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Prawitt D, Eggermann T. Molecular mechanisms of human overgrowth and use of omics in its diagnostics: chances and challenges. Front Genet 2024; 15:1382371. [PMID: 38894719 PMCID: PMC11183334 DOI: 10.3389/fgene.2024.1382371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 05/14/2024] [Indexed: 06/21/2024] Open
Abstract
Overgrowth disorders comprise a group of entities with a variable phenotypic spectrum ranging from tall stature to isolated or lateralized overgrowth of body parts and or organs. Depending on the underlying physiological pathway affected by pathogenic genetic alterations, overgrowth syndromes are associated with a broad spectrum of neoplasia predisposition, (cardio) vascular and neurodevelopmental anomalies, and dysmorphisms. Pathologic overgrowth may be of prenatal or postnatal onset. It either results from an increased number of cells (intrinsic cellular hyperplasia), hypertrophy of the normal number of cells, an increase in interstitial spaces, or from a combination of all of these. The underlying molecular causes comprise a growing number of genetic alterations affecting skeletal growth and Growth-relevant signaling cascades as major effectors, and they can affect the whole body or parts of it (mosaicism). Furthermore, epigenetic modifications play a critical role in the manifestation of some overgrowth diseases. The diagnosis of overgrowth syndromes as the prerequisite of a personalized clinical management can be challenging, due to their clinical and molecular heterogeneity. Physicians should consider molecular genetic testing as a first diagnostic step in overgrowth syndromes. In particular, the urgent need for a precise diagnosis in tumor predisposition syndromes has to be taken into account as the basis for an early monitoring and therapy. With the (future) implementation of next-generation sequencing approaches and further omic technologies, clinical diagnoses can not only be verified, but they also confirm the clinical and molecular spectrum of overgrowth disorders, including unexpected findings and identification of atypical cases. However, the limitations of the applied assays have to be considered, for each of the disorders of interest, the spectrum of possible types of genomic variants has to be considered as they might require different methodological strategies. Additionally, the integration of artificial intelligence (AI) in diagnostic workflows significantly contribute to the phenotype-driven selection and interpretation of molecular and physiological data.
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Affiliation(s)
- Dirk Prawitt
- Center for Pediatrics and Adolescent Medicine, University Medical Center, Mainz, Germany
| | - Thomas Eggermann
- Institute for Human Genetics and Genome Medicine, Medical Faculty, RWTH Aachen, Aachen, Germany
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Wilke MVMB, Klee EW, Dhamija R, Fervenza FC, Thomas B, Leung N, Hogan MC, Hager MM, Kolbert KJ, Kemppainen JL, Loftus EC, Leitzen KM, Vitek CR, McAllister T, Lazaridis KN, Pinto E Vairo F. Diagnostic yield of exome and genome sequencing after non-diagnostic multi-gene panels in patients with single-system diseases. Orphanet J Rare Dis 2024; 19:216. [PMID: 38790019 PMCID: PMC11127317 DOI: 10.1186/s13023-024-03213-x] [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: 01/30/2024] [Accepted: 05/09/2024] [Indexed: 05/26/2024] Open
Abstract
BACKGROUND Though next-generation sequencing (NGS) tests like exome sequencing (ES), genome sequencing (GS), and panels derived from exome and genome data (EGBP) are effective for rare diseases, the ideal diagnostic approach is debated. Limited research has explored reanalyzing raw ES and GS data post-negative EGBP results for diagnostics. RESULTS We analyzed complete ES/GS raw sequencing data from Mayo Clinic's Program for Rare and Undiagnosed Diseases (PRaUD) patients to assess whether supplementary findings could augment diagnostic yield. ES data from 80 patients (59 adults) and GS data from 20 patients (10 adults), averaging 43 years in age, were analyzed. Most patients had renal (n=44) and auto-inflammatory (n=29) phenotypes. Ninety-six cases had negative findings and in four cases additional genetic variants were found, including a variant related to a recently described disease (RRAGD-related hypomagnesemia), a variant missed due to discordant inheritance pattern (COL4A3), a variant with high allelic frequency (NPHS2) in the general population, and a variant associated with an initially untargeted phenotype (HNF1A). CONCLUSION ES and GS show diagnostic yields comparable to EGBP for single-system diseases. However, EGBP's limitations in detecting new disease-associated genes underscore the necessity for periodic updates.
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Affiliation(s)
| | - Eric W Klee
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Radhika Dhamija
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | | | | | - Nelson Leung
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA
| | - Marie C Hogan
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA
| | | | - Kayla J Kolbert
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | | | - Elle C Loftus
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Katie M Leitzen
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Carolyn R Vitek
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Tammy McAllister
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Konstantinos N Lazaridis
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
- Division of Gastroenterology & Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Filippo Pinto E Vairo
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA.
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA.
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Urbaneja E, Bonet N, Solis-Moruno M, Mensa-Vilaro A, de Landazuri IO, Tormo M, Lara R, Plaza S, Fabregat V, Yagüe J, Casals F, Arostegui JI. Case report: Novel compound heterozygous IL1RN mutations as the likely cause of a lethal form of deficiency of interleukin-1 receptor antagonist. Front Immunol 2024; 15:1381447. [PMID: 38646532 PMCID: PMC11026629 DOI: 10.3389/fimmu.2024.1381447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Accepted: 03/04/2024] [Indexed: 04/23/2024] Open
Abstract
Undiagnosed monogenic diseases represent a challenging group of human conditions highly suspicious to have a genetic origin, but without conclusive evidences about it. We identified two brothers born prematurely from a non-consanguineous healthy couple, with a neonatal-onset, chronic disease characterized by severe skin and bone inflammatory manifestations and a fatal outcome in infancy. We conducted DNA and mRNA analyses in the patients' healthy relatives to identify the genetic cause of the patients' disease. DNA analyses were performed by both Sanger and next-generation sequencing, which identified two novel heterozygous IL1RN variants: the intronic c.318 + 2T>G variant in the father and a ≈2,600-bp intragenic deletion in the mother. IL1RN mRNA production was markedly decreased in both progenitors when compared with healthy subjects. The mRNA sequencing performed in each parent identified two novel, truncated IL1RN transcripts. Additional experiments revealed a perfect intrafamilial phenotype-genotype segregation following an autosomal recessive inheritance pattern. The evidences shown here supported for the presence of two novel loss-of-function (LoF) IL1RN pathogenic variants in the analyzed family. Biallelic LoF variants at the IL1RN gene cause the deficiency of interleukin-1 receptor antagonist (DIRA), a monogenic autoinflammatory disease with marked similarities with the patients described here. Despite the non-availability of the patients' samples representing the main limitation of this study, the collected evidences strongly suggest that the patients described here suffered from a lethal form of DIRA likely due to a compound heterozygous genotype at IL1RN, thus providing a reliable genetic diagnosis based on the integration of old medical information with currently obtained genetic data.
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Affiliation(s)
- Elena Urbaneja
- Department of Immunology and Pediatric Rheumatology, Hospital Clínico Universitario de Valladolid, Valladolid, Spain
| | - Nuria Bonet
- Genomics Core Facility, Departament de Medicina i Ciències de la Vida (MELIS), Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
| | - Manuel Solis-Moruno
- Genomics Core Facility, Departament de Medicina i Ciències de la Vida (MELIS), Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
| | - Anna Mensa-Vilaro
- Department of Immunology, Hospital Clínic, Barcelona, Spain
- Institut d’Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
| | - Iñaki Ortiz de Landazuri
- Department of Immunology, Hospital Clínic, Barcelona, Spain
- Institut d’Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
| | - Marc Tormo
- Genomics Core Facility, Departament de Medicina i Ciències de la Vida (MELIS), Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
- Scientific Computing Core Facility, Departament de Medicina i Ciències de la Vida (MELIS), Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
| | - Rocio Lara
- Department of Immunology, Hospital Clínic, Barcelona, Spain
| | - Susana Plaza
- Department of Immunology, Hospital Clínic, Barcelona, Spain
| | | | - Jordi Yagüe
- Department of Immunology, Hospital Clínic, Barcelona, Spain
- Institut d’Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
- School of Medicine, Universitat de Barcelona, Barcelona, Spain
| | - Ferran Casals
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Institut de Biomedicina de la Universitat de Barcelona (IBUB), Universitat de Barcelona, Barcelona, Spain
- Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Juan I. Arostegui
- Department of Immunology, Hospital Clínic, Barcelona, Spain
- Institut d’Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
- School of Medicine, Universitat de Barcelona, Barcelona, Spain
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Wu J, Cui Y, Liu T, Gu C, Ma X, Yu C, Cai Y, Shu J, Wang W, Cai C. Whole exome sequencing approach for identification of the molecular etiology in pediatric patients with hematuria. Clin Chim Acta 2024; 554:117795. [PMID: 38262496 DOI: 10.1016/j.cca.2024.117795] [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: 10/05/2023] [Revised: 12/25/2023] [Accepted: 01/20/2024] [Indexed: 01/25/2024]
Abstract
BACKGROUND Hematuria is a common condition in clinical practice of pediatric patients. It is related to a wide spectrum of disorders and has high heterogeneity both clinically and genetically, which contributes to challenges of diagnosis and lead many pediatric patients with hematuria not to receive accurate diagnosis and early management. METHODS In this single center study, 42 children with hematuria were included in Tianjin Children's Hospital between 2019 and 2020. We analyzed the clinical information and performed WES (Whole exome sequencing) for all cases. Then the classification of identified variants was performed according to the American College of Medical Genetics and Genomics (ACMG) guidelines for interpreting sequence variants. For the fragment deletion, qPCR was performed to validate and confirm the inherited pattern. RESULTS For the 42 patients, 16 cases had gross hematuria and 26 had microscopic hematuria. Molecular genetic causes were uncovered in 9 (21.4%) children, including 7 with Alport syndrome (AS), one with polycystic nephropathy and one with lipoprotein glomerulopathy. The genetic causes for other patients were not related with hematuria. CONCLUSIONS WES is a rapid and effective way to evaluate patients with hematuria. The analysis of genotype-phenotype correlations of patients with AS indicated that severe variants were associated with early kidney failure. Secondary findings were not rare in Chinese children, thus the clinician should pay more attention to the clinical interpretation of sequencing results and properly interaction with patients and their family.
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Affiliation(s)
- Jinying Wu
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin 300134, China
| | - Yaqiong Cui
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin 300134, China
| | - Tao Liu
- The department of nephrology, Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin 300134, China
| | - Chunyu Gu
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin 300134, China
| | - Ximeng Ma
- Basic Medical College, Tianjin Medical University, Tianjin 30070, China
| | - Changshun Yu
- Tianjin KingMed Center for Clinical Laboratory Co. Ltd., Tianjin 300392, China
| | - Yingzi Cai
- Department of Medicine,Tianjin University, Tianjin 300110, China
| | - Jianbo Shu
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin 300134, China.
| | - Wenhong Wang
- The department of nephrology, Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin 300134, China.
| | - Chunquan Cai
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin 300134, China.
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McNeill A. 2023 in the European Journal of Human Genetics. Eur J Hum Genet 2024; 32:135-137. [PMID: 38332347 PMCID: PMC10853252 DOI: 10.1038/s41431-024-01540-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2024] Open
Affiliation(s)
- Alisdair McNeill
- Division of Neuroscience and Neuroscience Institute, The University of Sheffield, Sheffield, UK.
- Sheffield Clinical Genetics Service, Sheffield Children's Hospital NHS Foundation Trust, Sheffield, UK.
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Bartolomaeus T, Hentschel J, Jamra RA, Popp B. Re-evaluation and re-analysis of 152 research exomes five years after the initial report reveals clinically relevant changes in 18. Eur J Hum Genet 2023; 31:1154-1164. [PMID: 37460657 PMCID: PMC10545662 DOI: 10.1038/s41431-023-01425-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 06/16/2023] [Accepted: 06/28/2023] [Indexed: 07/22/2023] Open
Abstract
Iterative re-analysis of NGS results is not well investigated for published research cohorts of rare diseases. We revisited a cohort of 152 consanguineous families with developmental disorders (NDD) reported five years ago. We re-evaluated all reported variants according to diagnostic classification guidelines or our candidate gene scoring system (AutoCaSc) and systematically scored the validity of gene-disease associations (GDA). Sequencing data was re-processed using an up-to-date pipeline for case-level re-analysis. In 28/152 (18%) families, we identified a clinically relevant change. Ten previously reported (likely) pathogenic variants were re-classified as VUS/benign. In one case, the GDA (TSEN15) validity was judged as limited, and in five cases GDAs are meanwhile established. We identified 12 new disease causing variants. Two previously reported variants were missed by our updated pipeline due to alignment or reference issues. Our results support the need to re-evaluate screening studies, not only the negative cases but including supposedly solved ones. This also applies in a diagnostic setting. We highlight that the complexity of computational re-analysis for old data should be weighed against the decreasing re-testing costs. Since extensive re-analysis per case is beyond the resources of most institutions, we recommend a screening procedure that would quickly identify the majority (83%) of new variants.
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Affiliation(s)
- Tobias Bartolomaeus
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, 04103, Germany
| | - Julia Hentschel
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, 04103, Germany
| | - Rami Abou Jamra
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, 04103, Germany.
| | - Bernt Popp
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, 04103, Germany.
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Center of Functional Genomics, Hessische Straße 4A, 10115, Berlin, Germany.
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McNeill A. Expanding what we know about rare genetic diseases. Eur J Hum Genet 2023; 31:1091-1092. [PMID: 37783763 PMCID: PMC10545818 DOI: 10.1038/s41431-023-01453-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023] Open
Affiliation(s)
- Alisdair McNeill
- Division of Neuroscience, The University of Sheffield, Sheffield, UK.
- Sheffield Children's Hospital NHS Foundation Trust, Sheffield, UK.
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Bayat A. Unveiling the hidden: revisiting the potential of old genetic data for rare disease research. Eur J Hum Genet 2023; 31:1093-1094. [PMID: 37474787 PMCID: PMC10545786 DOI: 10.1038/s41431-023-01435-4] [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: 07/10/2023] [Accepted: 07/13/2023] [Indexed: 07/22/2023] Open
Affiliation(s)
- Allan Bayat
- Department of Epilepsy Genetics and Personalized Medicine, Danish Epilepsy Center, Dianalund, Denmark.
- Department of Regional Health Research, University of Southern Denmark, Odense, Denmark.
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark.
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