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Moch J, Radtke M, Liehr T, Eggermann T, Gilissen C, Pfundt R, Astuti G, Hentschel J, Schumann I. Automatized detection of uniparental disomies in a large cohort. Hum Genet 2024; 143:955-964. [PMID: 39012485 PMCID: PMC11303498 DOI: 10.1007/s00439-024-02687-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: 04/16/2024] [Accepted: 07/03/2024] [Indexed: 07/17/2024]
Abstract
Uniparental disomy (UPD) is the inheritance of both homologues of a chromosome from only one parent. The detection of UPDs in sequencing data is not well established and a common gap in genetic diagnostics. We applied our in-house UPD detection pipeline to evaluate a cohort of 9212 samples, including multigene panels as well as exome sequencing data in a single, duo or trio constellation. We used the results to inform the design of our publicly available web app altAFplotter. UPDs categorized as heterodisomy, whole chromosome or segmental isodisomy were identified and validated with microsatellites, multiplex ligation-dependent probe amplification as well as Sanger sequencing. We detected 14 previously undiagnosed UPDs including nine isodisomies, four segmental isodisomies as well as one heterodisomy on chromosome 22. We characterized eight findings as potentially causative through homozygous pathogenic variants or imprinting disorders. Overall, our study demonstrates the utility of our UPD detection pipeline with our web app, altAFplotter, to reliably identify UPDs. This not only increases the diagnostic yield of cases with growth and metabolic disturbances, as well as developmental delay, but also enhances the understanding of UPDs that may be relevant for recurrence risks and genetic counseling.
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Affiliation(s)
- Johanna Moch
- Institute of Human Genetics, Leipzig University, Leipzig, Germany
| | | | - Thomas Liehr
- Institute of Human Genetics, Jena University, Jena, Germany
| | - Thomas Eggermann
- Institute of Human Genetics and Genomic Medicine, Aachen University, Aachen, Germany
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Galuh Astuti
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Julia Hentschel
- Institute of Human Genetics, Leipzig University, Leipzig, Germany
| | - Isabell Schumann
- Institute of Human Genetics, Leipzig University, Leipzig, Germany.
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Moch J, Radtke M, Gburek-Augustat J, Karnstedt M, Schönnagel S, Drukewitz SH, Pilgram L, Hentschel J, Schumann I. Case report: Complete paternal isodisomy on chromosome 18 induces methylation changes in PARD6G-AS1 promotor in a case with arthrogryposis. Front Genet 2023; 14:1297754. [PMID: 38188501 PMCID: PMC10768175 DOI: 10.3389/fgene.2023.1297754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 11/28/2023] [Indexed: 01/09/2024] Open
Abstract
Uniparental disomy (UPD) is the inheritance of both alleles of a chromosome from only one parent. So far, the detection of UPDs in sequencing data is not well established and a known gap in next-generation sequencing (NGS) diagnostics. By developing a new tool for UPD detection, we re-evaluated an eight-year-old individual presenting with scoliosis, muscle weakness and global developmental delay. Previous panel analysis identified a homozygous likely pathogenic loss-of-function variant in the PIEZO2-gene associated with arthrogryposis (OMIM # 617146). Interestingly, during a re-evaluation process, we identified a region of homozygosity (ROH) covering over 95% of chromosome 18. Segregation and microsatellite analysis within the family revealed that only the father is a heterozygous carrier of the variant in PIEZO2 and confirmed paternal uniparental isodisomy (iUPD) on chromosome 18 in the individual. Further methylation analysis indicated demethylation of the promotor region of PARD6G-AS1, which is described to be maternally imprinted and could possibly influence the individuals' phenotype. Our report describes the first complete iUPD on chromosome 18 and highlights that UPDs can be a cause for homozygous pathogenic variants, which reduces the risk of reoccurrence in case of a new pregnancy in comparison to an autosomal recessive inheritance trait significantly.
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Affiliation(s)
- Johanna Moch
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Maximilian Radtke
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Janina Gburek-Augustat
- Division of Neuropaediatrics, Hospital for Children and Adolescents, University of Leipzig Medical Center, Leipzig, Germany
| | - Maike Karnstedt
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Senta Schönnagel
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Stephan H. Drukewitz
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Laura Pilgram
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Julia Hentschel
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Isabell Schumann
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
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Ohno K, Ohkawara B, Shen XM, Selcen D, Engel AG. Clinical and Pathologic Features of Congenital Myasthenic Syndromes Caused by 35 Genes-A Comprehensive Review. Int J Mol Sci 2023; 24:ijms24043730. [PMID: 36835142 PMCID: PMC9961056 DOI: 10.3390/ijms24043730] [Citation(s) in RCA: 34] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 02/09/2023] [Accepted: 02/09/2023] [Indexed: 02/16/2023] Open
Abstract
Congenital myasthenic syndromes (CMS) are a heterogeneous group of disorders characterized by impaired neuromuscular signal transmission due to germline pathogenic variants in genes expressed at the neuromuscular junction (NMJ). A total of 35 genes have been reported in CMS (AGRN, ALG14, ALG2, CHAT, CHD8, CHRNA1, CHRNB1, CHRND, CHRNE, CHRNG, COL13A1, COLQ, DOK7, DPAGT1, GFPT1, GMPPB, LAMA5, LAMB2, LRP4, MUSK, MYO9A, PLEC, PREPL, PURA, RAPSN, RPH3A, SCN4A, SLC18A3, SLC25A1, SLC5A7, SNAP25, SYT2, TOR1AIP1, UNC13A, VAMP1). The 35 genes can be classified into 14 groups according to the pathomechanical, clinical, and therapeutic features of CMS patients. Measurement of compound muscle action potentials elicited by repetitive nerve stimulation is required to diagnose CMS. Clinical and electrophysiological features are not sufficient to identify a defective molecule, and genetic studies are always required for accurate diagnosis. From a pharmacological point of view, cholinesterase inhibitors are effective in most groups of CMS, but are contraindicated in some groups of CMS. Similarly, ephedrine, salbutamol (albuterol), amifampridine are effective in most but not all groups of CMS. This review extensively covers pathomechanical and clinical features of CMS by citing 442 relevant articles.
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Affiliation(s)
- Kinji Ohno
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
- Correspondence: (K.O.); (A.G.E.)
| | - Bisei Ohkawara
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Xin-Ming Shen
- Department of Neurology and Neuromuscular Research Laboratory, Mayo Clinic, Rochester, MN 55905, USA
| | - Duygu Selcen
- Department of Neurology and Neuromuscular Research Laboratory, Mayo Clinic, Rochester, MN 55905, USA
| | - Andrew G. Engel
- Department of Neurology and Neuromuscular Research Laboratory, Mayo Clinic, Rochester, MN 55905, USA
- Correspondence: (K.O.); (A.G.E.)
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Villafuerte-De la Cruz R, Chacon-Camacho OF, Rodriguez-Martinez AC, Xilotl-De Jesus N, Arce-Gonzalez R, Rodriguez-De la Torre C, Valdez-Garcia JE, Rojas-Martinez A, Zenteno JC. Case report: Disease phenotype associated with simultaneous biallelic mutations in ABCA4 and USH2A due to uniparental disomy of chromosome 1. Front Genet 2022; 13:949437. [PMID: 36051698 PMCID: PMC9424670 DOI: 10.3389/fgene.2022.949437] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 07/18/2022] [Indexed: 11/29/2022] Open
Abstract
Inherited retinal diseases (IRDs) represent a spectrum of clinically and genetically heterogeneous disorders. Our study describes an IRD patient carrying ABCA4 and USH2A pathogenic biallelic mutations as a result of paternal uniparental disomy (UPD) in chromosome 1. The proband is a 9-year-old girl born from non-consanguineous parents. Both parents were asymptomatic and denied family history of ocular disease. Clinical history and ophthalmologic examination of the proband were consistent with Stargardt disease. Whispered voice testing disclosed moderate hearing loss. Next-generation sequencing and Sanger sequencing identified pathogenic variants in ABCA4 (c.4926C>G and c.5044_5058del) and USH2A (c.2276G>T). All variants were present homozygously in DNA from the proband and heterozygously in DNA from the father. No variants were found in maternal DNA. Further analysis of single nucleotide polymorphisms confirmed paternal UPD of chromosome 1. This is the first known patient with confirmed UPD for two recessively mutated IRD genes. Our study expands on the genetic heterogeneity of IRDs and highlights the importance of UPD as a mechanism of autosomal recessive disease in non-consanguineous parents. Moreover, a long-term follow-up is essential for the identification of retinal features that may develop as a result of USH2A-related conditions.
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Affiliation(s)
| | - O. F. Chacon-Camacho
- Carrera Médico Cirujano, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Genetics Department, Institute of Ophthalmology “Conde de Valenciana”, Mexico City, Mexico
| | - A. C. Rodriguez-Martinez
- Department of Ophthalmology, University Hospital and Faculty of Medicine, Autonomous University of Nuevo Leon (UANL), Monterrey, Mexico
| | - N. Xilotl-De Jesus
- Genetics Department, Institute of Ophthalmology “Conde de Valenciana”, Mexico City, Mexico
| | - R. Arce-Gonzalez
- Genetics Department, Institute of Ophthalmology “Conde de Valenciana”, Mexico City, Mexico
| | | | - J. E. Valdez-Garcia
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, Mexico
| | - A. Rojas-Martinez
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, Mexico
- Institute for Obesity Research, Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, Mexico
- *Correspondence: A. Rojas-Martinez, ; J. C. Zenteno,
| | - J. C. Zenteno
- Genetics Department, Institute of Ophthalmology “Conde de Valenciana”, Mexico City, Mexico
- Biochemistry Department, Faculty of Medicine, National Autonomous University of Mexico (UNAM), Mexico City, Mexico
- *Correspondence: A. Rojas-Martinez, ; J. C. Zenteno,
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Jacobs MF, Robinson D, Wu YM, Opipari VP, Mody R. Homozygous ATM mutation due to germline uniparental isodisomy in patient with T acute lymphoblastic leukemia and hepatosplenic T-cell lymphoma. Cancer Genet 2022; 266-267:15-18. [DOI: 10.1016/j.cancergen.2022.05.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 03/05/2022] [Accepted: 05/16/2022] [Indexed: 11/16/2022]
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Wang H, Huo L, Wang Y, Sun W, Gu W. Usher syndrome type 2A complicated with glycogen storage disease type 3 due to paternal uniparental isodisomy of chromosome 1 in a sporadic patient. Mol Genet Genomic Med 2021; 9:e1779. [PMID: 34405590 PMCID: PMC8580083 DOI: 10.1002/mgg3.1779] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 05/01/2021] [Accepted: 07/08/2021] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND The condition of uniparental disomy (UPD) occurs when an individual inherits two copies of a chromosome, or part of a chromosome, from one parent. Most cases of uniparental heterodisomy (UPhD) do not cause diseases, whereas cases of uniparental isodisomy (UPiD), while rare, may be pathogenic. Theoretically, UPiD may cause rare genetic diseases in a homozygous recessive manner. METHODS A 4-year-old girl presented with congenital hearing loss, developmental delay, hepatomegaly, and other clinical features. She and her parents were genetically tested using trio whole exome sequencing (Trio-WES) and copy number variation sequencing (CNV-seq). In addition, we built a structural model to further examine the pathogenicity of the UPiD variants. RESULTS Trio-WES identified a paternal UPiD in chromosome 1, and two homozygous pathogenic variants AGL c.4284T>G/p.Tyr1428* and USH2A c.6528T>A/p.Tyr2176* in the UPiD region. We further analyzed the pathogenicity of these two variations. The patient was diagnosed with Usher syndrome type 2A (USH2A) and glycogen storage disease type III (GSD3). CONCLUSIONS Our study reports a rare case of a patient carrying two pathogenic variants of different genes caused by paternal UPiD, supporting the potential application of Trio-WES in detecting and facilitating the diagnosis of UPD.
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Affiliation(s)
- Hua Wang
- Department of Pediatric Neurology, Shengjing Hospital of China Medical University, Shenyang, P.R. China
| | - Liang Huo
- Department of Pediatric Neurology, Shengjing Hospital of China Medical University, Shenyang, P.R. China
| | - Yajian Wang
- Chigene (Beijing) Translational Medical Research Center Co., Ltd., Beijing, P.R. China
| | - Weiwei Sun
- Chigene (Beijing) Translational Medical Research Center Co., Ltd., Beijing, P.R. China
| | - Weiyue Gu
- Chigene (Beijing) Translational Medical Research Center Co., Ltd., Beijing, P.R. China
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González-Quintana A, Trujillo-Tiebas MJ, Fernández-Perrone AL, Blázquez A, Lucia A, Morán M, Ugalde C, Arenas J, Ayuso C, Martín MA. Uniparental isodisomy as a cause of mitochondrial complex I respiratory chain disorder due to a novel splicing NDUFS4 mutation. Mol Genet Metab 2020; 131:341-348. [PMID: 33093004 DOI: 10.1016/j.ymgme.2020.10.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 09/16/2020] [Accepted: 10/12/2020] [Indexed: 01/21/2023]
Abstract
Uniparental disomy (UPD) is an underestimated cause of autosomal recessive disorders. In this study, we aim to raise awareness about the possibility of UPD in mitochondrial disorders - where it is a hardly described event -, by functionally characterizing a novel variant in a structural subunit of complex I (CI) of the mitochondrial oxidative phosphorylation system. Using next-generation sequencing, we identified a new intronic homozygous c.350 + 5G > A variant in the NDUFS4 gene in a one-year-old girl (being alive at the age of 7) belonging to a non-consanguineous family presenting with encephalopathy, psychomotor delay, lactic acidosis and a single CI deficiency, a less severe phenotype than those previously reported in most NDUFS4 patients. One parent lacked the variant, and microsatellite genotyping showed complete paternal uniparental isodisomy of the non-imprinted chromosome 5. We demonstrated in patient's skeletal muscle and fibroblasts splicing abnormalities, low expression of NDUFS4, undetectable NDUFS4 protein, defects in cellular respiration (decreased oxygen consumption and ATP production), and impaired assembly or stability of mitochondrial supercomplexes containing CI. Our findings support that c.350 + 5G > A variant is pathogenic, and reinforce that UPD, although rare, should be considered as a possible cause of mitochondrial diseases in order to provide accurate genetic counselling.
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Affiliation(s)
- Adrián González-Quintana
- Mitochondrial Diseases Laboratory, Hospital Universitario '12 de Octubre', Madrid, Spain; Center for Biomedical Network Research on Rare Diseases (CIBERER), Madrid, Spain
| | - María J Trujillo-Tiebas
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Madrid, Spain; Department of Genetics, IIS-Fundación Jiménez Díaz University Hospital (IIS-FJD, UAM), Madrid, Spain
| | | | - Alberto Blázquez
- Mitochondrial Diseases Laboratory, Hospital Universitario '12 de Octubre', Madrid, Spain; Center for Biomedical Network Research on Rare Diseases (CIBERER), Madrid, Spain; Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Madrid, Spain
| | - Alejandro Lucia
- Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Madrid, Spain; Faculty of Sport Sciences, Universidad Europea de Madrid, Madrid, Spain; Center for Biomedical Research Network on Frailty and Healthy Aging (CIBERFES), Madrid, Spain
| | - María Morán
- Mitochondrial Diseases Laboratory, Hospital Universitario '12 de Octubre', Madrid, Spain; Center for Biomedical Network Research on Rare Diseases (CIBERER), Madrid, Spain; Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Madrid, Spain
| | - Cristina Ugalde
- Mitochondrial Diseases Laboratory, Hospital Universitario '12 de Octubre', Madrid, Spain; Center for Biomedical Network Research on Rare Diseases (CIBERER), Madrid, Spain; Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Madrid, Spain
| | - Joaquín Arenas
- Mitochondrial Diseases Laboratory, Hospital Universitario '12 de Octubre', Madrid, Spain; Center for Biomedical Network Research on Rare Diseases (CIBERER), Madrid, Spain; Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Madrid, Spain
| | - Carmen Ayuso
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Madrid, Spain; Department of Genetics, IIS-Fundación Jiménez Díaz University Hospital (IIS-FJD, UAM), Madrid, Spain
| | - Miguel A Martín
- Mitochondrial Diseases Laboratory, Hospital Universitario '12 de Octubre', Madrid, Spain; Center for Biomedical Network Research on Rare Diseases (CIBERER), Madrid, Spain; Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Madrid, Spain.
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Hepatosplenic αβ T-Cell Lymphoma as Second Malignancy in Young Adult Patient With Previously Undiagnosed Ataxia-Telangiectasia. J Pediatr Hematol Oncol 2020; 42:e463-e465. [PMID: 31259827 PMCID: PMC6933092 DOI: 10.1097/mph.0000000000001537] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Ataxia-telangiectasia is a rare autosomal recessive neurodegenerative disease characterized by ataxia, radiosensitivity, telangiectases, and increased risk for hematologic malignancies. We present a case of a female individual diagnosed with T-cell acute lymphocytic leukemia at 13 years and subsequently with αβ subtype of hepatosplenic T-cell lymphoma (HSTCL) at 20 years. During her diagnostic work up for HSTCL, paired tumor-germline sequencing identified a diagnosis of ataxia-telangiectasia. We also describe a very refractory clinical course of her αβ HSTCL, including only a brief response to multiagent chemotherapy and an allogenic bone marrow transplant.
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Yauy K, de Leeuw N, Yntema HG, Pfundt R, Gilissen C. Accurate detection of clinically relevant uniparental disomy from exome sequencing data. Genet Med 2019; 22:803-808. [PMID: 31767986 PMCID: PMC7118024 DOI: 10.1038/s41436-019-0704-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 11/07/2019] [Indexed: 12/13/2022] Open
Abstract
Purpose Uniparental disomy (UPD) is the rare occurrence of two homologous chromosomes originating from the same parent and is typically identified by marker analysis or single-nucleotide polymorphism (SNP)-based microarrays. UPDs may lead to disease due to imprinting effects, underlying homozygous pathogenic variants, or low-level mosaic aneuploidies. In this study we detected clinically relevant UPD events in both trio and single exome sequencing (ES) data. Methods UPD was detected by applying a method based on Mendelian inheritance errors to a cohort of 4912 ES trios (all UPD types) and by using median absolute deviation–scaled regions of homozygosity to a cohort of 29,723 single ES samples (isodisomy only). Results As positive controls, we accurately identified three mixed UPD, three isodisomy, as well as two segmental UPD events that were all previously reported by SNP-based microarrays. In addition, we identified three segmental UPD and 11 isodisomy events. This resulted in a novel diagnosis based on imprinting for one patient, and adjusted genetic counseling for another patient. Conclusion UPD can easily be identified using both single and trio ES and may be clinically relevant to patients. UPD analysis should become routine in clinical ES, because it increases the diagnostic yield and could affect genetic counseling.
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Affiliation(s)
- Kevin Yauy
- Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, Génétique clinique, CHU Montpellier, Université de Montpellier, Centre de référence anomalies du développement SORO, INSERM U1183, Montpellier, France.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Nicole de Leeuw
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University 6525 HR, Nijmegen, The Netherlands
| | - Helger G Yntema
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands. .,Donders Institute for Brain, Cognition and Behaviour, Radboud University 6525 HR, Nijmegen, The Netherlands.
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands. .,Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands.
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