROUND The T-cell receptor (TCR)/CD3 complex plays a crucial role in T-cell development and immune regulation. CD3G gene encodes one of the CD3 subunits named CD3γ, and its deficiency can cause autoimmune disorders, immunodeficiency and recurrent infections. To date, only 13 patients with CD3G variants have been reported. CASE REPORT We report a 10-year-old Chinese boy presented with lupus-like disease in addition to autoimmune thyroiditis, asthma, immunodeficiency and recurrent infection. Flow cytometric analysis revealed apparently decreased levels of CD3+ and CD8+ T cells but mildly decreased CD4+ T cells. However, the activation of T cells and B cells increased. RESULTS Trio-based whole-exome sequencing revealed a homozygous pathogenic variant (c.213delA, p.Lys71fs) of CD3G gene in the proband. His parents were both heterozygous carriers of this variant. CONCLUSION This is the first patient who met the diagnostic criteria for systemic lupus erythematosus by the Systemic Lupus International Collaborating Clinics (SLICC) group. In addition to low T cells and low Treg cells, our study further revealed T cells and B cells activation enhanced in CD3γ deficiency patient, which may play an important role in autoimmunity. We believe that our study makes a significant contribution to the literature and will provide further insight into CD3γ deficiency and monogenic lupus.
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Affiliation(s)
- Hongrong Lin
- Department of Pediatrics, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong Province, China
| | - Shuai Chu
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong Province, China
| | - Cui Tang
- Department of Pediatrics, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong Province, China
| | - Sijin Wang
- Department of Pediatrics, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong Province, China
| | - Yong Cai
- Department of Pediatrics, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong Province, China.
| | - Liangzhong Sun
- Department of Pediatrics, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong Province, China.
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Strålfors A, Lagerstedt-Robinson K, Landin B. Atypical Interference in Hb A1c Measurements Might Be Due to Mosaic Expression of Hemoglobin Variants. Clin Chem 2024; 70:1185-1187. [PMID: 38958122 DOI: 10.1093/clinchem/hvae091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 06/03/2024] [Indexed: 07/04/2024]
Affiliation(s)
- Annelie Strålfors
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | | | - Britta Landin
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Chemistry, Karolinska University Hospital, Stockholm, Sweden
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Parrini E, Balestrini S, Rutigliano D, Ricci ML, Mei D, Guerrini R. Bilateral Perisylvian Polymicrogyria, Intellectual Disability and Nephronophthisis Associated With Compound Heterozygous Pathogenic Variants in the CEP83 Gene. Am J Med Genet A 2024:e63863. [PMID: 39219159 DOI: 10.1002/ajmg.a.63863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 08/11/2024] [Accepted: 08/18/2024] [Indexed: 09/04/2024]
Abstract
The centrosomal protein 83 (CEP83) is a centriolar protein involved in primary cilium assembly, an early and critical step in ciliogenesis. Bi-allelic pathogenic variants in the CEP83 gene have been associated with infantile nephronophthisis and, in a few patients, retinitis pigmentosa. We describe a 5-year-old boy with bilateral perisylvian polymicrogyria, intellectual disability, and nephronophthisis in whom, using exome sequencing, we identified the c.1052T>G p.(Leu351*) stopgain variant inherited from the father and the c.2024T>C p.(Leu675Pro) missense variant inherited from the mother, in a compound heterozygous pattern. Polymicrogyria or, in general, malformations of cortical development had not been previously observed in patients with pathogenic CEP83 variants. However, defects in CEP83 can affect the formation and function of cilia or centrosomal structures, resulting in a polymicrogyric pattern overlapping with that associated with pathogenic variants affecting other genes coding for centrosomal components. This observation expands the spectrum of phenotypes associated with the CEP83 gene and adds it to the list of genes associated with bilateral perisylvian polymicrogyria.
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Affiliation(s)
- Elena Parrini
- Neuroscience and Medical Genetics Department, Meyer Children's Hospital IRCCS, Florence, Italy
| | - Simona Balestrini
- Neuroscience and Medical Genetics Department, Meyer Children's Hospital IRCCS, Florence, Italy
- NEUROFARBA Department, University of Florence, Florence, Italy
| | - Domenico Rutigliano
- Neuroscience and Medical Genetics Department, Meyer Children's Hospital IRCCS, Florence, Italy
| | - Maria Luisa Ricci
- Neuroscience and Medical Genetics Department, Meyer Children's Hospital IRCCS, Florence, Italy
| | - Davide Mei
- Neuroscience and Medical Genetics Department, Meyer Children's Hospital IRCCS, Florence, Italy
| | - Renzo Guerrini
- Neuroscience and Medical Genetics Department, Meyer Children's Hospital IRCCS, Florence, Italy
- NEUROFARBA Department, University of Florence, Florence, Italy
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Wachtmeister A, Tettamanti G, Nordgren I, Norrby C, Laurell T, Lu Y, Skarin Nordenvall A, Nordgren A. Cancer risk in individuals with polydactyly: a Swedish population-based cohort study. Br J Cancer 2024; 131:755-762. [PMID: 38951698 PMCID: PMC11333495 DOI: 10.1038/s41416-024-02770-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 06/13/2024] [Accepted: 06/17/2024] [Indexed: 07/03/2024] Open
Abstract
BACKGROUND Polydactyly is a feature of several cancer predisposition syndromes (CPS), however, cancer risk in individuals with polydactyly is largely unknown. METHODS We performed a matched cohort study using data from Swedish national registers. We included 6694 individuals with polydactyly, born in Sweden between 1970-2017. Polydactyly was categorised as thumb polydactyly, finger polydactyly, polydactyly+ (additional birth defects and/or intellectual disability) or isolated polydactyly. Each exposed individual was matched to 50 comparisons by sex, birth year and birth county. Associations were estimated through Cox proportional hazard models. FINDINGS An increased childhood cancer risk was found in males (HR 4.24, 95% CI 2.03-8.84) and females (HR 3.32, 95% CI 1.44-7.63) with polydactyly+. Isolated polydactyly was associated with cancer in childhood (HR 1.87, 95% CI 1.05-3.33) and young adulthood (HR 2.30, 95% CI 1.17-4.50) in males but not in females. The increased cancer risk remained after exclusion of two known CPS: Down syndrome and neurofibromatosis. The highest site-specific cancer risk was observed for kidney cancer and leukaemia. CONCLUSIONS An increased cancer risk was found in individuals with polydactyly, especially in males and in individuals with polydactyly+. We encourage future research about polydactyly and cancer associations and emphasise the importance of clinical phenotyping.
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Affiliation(s)
| | - Giorgio Tettamanti
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Unit of Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Ida Nordgren
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Christina Norrby
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Tobias Laurell
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Hand Surgery, Södersjukhuset, Stockholm, Sweden
| | - Yunxia Lu
- Department of Population Health and Disease Prevention & Department of Epidemiology and Biostatistics, Program in Public Health, University of California, Irvine, CA, USA
| | - Anna Skarin Nordenvall
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Radiology, Karolinska University Hospital, Stockholm, Sweden
| | - Ann Nordgren
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
- Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
- Institute of Biomedicine, Department of Laboratory Medicine, University of Gothenburg, Gothenburg, Sweden
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Moya Quiros V, Adham A, Convers P, Lesca G, Mauguiere F, Soulier H, Arzimanoglou A, Bayat A, Braakman H, Camdessanche JP, Casenave P, Chaton L, Chaix Y, Chochoi M, Depienne C, Desportes V, De Ridder J, Dinkelacker V, Gardella E, Kluger GJ, Jung J, Lemesle Martin M, Mancardi MM, Mueller M, Poulat AL, Platzer K, Roubertie A, Stokman MF, Vulto-van Silfhout AT, Wiegand G, Mazzola L. Electro-Clinical Features and Functional Connectivity Analysis in SYN1-Related Epilepsy. Ann Neurol 2024. [PMID: 39177219 DOI: 10.1002/ana.27063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Revised: 08/07/2024] [Accepted: 08/07/2024] [Indexed: 08/24/2024]
Abstract
OBJECTIVE There is currently scarce data on the electroclinical characteristics of epilepsy associated with synapsin 1 (SYN1) pathogenic variations. We examined clinical and electro-encephalographic (EEG) features in patients with epilepsy and SYN1 variants, with the aim of identifying a distinctive electroclinical pattern. METHODS In this retrospective multicenter study, we collected and reviewed demographic, genetic, and epilepsy data of 19 male patients with SYN1 variants. Specifically, we analyzed interictal EEG data for all patients, and electro-clinical data from 10 epileptic seizures in 5 patients, using prolonged video-EEG monitoring recordings. Inter-ictal EEG functional connectivity parameters and frequency spectrum of the 10 patients over 12 years of age, were computed and compared with those of 56 age- and sex-matched controls. RESULTS The main electroclinical features of epilepsy in patients with SYN1 were (1) EEG background and organization mainly normal; (2) interictal abnormalities are often rare or not visible on EEG; (3) more than 60% of patients had reflex seizures (cutaneous contact with water and defecation being the main triggers) isolated or associated with spontaneous seizures; (4) electro-clinical semiology of seizures was mainly temporal or temporo-insulo/perisylvian with a notable autonomic component; and (5) ictal EEG showed a characteristic rhythmic theta/delta activity predominating in temporo-perisylvian regions at the beginning of most seizures. Comparing patients with SYN1 to healthy subjects, we observed a shift to lower frequency bands in power spectrum of interictal EEG and an increased connectivity in both temporal regions. INTERPRETATION A distinct epilepsy syndrome emerges in patients with SYN1, with a rather characteristic clinical and EEG pattern suggesting predominant temporo-insular involvement. ANN NEUROL 2024.
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Affiliation(s)
| | - Ahmed Adham
- Physical Medicine and Rehabilitation Department, University Hospital of Saint-Étienne, Saint-Étienne, France
- CEA, LETI, CLINATEC, University Grenoble Alpes, Grenoble, France
| | - Philippe Convers
- Neurology Department, University Hospital, Saint-Etienne, France
- NeuroPain Lab, Lyon Neuroscience Research Centre, CRNL-INSERM U 1028/CNRS UMR 5292, University of Lyon, Lyon, France
| | - Gaetan Lesca
- Department of Genetics, Member of the ERN EpiCARE, Hospices Civils de Lyon, Bron, France
- Institute NeuroMyoGène, Laboratoire Physiopathologie et Génétique du Neurone et du Muscle, CNRS UMR 5261-INSERM U1315, Université de Lyon-Université Claude Bernard Lyon 1, Lyon, France
| | - François Mauguiere
- NeuroPain Lab, Lyon Neuroscience Research Centre, CRNL-INSERM U 1028/CNRS UMR 5292, University of Lyon, Lyon, France
- Department of Functional Neurology and Epileptology, Member of the ERN EpiCARE, Hospices Civils de Lyon, Université de Lyon, Lyon, France
| | - Hugo Soulier
- Neurology Department, University Hospital, Saint-Etienne, France
| | - Alexis Arzimanoglou
- Department of Clinical Epileptology, Sleep Disorders and Functional Pediatric Neurology, coordinating member of the ERN EpiCARE, University Hospitals of Lyon (HCL), Lyon, France
- Sección Epilepsia, Sueño y Neurofisiología, Department of Neurology, coordinating member of the ERN EpiCARE, Hospital Sant Joan de Déu Barcelona, Barcelona, Spain
| | - Allan Bayat
- Institute for Regional Health Services, University of Southern Denmark, Odense, Denmark
- Department of Epilepsy Genetics and Personalized Medicine, Danish Epilepsy Center, Member of the ERN EpiCARE, Dianalund, Denmark
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Hilde Braakman
- Department of Paediatric Neurology, Radboud University Medical Centre, Amalia Children's Hospital, Nijmegen, The Netherlands
| | | | | | - Laurence Chaton
- Department of Neurology, Neurophysiology Unit, CHU Lille, Lille, France
| | - Yves Chaix
- Toulouse NeuroImaging Center, University of Toulouse, INSERM, Université Paul Sabatier, Toulouse, France
- Pediatric Neurology Unit, Children's Hospital, Toulouse-Purpan University Hospital, Toulouse, France
| | - Maxime Chochoi
- Department of Neurology, Neurophysiology Unit, CHU Lille, Lille, France
| | - Christel Depienne
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Vincent Desportes
- Hospices Civils de Lyon, Department of Pediatric Neurology, Member of the ERN EpiCARE, Hôpital Femme Mère Enfant, Lyon, France
| | - Jessie De Ridder
- Department of Neurology, Academic Center for Epileptology, Kempenhaeghe, Heeze, The Netherlands
| | - Vera Dinkelacker
- Department of Neurology, University Hospital Strasbourg, Strasbourg, France
| | - Elena Gardella
- Institute for Regional Health Services, University of Southern Denmark, Odense, Denmark
- Department of Epilepsy Genetics and Personalized Medicine, Danish Epilepsy Center, Member of the ERN EpiCARE, Dianalund, Denmark
| | - Gerhard J Kluger
- Schön Klinik Vogtareuth, Center for Pediatric Neurology, Neurorehabilitation and Epileptology, Collaborating Partner of the ERN EpiCARE, PMU, Vogtareuth, Salzburg, Germany
| | - Julien Jung
- Department of Functional Neurology and Epileptology, Member of the ERN EpiCARE, Hospices Civils de Lyon, Université de Lyon, Lyon, France
- Department of Neurology, University Hospital, Lyon Neuroscience Research Center (CRNL), INSERM U1028, CNRS UMR5292, Lyon, France
| | | | - Maria Margherita Mancardi
- Unit of Child Neuropsychiatry, Epilepsy Center, Member of the ERN EpiCARE, Istituto Giannina Gaslini, Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics and Maternal and Child Health, University of Genoa, Genoa, Italy
| | - Markus Mueller
- Department of Epileptology, Krankenhaus Mara, Bethel Epilepsy Center, Bielefeld University, Bielefeld, Germany
| | - Anne-Lise Poulat
- Hospices Civils de Lyon, Department of Pediatric Neurology, Member of the ERN EpiCARE, Hôpital Femme Mère Enfant, Lyon, France
| | - Konrad Platzer
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Agathe Roubertie
- Department of Pediatric Neurology, INSERM, University Hospital Montpellier, Montpellier, France
| | - Marijn F Stokman
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Gert Wiegand
- Division of Pediatric Neurology, Department of Pediatrics, Asklepios Klinik Nord-Heidberg, Hamburg, Germany
- Department of Pediatric and Adolescent Medicine II (Neuropediatrics, Social Pediatrics), University Medical Centre Schleswig-Holstein, Kiel, Germany
| | - Laure Mazzola
- Neurology Department, University Hospital, Saint-Etienne, France
- NeuroPain Lab, Lyon Neuroscience Research Centre, CRNL-INSERM U 1028/CNRS UMR 5292, University of Lyon, Lyon, France
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Yan J, Huang Y, Cao L, Dong Y, Xu Z, Wang F, Gao Y, Feng D, Zhang M. Clinical, pathological and genetic characteristics of 17 unrelated children with Alagille Syndrome. BMC Pediatr 2024; 24:532. [PMID: 39164659 PMCID: PMC11334458 DOI: 10.1186/s12887-024-04973-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 07/25/2024] [Indexed: 08/22/2024] Open
Abstract
BACKGROUND Alagille syndrome (ALGS) is a multisystem genetic disorder frequently characterized by hepatic manifestations. This study analyzed the clinical, pathological, and molecular genetic features of ALGS to improve the efficiency of clinical diagnosis. METHODS We retrospectively analyzed the clinical manifestations, pathological examination findings, and genetic testing results of 17 children diagnosed with ALGS based on the revised criteria and hospitalized at our center from January 2012 to January 2022. RESULTS The clinical manifestations are as follows: Cholestasis (16/17, 94%), characteristic facies (15/17, 88%), heart disease (12/16, 75%), butterfly vertebrae (12/17, 71%) and posterior embryotoxon (7/12, 58%). Among the 15 patients who underwent liver pathology examination, 13 (87%) were found to have varying degrees of bile duct paucity. Genetic testing was performed on 15 children, and pathogenic variants of the jagged canonical Notch ligand 1 (JAG1) gene were identified in 13 individuals, including 4 novel variants. No pathogenic variant in the notch homolog 2 (NOTCH2) gene were identified, and 2 children exhibited none of the aforementioned gene pathogenic variants. The median follow-up duration was 7 years. Of the remaining 15 patients (excluding 2 lost to follow-up), 11 remained stable, 4 deteriorated, and no patient died during the follow-up period. CONCLUSIONS Among children diagnosed with ALGS, cholestasis stands as the most common feature. To minimize the risk of misdiagnosis, genetic testing should be performed on children exhibiting cholestasis, followed by the application of the revised diagnostic criteria for ALGS. While pharmacological therapy has shown effectiveness for ALGS patients, liver transplantation may be considered in instances of severe pruritus.
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Affiliation(s)
- Jianguo Yan
- Senior Department of Liver Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Yuanzhi Huang
- Peking University 302 Clinical Medical School, 38 Xueyuan Road, 100191, Beijing, China
- Senior Department of Liver Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Lili Cao
- Senior Department of Liver Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Yi Dong
- Senior Department of Liver Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Zhiqiang Xu
- Senior Department of Liver Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Fuchuan Wang
- Senior Department of Liver Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Yinjie Gao
- Senior Department of Liver Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Danni Feng
- Senior Department of Liver Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Min Zhang
- Peking University 302 Clinical Medical School, 38 Xueyuan Road, 100191, Beijing, China.
- Senior Department of Liver Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China.
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9
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Chi CS, Tsai CR, Lee HF. Resolving unsolved whole-genome sequencing data in paediatric neurological disorders: a cohort study. Arch Dis Child 2024; 109:730-735. [PMID: 38789118 PMCID: PMC11347223 DOI: 10.1136/archdischild-2024-326985] [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: 02/10/2024] [Accepted: 05/11/2024] [Indexed: 05/26/2024]
Abstract
OBJECTIVE To resolve unsolved whole-genome sequencing (WGS) data in individuals with paediatric neurological disorders. DESIGN A cohort study method using updated bioinformatic tools, new analysis targets, clinical information and literature databases was employed to reanalyse existing unsolved genome data. PARTICIPANTS From January 2016 to September 2023, a total of 615 individuals who aged under 18 years old, exhibited neurological disorders and received singleton WGS were recruited. 364 cases were unsolved during initial WGS analysis, in which 102 consented to reanalyse existing singleton WGS data. RESULTS Median duration for reanalysis after initial negative WGS results was 2 years and 4 months. The diagnostic yield was 29 of 102 individuals (28.4%) through reanalysis. New disease gene discovery and new target acquisitions contributed to 13 of 29 solved cases (44.8%). The reasons of non-detected causative variants during initial WGS analysis were variant reclassification in 9 individuals (31%), analytical issue in 9 (31%), new emerging disease-gene association in 8 (27.6%) and clinical update in 3 (10.3%). The 29 new diagnoses increased the cumulative diagnostic yield of clinical WGS in the entire study cohort to 45.5% after reanalysis. CONCLUSIONS Unsolved paediatric WGS individuals with neurological disorders could obtain molecular diagnoses through reanalysis within a timeframe of 2-2.5 years. New disease gene, structural variations and deep intronic splice variants make a significant contribution to diagnostic yield. This approach can provide precise genetic counselling to positive reanalysis results and end a diagnostic odyssey.
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Affiliation(s)
- Ching-Shiang Chi
- Division of Pediatric Neurology, Children's Medical Center, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Chi-Ren Tsai
- Division of Pediatric Neurology, Children's Medical Center, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Hsiu-Fen Lee
- Division of Pediatric Neurology, Children's Medical Center, Taichung Veterans General Hospital, Taichung, Taiwan
- Department of Post-Baccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung, Taiwan
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10
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Wincent J, Helgadóttir HT, Sergouniotis F, Salazar Mantero A, Carvalho CMB, Malmgren H, Lindstrand A, Iwarsson E. Genome sequencing differentiates a paracentric inversion from a balanced insertion enabling more accurate preimplantation genetic testing. Acta Obstet Gynecol Scand 2024; 103:1564-1569. [PMID: 38872454 PMCID: PMC11266630 DOI: 10.1111/aogs.14898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 05/13/2024] [Accepted: 05/26/2024] [Indexed: 06/15/2024]
Abstract
INTRODUCTION Distinguishing paracentric inversions (PAIs) from chromosomal insertions has traditionally relied on fluorescent in situ hybridization (FISH) techniques, but recent advancements in high-throughput sequencing have enabled the use of genome sequencing for such differentiation. In this study, we present a 38-year-old male carrier of a paracentric inversion on chromosome 2q, inv (2)(q31.2q34), whose partner experienced recurrent miscarriages. MATERIAL AND METHODS FISH analysis confirmed the inversion, and genome sequencing was employed for detailed characterization. RESULTS Preimplantation genetic testing (PGT) revealed that all assessed embryos were balanced, consistent with the low risk of unbalanced offspring associated with PAIs. While PAI carriers traditionally exhibit low risk of producing unbalanced offspring, exceptions exist due to crossover events within the inversion loop. Although the sample size was limited, the findings align with existing sperm study data, supporting the rare occurrence of unbalanced progeny in PAI carriers. CONCLUSIONS This study highlights the possibility of characterizing PAIs using genome sequencing to enable correct reproductive counseling and PGT decisions. Detailed characterization of a PAI is crucial for understanding potential outcomes and guiding PGT strategies, as accurate knowledge of the inversion size is essential for appropriate method selection in PGT. Given the very low risk of unbalanced offspring in PAI carriers, routine PGT may not be warranted but should be considered in specific cases with a history of unbalanced progeny or recurrent miscarriages. This study contributes to our understanding of PAI segregation and its implications for reproductive outcomes.
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Affiliation(s)
- Josephine Wincent
- Department of Molecular Medicine and SurgeryKarolinska InstitutetStockholmSweden
- Clinical Genetics and GenomicsKarolinska University HospitalStockholmSweden
| | - Hafdís T. Helgadóttir
- Department of Molecular Medicine and SurgeryKarolinska InstitutetStockholmSweden
- Clinical Genetics and GenomicsKarolinska University HospitalStockholmSweden
| | - Fotios Sergouniotis
- Department of Reproductive MedicineKarolinska University HospitalStockholmSweden
- Department of Obstetrics and GynecologyKarolinska University HospitalStockholmSweden
| | - Angelo Salazar Mantero
- Department of Molecular Medicine and SurgeryKarolinska InstitutetStockholmSweden
- Clinical Genetics and GenomicsKarolinska University HospitalStockholmSweden
| | | | - Helena Malmgren
- Department of Molecular Medicine and SurgeryKarolinska InstitutetStockholmSweden
- Clinical Genetics and GenomicsKarolinska University HospitalStockholmSweden
| | - Anna Lindstrand
- Department of Molecular Medicine and SurgeryKarolinska InstitutetStockholmSweden
- Clinical Genetics and GenomicsKarolinska University HospitalStockholmSweden
| | - Erik Iwarsson
- Department of Molecular Medicine and SurgeryKarolinska InstitutetStockholmSweden
- Clinical Genetics and GenomicsKarolinska University HospitalStockholmSweden
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11
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Drackley A, Peter M, Rathbun P, Ing A, Prada CE, Yap KL. Homozygosity for disease-causing variants in AMT and GLDC in a patient with severe nonketotic hyperglycinemia. Am J Med Genet A 2024; 194:e63622. [PMID: 38572626 DOI: 10.1002/ajmg.a.63622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 03/07/2024] [Accepted: 03/25/2024] [Indexed: 04/05/2024]
Abstract
Nonketotic hyperglycinemia (NKH) is a relatively well-characterized inborn error of metabolism that results in a combination of lethargy, hypotonia, seizures, developmental arrest, and, in severe cases, death early in life. Three genes encoding components of the glycine cleavage enzyme system-GLDC, AMT, and GCSH-are independently associated with NKH. We report on a patient with severe NKH in whom the homozygous pathogenic variant in AMT (NM_000481.3):c.602_603del (p.Lys201Thrfs*75) and the homozygous likely pathogenic variant in GLDC(NM_000170.2):c.2852C>A (p.Ser951Tyr) were both identified. Our patient demonstrates a novel combination of two homozygous disease-causing variants impacting the glycine cleavage pathway at two different components, and elicits management- and genetic counseling-related challenges for the family.
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Affiliation(s)
- Andy Drackley
- Department of Pathology & Laboratory Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
- Division of Genetics, Genomics, and Metabolism, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
| | - Merlene Peter
- Division of Genetics, Genomics, and Metabolism, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
| | - Pamela Rathbun
- Department of Pathology & Laboratory Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Alexander Ing
- Department of Pathology & Laboratory Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
- Division of Genetics, Genomics, and Metabolism, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Carlos E Prada
- Division of Genetics, Genomics, and Metabolism, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Kai Lee Yap
- Department of Pathology & Laboratory Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
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12
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Pei Y, Tanguy M, Giess A, Dixit A, Wilson LC, Gibbons RJ, Twigg SRF, Elgar G, Wilkie AOM. A Comparison of Structural Variant Calling from Short-Read and Nanopore-Based Whole-Genome Sequencing Using Optical Genome Mapping as a Benchmark. Genes (Basel) 2024; 15:925. [PMID: 39062704 PMCID: PMC11276380 DOI: 10.3390/genes15070925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Revised: 07/03/2024] [Accepted: 07/11/2024] [Indexed: 07/28/2024] Open
Abstract
The identification of structural variants (SVs) in genomic data represents an ongoing challenge because of difficulties in reliable SV calling leading to reduced sensitivity and specificity. We prepared high-quality DNA from 9 parent-child trios, who had previously undergone short-read whole-genome sequencing (Illumina platform) as part of the Genomics England 100,000 Genomes Project. We reanalysed the genomes using both Bionano optical genome mapping (OGM; 8 probands and one trio) and Nanopore long-read sequencing (Oxford Nanopore Technologies [ONT] platform; all samples). To establish a "truth" dataset, we asked whether rare proband SV calls (n = 234) made by the Bionano Access (version 1.6.1)/Solve software (version 3.6.1_11162020) could be verified by individual visualisation using the Integrative Genomics Viewer with either or both of the Illumina and ONT raw sequence. Of these, 222 calls were verified, indicating that Bionano OGM calls have high precision (positive predictive value 95%). We then asked what proportion of the 222 true Bionano SVs had been identified by SV callers in the other two datasets. In the Illumina dataset, sensitivity varied according to variant type, being high for deletions (115/134; 86%) but poor for insertions (13/58; 22%). In the ONT dataset, sensitivity was generally poor using the original Sniffles variant caller (48% overall) but improved substantially with use of Sniffles2 (36/40; 90% and 17/23; 74% for deletions and insertions, respectively). In summary, we show that the precision of OGM is very high. In addition, when applying the Sniffles2 caller, the sensitivity of SV calling using ONT long-read sequence data outperforms Illumina sequencing for most SV types.
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Affiliation(s)
- Yang Pei
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK; (Y.P.); (S.R.F.T.)
| | - Melanie Tanguy
- Genomics England Limited, One Canada Square, London E14 5AB, UK
| | - Adam Giess
- Genomics England Limited, One Canada Square, London E14 5AB, UK
| | - Abhijit Dixit
- Clinical Genetics Service, Nottingham University Hospitals NHS Foundation Trust, City Hospital, Nottingham NG5 1PB, UK
| | - Louise C. Wilson
- North East Thames Regional Genetics Service, Great Ormond Street Hospital for Children NHS Foundation Trust, Great Ormond Street Hospital, London WC1N 3JH, UK
| | - Richard J. Gibbons
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Stephen R. F. Twigg
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK; (Y.P.); (S.R.F.T.)
| | - Greg Elgar
- Genomics England Limited, One Canada Square, London E14 5AB, UK
| | - Andrew O. M. Wilkie
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK; (Y.P.); (S.R.F.T.)
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13
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Harsono IW, Ariani Y, Benyamin B, Fadilah F, Pujianto DA, Hafifah CN. IDeRare: a lightweight and extensible open-source phenotype and exome analysis pipeline for germline rare disease diagnosis. JAMIA Open 2024; 7:ooae052. [PMID: 38883202 PMCID: PMC11179852 DOI: 10.1093/jamiaopen/ooae052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 05/20/2024] [Accepted: 05/27/2024] [Indexed: 06/18/2024] Open
Abstract
Objectives Diagnosing rare diseases is an arduous and challenging process in clinical settings, resulting in the late discovery of novel variants and referral loops. To help clinicians, we built IDeRare pipelines to accelerate phenotype-genotype analysis for patients with suspected rare diseases. Materials and Methods IDeRare pipeline is separated into phenotype and genotype parts. The phenotype utilizes our handmade Python library, while the genotype part utilizes command line (bash) and Python script to combine bioinformatics executable and Docker image. Results We described various implementations of IDeRare phenotype and genotype parts with real-world clinical and exome data using IDeRare, accelerating the terminology conversion process and giving insight on the diagnostic pathway based on disease linkage analysis until exome analysis and HTML-based reporting for clinicians. Conclusion IDeRare is freely available under the BSD-3 license, obtainable via GitHub. The portability of IDeRare pipeline could be easily implemented for semi-technical users and extensible for advanced users.
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Affiliation(s)
- Ivan William Harsono
- Doctoral Program in Biomedical Sciences, Faculty of Medicine, Universitas Indonesia, Jakarta 10430, Indonesia
| | - Yulia Ariani
- Department of Medical Biology, Faculty of Medicine, Universitas Indonesia, Jakarta 10430, Indonesia
| | - Beben Benyamin
- Australian Centre for Precision Health, University of South Australia, Adelaide 5000, Australia
- UniSA Allied Health and Human Performance, University of South Australia, Adelaide 5000, Australia
- South Australian Health and Medical Research Institute (SAHMRI), University of South Australia, Adelaide 5000, Australia
| | - Fadilah Fadilah
- Department of Medical Chemistry, Faculty of Medicine, Universitas Indonesia, Jakarta 10430, Indonesia
- Bioinformatics Core Facilities-IMERI, Faculty of Medicine, Universitas Indonesia, Jakarta 10430, Indonesia
| | - Dwi Ari Pujianto
- Department of Medical Biology, Faculty of Medicine, Universitas Indonesia, Jakarta 10430, Indonesia
| | - Cut Nurul Hafifah
- Department of Child Health, Dr Cipto Mangunkusumo Hospital, Faculty of Medicine, University of Indonesia, Jakarta 10430, Indonesia
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14
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Marchionni E, Guadagnolo D, Mastromoro G, Pizzuti A. Prenatal Genome-Wide Sequencing analysis (Exome or Genome) in detecting pathogenic Single Nucleotide Variants in fetal Central Nervous System Anomalies: systematic review and meta-analysis. Eur J Hum Genet 2024; 32:759-769. [PMID: 38486024 PMCID: PMC11219734 DOI: 10.1038/s41431-024-01590-2] [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: 09/16/2023] [Revised: 02/04/2024] [Accepted: 03/05/2024] [Indexed: 03/20/2024] Open
Abstract
Prenatal Exome (pES) or Genome (pGS) Sequencing analysis showed a significant incremental diagnostic yield over karyotype and chromosomal microarray analysis (CMA) in fetal structural anomalies. Optimized indications and detection rates in different fetal anomalies are still under investigation. The aim of this study was to assess the incremental diagnostic yield in prenatally diagnosed Central Nervous System (CNS) anomalies. A systematic review on antenatal CNS anomalies was performed according to PRISMA guidelines, including n = 12 paper, accounting for 428 fetuses. Results were pooled in a meta-analysis fitting a logistic random mixed-effect model. The effect of interest was the incremental diagnostic rate of pES over karyotype/CMA in detecting likely pathogenic/pathogenic Single Nucleotide Variants (SNVs). A further meta-analysis adding the available pGS studies (including diagnostic coding SNVs only) and submeta-analysis on three CNS subcategories were also performed. The pooled incremental diagnostic yield estimate of pES studies was 38% (95% C.I.: [29%;47%]) and 36% (95% C.I.: [28%;45%]) when including diagnostic SNVs of pGS studies. The point estimate of the effect resulted 22% (95% C.I.: [15%;31%]) in apparently isolated anomalies, 33% (95% C.I.: [22%;46%]) in CNS-only related anomalies (≥1) and 46% (95% C.I.: [38%;55%]) in non-isolated anomalies (either ≥ 2 anomalies in CNS, or CNS and extra-CNS). Meta-analysis showed a substantial diagnostic improvement in performing Prenatal Genome-Wide Sequencing analysis (Exome or Genome) over karyotype and CMA in CNS anomalies.
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Affiliation(s)
- Enrica Marchionni
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy.
| | - Daniele Guadagnolo
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Gioia Mastromoro
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Antonio Pizzuti
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
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15
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Tanudisastro HA, Deveson IW, Dashnow H, MacArthur DG. Sequencing and characterizing short tandem repeats in the human genome. Nat Rev Genet 2024; 25:460-475. [PMID: 38366034 DOI: 10.1038/s41576-024-00692-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/06/2023] [Indexed: 02/18/2024]
Abstract
Short tandem repeats (STRs) are highly polymorphic sequences throughout the human genome that are composed of repeated copies of a 1-6-bp motif. Over 1 million variable STR loci are known, some of which regulate gene expression and influence complex traits, such as height. Moreover, variants in at least 60 STR loci cause genetic disorders, including Huntington disease and fragile X syndrome. Accurately identifying and genotyping STR variants is challenging, in particular mapping short reads to repetitive regions and inferring expanded repeat lengths. Recent advances in sequencing technology and computational tools for STR genotyping from sequencing data promise to help overcome this challenge and solve genetically unresolved cases and the 'missing heritability' of polygenic traits. Here, we compare STR genotyping methods, analytical tools and their applications to understand the effect of STR variation on health and disease. We identify emergent opportunities to refine genotyping and quality-control approaches as well as to integrate STRs into variant-calling workflows and large cohort analyses.
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Affiliation(s)
- Hope A Tanudisastro
- Centre for Population Genomics, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Faculty of Medicine and Health, University of New South Wales, Sydney, New South Wales, Australia
- Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia
| | - Ira W Deveson
- Faculty of Medicine and Health, University of New South Wales, Sydney, New South Wales, Australia
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Harriet Dashnow
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA.
| | - Daniel G MacArthur
- Centre for Population Genomics, Garvan Institute of Medical Research, Sydney, New South Wales, Australia.
- Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.
- Faculty of Medicine and Health, University of New South Wales, Sydney, New South Wales, Australia.
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16
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Uehara T, Seki E, Nonoda Y, Kumaki T, Tsuyusaki Y, Aida N, Enomoto Y, Ishikura K, Kurosawa K. Two siblings with acute necrotizing encephalopathy associated with variants of LARS1. Am J Med Genet A 2024:e63803. [PMID: 38923116 DOI: 10.1002/ajmg.a.63803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Revised: 05/18/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024]
Abstract
Acute necrotizing encephalopathy (ANE) is a rapidly progressive encephalopathy of unknown etiology. The underlying mechanisms are highly heterogeneous, often including genetic backgrounds. Variants of LARS1, encoding the leucyl-tRNA synthetase 1, are responsible for infantile liver failure syndrome 1. We describe two siblings with ANE caused by compound heterozygous variants of LARS1. Patient 1 was a 17-month-old girl. She presented with generalized seizure and liver dysfunction due to influenza type A infection. Brain magnetic resonance imaging on day 4 of onset showed diffuse high-intensity signals consistent with ANE. She died on day 10. Patient 2, a younger male sibling of patient 1, had mild to moderate developmental delay and growth failure at the age of 18 months. He showed a markedly elevated level of transaminases triggered by infection with human herpesvirus 6. On day 4 of onset, he had generalized seizures. Brain computed tomography showed a diffuse symmetrical hypodensity consistent with ANE. He died on day 7. Whole exome sequencing identified the compound heterozygous variants in LARS1 (NM_020117.11) as c.83_88delinsAATGGGATA, p.(Arg28_Phe30delinsLysTryAspIle) and c.1283C>T, p.(Pro428Leu) in both siblings. The severe neurologic phenotype, found in our patients, reflects the complicated pathogenesis of LARS1-related disorder.
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Affiliation(s)
- Takeshi Uehara
- Division of Medical Genetics, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Eijun Seki
- Department of Neurology, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Yutaka Nonoda
- Department of Pediatrics, Kitasato University School of Medicine, Sagamihara, Japan
| | - Tatsuro Kumaki
- Division of Medical Genetics, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Yu Tsuyusaki
- Department of Neurology, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Noriko Aida
- Department of Radiology, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Yumi Enomoto
- Clinical Research Institute, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Kenji Ishikura
- Department of Pediatrics, Kitasato University School of Medicine, Sagamihara, Japan
| | - Kenji Kurosawa
- Division of Medical Genetics, Kanagawa Children's Medical Center, Yokohama, Japan
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17
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Ashenden AJ, Chowdhury A, Anastasi LT, Lam K, Rozek T, Ranieri E, Siu CWK, King J, Mas E, Kassahn KS. The Multi-Omic Approach to Newborn Screening: Opportunities and Challenges. Int J Neonatal Screen 2024; 10:42. [PMID: 39051398 PMCID: PMC11270328 DOI: 10.3390/ijns10030042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 06/13/2024] [Accepted: 06/13/2024] [Indexed: 07/27/2024] Open
Abstract
Newborn screening programs have seen significant evolution since their initial implementation more than 60 years ago, with the primary goal of detecting treatable conditions within the earliest possible timeframe to ensure the optimal treatment and outcomes for the newborn. New technologies have driven the expansion of screening programs to cover additional conditions. In the current era, the breadth of screened conditions could be further expanded by integrating omic technologies such as untargeted metabolomics and genomics. Genomic screening could offer opportunities for lifelong care beyond the newborn period. For genomic newborn screening to be effective and ready for routine adoption, it must overcome barriers such as implementation cost, public acceptability, and scalability. Metabolomics approaches, on the other hand, can offer insight into disease phenotypes and could be used to identify known and novel biomarkers of disease. Given recent advances in metabolomic technologies, alongside advances in genomics including whole-genome sequencing, the combination of complementary multi-omic approaches may provide an exciting opportunity to leverage the best of both approaches and overcome their respective limitations. These techniques are described, along with the current outlook on multi-omic-based NBS research.
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Affiliation(s)
- Alex J. Ashenden
- Department of Biochemical Genetics, SA Pathology, Women’s and Children’s Hospital, Adelaide, SA 5006, Australia (T.R.)
| | - Ayesha Chowdhury
- Department of Molecular Pathology, SA Pathology, Adelaide, SA 5000, Australia; (A.C.); (L.T.A.)
| | - Lucy T. Anastasi
- Department of Molecular Pathology, SA Pathology, Adelaide, SA 5000, Australia; (A.C.); (L.T.A.)
| | - Khoa Lam
- Department of Biochemical Genetics, SA Pathology, Women’s and Children’s Hospital, Adelaide, SA 5006, Australia (T.R.)
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA 5000, Australia
| | - Tomas Rozek
- Department of Biochemical Genetics, SA Pathology, Women’s and Children’s Hospital, Adelaide, SA 5006, Australia (T.R.)
| | - Enzo Ranieri
- Department of Biochemical Genetics, SA Pathology, Women’s and Children’s Hospital, Adelaide, SA 5006, Australia (T.R.)
| | - Carol Wai-Kwan Siu
- Department of Biochemical Genetics, SA Pathology, Women’s and Children’s Hospital, Adelaide, SA 5006, Australia (T.R.)
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA 5000, Australia
| | - Jovanka King
- Immunology Directorate, SA Pathology, Adelaide, SA 5000, Australia
- Department of Allergy and Clinical Immunology, Women’s and Children’s Hospital, Adelaide, SA 5006, Australia
- Discipline of Paediatrics, Women’s and Children’s Hospital, The University of Adelaide, Adelaide, SA 5006, Australia
| | - Emilie Mas
- Department of Biochemical Genetics, SA Pathology, Women’s and Children’s Hospital, Adelaide, SA 5006, Australia (T.R.)
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA 5000, Australia
| | - Karin S. Kassahn
- Department of Molecular Pathology, SA Pathology, Adelaide, SA 5000, Australia; (A.C.); (L.T.A.)
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA 5000, Australia
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18
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Öfverholm I, Wallander K, Haglund C, Chellappa V, Wejde J, Gellerbring A, Wirta V, Renevey A, Caceres E, Tsagkozis P, Mayrhofer M, Papakonstantinou A, Linder-Stragliotto C, Bränström R, Larsson O, Lindberg J, Lin Y, Haglund de Flon F. Comprehensive Genomic Profiling Alters Clinical Diagnoses in a Significant Fraction of Tumors Suspicious of Sarcoma. Clin Cancer Res 2024; 30:2647-2658. [PMID: 38573684 DOI: 10.1158/1078-0432.ccr-24-0384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 03/13/2024] [Accepted: 04/01/2024] [Indexed: 04/05/2024]
Abstract
PURPOSE Tumor classification is a key component in personalized cancer care. For soft-tissue and bone tumors, this classification is currently based primarily on morphology assessment and IHC staining. However, these standard-of-care methods can pose challenges for pathologists. We therefore assessed how whole-genome and whole-transcriptome sequencing (WGTS) impacted tumor classification and clinical management when interpreted together with histomorphology. EXPERIMENTAL DESIGN We prospectively evaluated WGTS in routine diagnostics of 200 soft-tissue and bone tumors suspicious for malignancy, including DNA and RNA isolation from the tumor, and DNA isolation from a peripheral blood sample or any non-tumor tissue. RESULTS On the basis of specific genomic alterations or absence of presumed findings, WGTS resulted in reclassification of 7% (13/197) of the histopathologic diagnoses. Four cases were downgraded from low-grade sarcomas to benign lesions, and two cases were reclassified as metastatic malignant melanomas. Fusion genes associated with specific tumor entities were found in 30 samples. For malignant soft-tissue and bone tumors, we identified treatment relevant variants in 15% of cases. Germline pathogenic variants associated with a hereditary cancer syndrome were found in 22 participants (11%). CONCLUSIONS WGTS provides an important dimension of data that aids in the classification of soft-tissue and bone tumors, correcting a significant fraction of clinical diagnoses, and identifies molecular targets relevant for precision medicine. However, genetic findings need to be evaluated in their morphopathologic context, just as germline findings need to be evaluated in the context of patient phenotype and family history.
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Affiliation(s)
- Ingegerd Öfverholm
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Karin Wallander
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Cecilia Haglund
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Department of Pathology and Cancer Diagnostics, Karolinska University Hospital, Stockholm, Sweden
| | - Venkatesh Chellappa
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Johan Wejde
- Department of Pathology and Cancer Diagnostics, Karolinska University Hospital, Stockholm, Sweden
| | - Anna Gellerbring
- Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Valtteri Wirta
- Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, School of Chemistry, Biotechnology and Health, Royal Institute of Technology, Stockholm, Sweden
- Genomic Medicine Center Karolinska, Karolinska University Hospital, Stockholm, Sweden
| | - Annick Renevey
- Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Eva Caceres
- Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Genomic Medicine Center Karolinska, Karolinska University Hospital, Stockholm, Sweden
| | - Panagiotis Tsagkozis
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Markus Mayrhofer
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Andri Papakonstantinou
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Department of Breast Cancer, Endocrine Tumors and Sarcoma, Karolinska University Hospital, Stockholm, Sweden
| | | | - Robert Bränström
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Breast Cancer, Endocrine Tumors and Sarcoma, Karolinska University Hospital, Stockholm, Sweden
| | - Olle Larsson
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Johan Lindberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Yingbo Lin
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Felix Haglund de Flon
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Department of Pathology and Cancer Diagnostics, Karolinska University Hospital, Stockholm, Sweden
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19
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Joustra SD, Isik E, Wit JM, Catli G, Anik A, Haliloglu B, Kandemir N, Ozsu E, Hendriks YMC, de Bruin C, Kant SG, Campos-Barros A, Challis RC, Parry D, Harley ME, Jackson A, Losekoot M, van Duyvenvoorde HA. Genetic Findings in Short Turkish Children Born to Consanguineous Parents. Horm Res Paediatr 2024:1-11. [PMID: 38838658 PMCID: PMC7616538 DOI: 10.1159/000539696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 05/30/2024] [Indexed: 06/07/2024] Open
Abstract
INTRODUCTION The diagnostic yield of genetic analysis in the evaluation of children with short stature depends on associated clinical characteristics, but the additional effect of parental consanguinity has not been well documented. METHODS This observational case series of 42 short children from 34 consanguineous families was collected by six referral centres of paediatric endocrinology (inclusion criteria: short stature and parental consanguinity). In 18 patients (12 families, group 1), the clinical features suggested a specific genetic defect in the growth hormone (GH) insulin-like growth factor I (IGF-I) axis, and a candidate gene approach was used. In others (group 2), a hypothesis-free approach was chosen (gene panels, microarray analysis, and whole exome sequencing) and further subdivided into 11 patients with severe short stature (height <-3.5 standard deviation score [SDS]) and microcephaly (head circumference <-3.0 SDS) (group 2a), 10 patients with syndromic short stature (group 2b), and 3 patients with nonspecific isolated GH deficiency (group 2c). RESULTS In all 12 families from group 1, (likely) pathogenic variants were identified in GHR, IGFALS, GH1, and STAT5B. In 9/12 families from group 2a, variants were detected in PCNT, SMARCAL1, SRCAP, WDR4, and GHSR. In 5/9 families from group 2b, variants were found in TTC37, SCUBE3, NSD2, RABGAP1, and 17p13.3 microdeletions. In group 2c, no genetic cause was found. Homozygous, compound heterozygous, and heterozygous variants were found in 21, 1, and 4 patients, respectively. CONCLUSION Genetic testing in short children from consanguineous parents has a high diagnostic yield, especially in cases of severe GH deficiency or insensitivity, microcephaly, and syndromic short stature.
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Affiliation(s)
- Sjoerd D Joustra
- Department of Paediatrics, Division of Pediatric Endocrinology, Willem-Alexander Children's Hospital, Leiden University Medical Center, Leiden, The Netherlands
| | - Emregul Isik
- Department of Paediatrics, Ankara Bilkent City Hospital, Ankara, Turkey
| | - Jan M Wit
- Department of Paediatrics, Division of Pediatric Endocrinology, Willem-Alexander Children's Hospital, Leiden University Medical Center, Leiden, The Netherlands
| | - Gonul Catli
- Department of Paediatric Endocrinology, Izmir Katip Celebi University Faculty of Medicine, Izmir, Turkey
- Department of Paediatric Endocrinology, Istinye University Faculty of Medicine, Istanbul, Turkey
| | - Ahmet Anik
- Department of Paediatric Endocrinology, Dokuz Eylul University, Izmir, Turkey
| | - Belma Haliloglu
- Department of Paediatric Endocrinology and Diabetology, Marmara University School of Medicine, Istanbul, Turkey
| | - Nurgun Kandemir
- Department of Paediatric Endocrinology, Hacettepe University, Faculty of Medicine, Ankara, Turkey
| | - Elif Ozsu
- Department of Paediatric Endocrinology and Diabetes, University of Ankara, Ankara, Turkey
| | - Yvonne M C Hendriks
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Christiaan de Bruin
- Department of Paediatrics, Division of Pediatric Endocrinology, Willem-Alexander Children's Hospital, Leiden University Medical Center, Leiden, The Netherlands
| | - Sarina G Kant
- Department of Clinical Genetics, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Angel Campos-Barros
- Institute of Medical and Molecular Genetics (INGEMM), IdiPAZ, Hospital Universitario La Paz, Madrid, Spain
- Rare Diseases Biomedical Research Network (CIBERER; U 753), ISCIII, Madrid, Spain
| | - Rachel C Challis
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - David Parry
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Margaret E Harley
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Andrew Jackson
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Monique Losekoot
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
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20
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Fehlberg Z, Goranitis I, Mallett AJ, Stark Z, Best S. Determining priority indicators of utility for genomic testing in rare disease: A Delphi study. Genet Med 2024; 26:101116. [PMID: 38459833 DOI: 10.1016/j.gim.2024.101116] [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: 10/25/2023] [Revised: 03/01/2024] [Accepted: 03/04/2024] [Indexed: 03/10/2024] Open
Abstract
PURPOSE Determining the value of genomic tests in rare disease necessitates a broader conceptualization of genomic utility beyond diagnostic yield. Despite widespread discussion, consensus toward which aspects of value to consider is lacking. This study aimed to use expert opinion to identify and refine priority indicators of utility in rare disease genomic testing. METHODS We used 2 survey rounds following Delphi methodology to obtain consensus on indicators of utility among experts involved in policy, clinical, research, and consumer advocacy leadership in Australia. We analyzed quantitative and qualitative data to identify, define, and determine priority indicators. RESULTS Twenty-five experts completed round 1 and 18 completed both rounds. Twenty indicators reached consensus as a priority in value assessment, including those relating to prognostic information, timeliness of results, practical and health care outcomes, clinical accreditation, and diagnostic yield. Whereas indicators pertaining to discovery research, disutility, and factors secondary to primary reason for testing were considered less of a priority and were removed. CONCLUSION This study obtained expert consensus on different utility indicators that are considered a priority in determining the value of genomic testing in rare disease in Australia. Indicators may inform a standardized approach to evidence generation and assessment to guide future research, decision making, and implementation efforts.
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Affiliation(s)
- Zoe Fehlberg
- Australian Genomics, Melbourne, VIC, Australia; University of Melbourne, Melbourne, VIC, Australia
| | - Ilias Goranitis
- Australian Genomics, Melbourne, VIC, Australia; University of Melbourne, Melbourne, VIC, Australia
| | - Andrew J Mallett
- Australian Genomics, Melbourne, VIC, Australia; College of Medicine and Dentistry, James Cook University, Douglas, QLD, Australia; Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, Australia; Department of Renal Medicine, Townsville University Hospital, Douglas, QLD, Australia
| | - Zornitza Stark
- Australian Genomics, Melbourne, VIC, Australia; University of Melbourne, Melbourne, VIC, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Stephanie Best
- Australian Genomics, Melbourne, VIC, Australia; University of Melbourne, Melbourne, VIC, Australia; Department of Health Services Research, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia; Victorian Comprehensive Cancer Centre Alliance, Melbourne, VIC, Australia.
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21
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Kernohan KD, Boycott KM. The expanding diagnostic toolbox for rare genetic diseases. Nat Rev Genet 2024; 25:401-415. [PMID: 38238519 DOI: 10.1038/s41576-023-00683-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/22/2023] [Indexed: 05/23/2024]
Abstract
Genomic technologies, such as targeted, exome and short-read genome sequencing approaches, have revolutionized the care of patients with rare genetic diseases. However, more than half of patients remain without a diagnosis. Emerging approaches from research-based settings such as long-read genome sequencing and optical genome mapping hold promise for improving the identification of disease-causal genetic variants. In addition, new omic technologies that measure the transcriptome, epigenome, proteome or metabolome are showing great potential for variant interpretation. As genetic testing options rapidly expand, the clinical community needs to be mindful of their individual strengths and limitations, as well as remaining challenges, to select the appropriate diagnostic test, correctly interpret results and drive innovation to address insufficiencies. If used effectively - through truly integrative multi-omics approaches and data sharing - the resulting large quantities of data from these established and emerging technologies will greatly improve the interpretative power of genetic and genomic diagnostics for rare diseases.
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Affiliation(s)
- Kristin D Kernohan
- CHEO Research Institute, University of Ottawa, Ottawa, ON, Canada
- Newborn Screening Ontario, CHEO, Ottawa, ON, Canada
| | - Kym M Boycott
- CHEO Research Institute, University of Ottawa, Ottawa, ON, Canada.
- Department of Genetics, CHEO, Ottawa, ON, Canada.
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22
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Xu W, Chen K, Yuan Y, Guo M, Dong Q, Cui M. Ring finger protein 216 loss-of-function induces white matter hyperintensities by inhibiting oligodendroglia proliferation. Cell Biochem Funct 2024; 42:e4057. [PMID: 38853469 DOI: 10.1002/cbf.4057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 04/12/2024] [Accepted: 05/12/2024] [Indexed: 06/11/2024]
Abstract
White matter hyperintensities (WMHs) refer to a group of diseases with numerous etiologies while oligodendrocytes remain the centerpiece in the pathogenesis of WMHs. Ring Finger Protein 216 (RNF216) encodes a ubiquitin ligase, and its mutation begets WMHs, ataxia, and cognitive decline in patients. Yet no study has revealed the function of RNF216 in oligodendroglia and WHIs before. In this study, we summarized the phenotypes of RNF216-mutation cases and explored the normal distribution of RNF216 in distinct brain regions and neuronal cells by bioinformatic analysis. Furthermore, MO3.13, a human oligodendrocyte cell line, was applied to study the function alteration after RNF216 knockdown. As a result, WMHs were the most common symptom in RNF216-mutated diseases, and RNF216 was indeed relatively enriched in corpus callosum and oligodendroglia in humans. The downregulation of RNF216 in oligodendroglia remarkably hampered cell proliferation by inhibiting the Akt pathway while having no significant effect on cell injury and oligodendrocyte maturation. Combining clinical, bioinformatical, and experimental evidence, our study implied the pivotal role of RNF216 in WMHs which might serve as a potent target in the therapy of WMHs.
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Affiliation(s)
- Wenqing Xu
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China
| | - Keliang Chen
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China
| | - Yiwen Yuan
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China
| | - Min Guo
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China
| | - Qiang Dong
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China
- National Center for Neurological Disorders, Huashan Hospital, Fudan University, Shanghai, China
| | - Mei Cui
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China
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23
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Lyander A, Gellerbring A, Hägglund M, Elhami K, Wirta V. NGS method for parallel processing of high quality, damaged or fragmented input material using target enrichment. PLoS One 2024; 19:e0304411. [PMID: 38809937 PMCID: PMC11135680 DOI: 10.1371/journal.pone.0304411] [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: 12/12/2023] [Accepted: 05/10/2024] [Indexed: 05/31/2024] Open
Abstract
Next-generation sequencing (NGS) has been increasingly popular in genomics studies over the last decade and is now commonly used in clinical applications for precision diagnostics. Many disease areas typically involve different kinds of sample specimens, sample qualities and quantities. The quality of the DNA can range from intact, high molecular weight molecules to degraded, damaged and very short molecules. The differences in quality and quantity pose challenges for downstream molecular analyses. To overcome the challenge with the need of different molecular methods for different types of samples, we have developed a joint procedure for preparing enriched DNA libraries from high molecular weight DNA and DNA from formalin-fixed, paraffin-embedded tissue, fresh frozen tissue material, as well as cell-free DNA.
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Affiliation(s)
- Anna Lyander
- Science for Life Laboratory, KTH Royal Institute of Technology, Clinical Genomics Stockholm, School of Engineering Sciences in Chemistry, Biotechnology and Health, Stockholm, Sweden
- Department of Microbiology, Science for Life Laboratory, Karolinska Institutet, Clinical Genomics Stockholm, Tumor and Cell Biology, Stockholm, Sweden
| | - Anna Gellerbring
- Department of Microbiology, Science for Life Laboratory, Karolinska Institutet, Clinical Genomics Stockholm, Tumor and Cell Biology, Stockholm, Sweden
| | - Moa Hägglund
- Department of Microbiology, Science for Life Laboratory, Karolinska Institutet, Clinical Genomics Stockholm, Tumor and Cell Biology, Stockholm, Sweden
| | - Keyvan Elhami
- Department of Microbiology, Science for Life Laboratory, Karolinska Institutet, Clinical Genomics Stockholm, Tumor and Cell Biology, Stockholm, Sweden
| | - Valtteri Wirta
- Science for Life Laboratory, KTH Royal Institute of Technology, Clinical Genomics Stockholm, School of Engineering Sciences in Chemistry, Biotechnology and Health, Stockholm, Sweden
- Department of Microbiology, Science for Life Laboratory, Karolinska Institutet, Clinical Genomics Stockholm, Tumor and Cell Biology, Stockholm, Sweden
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24
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Sennfält S, Gustavsson P, Malmgren H, Gilland E, Almqvist H, Oscarson M, Engvall M, Björkhem I, Nilsson D, Lagerstedt-Robinson K, Svenningsson P, Paucar M. Novel findings in a Swedish primary familial brain calcification cohort. J Neurol Sci 2024; 460:123020. [PMID: 38642488 DOI: 10.1016/j.jns.2024.123020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 04/10/2024] [Accepted: 04/16/2024] [Indexed: 04/22/2024]
Abstract
INTRODUCTION Brain calcifications are frequent findings on imaging. In a small proportion of cases, these calcifications are associated with pathogenic gene variants, hence termed primary familial brain calcification (PFBC). The clinical penetrance is incomplete and phenotypic variability is substantial. This paper aims to characterize a Swedish PFBC cohort including 25 patients: 20 from seven families and five sporadic cases. METHODS Longitudinal clinical assessment and CT imaging were conducted, abnormalities were assessed using the total calcification score (TCS). Genetic analyses, including a panel of six known PFBC genes, were performed in all index and sporadic cases. Additionally, three patients carrying a novel pathogenic copy number variant in SLC20A2 had their cerebrospinal fluid phosphate (CSF-Pi) levels measured. RESULTS Among the 25 patients, the majority (76%) displayed varying symptoms during the initial assessment including motor (60%), psychiatric (40%), and/or cognitive abnormalities (24%). Clinical progression was observed in most patients (78.6%), but there was no significant difference in calcification between the first and second scans, with mean scores of 27.3 and 32.8, respectively. In three families and two sporadic cases, pathogenic genetic variants were identified, including a novel finding, in the SLC20A2 gene. In the three tested patients, the CSF-Pi levels were normal. CONCLUSIONS This report demonstrates the variable expressivity seen in PFBC and includes a novel pathogenic variant in the SLC20A2 gene. In four families and three sporadic cases, no pathogenic variants were found, suggesting that new PFBC genes remain to be discovered.
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Affiliation(s)
- Stefan Sennfält
- Department of Neurology, Karolinska University Hospital, Hälsovägen 13 R52, 141 86 Stockholm, Sweden; Department of Clinical Neuroscience, Karolinska Institutet, Nobels väg 6, 171 77 Stockholm, Sweden.
| | - Peter Gustavsson
- Department of Clinical Genetics, Karolinska University Hospital, Karolinska Vägen, 171 76500 Solna, Sweden; Department of Molecular Medicine and Surgery, Karolinska Institutet, Nobels väg 6, 171 77 Stockholm, Sweden.
| | - Helena Malmgren
- Department of Clinical Genetics, Karolinska University Hospital, Karolinska Vägen, 171 76500 Solna, Sweden; Department of Molecular Medicine and Surgery, Karolinska Institutet, Nobels väg 6, 171 77 Stockholm, Sweden.
| | - Eric Gilland
- Department of Neurology, Sahlgrenska University Hospital, Gothenburg, Blå stråket 7, 413 46 Göteborg, Sweden.
| | - Håkan Almqvist
- Department of Clinical Neuroscience, Karolinska Institutet, Nobels väg 6, 171 77 Stockholm, Sweden; Department of Radiology, Capio S:t Goran Hospital, Sankt Göransplan 1, 112 19 Stockholm, Sweden.
| | - Mikael Oscarson
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Anna Steckséns g 47, 171 76 Solna, Sweden.
| | - Martin Engvall
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Anna Steckséns g 47, 171 76 Solna, Sweden.
| | - Ingemar Björkhem
- Science for Life Laboratory, Stockholm, Tomtebodavägen 23, 171 65 Solna, Sweden.
| | - Daniel Nilsson
- Department of Clinical Genetics, Karolinska University Hospital, Karolinska Vägen, 171 76500 Solna, Sweden; Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Alfred Nobels Allé 8, 141 52 Huddinge, Sweden.
| | - Kristina Lagerstedt-Robinson
- Department of Clinical Genetics, Karolinska University Hospital, Karolinska Vägen, 171 76500 Solna, Sweden; Department of Molecular Medicine and Surgery, Karolinska Institutet, Nobels väg 6, 171 77 Stockholm, Sweden.
| | - Per Svenningsson
- Department of Neurology, Karolinska University Hospital, Hälsovägen 13 R52, 141 86 Stockholm, Sweden; Department of Clinical Neuroscience, Karolinska Institutet, Nobels väg 6, 171 77 Stockholm, Sweden.
| | - Martin Paucar
- Department of Neurology, Karolinska University Hospital, Hälsovägen 13 R52, 141 86 Stockholm, Sweden; Department of Clinical Neuroscience, Karolinska Institutet, Nobels väg 6, 171 77 Stockholm, Sweden.
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25
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Westenius E, Conner P, Pettersson M, Sahlin E, Papadogiannakis N, Lindstrand A, Iwarsson E. Whole-genome sequencing in prenatally detected congenital malformations: prospective cohort study in clinical setting. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2024; 63:658-663. [PMID: 38268232 DOI: 10.1002/uog.27592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 12/26/2023] [Accepted: 01/16/2024] [Indexed: 01/26/2024]
Abstract
OBJECTIVE To investigate the diagnostic yield of trio whole-genome sequencing (WGS) in fetuses with various congenital malformations referred to a tertiary center for prenatal diagnosis. METHODS In this prospective study, 50 pregnancies with different congenital malformations, negative for trisomies and causative copy-number variants, were analyzed further with fetal-parental trio WGS analysis. Parents were eligible for inclusion if they accepted further investigation following the detection of isolated or multiple malformations on prenatal ultrasound. Cases with isolated increased nuchal translucency, gamete donation or multiple pregnancy were excluded. WGS with the Illumina Inc. 30× polymerase-chain-reaction-free short-read sequencing included analysis of single-nucleotide variants, insertions and deletions, structural variants, short tandem repeats and copy-number identification of SMN1 and SMN2 genes. RESULTS A molecular diagnosis was achieved in 13/50 (26%) cases. Causative sequence variants were identified in 12 genes: FGFR3 (n = 2), ACTA1 (n = 1), CDH2 (n = 1), COL1A2 (n = 1), DHCR7 (n = 1), EYA1 (n = 1), FBXO11 (n = 1), FRAS1 (n = 1), L1CAM (n = 1), OFD1 (n = 1), PDHA1 (n = 1) and SOX9 (n = 1). The phenotypes of the cases were divided into different groups, with the following diagnostic yields: skeletal malformation (4/9 (44%)), multisystem malformation (3/7 (43%)), central nervous system malformation (5/15 (33%)) and thoracic malformation (1/10 (10%)). Additionally, two cases carried variants that were considered potentially clinically relevant, even though they were assessed as variants of uncertain significance, according to the guidelines provided by the American College of Medical Genetics and Genomics. Overall, we identified a causative or potentially clinically relevant variant in 15/50 (30%) cases. CONCLUSIONS We demonstrate a diagnostic yield of 26% with clinical WGS in prenatally detected congenital malformations. This study emphasizes the benefits that WGS can bring to the diagnosis of fetal structural anomalies. It is important to note that causative chromosomal aberrations were excluded from our cohort before WGS. As chromosomal aberrations are a well-known cause of prenatally detected congenital malformations, future studies using WGS as a primary diagnostic test, including assessment of chromosomal aberrations, may show that the detection rate exceeds the diagnostic yield of this study. WGS can add clinically relevant information, explaining the underlying cause of the fetal anomaly, which will provide information concerning the specific prognosis of the condition, as well as estimate the risk of recurrence. A genetic diagnosis can also provide more reproductive choice for future pregnancies. © 2024 The Authors. Ultrasound in Obstetrics & Gynecology published by John Wiley & Sons Ltd on behalf of International Society of Ultrasound in Obstetrics and Gynecology.
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Affiliation(s)
- E Westenius
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics and Genomics, Karolinska University Hospital, Stockholm, Sweden
| | - P Conner
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
- Center for Fetal Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - M Pettersson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics and Genomics, Karolinska University Hospital, Stockholm, Sweden
| | - E Sahlin
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics and Genomics, Karolinska University Hospital, Stockholm, Sweden
| | - N Papadogiannakis
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Pathology, Karolinska University Hospital, Stockholm, Sweden
| | - A Lindstrand
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics and Genomics, Karolinska University Hospital, Stockholm, Sweden
| | - E Iwarsson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics and Genomics, Karolinska University Hospital, Stockholm, Sweden
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26
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Filograna R, Gerlach J, Choi HN, Rigoni G, Barbaro M, Oscarson M, Lee S, Tiklova K, Ringnér M, Koolmeister C, Wibom R, Riggare S, Nennesmo I, Perlmann T, Wredenberg A, Wedell A, Motori E, Svenningsson P, Larsson NG. PARKIN is not required to sustain OXPHOS function in adult mammalian tissues. NPJ Parkinsons Dis 2024; 10:93. [PMID: 38684669 PMCID: PMC11058849 DOI: 10.1038/s41531-024-00707-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 04/11/2024] [Indexed: 05/02/2024] Open
Abstract
Loss-of-function variants in the PRKN gene encoding the ubiquitin E3 ligase PARKIN cause autosomal recessive early-onset Parkinson's disease (PD). Extensive in vitro and in vivo studies have reported that PARKIN is involved in multiple pathways of mitochondrial quality control, including mitochondrial degradation and biogenesis. However, these findings are surrounded by substantial controversy due to conflicting experimental data. In addition, the existing PARKIN-deficient mouse models have failed to faithfully recapitulate PD phenotypes. Therefore, we have investigated the mitochondrial role of PARKIN during ageing and in response to stress by employing a series of conditional Parkin knockout mice. We report that PARKIN loss does not affect oxidative phosphorylation (OXPHOS) capacity and mitochondrial DNA (mtDNA) levels in the brain, heart, and skeletal muscle of aged mice. We also demonstrate that PARKIN deficiency does not exacerbate the brain defects and the pro-inflammatory phenotype observed in mice carrying high levels of mtDNA mutations. To rule out compensatory mechanisms activated during embryonic development of Parkin-deficient mice, we generated a mouse model where loss of PARKIN was induced in adult dopaminergic (DA) neurons. Surprisingly, also these mice did not show motor impairment or neurodegeneration, and no major transcriptional changes were found in isolated midbrain DA neurons. Finally, we report a patient with compound heterozygous PRKN pathogenic variants that lacks PARKIN and has developed PD. The PARKIN deficiency did not impair OXPHOS activities or induce mitochondrial pathology in skeletal muscle from the patient. Altogether, our results argue that PARKIN is dispensable for OXPHOS function in adult mammalian tissues.
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Affiliation(s)
- Roberta Filograna
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
| | - Jule Gerlach
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Hae-Na Choi
- Institute for Biochemistry, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Giovanni Rigoni
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Michela Barbaro
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Mikael Oscarson
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Seungmin Lee
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Katarina Tiklova
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Markus Ringnér
- Department of Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Lund University, Lund, Sweden
| | - Camilla Koolmeister
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Rolf Wibom
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Sara Riggare
- Department of Women's and Children's Health, Uppsala University, Uppsala, Sweden
| | - Inger Nennesmo
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Thomas Perlmann
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Anna Wredenberg
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Anna Wedell
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden
| | - Elisa Motori
- Institute for Biochemistry, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Per Svenningsson
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
- Department of Neurology, Karolinska University Hospital, Stockholm, Sweden
| | - Nils-Göran Larsson
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
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27
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Cui Y, Ye W, Li JS, Li JJ, Vilain E, Sallam T, Li W. A genome-wide spectrum of tandem repeat expansions in 338,963 humans. Cell 2024; 187:2336-2341.e5. [PMID: 38582080 PMCID: PMC11065452 DOI: 10.1016/j.cell.2024.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 01/23/2024] [Accepted: 03/05/2024] [Indexed: 04/08/2024]
Abstract
The Genome Aggregation Database (gnomAD), widely recognized as the gold-standard reference map of human genetic variation, has largely overlooked tandem repeat (TR) expansions, despite the fact that TRs constitute ∼6% of our genome and are linked to over 50 human diseases. Here, we introduce the TR-gnomAD (https://wlcb.oit.uci.edu/TRgnomAD), a biobank-scale reference of 0.86 million TRs derived from 338,963 whole-genome sequencing (WGS) samples of diverse ancestries (39.5% non-European samples). TR-gnomAD offers critical insights into ancestry-specific disease prevalence using disparities in TR unit number frequencies among ancestries. Moreover, TR-gnomAD is able to differentiate between common, presumably benign TR expansions, which are prevalent in TR-gnomAD, from those potentially pathogenic TR expansions, which are found more frequently in disease groups than within TR-gnomAD. Together, TR-gnomAD is an invaluable resource for researchers and physicians to interpret TR expansions in individuals with genetic diseases.
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Affiliation(s)
- Ya Cui
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA 92697, USA.
| | - Wenbin Ye
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA 92697, USA
| | - Jason Sheng Li
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA 92697, USA
| | - Jingyi Jessica Li
- Department of Statistics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Eric Vilain
- Institute for Clinical and Translational Science, University of California, Irvine, Irvine, CA 92697, USA; Department of Pediatrics, University of California, Irvine, Irvine, CA 92697, USA
| | - Tamer Sallam
- Division of Cardiology, Department of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Wei Li
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA 92697, USA.
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28
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Tesi B, Robinson KL, Abel F, Díaz de Ståhl T, Orrsjö S, Poluha A, Hellberg M, Wessman S, Samuelsson S, Frisk T, Vogt H, Henning K, Sabel M, Ek T, Pal N, Nyman P, Giraud G, Wille J, Pronk CJ, Norén-Nyström U, Borssén M, Fili M, Stålhammar G, Herold N, Tettamanti G, Maya-Gonzalez C, Arvidsson L, Rosén A, Ekholm K, Kuchinskaya E, Hallbeck AL, Nordling M, Palmebäck P, Kogner P, Smoler GK, Lähteenmäki P, Fransson S, Martinsson T, Shamik A, Mertens F, Rosenquist R, Wirta V, Tham E, Grillner P, Sandgren J, Ljungman G, Gisselsson D, Taylan F, Nordgren A. Diagnostic yield and clinical impact of germline sequencing in children with CNS and extracranial solid tumors-a nationwide, prospective Swedish study. THE LANCET REGIONAL HEALTH. EUROPE 2024; 39:100881. [PMID: 38803632 PMCID: PMC11129334 DOI: 10.1016/j.lanepe.2024.100881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 02/04/2024] [Accepted: 02/23/2024] [Indexed: 05/29/2024]
Abstract
Background Childhood cancer predisposition (ChiCaP) syndromes are increasingly recognized as contributing factors to childhood cancer development. Yet, due to variable availability of germline testing, many children with ChiCaP might go undetected today. We report results from the nationwide and prospective ChiCaP study that investigated diagnostic yield and clinical impact of integrating germline whole-genome sequencing (gWGS) with tumor sequencing and systematic phenotyping in children with solid tumors. Methods gWGS was performed in 309 children at diagnosis of CNS (n = 123, 40%) or extracranial (n = 186, 60%) solid tumors and analyzed for disease-causing variants in 189 known cancer predisposing genes. Tumor sequencing data were available for 74% (227/309) of patients. In addition, a standardized clinical assessment for underlying predisposition was performed in 95% (293/309) of patients. Findings The prevalence of ChiCaP diagnoses was 11% (35/309), of which 69% (24/35) were unknown at inclusion (diagnostic yield 8%, 24/298). A second-hit and/or relevant mutational signature was observed in 19/21 (90%) tumors with informative data. ChiCaP diagnoses were more prevalent among patients with retinoblastomas (50%, 6/12) and high-grade astrocytomas (37%, 6/16), and in those with non-cancer related features (23%, 20/88), and ≥2 positive ChiCaP criteria (28%, 22/79). ChiCaP diagnoses were autosomal dominant in 80% (28/35) of patients, yet confirmed de novo in 64% (18/28). The 35 ChiCaP findings resulted in tailored surveillance (86%, 30/35) and treatment recommendations (31%, 11/35). Interpretation Overall, our results demonstrate that systematic phenotyping, combined with genomics-based diagnostics of ChiCaP in children with solid tumors is feasible in large-scale clinical practice and critically guides personalized care in a sizable proportion of patients. Funding The study was supported by the Swedish Childhood Cancer Fund and the Ministry of Health and Social Affairs.
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Affiliation(s)
- Bianca Tesi
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Clinical Genetics and Genomics, Karolinska University Hospital, Solna, Sweden
- Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Kristina Lagerstedt Robinson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Clinical Genetics and Genomics, Karolinska University Hospital, Solna, Sweden
| | - Frida Abel
- Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Teresita Díaz de Ståhl
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Clinical Pathology and Cancer Diagnostics, Karolinska University Hospital, Stockholm, Sweden
| | - Sara Orrsjö
- Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Anna Poluha
- Clinical Genetics, Uppsala University Hospital, Uppsala, Sweden
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Maria Hellberg
- Department of Clinical Genetics, Pathology and Molecular Diagnostics, Office of Medical Services, Region Skåne, Lund, Sweden
| | - Sandra Wessman
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Clinical Pathology and Cancer Diagnostics, Karolinska University Hospital, Stockholm, Sweden
| | - Sofie Samuelsson
- Department of Clinical Genetics, Pathology and Molecular Diagnostics, Office of Medical Services, Region Skåne, Lund, Sweden
| | - Tony Frisk
- Department of Pediatric Hematology and Oncology, Karolinska University Hospital, Stockholm, Sweden
- Childhood Cancer Research Unit, Department of Women’s and Children’s Health, Karolinska Institutet, Stockholm, Sweden
| | - Hartmut Vogt
- Crown Princess Victoria Children’s Hospital, and Division of Children’s and Women’s Health, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Karin Henning
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Pediatric Hematology and Oncology, Karolinska University Hospital, Stockholm, Sweden
| | - Magnus Sabel
- Department of Pediatrics, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Sweden
- Queen Silvia Children’s Hospital, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Torben Ek
- Department of Pediatrics, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Sweden
- Queen Silvia Children’s Hospital, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Niklas Pal
- Department of Pediatric Hematology and Oncology, Karolinska University Hospital, Stockholm, Sweden
| | - Per Nyman
- Department of Health, Medicine and Caring Sciences, Linköping University, Linköping, Sweden
- Centre for Medical Image Science and Visualization (CMIV), Linköping University, Linköping, Sweden
| | - Geraldine Giraud
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
- Pediatric Oncology, Uppsala University Children’s Hospital, Uppsala, Sweden
- Department of Women’s and Children’s Health, Uppsala University, Sweden
| | - Joakim Wille
- Childhood Cancer Center, Skåne University Hospital, Lund, Sweden
| | - Cornelis Jan Pronk
- Childhood Cancer Center, Skåne University Hospital, Lund, Sweden
- Division of Molecular Hematology/Wallenberg Center for Molecular Medicine, Lund University, Sweden
| | | | - Magnus Borssén
- Department of Clinical Sciences, Pediatrics, Umeå University, Umeå, Sweden
| | - Maria Fili
- Division of Eye and Vision, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
- St. Erik Eye Hospital, Stockholm, Sweden
| | - Gustav Stålhammar
- Division of Eye and Vision, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
- St. Erik Eye Hospital, Stockholm, Sweden
| | - Nikolas Herold
- Department of Pediatric Hematology and Oncology, Karolinska University Hospital, Stockholm, Sweden
- Childhood Cancer Research Unit, Department of Women’s and Children’s Health, Karolinska Institutet, Stockholm, Sweden
| | - Giorgio Tettamanti
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Unit of Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | | | - Linda Arvidsson
- Department of Clinical Genetics, Pathology and Molecular Diagnostics, Office of Medical Services, Region Skåne, Lund, Sweden
| | - Anna Rosén
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Katja Ekholm
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Clinical Genetics and Genomics, Karolinska University Hospital, Solna, Sweden
| | | | - Anna-Lotta Hallbeck
- Department of Clinical Genetics, Linköping University Hospital, Linköping, Sweden
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Margareta Nordling
- Department of Clinical Genetics, Linköping University Hospital, Linköping, Sweden
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Pia Palmebäck
- Department of Clinical Genetics, Linköping University Hospital, Linköping, Sweden
| | - Per Kogner
- Department of Pediatric Hematology and Oncology, Karolinska University Hospital, Stockholm, Sweden
- Childhood Cancer Research Unit, Department of Women’s and Children’s Health, Karolinska Institutet, Stockholm, Sweden
| | - Gunilla Kanter Smoler
- Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Päivi Lähteenmäki
- Childhood Cancer Research Unit, Department of Women’s and Children’s Health, Karolinska Institutet, Stockholm, Sweden
| | - Susanne Fransson
- Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Tommy Martinsson
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Alia Shamik
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Clinical Pathology and Cancer Diagnostics, Karolinska University Hospital, Stockholm, Sweden
| | - Fredrik Mertens
- Department of Clinical Genetics, Pathology and Molecular Diagnostics, Office of Medical Services, Region Skåne, Lund, Sweden
| | - Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Clinical Genetics and Genomics, Karolinska University Hospital, Solna, Sweden
- Genomic Medicine Center Karolinska, Karolinska University Hospital, Stockholm, Sweden
| | - Valtteri Wirta
- Genomic Medicine Center Karolinska, Karolinska University Hospital, Stockholm, Sweden
- Science for Life Laboratory, Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institutet of Technology, Stockholm, Sweden
| | - Emma Tham
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Clinical Genetics and Genomics, Karolinska University Hospital, Solna, Sweden
| | - Pernilla Grillner
- Department of Pediatric Hematology and Oncology, Karolinska University Hospital, Stockholm, Sweden
- Childhood Cancer Research Unit, Department of Women’s and Children’s Health, Karolinska Institutet, Stockholm, Sweden
| | - Johanna Sandgren
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Clinical Pathology and Cancer Diagnostics, Karolinska University Hospital, Stockholm, Sweden
| | - Gustaf Ljungman
- Pediatric Oncology, Uppsala University Children’s Hospital, Uppsala, Sweden
- Department of Women’s and Children’s Health, Uppsala University, Sweden
| | - David Gisselsson
- Department of Clinical Genetics, Pathology and Molecular Diagnostics, Office of Medical Services, Region Skåne, Lund, Sweden
| | - Fulya Taylan
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Clinical Genetics and Genomics, Karolinska University Hospital, Solna, Sweden
| | - Ann Nordgren
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Clinical Genetics and Genomics, Karolinska University Hospital, Solna, Sweden
- Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Genomic Medicine Center Karolinska, Karolinska University Hospital, Stockholm, Sweden
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Shen NX, Qu XC, Yu J, Fan CX, Min FL, Li LY, Zhang MR, Li BM, Wang J, He N, Liao WP, Shi YW, Li WB. NUS1 Variants Cause Lennox-Gastaut Syndrome Related to Unfolded Protein Reaction Activation. Mol Neurobiol 2024:10.1007/s12035-024-04123-6. [PMID: 38520610 DOI: 10.1007/s12035-024-04123-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 03/12/2024] [Indexed: 03/25/2024]
Abstract
NUS1 encodes the Nogo-B receptor, a critical regulator for unfolded protein reaction (UPR) signaling. Although several loss-of-function variants of NUS1 have been identified in patients with developmental and epileptic encephalopathy (DEE), the role of the NUS1 variant in Lennox-Gastaut syndrome (LGS), a severe child-onset DEE, remains unknown. In this study, we identified two de novo variants of NUS1, a missense variant (c.868 C > T/p.R290C) and a splice site variant (c.792-2 A > G), in two unrelated LGS patients using trio-based whole-exome sequencing performed in a cohort of 165 LGS patients. Both variants were absent in the gnomAD population and showed a significantly higher observed number of variants than expected genome-wide. The R290C variant was predicted to damage NUS1 and decrease its protein stability. The c.792-2 A > G variant caused premature termination of the protein. Knockdown of NUS1 activated the UPR pathway, resulting in apoptosis of HEK293T cells. Supplementing cells with expression of wild-type NUS1, but not the mutant (R290C), rescued UPR activation and apoptosis in NUS1 knockdown cells. Compared to wild-type Drosophila, seizure-like behaviors and excitability in projection neurons were significantly increased in Tango14 (homolog of human NUS1) knockdown and Tango14R290C/+ knock-in Drosophila. Additionally, abnormal development and a small body size were observed in both mutants. Activated UPR signaling was also detected in both mutants. Thus, NUS1 is a causative gene for LGS with dominant inheritance. The pathogenicity of these variants is related to the UPR signaling activation, which may be a common pathogenic mechanism of DEE.
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Affiliation(s)
- Nan-Xiang Shen
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, China
| | - Xiao-Chong Qu
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, China
| | - Jing Yu
- Neurology Department, Children's Hospital of Xinjiang Uygur Autonomous Region, Urumchi, China
| | - Cui-Xia Fan
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, China
| | - Fu-Li Min
- Department of Neurology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Ling-Ying Li
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, China
| | - Ming-Rui Zhang
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, China
| | - Bing-Mei Li
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, China
| | - Jie Wang
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, China
| | - Na He
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, China
| | - Wei-Ping Liao
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, China
| | - Yi-Wu Shi
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, China.
| | - Wen-Bin Li
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, China.
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30
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Franzén B, Auer G, Lewensohn R. Minimally invasive biopsy-based diagnostics in support of precision cancer medicine. Mol Oncol 2024. [PMID: 38519839 DOI: 10.1002/1878-0261.13640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 01/31/2024] [Accepted: 03/14/2024] [Indexed: 03/25/2024] Open
Abstract
Precision cancer medicine (PCM) to support the treatment of solid tumors requires minimally invasive diagnostics. Here, we describe the development of fine-needle aspiration biopsy-based (FNA) molecular cytology which will be increasingly important in diagnostics and adaptive treatment. We provide support for FNA-based molecular cytology having a significant potential to replace core needle biopsy (CNB) as a patient-friendly potent technique for tumor sampling for various tumor types. This is not only because CNB is a more traumatic procedure and may be associated with more complications compared to FNA-based sampling, but also due to the recently developed molecular methods used with FNA. Recent studies show that image-guided FNA in combination with ultrasensitive molecular methods also offers opportunities for characterization of the tumor microenvironment which can aid therapeutic decisions. Here we provide arguments for an increased implementation of molecular FNA-based sampling as a patient-friendly diagnostic method, which may, due to its repeatability, facilitate regular sampling that is needed during different treatment lines, to provide tumor information, supporting treatment decisions, shortening lead times in healthcare, and benefit healthcare economics.
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Affiliation(s)
- Bo Franzén
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Cancer Centre Karolinska (CCK) Foundation, Karolinska University Hospital, Stockholm, Sweden
| | - Gert Auer
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Rolf Lewensohn
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Theme Cancer, Medical Unit Head and Neck, Lung, and Skin Tumors, Thoracic Oncology Center, Karolinska University Hospital, Stockholm, Sweden
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31
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Lin ZJ, Li B, Lin PX, Song W, Yan LM, Meng H, He N. Clinical application of trio-based whole-exome sequencing in idiopathic generalized epilepsy. Seizure 2024; 116:24-29. [PMID: 36842888 DOI: 10.1016/j.seizure.2023.02.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/07/2023] [Accepted: 02/10/2023] [Indexed: 02/13/2023] Open
Abstract
PURPOSE Idiopathic generalized epilepsies (IGEs) are a common group of genetic generalized epilepsies with high genetic heterogeneity and complex inheritance. However, the genetic basis is still largely unknown. This study aimed to explore the genetic etiologies in IGEs. METHODS Trio-based whole-exome sequencing was performed in 60 cases with IGEs. The pathogenicity of candidate genetic variants was evaluated by the criteria of the American College of Medical Genetics and Genomics (ACMG), and the clinical causality was assessed by concordance between the observed phenotype and the reported phenotype. RESULTS Seven candidate variants were detected in seven unrelated cases with IGE (11.7%, 7/60). According to ACMG, a de novo SLC2A1 (c.376C>T/p.Arg126Cys) variant identified in childhood absence epilepsy was evaluated as pathogenic with clinical concordance. Six variants were assessed to be uncertain significance by ACMG, but then considered causative after evaluation of clinical concordance. These variants included CLCN4 hemizygous variant (c.2044G>A/p.Glu682Lys) and IQSEC2 heterozygous variant (c.4315C>T/p.Pro1439Ser) in juvenile absence epilepsy, EFHC1 variant (c.1504C>T/p.Arg502Trp) and CACNA1H (c.589G>T/p.Ala197Ser) both with incomplete penetrance in juvenile myoclonic epilepsy, and GRIN2A variant (c.2011C>G/p.Gln671Glu) and GABRB1 variant (c.1075G>A/p.Val359Ile) both co-segregated with juvenile myoclonic epilepsy. Among them, GABRB1 was for the first time identified as potential novel causative gene for IGE. SIGNIFICANCE Considering the genetic heterogeneity and complex inheritance of IGEs, a comprehensive evaluation combined the ACMG scoring and assessment of clinical concordance is suggested for the pathogenicity analysis of variants identified in clinical screening. GABRB1 is probably a novel causative gene for IGE, which warrants further studies.
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Affiliation(s)
- Zhi-Jian Lin
- Department of Neurology, the Affiliated Hospital of Putian University, Putian 351100, Fujian Province, China; Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Bin Li
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Peng-Xing Lin
- Department of Neurology, the Affiliated Hospital of Putian University, Putian 351100, Fujian Province, China
| | - Wang Song
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Li-Min Yan
- Department of Neurology, The Second Affiliated Hospital of Hainan Medical University, 570311 Haikou, Hainan, China
| | - Heng Meng
- Department of Neurology, the First Affiliated Hospital of Jinan University, Guangzhou 510632, China.
| | - Na He
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China.
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32
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Johansson J, Lidéus S, Frykholm C, Gunnarsson C, Mihalic F, Gudmundsson S, Ekvall S, Molin AM, Pham M, Vihinen M, Lagerstedt-Robinson K, Nordgren A, Jemth P, Ameur A, Annerén G, Wilbe M, Bondeson ML. Gustavson syndrome is caused by an in-frame deletion in RBMX associated with potentially disturbed SH3 domain interactions. Eur J Hum Genet 2024; 32:333-341. [PMID: 37277488 PMCID: PMC10923852 DOI: 10.1038/s41431-023-01392-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 03/07/2023] [Accepted: 05/12/2023] [Indexed: 06/07/2023] Open
Abstract
RNA binding motif protein X-linked (RBMX) encodes the heterogeneous nuclear ribonucleoprotein G (hnRNP G) that regulates splicing, sister chromatid cohesion and genome stability. RBMX knock down experiments in various model organisms highlight the gene's importance for brain development. Deletion of the RGG/RG motif in hnRNP G has previously been associated with Shashi syndrome, however involvement of other hnRNP G domains in intellectual disability remain unknown. In the current study, we present the underlying genetic and molecular cause of Gustavson syndrome. Gustavson syndrome was first reported in 1993 in a large Swedish five-generation family presented with profound X-linked intellectual disability and an early death. Extensive genomic analyses of the family revealed hemizygosity for a novel in-frame deletion in RBMX in affected individuals (NM_002139.4; c.484_486del, p.(Pro162del)). Carrier females were asymptomatic and presented with skewed X-chromosome inactivation, indicating silencing of the pathogenic allele. Affected individuals presented minor phenotypic overlap with Shashi syndrome, indicating a different disease-causing mechanism. Investigation of the variant effect in a neuronal cell line (SH-SY5Y) revealed differentially expressed genes enriched for transcription factors involved in RNA polymerase II transcription. Prediction tools and a fluorescence polarization assay imply a novel SH3-binding motif of hnRNP G, and potentially a reduced affinity to SH3 domains caused by the deletion. In conclusion, we present a novel in-frame deletion in RBMX segregating with Gustavson syndrome, leading to disturbed RNA polymerase II transcription, and potentially reduced SH3 binding. The results indicate that disruption of different protein domains affects the severity of RBMX-associated intellectual disabilities.
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Affiliation(s)
- Josefin Johansson
- Department of Immunology, Genetics and Pathology, Biomedical Centre, Uppsala University, Uppsala, Sweden
| | - Sarah Lidéus
- Department of Immunology, Genetics and Pathology, Biomedical Centre, Uppsala University, Uppsala, Sweden
| | - Carina Frykholm
- Department of Immunology, Genetics and Pathology, Biomedical Centre, Uppsala University, Uppsala, Sweden
| | - Cecilia Gunnarsson
- Department of Clinical Genetics, and Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
- Centre for Rare Diseases in South East Region of Sweden, Linköping University, Linköping, Sweden
| | - Filip Mihalic
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, Husargatan 3, 751 23, Uppsala, Sweden
| | - Sanna Gudmundsson
- Department of Immunology, Genetics and Pathology, Biomedical Centre, Uppsala University, Uppsala, Sweden
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Sara Ekvall
- Department of Immunology, Genetics and Pathology, Biomedical Centre, Uppsala University, Uppsala, Sweden
| | - Anna-Maja Molin
- Department of Immunology, Genetics and Pathology, Biomedical Centre, Uppsala University, Uppsala, Sweden
| | - Mai Pham
- Department of Immunology, Genetics and Pathology, Biomedical Centre, Uppsala University, Uppsala, Sweden
| | - Mauno Vihinen
- Department of Experimental Medical Science, BMC B13, Lund University, SE-22 184, Lund, Sweden
| | - Kristina Lagerstedt-Robinson
- Clinical Genetics, Karolinska University Hospital, Solna, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Ann Nordgren
- Clinical Genetics, Karolinska University Hospital, Solna, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
- Institute of Biomedicine, Department of Laboratory Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Per Jemth
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, Husargatan 3, 751 23, Uppsala, Sweden
| | - Adam Ameur
- Department of Immunology, Genetics and Pathology, Biomedical Centre, Uppsala University, Uppsala, Sweden
| | - Göran Annerén
- Department of Immunology, Genetics and Pathology, Biomedical Centre, Uppsala University, Uppsala, Sweden
| | - Maria Wilbe
- Department of Immunology, Genetics and Pathology, Biomedical Centre, Uppsala University, Uppsala, Sweden
| | - Marie-Louise Bondeson
- Department of Immunology, Genetics and Pathology, Biomedical Centre, Uppsala University, Uppsala, Sweden.
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Chaouch A, Ulph F, Alder J, Hamdalla H, Ealing J, Clancy T, Macleod R, Clarke AJ. Informed consent for whole genome sequencing in mainstream clinics: logistical constraints and possible solutions. Eur J Hum Genet 2024; 32:260-262. [PMID: 38177407 PMCID: PMC10924082 DOI: 10.1038/s41431-023-01520-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Revised: 11/21/2023] [Accepted: 12/04/2023] [Indexed: 01/06/2024] Open
Affiliation(s)
- Amina Chaouch
- Manchester Centre for Clinical Neurosciences, Salford Royal NHS Foundation Trust, Manchester, M8 6HD, UK.
- University of Manchester, Manchester, UK.
| | - Fiona Ulph
- School of Psychological Sciences, University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - James Alder
- Manchester Medical School, Manchester University, Manchester, M13 9PL, UK
| | - Hisham Hamdalla
- Manchester Centre for Clinical Neurosciences, Salford Royal NHS Foundation Trust, Manchester, M8 6HD, UK
| | - John Ealing
- Manchester Centre for Clinical Neurosciences, Salford Royal NHS Foundation Trust, Manchester, M8 6HD, UK
| | | | - Rhona Macleod
- St Mary's Hospital, Manchester University Hospitals NHS Foundation Trust, Manchester Centre for Genomic Medicine, Manchester, UK
| | - Angus John Clarke
- Cardiff University School of Medicine, Institute of Medical Genetics, University Hospital of Wales, Cardiff, UK
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Jefferis J, Mallett AJ. Exploring the impact and utility of genomic sequencing in established CKD. Clin Kidney J 2024; 17:sfae043. [PMID: 38464959 PMCID: PMC10921391 DOI: 10.1093/ckj/sfae043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Indexed: 03/12/2024] Open
Abstract
Clinical genetics is increasingly recognized as an important area within nephrology care. Clinicians require awareness of genetic kidney disease to recognize clinical phenotypes, consider use of genomics to aid diagnosis, and inform treatment decisions. Understanding the broad spectrum of clinical phenotypes and principles of genomic sequencing is becoming increasingly required in clinical nephrology, with nephrologists requiring education and support to achieve meaningful patient outcomes. Establishment of effective clinical resources, multi-disciplinary teams and education is important to increase application of genomics in clinical care, for the benefit of patients and their families. Novel applications of genomics in chronic kidney disease include pharmacogenomics and clinical translation of polygenic risk scores. This review explores established and emerging impacts and utility of genomics in kidney disease.
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Affiliation(s)
- Julia Jefferis
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, Australia
- Faculty of Medicine, The University of Queensland, Brisbane, Australia
- Kidney Health Service, Royal Brisbane and Women's Hospital, Brisbane, Australia
| | - Andrew J Mallett
- Faculty of Medicine, The University of Queensland, Brisbane, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
- Department of Renal Medicine, Townsville University Hospital, Douglas, Australia
- College of Medicine and Dentistry, James Cook University, Douglas, Australia
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35
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Schobers G, Derks R, den Ouden A, Swinkels H, van Reeuwijk J, Bosgoed E, Lugtenberg D, Sun SM, Corominas Galbany J, Weiss M, Blok MJ, Olde Keizer RACM, Hofste T, Hellebrekers D, de Leeuw N, Stegmann A, Kamsteeg EJ, Paulussen ADC, Ligtenberg MJL, Bradley XZ, Peden J, Gutierrez A, Pullen A, Payne T, Gilissen C, van den Wijngaard A, Brunner HG, Nelen M, Yntema HG, Vissers LELM. Genome sequencing as a generic diagnostic strategy for rare disease. Genome Med 2024; 16:32. [PMID: 38355605 PMCID: PMC10868087 DOI: 10.1186/s13073-024-01301-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 02/02/2024] [Indexed: 02/16/2024] Open
Abstract
BACKGROUND To diagnose the full spectrum of hereditary and congenital diseases, genetic laboratories use many different workflows, ranging from karyotyping to exome sequencing. A single generic high-throughput workflow would greatly increase efficiency. We assessed whether genome sequencing (GS) can replace these existing workflows aimed at germline genetic diagnosis for rare disease. METHODS We performed short-read GS (NovaSeq™6000; 150 bp paired-end reads, 37 × mean coverage) on 1000 cases with 1271 known clinically relevant variants, identified across different workflows, representative of our tertiary diagnostic centers. Variants were categorized into small variants (single nucleotide variants and indels < 50 bp), large variants (copy number variants and short tandem repeats) and other variants (structural variants and aneuploidies). Variant calling format files were queried per variant, from which workflow-specific true positive rates (TPRs) for detection were determined. A TPR of ≥ 98% was considered the threshold for transition to GS. A GS-first scenario was generated for our laboratory, using diagnostic efficacy and predicted false negative as primary outcome measures. As input, we modeled the diagnostic path for all 24,570 individuals referred in 2022, combining the clinical referral, the transition of the underlying workflow(s) to GS, and the variant type(s) to be detected. RESULTS Overall, 95% (1206/1271) of variants were detected. Detection rates differed per variant category: small variants in 96% (826/860), large variants in 93% (341/366), and other variants in 87% (39/45). TPRs varied between workflows (79-100%), with 7/10 being replaceable by GS. Models for our laboratory indicate that a GS-first strategy would be feasible for 84.9% of clinical referrals (750/883), translating to 71% of all individuals (17,444/24,570) receiving GS as their primary test. An estimated false negative rate of 0.3% could be expected. CONCLUSIONS GS can capture clinically relevant germline variants in a 'GS-first strategy' for the majority of clinical indications in a genetics diagnostic lab.
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Affiliation(s)
- Gaby Schobers
- Department of Human Genetics, Radboudumc, Nijmegen, Netherlands
- Research Institute for Medical Innovation, Radboudumc, Nijmegen, Netherlands
| | - Ronny Derks
- Department of Human Genetics, Radboudumc, Nijmegen, Netherlands
| | - Amber den Ouden
- Department of Human Genetics, Radboudumc, Nijmegen, Netherlands
| | - Hilde Swinkels
- Department of Human Genetics, Radboudumc, Nijmegen, Netherlands
| | - Jeroen van Reeuwijk
- Department of Human Genetics, Radboudumc, Nijmegen, Netherlands
- Research Institute for Medical Innovation, Radboudumc, Nijmegen, Netherlands
| | - Ermanno Bosgoed
- Department of Human Genetics, Radboudumc, Nijmegen, Netherlands
| | | | - Su Ming Sun
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, Netherlands
| | - Jordi Corominas Galbany
- Department of Human Genetics, Radboudumc, Nijmegen, Netherlands
- Research Institute for Medical Innovation, Radboudumc, Nijmegen, Netherlands
| | - Marjan Weiss
- Department of Human Genetics, Radboudumc, Nijmegen, Netherlands
| | - Marinus J Blok
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, Netherlands
| | - Richelle A C M Olde Keizer
- Department of Human Genetics, Radboudumc, Nijmegen, Netherlands
- Research Institute for Medical Innovation, Radboudumc, Nijmegen, Netherlands
| | - Tom Hofste
- Department of Human Genetics, Radboudumc, Nijmegen, Netherlands
| | - Debby Hellebrekers
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, Netherlands
| | - Nicole de Leeuw
- Department of Human Genetics, Radboudumc, Nijmegen, Netherlands
| | - Alexander Stegmann
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, Netherlands
| | | | - Aimee D C Paulussen
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, Netherlands
| | - Marjolijn J L Ligtenberg
- Department of Human Genetics, Radboudumc, Nijmegen, Netherlands
- Research Institute for Medical Innovation, Radboudumc, Nijmegen, Netherlands
| | | | | | | | | | | | - Christian Gilissen
- Department of Human Genetics, Radboudumc, Nijmegen, Netherlands
- Research Institute for Medical Innovation, Radboudumc, Nijmegen, Netherlands
| | | | - Han G Brunner
- Department of Human Genetics, Radboudumc, Nijmegen, Netherlands
- Research Institute for Medical Innovation, Radboudumc, Nijmegen, Netherlands
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, Netherlands
| | - Marcel Nelen
- Department of Human Genetics, Radboudumc, Nijmegen, Netherlands
| | - Helger G Yntema
- Department of Human Genetics, Radboudumc, Nijmegen, Netherlands
- Research Institute for Medical Innovation, Radboudumc, Nijmegen, Netherlands
| | - Lisenka E L M Vissers
- Department of Human Genetics, Radboudumc, Nijmegen, Netherlands.
- Research Institute for Medical Innovation, Radboudumc, Nijmegen, Netherlands.
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36
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Bagger FO, Borgwardt L, Jespersen AS, Hansen AR, Bertelsen B, Kodama M, Nielsen FC. Whole genome sequencing in clinical practice. BMC Med Genomics 2024; 17:39. [PMID: 38287327 PMCID: PMC10823711 DOI: 10.1186/s12920-024-01795-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 01/01/2024] [Indexed: 01/31/2024] Open
Abstract
Whole genome sequencing (WGS) is becoming the preferred method for molecular genetic diagnosis of rare and unknown diseases and for identification of actionable cancer drivers. Compared to other molecular genetic methods, WGS captures most genomic variation and eliminates the need for sequential genetic testing. Whereas, the laboratory requirements are similar to conventional molecular genetics, the amount of data is large and WGS requires a comprehensive computational and storage infrastructure in order to facilitate data processing within a clinically relevant timeframe. The output of a single WGS analyses is roughly 5 MIO variants and data interpretation involves specialized staff collaborating with the clinical specialists in order to provide standard of care reports. Although the field is continuously refining the standards for variant classification, there are still unresolved issues associated with the clinical application. The review provides an overview of WGS in clinical practice - describing the technology and current applications as well as challenges connected with data processing, interpretation and clinical reporting.
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Affiliation(s)
- Frederik Otzen Bagger
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Line Borgwardt
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Andreas Sand Jespersen
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Anna Reimer Hansen
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Birgitte Bertelsen
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Miyako Kodama
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Finn Cilius Nielsen
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark.
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37
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Covill LE, Sendel A, Campbell TM, Piiroinen I, Enoksson SL, Borgström EW, Hansen S, Ma K, Marits P, Norlin AC, Smith CIE, Kåhlin J, Eriksson LI, Bergman P, Bryceson YT. Evaluation of Genetic or Cellular Impairments in Type I IFN Immunity in a Cohort of Young Adults with Critical COVID-19. J Clin Immunol 2024; 44:50. [PMID: 38231281 PMCID: PMC10794435 DOI: 10.1007/s10875-023-01641-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 12/13/2023] [Indexed: 01/18/2024]
Abstract
Several genetic and immunological risk factors for severe COVID-19 have been identified, with monogenic conditions relating to 13 genes of type I interferon (IFN) immunity proposed to explain 4.8% of critical cases. However, previous cohorts have been clinically heterogeneous and were not subjected to thorough genetic and immunological analyses. We therefore aimed to systematically investigate the prevalence of rare genetic variants causing inborn errors of immunity (IEI) and functionally interrogate the type I IFN pathway in young adults that suffered from critical COVID-19 yet lacked comorbidities. We selected and clinically characterized a cohort of 38 previously healthy individuals under 50 years of age who were treated in intensive care units due to critical COVID-19. Blood samples were collected after convalescence. Two patients had IFN-α autoantibodies. Genome sequencing revealed very rare variants in the type I IFN pathway in 31.6% of the patients, which was similar to controls. Analyses of cryopreserved leukocytes did not indicate any defect in plasmacytoid dendritic cell sensing of TLR7 and TLR9 agonists in patients carrying variants in these pathways. However, lymphocyte STAT phosphorylation and protein upregulation upon IFN-α stimulation revealed three possible cases of impaired type I IFN signaling in carriers of rare variants. Together, our results suggest a strategy of functional screening followed by genome analyses and biochemical validation to uncover undiagnosed causes of critical COVID-19.
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Affiliation(s)
- L E Covill
- Center for Hematology and Regenerative Medicine, Department of Medicine, Karolinska Institute, Stockholm, Sweden
| | - A Sendel
- Division of Clinical Immunology and Transfusion Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - T M Campbell
- Center for Hematology and Regenerative Medicine, Department of Medicine, Karolinska Institute, Stockholm, Sweden
| | - I Piiroinen
- Center for Hematology and Regenerative Medicine, Department of Medicine, Karolinska Institute, Stockholm, Sweden
| | - S Lind Enoksson
- Division of Clinical Immunology and Transfusion Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - E Wahren Borgström
- Division of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - S Hansen
- Division of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - K Ma
- Center for Hematology and Regenerative Medicine, Department of Medicine, Karolinska Institute, Stockholm, Sweden
| | - P Marits
- Division of Clinical Immunology and Transfusion Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - A C Norlin
- Division of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - C I E Smith
- Division of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - J Kåhlin
- Division of Perioperative Medicine and Intensive Care, Karolinska University Hospital, Stockholm, Sweden
| | - L I Eriksson
- Division of Perioperative Medicine and Intensive Care, Karolinska University Hospital, Stockholm, Sweden
| | - P Bergman
- Division of Clinical Immunology and Transfusion Medicine, Karolinska University Hospital, Stockholm, Sweden
- Division of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Y T Bryceson
- Center for Hematology and Regenerative Medicine, Department of Medicine, Karolinska Institute, Stockholm, Sweden.
- Division of Clinical Immunology and Transfusion Medicine, Karolinska University Hospital, Stockholm, Sweden.
- Broegelmann Laboratory, Department of Clinical Sciences, University of Bergen, Bergen, Norway.
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38
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Leigh S, Baines R, Stevens S, Garba-Sani Z, Austin D, Chatterjee A. Walk a mile in my shoes: perspectives towards sharing of health and experience data among individuals living with sickle cell disorder. Mhealth 2024; 10:4. [PMID: 38323148 PMCID: PMC10839506 DOI: 10.21037/mhealth-23-18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 11/29/2023] [Indexed: 02/08/2024] Open
Abstract
Background Advancements in digital health technologies (DHTs) mean people are increasingly recording and managing personal health data. As observed during the COVID-19 pandemic, sharing of such data may provide unrivalled opportunities in advancing our understanding of conditions otherwise poorly understood, including rare conditions. Methods A semi-structured focus group (n=25) explored perspectives and experiences of sharing health data among those with a group of rare haematological conditions, sickle cell disorder (SCD). The focus group explored (I) what 'feeling well' looks like; (II) how this could be monitored using DHTs; (III) which data healthcare professionals (HCPs) should pay greater attention to and; (IV) types of data willing to be shared, with whom, and under which conditions. Key themes were further assessed via an online survey (n=50). Results Patient-relevant measures of condition-management focused on "everything else that comes with" SCD, suggesting HCPs did not pay sufficient attention to day-to-day symptom variability. This was juxtaposed against the "fixed and one-off" electronic health record (EHR), collecting pre-specified data at pre-determined snapshots of time, not considered reflective of outcomes associated with "feeling well" day-to-day. Forty-four-point-seven percent of respondents had previously shared health data. Most were willing to share data concerning symptoms and health service utilisation, but were less willing to share genomic and EHR data. Sixty-one-point-seven percent believed HCPs did not pay enough attention to daily fluctuations in mental and physical health. Financial benefits (74.5%), trust in organisations seeking data (72.3%), and knowing how data will be used (61.7%) were key facilitators of data sharing. Seventy-one percent, 70% and 65.2% had not previously shared health data with the pharmaceutical industry, charitable organisations and digital health interventions respectively, but were open to doing so in the future. Conclusions Those living with the rare condition SCD were supportive of collecting and sharing data to foster research and improve understanding and outcomes. However, specific requirements were identified to respect privacy and informational needs regarding future use of data. DHTs can be a valuable tool in improving understanding of the day-to-day impact of health conditions, but understanding patient needs is critical in ensuring involvement in the process, as not all data types are considered of equal value, benefit, or risk.
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Affiliation(s)
- Simon Leigh
- Prometheus Health Technologies, Mor Workspace, Newquay, UK
- Warwick Medical School, University of Warwick, Coventry, UK
| | - Rebecca Baines
- Centre for Health Technology, University of Plymouth, Plymouth, UK
| | - Sebastian Stevens
- Prometheus Health Technologies, Mor Workspace, Newquay, UK
- Centre for Health Technology, University of Plymouth, Plymouth, UK
| | | | - Daniella Austin
- School of Psychology, Faculty of Health, University of Plymouth, Plymouth, UK
| | - Arunangsu Chatterjee
- Centre for Health Technology, University of Plymouth, Plymouth, UK
- School of Medicine, University of Leeds, Leeds, UK
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39
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Lord J, Oquendo CJ, Wai HA, Douglas AGL, Bunyan DJ, Wang Y, Hu Z, Zeng Z, Danis D, Katsonis P, Williams A, Lichtarge O, Chang Y, Bagnall RD, Mount SM, Matthiasardottir B, Lin C, Hansen TVO, Leman R, Martins A, Houdayer C, Krieger S, Bakolitsa C, Peng Y, Kamandula A, Radivojac P, Baralle D. Predicting the impact of rare variants on RNA splicing in CAGI6. Hum Genet 2024:10.1007/s00439-023-02624-3. [PMID: 38170232 DOI: 10.1007/s00439-023-02624-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 11/18/2023] [Indexed: 01/05/2024]
Abstract
Variants which disrupt splicing are a frequent cause of rare disease that have been under-ascertained clinically. Accurate and efficient methods to predict a variant's impact on splicing are needed to interpret the growing number of variants of unknown significance (VUS) identified by exome and genome sequencing. Here, we present the results of the CAGI6 Splicing VUS challenge, which invited predictions of the splicing impact of 56 variants ascertained clinically and functionally validated to determine splicing impact. The performance of 12 prediction methods, along with SpliceAI and CADD, was compared on the 56 functionally validated variants. The maximum accuracy achieved was 82% from two different approaches, one weighting SpliceAI scores by minor allele frequency, and one applying the recently published Splicing Prediction Pipeline (SPiP). SPiP performed optimally in terms of sensitivity, while an ensemble method combining multiple prediction tools and information from databases exceeded all others for specificity. Several challenge methods equalled or exceeded the performance of SpliceAI, with ultimate choice of prediction method likely to depend on experimental or clinical aims. One quarter of the variants were incorrectly predicted by at least 50% of the methods, highlighting the need for further improvements to splicing prediction methods for successful clinical application.
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Affiliation(s)
- Jenny Lord
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | | | - Htoo A Wai
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Andrew G L Douglas
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - David J Bunyan
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
- Wessex Regional Genetics Laboratory, Salisbury District Hospital, Salisbury, UK
| | - Yaqiong Wang
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, 201102, China
| | - Zhiqiang Hu
- University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Zishuo Zeng
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, 08873, USA
| | - Daniel Danis
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06032, USA
| | - Panagiotis Katsonis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Amanda Williams
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Olivier Lichtarge
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Yuchen Chang
- Agnes Ginges Centre for Molecular Cardiology at Centenary Institute, University of Sydney, Sydney, Australia
- Faculty of Medicine and Health, University of Sydney, Sydney, Australia
| | - Richard D Bagnall
- Agnes Ginges Centre for Molecular Cardiology at Centenary Institute, University of Sydney, Sydney, Australia
- Faculty of Medicine and Health, University of Sydney, Sydney, Australia
| | - Stephen M Mount
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA
| | - Brynja Matthiasardottir
- Graduate Program in Biological Sciences and Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA
- Inflammatory Disease Section, National Human Genome Research Institute, Bethesda, MD, USA
| | | | - Thomas van Overeem Hansen
- Department of Clinical Genetics, University Hospital of Copenhagen, Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Raphael Leman
- Laboratoire de Biologie et Génétique du Cancer, Centre François Baclesse, Caen, France
- Inserm U1245, Cancer Brain and Genomics, Normandie Université, UNICAEN, FHU G4 génomique, Rouen, France
| | - Alexandra Martins
- Inserm U1245, Cancer Brain and Genomics, Normandie Université, UNIROUEN, FHU G4 génomique, Rouen, France
| | - Claude Houdayer
- Inserm U1245, Cancer Brain and Genomics, Normandie Université, UNIROUEN, FHU G4 génomique, Rouen, France
- Department of Genetics, Univ Rouen Normandie, INSERM U1245, FHU-G4 Génomique and CHU Rouen, 76000, Rouen, France
| | - Sophie Krieger
- Laboratoire de Biologie et Génétique du Cancer, Centre François Baclesse, Caen, France
- Inserm U1245, Cancer Brain and Genomics, Normandie Université, UNICAEN, FHU G4 génomique, Rouen, France
| | | | - Yisu Peng
- Khoury College of Computer Sciences, Northeastern University, Boston, MA, 02115, USA
| | - Akash Kamandula
- Khoury College of Computer Sciences, Northeastern University, Boston, MA, 02115, USA
| | - Predrag Radivojac
- Khoury College of Computer Sciences, Northeastern University, Boston, MA, 02115, USA
| | - Diana Baralle
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK.
- Wessex Clinical Genetics Service, University Hospital Southampton NHS Foundation Trust, Southampton, UK.
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40
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James KN, Chowdhury S, Ding Y, Batalov S, Watkins K, Kwon YH, Van Der Kraan L, Ellsworth K, Kingsmore SF, Guidugli L. Genome sequencing detects a wide range of clinically relevant copy-number variants and other genomic alterations. Genet Med 2024; 26:101006. [PMID: 37869996 DOI: 10.1016/j.gim.2023.101006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 10/03/2023] [Accepted: 10/06/2023] [Indexed: 10/24/2023] Open
Abstract
PURPOSE Copy-number variants (CNVs) and other non-single nucleotide variant/indel variant types contribute an important proportion of diagnoses in individuals with suspected genetic disease. This study describes the range of such variants detected by genome sequencing (GS). METHODS For a pediatric cohort of 1032 participants undergoing clinical GS, we characterize the CNVs and other non-single nucleotide variant/indel variant types that were reported, including aneuploidies, mobile element insertions, and uniparental disomies, and we describe the bioinformatic pipeline used to detect these variants. RESULTS Together, these genetic alterations accounted for 15.8% of reported variants. Notably, 67.9% of these were deletions, 32.9% of which overlapped a single gene, and many deletions were reported together with a second variant in the same gene in cases of recessive disease. A retrospective medical record review in a subset of this cohort revealed that up to 6 additional genetic tests were ordered in 68% (26/38) of cases, some of which failed to report the CNVs/rare variants reported on GS. CONCLUSION GS detected a broad range of reported variant types, including CNVs ranging in size from 1 Kb to 46 Mb.
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Affiliation(s)
- Kiely N James
- Rady Children's Institute for Genomic Medicine, San Diego, CA
| | | | - Yan Ding
- Rady Children's Institute for Genomic Medicine, San Diego, CA
| | - Sergey Batalov
- Rady Children's Institute for Genomic Medicine, San Diego, CA
| | - Kelly Watkins
- Rady Children's Institute for Genomic Medicine, San Diego, CA
| | - Yong Hyun Kwon
- Rady Children's Institute for Genomic Medicine, San Diego, CA
| | | | | | | | - Lucia Guidugli
- Rady Children's Institute for Genomic Medicine, San Diego, CA.
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41
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Dong L, Zhang L, Li X, Mei S, Shen Y, Fu L, Zhao S, Tang X, Tang Y. Clinical and genetic analysis of two patients with primary ciliary dyskinesia caused by a novel variant of DNAAF2. BMC Pediatr 2023; 23:616. [PMID: 38053031 PMCID: PMC10696777 DOI: 10.1186/s12887-023-04185-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 07/08/2023] [Indexed: 12/07/2023] Open
Abstract
BACKGROUND The study describes the clinical manifestations and variant screening of two Chinese siblings with primary ciliary dyskinesia (PCD). They carry the same DNAAF2 genotype, which is an extremely rare PCD genotype in the Chinese population. In addition, the study illustrated an overview of published variants on DNAAF2 to date. METHODS A two-child family was recruited for the study. Clinical manifestations, laboratory tests, bronchoscopic and otoscopic images, and radiographic data were collected. Whole blood was collected from siblings and their parents for whole-exome sequencing (WES) and Sanger sequencing to screen variants. RESULTS The two siblings exhibited typical clinical manifestations of PCD. Two compound heterozygous variants in DNAAF2 were detected in both by WES. Nonsense variant c.156 C>A and frameshift variant c.177_178insA, which was a novel variant. CONCLUSION The study identified a novel variant of DNAAF2 in Chinese children with a typical phenotype of PCD, which may enrich our knowledge of the clinical, diagnostic and genetic information of DNAAF2-induced PCD in children.
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Affiliation(s)
- Lili Dong
- Department of Respiratory Medicine, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, China
| | - Lei Zhang
- Department of Respiratory Medicine, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, China
| | - Xiao Li
- Department of Respiratory Medicine, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, China
| | - Shiyue Mei
- Henan Provincial Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, China
| | - Yuelin Shen
- Department of Respiratory Medicine, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, China
- Department of Respiratory Medicine, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Libing Fu
- Department of Pathology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Shunying Zhao
- Department of Respiratory Medicine, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Xiaolei Tang
- Department of Respiratory Medicine, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, China.
- Department of Respiratory Medicine, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China.
| | - Yu Tang
- Department of Respiratory Medicine, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, China.
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Uhlen M, Quake SR. Sequential sequencing by synthesis and the next-generation sequencing revolution. Trends Biotechnol 2023; 41:1565-1572. [PMID: 37482467 DOI: 10.1016/j.tibtech.2023.06.007] [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: 05/08/2023] [Revised: 06/11/2023] [Accepted: 06/15/2023] [Indexed: 07/25/2023]
Abstract
The impact of next-generation sequencing (NGS) cannot be overestimated. The technology has transformed the field of life science, contributing to a dramatic expansion in our understanding of human health and disease and our understanding of biology and ecology. The vast majority of the major NGS systems today are based on the concept of 'sequencing by synthesis' (SBS) with sequential detection of nucleotide incorporation using an engineered DNA polymerase. Based on this strategy, various alternative platforms have been developed, including the use of either native nucleotides or reversible terminators and different strategies for the attachment of DNA to a solid support. In this review, some of the key concepts leading to this remarkable development are discussed.
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Affiliation(s)
- Mathias Uhlen
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden; Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden.
| | - Stephen R Quake
- Departments of Bioengineering and Applied Physics, Stanford University, Stanford, CA, USA; Chan Zuckerberg Initiative, Redwood City, California, USA, Stanford, CA, USA
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43
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Ren M, Zheng H, Lu X, Lian W, Feng B. Expanding the genotypic and phenotypic spectrum associated with TBL1XR1 de novo variants. Gene 2023; 886:147777. [PMID: 37683765 DOI: 10.1016/j.gene.2023.147777] [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: 03/20/2023] [Revised: 09/01/2023] [Accepted: 09/05/2023] [Indexed: 09/10/2023]
Abstract
BACKGROUND The TBL1XR1 gene encodes the protein transducin-beta-like 1 receptor1, widely distributed in the pituitary, hypothalamus, white and brown adipose tissue, muscle, and liver. Current evidence suggests that heterozygous TBL1XR1 pathogenic variants can lead to a wide spectrum of phenotypes. This study aims to reveal the clinical phenotype and genetic profiles of de novo TBL1XR1 variations and summarize the relevant clinical and genetic features. METHODS We analyzed four new cases harboring de novo TBL1XR1 variants and reviewed all reported cases. RESULTS All probands suffered from global developmental delay. Moreover, patient 1 exhibited susceptibility to startle, patient 2 had hypovitaminosis D, short stature and hyponatremia, and patients 3 and 4 both presented with ASD (Autism spectrum disorder) and short stature. They all had a de novo TBL1XR1 variant (NM_024665.7), c.1184A > G (p.Tyr395Cys), c.1108G > A (p.Asp370Asn), c.1047 + 1G > C, and c.1097C > T (p.Ser366Phe) respectively. In addition, pooled analysis of 51 cases showed that they had speech impairment (38/39), intellectual developmental disorder (28/28), global developmental delay (42/42), and hypotonia (24/27), and some of them had epilepsy (10/22), ASD (13/25), and developmental regression (4/13). CONCLUSIONS We report four new patients with de novo TBL1XR1 variants and provide a comprehensive overview of 47 previously reported individuals with TBL1XR1 variants, enriching the genotypic and phenotypic spectrum of TBL1XR1-related disease. This report further validates the pathogenicity de novo TBL1XR1 variants.
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Affiliation(s)
- Mingyue Ren
- School of Pediatrics, Henan University of Chinese Medicine, Zhengzhou, China
| | - Hong Zheng
- School of Pediatrics, Henan University of Chinese Medicine, Zhengzhou, China; The First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, China.
| | - Xiangpeng Lu
- The First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, China
| | - Wenjun Lian
- The First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, China
| | - Bin Feng
- School of Pediatrics, Henan University of Chinese Medicine, Zhengzhou, China; The First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, China
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44
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Pagnamenta AT, Camps C, Giacopuzzi E, Taylor JM, Hashim M, Calpena E, Kaisaki PJ, Hashimoto A, Yu J, Sanders E, Schwessinger R, Hughes JR, Lunter G, Dreau H, Ferla M, Lange L, Kesim Y, Ragoussis V, Vavoulis DV, Allroggen H, Ansorge O, Babbs C, Banka S, Baños-Piñero B, Beeson D, Ben-Ami T, Bennett DL, Bento C, Blair E, Brasch-Andersen C, Bull KR, Cario H, Cilliers D, Conti V, Davies EG, Dhalla F, Dacal BD, Dong Y, Dunford JE, Guerrini R, Harris AL, Hartley J, Hollander G, Javaid K, Kane M, Kelly D, Kelly D, Knight SJL, Kreins AY, Kvikstad EM, Langman CB, Lester T, Lines KE, Lord SR, Lu X, Mansour S, Manzur A, Maroofian R, Marsden B, Mason J, McGowan SJ, Mei D, Mlcochova H, Murakami Y, Németh AH, Okoli S, Ormondroyd E, Ousager LB, Palace J, Patel SY, Pentony MM, Pugh C, Rad A, Ramesh A, Riva SG, Roberts I, Roy N, Salminen O, Schilling KD, Scott C, Sen A, Smith C, Stevenson M, Thakker RV, Twigg SRF, Uhlig HH, van Wijk R, Vona B, Wall S, Wang J, Watkins H, Zak J, Schuh AH, Kini U, Wilkie AOM, Popitsch N, Taylor JC. Structural and non-coding variants increase the diagnostic yield of clinical whole genome sequencing for rare diseases. Genome Med 2023; 15:94. [PMID: 37946251 PMCID: PMC10636885 DOI: 10.1186/s13073-023-01240-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 09/27/2023] [Indexed: 11/12/2023] Open
Abstract
BACKGROUND Whole genome sequencing is increasingly being used for the diagnosis of patients with rare diseases. However, the diagnostic yields of many studies, particularly those conducted in a healthcare setting, are often disappointingly low, at 25-30%. This is in part because although entire genomes are sequenced, analysis is often confined to in silico gene panels or coding regions of the genome. METHODS We undertook WGS on a cohort of 122 unrelated rare disease patients and their relatives (300 genomes) who had been pre-screened by gene panels or arrays. Patients were recruited from a broad spectrum of clinical specialties. We applied a bioinformatics pipeline that would allow comprehensive analysis of all variant types. We combined established bioinformatics tools for phenotypic and genomic analysis with our novel algorithms (SVRare, ALTSPLICE and GREEN-DB) to detect and annotate structural, splice site and non-coding variants. RESULTS Our diagnostic yield was 43/122 cases (35%), although 47/122 cases (39%) were considered solved when considering novel candidate genes with supporting functional data into account. Structural, splice site and deep intronic variants contributed to 20/47 (43%) of our solved cases. Five genes that are novel, or were novel at the time of discovery, were identified, whilst a further three genes are putative novel disease genes with evidence of causality. We identified variants of uncertain significance in a further fourteen candidate genes. The phenotypic spectrum associated with RMND1 was expanded to include polymicrogyria. Two patients with secondary findings in FBN1 and KCNQ1 were confirmed to have previously unidentified Marfan and long QT syndromes, respectively, and were referred for further clinical interventions. Clinical diagnoses were changed in six patients and treatment adjustments made for eight individuals, which for five patients was considered life-saving. CONCLUSIONS Genome sequencing is increasingly being considered as a first-line genetic test in routine clinical settings and can make a substantial contribution to rapidly identifying a causal aetiology for many patients, shortening their diagnostic odyssey. We have demonstrated that structural, splice site and intronic variants make a significant contribution to diagnostic yield and that comprehensive analysis of the entire genome is essential to maximise the value of clinical genome sequencing.
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Affiliation(s)
- Alistair T Pagnamenta
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Carme Camps
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Edoardo Giacopuzzi
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Human Technopole, Viale Rita Levi Montalcini 1, 20157, Milan, Italy
| | - John M Taylor
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Oxford Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Old Road, Oxford, OX3 7LE, UK
| | - Mona Hashim
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Eduardo Calpena
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Pamela J Kaisaki
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Akiko Hashimoto
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Jing Yu
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Edward Sanders
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Ron Schwessinger
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Jim R Hughes
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Gerton Lunter
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
- University Medical Center Groningen, Groningen University, PO Box 72, 9700 AB, Groningen, The Netherlands
| | - Helene Dreau
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Department of Oncology, Oxford Molecular Diagnostics Centre, University of Oxford, Level 4, John Radcliffe Hospital, Headley Way, Oxford, OX3 9DU, UK
| | - Matteo Ferla
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Lukas Lange
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Yesim Kesim
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Vassilis Ragoussis
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Dimitrios V Vavoulis
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Department of Oncology, Oxford Molecular Diagnostics Centre, University of Oxford, Level 4, John Radcliffe Hospital, Headley Way, Oxford, OX3 9DU, UK
| | - Holger Allroggen
- Neurosciences Department, UHCW NHS Trust, Clifford Bridge Road, Coventry, CV2 2DX, UK
| | - Olaf Ansorge
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
| | - Christian Babbs
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Siddharth Banka
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital, Oxford Road, Manchester, M13 9WL, UK
| | - Benito Baños-Piñero
- Oxford Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Old Road, Oxford, OX3 7LE, UK
| | - David Beeson
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
| | - Tal Ben-Ami
- Pediatric Hematology-Oncology Unit, Kaplan Medical Center, Rehovot, Israel
| | - David L Bennett
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
| | - Celeste Bento
- Hematology Department, Hospitais da Universidade de Coimbra, Coimbra, Portugal
| | - Edward Blair
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 7LE, UK
| | - Charlotte Brasch-Andersen
- Department of Clinical Genetics, Odense University Hospital and Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Katherine R Bull
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
| | - Holger Cario
- Department of Pediatrics and Adolescent Medicine, University Medical Center, Eythstrasse 24, 89075, Ulm, Germany
| | - Deirdre Cilliers
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 7LE, UK
| | - Valerio Conti
- Neuroscience Department, Meyer Children's Hospital IRCCS, Viale Pieraccini 24, 50139, Florence, Italy
| | - E Graham Davies
- Department of Immunology, Great Ormond Street Hospital for Children NHS Trust and UCL Great Ormond Street Institute of Child Health, Zayed Centre for Research, 2Nd Floor, 20C Guilford Street, London, WC1N 1DZ, UK
| | - Fatima Dhalla
- Department of Paediatrics, Institute of Developmental and Regenerative Medicine, IMS-Tetsuya Nakamura Building, Old Road Campus, Roosevelt Drive, Oxford, OX3 7TY, UK
| | - Beatriz Diez Dacal
- Oxford Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Old Road, Oxford, OX3 7LE, UK
| | - Yin Dong
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
| | - James E Dunford
- Oxford NIHR Musculoskeletal BRC and Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Nuffield Orthopaedic Centre, Old Road, Oxford, OX3 7HE, UK
| | - Renzo Guerrini
- Neuroscience Department, Meyer Children's Hospital IRCCS, Viale Pieraccini 24, 50139, Florence, Italy
| | - Adrian L Harris
- Department of Oncology, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK
| | - Jane Hartley
- Liver Unit, Birmingham Women's & Children's Hospital and University of Birmingham, Steelhouse Lane, Birmingham, B4 6NH, UK
| | - Georg Hollander
- Department of Paediatrics, University of Oxford, Level 2, Children's Hospital, John Radcliffe Hospital, Oxford, OX3 9DU, UK
| | - Kassim Javaid
- Oxford NIHR Musculoskeletal BRC and Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Nuffield Orthopaedic Centre, Old Road, Oxford, OX3 7HE, UK
| | - Maureen Kane
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Pharmacy Hall North, Room 731, 20 N. Pine Street, Baltimore, MD, 21201, USA
| | - Deirdre Kelly
- Liver Unit, Birmingham Women's & Children's Hospital and University of Birmingham, Steelhouse Lane, Birmingham, B4 6NH, UK
| | - Dominic Kelly
- Children's Hospital, OUH NHS Foundation Trust, NIHR Oxford BRC, Headley Way, Oxford, OX3 9DU, UK
| | - Samantha J L Knight
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Alexandra Y Kreins
- Department of Immunology, Great Ormond Street Hospital for Children NHS Trust and UCL Great Ormond Street Institute of Child Health, Zayed Centre for Research, 2Nd Floor, 20C Guilford Street, London, WC1N 1DZ, UK
| | - Erika M Kvikstad
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Craig B Langman
- Feinberg School of Medicine, Northwestern University, 211 E Chicago Avenue, Chicago, IL, MS37, USA
| | - Tracy Lester
- Oxford Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Old Road, Oxford, OX3 7LE, UK
| | - Kate E Lines
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- University of Oxford, Academic Endocrine Unit, OCDEM, Churchill Hospital, Oxford, OX3 7LJ, UK
| | - Simon R Lord
- Early Phase Clinical Trials Unit, Department of Oncology, University of Oxford, Cancer and Haematology Centre, Level 2 Administration Area, Churchill Hospital, Oxford, OX3 7LJ, UK
| | - Xin Lu
- Nuffield Department of Clinical Medicine, Ludwig Institute for Cancer Research, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK
| | - Sahar Mansour
- St George's University Hospitals NHS Foundation Trust, Blackshore Road, Tooting, London, SW17 0QT, UK
| | - Adnan Manzur
- MRC Centre for Neuromuscular Diseases, National Hospital for Neurology and Neurosurgery, Queen Square, London, WC1N 3BG, UK
| | - Reza Maroofian
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, WC1N 3BG, UK
| | - Brian Marsden
- Nuffield Department of Medicine, Kennedy Institute, University of Oxford, Oxford, OX3 7BN, UK
| | - Joanne Mason
- Yourgene Health Headquarters, Skelton House, Lloyd Street North, Manchester Science Park, Manchester, M15 6SH, UK
| | - Simon J McGowan
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Davide Mei
- Neuroscience Department, Meyer Children's Hospital IRCCS, Viale Pieraccini 24, 50139, Florence, Italy
| | - Hana Mlcochova
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Yoshiko Murakami
- Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Andrea H Németh
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 7LE, UK
| | - Steven Okoli
- Imperial College NHS Trust, Department of Haematology, Hammersmith Hospital, Du Cane Road, London, W12 0HS, UK
| | - Elizabeth Ormondroyd
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- University of Oxford, Level 6 West Wing, Oxford, OX3 9DU, JR, UK
| | - Lilian Bomme Ousager
- Department of Clinical Genetics, Odense University Hospital and Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Jacqueline Palace
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
| | - Smita Y Patel
- Clinical Immunology, John Radcliffe Hospital, Level 4A, Oxford, OX3 9DU, UK
| | - Melissa M Pentony
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Chris Pugh
- Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
| | - Aboulfazl Rad
- Department of Otolaryngology-Head & Neck Surgery, Tübingen Hearing Research Centre, Eberhard Karls University, Elfriede-Aulhorn-Str. 5, 72076, Tübingen, Germany
| | - Archana Ramesh
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
| | - Simone G Riva
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Irene Roberts
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
- Department of Paediatrics, University of Oxford, Level 2, Children's Hospital, John Radcliffe Hospital, Oxford, OX3 9DU, UK
| | - Noémi Roy
- Department of Haematology, Oxford University Hospitals NHS Foundation Trust, Level 4, Haematology, John Radcliffe Hospital, Oxford, OX3 9DU, UK
| | - Outi Salminen
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Department of Oncology, Oxford Molecular Diagnostics Centre, University of Oxford, Level 4, John Radcliffe Hospital, Headley Way, Oxford, OX3 9DU, UK
| | - Kyleen D Schilling
- Ann & Robert H. Lurie Children's Hospital of Chicago, 225 E Chicago Avenue, Chicago, IL, 60611, USA
| | - Caroline Scott
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Arjune Sen
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
| | - Conrad Smith
- Oxford Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Old Road, Oxford, OX3 7LE, UK
| | - Mark Stevenson
- University of Oxford, Academic Endocrine Unit, OCDEM, Churchill Hospital, Oxford, OX3 7LJ, UK
| | - Rajesh V Thakker
- University of Oxford, Academic Endocrine Unit, OCDEM, Churchill Hospital, Oxford, OX3 7LJ, UK
| | - Stephen R F Twigg
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Holm H Uhlig
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Department of Paediatrics, University of Oxford, Level 2, Children's Hospital, John Radcliffe Hospital, Oxford, OX3 9DU, UK
- Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford, OX3 9DU, UK
| | - Richard van Wijk
- UMC Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
| | - Barbara Vona
- Department of Otolaryngology-Head & Neck Surgery, Tübingen Hearing Research Centre, Eberhard Karls University, Elfriede-Aulhorn-Str. 5, 72076, Tübingen, Germany
- Institute of Human Genetics, University Medical Center Göttingen, Heinrich-Düker-Weg 12, 37073, Göttingen, Germany
- Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Germany
| | - Steven Wall
- Oxford Craniofacial Unit, John Radcliffe Hospital, Level LG1, West Wing, Oxford, OX3 9DU, UK
| | - Jing Wang
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
| | - Hugh Watkins
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- University of Oxford, Level 6 West Wing, Oxford, OX3 9DU, JR, UK
| | - Jaroslav Zak
- Nuffield Department of Clinical Medicine, Ludwig Institute for Cancer Research, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK
- Department of Immunology and Microbiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Anna H Schuh
- Department of Oncology, Oxford Molecular Diagnostics Centre, University of Oxford, Level 4, John Radcliffe Hospital, Headley Way, Oxford, OX3 9DU, UK
| | - Usha Kini
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 7LE, UK
| | - Andrew O M Wilkie
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Niko Popitsch
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna BioCenter(VBC), Dr.-Bohr-Gasse 9, 1030, Vienna, Austria
| | - Jenny C Taylor
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK.
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK.
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45
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Curic E, Ewans L, Pysar R, Taylan F, Botto LD, Nordgren A, Gahl W, Palmer EE. International Undiagnosed Diseases Programs (UDPs): components and outcomes. Orphanet J Rare Dis 2023; 18:348. [PMID: 37946247 PMCID: PMC10633944 DOI: 10.1186/s13023-023-02966-1] [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: 04/27/2023] [Accepted: 10/30/2023] [Indexed: 11/12/2023] Open
Abstract
Over the last 15 years, Undiagnosed Diseases Programs have emerged to address the significant number of individuals with suspected but undiagnosed rare genetic diseases, integrating research and clinical care to optimize diagnostic outcomes. This narrative review summarizes the published literature surrounding Undiagnosed Diseases Programs worldwide, including thirteen studies that evaluate outcomes and two commentary papers. Commonalities in the diagnostic and research process of Undiagnosed Diseases Programs are explored through an appraisal of available literature. This exploration allowed for an assessment of the strengths and limitations of each of the six common steps, namely enrollment, comprehensive clinical phenotyping, research diagnostics, data sharing and matchmaking, results, and follow-up. Current literature highlights the potential utility of Undiagnosed Diseases Programs in research diagnostics. Since participants have often had extensive previous genetic studies, research pipelines allow for diagnostic approaches beyond exome or whole genome sequencing, through reanalysis using research-grade bioinformatics tools and multi-omics technologies. The overall diagnostic yield is presented by study, since different selection criteria at enrollment and reporting processes make comparisons challenging and not particularly informative. Nonetheless, diagnostic yield in an undiagnosed cohort reflects the potential of an Undiagnosed Diseases Program. Further comparisons and exploration of the outcomes of Undiagnosed Diseases Programs worldwide will allow for the development and improvement of the diagnostic and research process and in turn improve the value and utility of an Undiagnosed Diseases Program.
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Affiliation(s)
- Ela Curic
- Discipline of Paediatrics and Child Health, Faculty of Medicine and Health, School of Clinical Medicine, University of New South Wales, Bright Alliance Building, Level 8, Randwick, NSW, Australia
| | - Lisa Ewans
- Discipline of Paediatrics and Child Health, Faculty of Medicine and Health, School of Clinical Medicine, University of New South Wales, Bright Alliance Building, Level 8, Randwick, NSW, Australia
- Centre for Clinical Genetics, Sydney Children's Hospital, Randwick, NSW, Australia
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Ryan Pysar
- Discipline of Paediatrics and Child Health, Faculty of Medicine and Health, School of Clinical Medicine, University of New South Wales, Bright Alliance Building, Level 8, Randwick, NSW, Australia
- Centre for Clinical Genetics, Sydney Children's Hospital, Randwick, NSW, Australia
- Department of Clinical Genetics, The Children's Hospital at Westmead, Westmead, NSW, Australia
| | - Fulya Taylan
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics and Genomics, Karolinska University Hospital, Stockholm, Sweden
| | - Lorenzo D Botto
- Division of Medical Genetics, Department of Pediatrics, University of Utah, Salt Lake City, Utah, USA
| | - Ann Nordgren
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics and Genomics, Karolinska University Hospital, Stockholm, Sweden
- Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - William Gahl
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Elizabeth Emma Palmer
- Discipline of Paediatrics and Child Health, Faculty of Medicine and Health, School of Clinical Medicine, University of New South Wales, Bright Alliance Building, Level 8, Randwick, NSW, Australia.
- Centre for Clinical Genetics, Sydney Children's Hospital, Randwick, NSW, Australia.
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46
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Wu D, Zheng Y, Li Y, Peng M, Lin H, Wang K. Exploring the molecular and clinical spectrum of COVID-19-related acute necrotizing encephalopathy in three pediatric cases. J Hum Genet 2023; 68:769-775. [PMID: 37491516 DOI: 10.1038/s10038-023-01171-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 06/04/2023] [Accepted: 06/04/2023] [Indexed: 07/27/2023]
Abstract
Acute necrotizing encephalopathy (ANE) is a rare disease that predominantly affects children and is associated with a high mortality rate. Here we report three cases of COVID-19-related ANE in children, with the mutation detection in two genes associated with mitochondrial dysfunction. The cases exhibited common ANE symptoms, such as fever, impaired consciousness, positive pathological reflex, increased cerebrospinal fluid protein, and multifocal and symmetric brain lesions identified through MRI. Using genotype-phenotype correlation analysis in trio-whole exome sequencing (WES), four potential pathogenic variants were identified in two genes associated with mitochondrial function (RANBP2 and MCCC2). Notably, MCCC2 was identified as being potentially associated with COVID-19-related ANE for the first time, and two of the four variants had not been previously reported. Our findings expand the clinical and mutation spectrum of COVID-19-related ANE in pediatric cases. The finding of these three new cases in our study further supports the previous hypothesis about the role of mitochondrial homeostatic imbalance in COVID-19-related ANE. It is essential to use genetic testing to identify this subset of patients with compromised mitochondrial function in order to improve patient management and prognosis.
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Affiliation(s)
- Dong Wu
- Institute of Eugenics, Department of Obstetrics and Gynecology, 900 Hospital of the Joint Logistics Team, Fuzhou Clinic Medical College, Fujian Medical University, Dongfang Affiliated Hospital of Xiamen University, Fuzhou, Fujian, 350025, People's Republic of China
| | - Yinan Zheng
- Pediatric Intensive Care Unit, Guangdong Women and Children Hospital, Guangzhou, Guangdong, 510010, People's Republic of China.
| | - Ying Li
- Pediatric Intensive Care Unit, Guangdong Women and Children Hospital, Guangzhou, Guangdong, 510010, People's Republic of China
| | - Mei Peng
- Fujungenetics Technologies, Shanghai, Shanghai, 200333, People's Republic of China
| | - Huaming Lin
- Guangzhou Daan Clinical Laboratory Center, Guangzhou, Guangdong, 510663, People's Republic of China
| | - Kaiyu Wang
- Fujungenetics Technologies, Shanghai, Shanghai, 200333, People's Republic of China.
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47
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Peng X, Kaviany S. Approach to Diagnosing Inborn Errors of Immunity. Rheum Dis Clin North Am 2023; 49:731-739. [PMID: 37821192 DOI: 10.1016/j.rdc.2023.06.001] [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] [Indexed: 10/13/2023]
Abstract
Inborn errors of immunity are now understood to encompass manifold features including but not limited to immunodeficiency, autoimmunity, autoinflammation, atopy, bone marrow defects, and/or increased malignancy risk. As such, it is essential to maintain a high index of suspicion, as these disorders are not limited to specific demographics such as children or those with recurrent infections. Clinical presentations and standard immunophenotyping are informative for suggesting potential underlying etiologies, but integration of data from multimodal approaches including genomics is often required to achieve diagnosis.
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Affiliation(s)
- Xiao Peng
- McKusick-Nathans, Department of Genetic Medicine, Johns Hopkins University School of Medicine, 600 North Wolfe Street, Blalock 1008, Baltimore, MD 21287, USA
| | - Saara Kaviany
- The University of Chicago & Biological Sciences, Department of Pediatrics, University of Chicago, 5841 South Maryland Avenue, Chicago, IL 60637, USA.
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48
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Abstract
Rare diseases are a leading cause of infant mortality and lifelong disability. To improve outcomes, timely diagnosis and effective treatments are needed. Genomic sequencing has transformed the traditional diagnostic process, providing rapid, accurate and cost-effective genetic diagnoses to many. Incorporating genomic sequencing into newborn screening programmes at the population scale holds the promise of substantially expanding the early detection of treatable rare diseases, with stored genomic data potentially benefitting health over a lifetime and supporting further research. As several large-scale newborn genomic screening projects launch internationally, we review the challenges and opportunities presented, particularly the need to generate evidence of benefit and to address the ethical, legal and psychosocial issues that genomic newborn screening raises.
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Affiliation(s)
- Zornitza Stark
- Australian Genomics, Melbourne, Victoria, Australia.
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia.
| | - Richard H Scott
- Great Ormond Street Hospital for Children, London, UK
- UCL Great Ormond Street Institute of Child Health, London, UK
- Genomics England, London, UK
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49
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Encarnação M, Ribeiro I, David H, Coutinho MF, Quelhas D, Alves S. Challenges in the Definitive Diagnosis of Niemann-Pick Type C-Leaky Variants and Alternative Transcripts. Genes (Basel) 2023; 14:1990. [PMID: 38002933 PMCID: PMC10671040 DOI: 10.3390/genes14111990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 10/17/2023] [Accepted: 10/23/2023] [Indexed: 11/26/2023] Open
Abstract
Niemann-Pick type C (NPC, ORPHA: 646) is a neuro-visceral, psychiatric disease caused predominantly by pathogenic variants in the NPC1 gene or seldom in NPC2. The rarity of the disease, and its wide range of clinical phenotypes and ages of onset, turn the diagnosis into a significant challenge. Other than the detailed clinical history, the typical diagnostic work-up for NPC includes the quantification of pathognomonic metabolites. However, the molecular basis diagnosis is still of utmost importance to fully characterize the disorder. Here, the authors provide an overview of splicing variants in the NPC1 and NPC2 genes and propose a new workflow for NPC diagnosis. Splicing variants cover a significant part of the disease-causing variants in NPC. The authors used cDNA analysis to study the impact of such variants, including the collection of data to classify them as leaky or non-leaky pathogenic variants. However, the presence of naturally occurring spliced transcripts can misdiagnose or mask a pathogenic variant and make the analysis even more difficult. Analysis of the NPC1 cDNA in NPC patients in parallel with controls is vital to assess and detect alternatively spliced forms. Moreover, nonsense-mediated mRNA decay (NMD) analysis plays an essential role in evaluating the naturally occurring transcripts during cDNA analysis and distinguishing them from other pathogenic variants' associated transcripts.
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Affiliation(s)
- Marisa Encarnação
- Research and Development Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, INSA I.P., Rua Alexandre Herculano, 321, 4000-055 Porto, Portugal; (M.E.); (H.D.); (M.F.C.)
- Center for the Study of Animal Science-Instituto de Ciências, Tecnologias e Agroambiente da Universidade do Porto, CECA-ICETA, University of Porto, Praça Gomes Teixeira, Apartado 55142, 4051-401 Porto, Portugal
- Associate Laboratory for Animal and Veterinary Sciences, AL4AnimalS, Faculdade de Medicina Veterinária Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
| | - Isaura Ribeiro
- Laboratório de Bioquímica Genética, Serviço de Genética Laboratorial, Centro de Genética Médica Jacinto Magalhães, Centro Hospitalar e Universitário de Santo António (CHUdSA), 4099-001 Porto, Portugal; (I.R.); (D.Q.)
- UMIB-Unit for Multidisciplinary Research in Biomedicine, ICBAS, University of Porto, 4099-002 Porto, Portugal
- ITR—Laboratory for Integrative and Translational Research in Population Health, 4050-600 Porto, Portugal
| | - Hugo David
- Research and Development Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, INSA I.P., Rua Alexandre Herculano, 321, 4000-055 Porto, Portugal; (M.E.); (H.D.); (M.F.C.)
- Center for the Study of Animal Science-Instituto de Ciências, Tecnologias e Agroambiente da Universidade do Porto, CECA-ICETA, University of Porto, Praça Gomes Teixeira, Apartado 55142, 4051-401 Porto, Portugal
- Associate Laboratory for Animal and Veterinary Sciences, AL4AnimalS, Faculdade de Medicina Veterinária Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
- Biology Department, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| | - Maria Francisca Coutinho
- Research and Development Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, INSA I.P., Rua Alexandre Herculano, 321, 4000-055 Porto, Portugal; (M.E.); (H.D.); (M.F.C.)
- Center for the Study of Animal Science-Instituto de Ciências, Tecnologias e Agroambiente da Universidade do Porto, CECA-ICETA, University of Porto, Praça Gomes Teixeira, Apartado 55142, 4051-401 Porto, Portugal
- Associate Laboratory for Animal and Veterinary Sciences, AL4AnimalS, Faculdade de Medicina Veterinária Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
| | - Dulce Quelhas
- Laboratório de Bioquímica Genética, Serviço de Genética Laboratorial, Centro de Genética Médica Jacinto Magalhães, Centro Hospitalar e Universitário de Santo António (CHUdSA), 4099-001 Porto, Portugal; (I.R.); (D.Q.)
- UMIB-Unit for Multidisciplinary Research in Biomedicine, ICBAS, University of Porto, 4099-002 Porto, Portugal
- ITR—Laboratory for Integrative and Translational Research in Population Health, 4050-600 Porto, Portugal
| | - Sandra Alves
- Research and Development Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, INSA I.P., Rua Alexandre Herculano, 321, 4000-055 Porto, Portugal; (M.E.); (H.D.); (M.F.C.)
- Center for the Study of Animal Science-Instituto de Ciências, Tecnologias e Agroambiente da Universidade do Porto, CECA-ICETA, University of Porto, Praça Gomes Teixeira, Apartado 55142, 4051-401 Porto, Portugal
- Associate Laboratory for Animal and Veterinary Sciences, AL4AnimalS, Faculdade de Medicina Veterinária Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
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50
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Ibarra-González I, Fernández-Lainez C, Vela-Amieva M, Guillén-López S, Belmont-Martínez L, López-Mejía L, Carrillo-Nieto RI, Guillén-Zaragoza NA. A Review of Disparities and Unmet Newborn Screening Needs over 33 Years in a Cohort of Mexican Patients with Inborn Errors of Intermediary Metabolism. Int J Neonatal Screen 2023; 9:59. [PMID: 37873850 PMCID: PMC10594536 DOI: 10.3390/ijns9040059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 09/26/2023] [Accepted: 10/02/2023] [Indexed: 10/25/2023] Open
Abstract
Advances in an early diagnosis by expanded newborn screening (NBS) have been achieved mainly in developed countries, while populations of middle- and low-income countries have poor access, leading to disparities. Expanded NBS in Mexico is not mandatory. Herein, we present an overview of the differences and unmet NBS needs of a group of Mexican patients with inborn errors of intermediary metabolism (IEiM), emphasizing the odyssey experienced to reach a diagnosis. We conducted a retrospective observational study of a historical cohort of patients with IEiM from a national reference center. A total of 924 patients with IEiM were included. Although 72.5% of the diseases identified are detectable by expanded NBS, only 35.4% of the patients were screened. The mortality in the unscreened group was almost two-fold higher than that in the screened group. Patients experienced a median diagnostic delay of 4 months, which is unacceptably long considering that to prevent disability and death, these disorders must be treated in the first days of life. Patients had to travel long distances to our reference center, contributing to their unacceptable diagnostic odyssey. This study highlights the urgent need to have an updated, expanded NBS program with adequate follow up in Mexico and promote the creation of regional medical care centers. We also provide compelling evidence that could prove valuable to decision makers overseeing public health initiatives for individuals impacted by IEiM from middle- and low-income countries.
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Affiliation(s)
- Isabel Ibarra-González
- Laboratorio de Errores Innatos del Metabolismo y Tamiz, Instituto Nacional de Pediatría, Secretaría de Salud, Ciudad de México 04530, Mexico
- Unidad de Genética de la Nutrición, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - Cynthia Fernández-Lainez
- Laboratorio de Errores Innatos del Metabolismo y Tamiz, Instituto Nacional de Pediatría, Secretaría de Salud, Ciudad de México 04530, Mexico
| | - Marcela Vela-Amieva
- Laboratorio de Errores Innatos del Metabolismo y Tamiz, Instituto Nacional de Pediatría, Secretaría de Salud, Ciudad de México 04530, Mexico
| | - Sara Guillén-López
- Laboratorio de Errores Innatos del Metabolismo y Tamiz, Instituto Nacional de Pediatría, Secretaría de Salud, Ciudad de México 04530, Mexico
| | - Leticia Belmont-Martínez
- Laboratorio de Errores Innatos del Metabolismo y Tamiz, Instituto Nacional de Pediatría, Secretaría de Salud, Ciudad de México 04530, Mexico
| | - Lizbeth López-Mejía
- Laboratorio de Errores Innatos del Metabolismo y Tamiz, Instituto Nacional de Pediatría, Secretaría de Salud, Ciudad de México 04530, Mexico
| | - Rosa Itzel Carrillo-Nieto
- Laboratorio de Errores Innatos del Metabolismo y Tamiz, Instituto Nacional de Pediatría, Secretaría de Salud, Ciudad de México 04530, Mexico
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