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Waldvogel SM, Posey JE, Goodell MA. Human embryonic genetic mosaicism and its effects on development and disease. Nat Rev Genet 2024; 25:698-714. [PMID: 38605218 PMCID: PMC11408116 DOI: 10.1038/s41576-024-00715-z] [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] [Accepted: 02/22/2024] [Indexed: 04/13/2024]
Abstract
Nearly every mammalian cell division is accompanied by a mutational event that becomes fixed in a daughter cell. When carried forward to additional cell progeny, a clone of variant cells can emerge. As a result, mammals are complex mosaics of clones that are genetically distinct from one another. Recent high-throughput sequencing studies have revealed that mosaicism is common, clone sizes often increase with age and specific variants can affect tissue function and disease development. Variants that are acquired during early embryogenesis are shared by multiple cell types and can affect numerous tissues. Within tissues, variant clones compete, which can result in their expansion or elimination. Embryonic mosaicism has clinical implications for genetic disease severity and transmission but is likely an under-recognized phenomenon. To better understand its implications for mosaic individuals, it is essential to leverage research tools that can elucidate the mechanisms by which expanded embryonic variants influence development and disease.
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Affiliation(s)
- Sarah M Waldvogel
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, USA
- Graduate Program in Cancer and Cell Biology, Baylor College of Medicine, Houston, TX, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Margaret A Goodell
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA.
- Graduate Program in Cancer and Cell Biology, Baylor College of Medicine, Houston, TX, USA.
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
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2
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Zsigmond A, Till Á, Bene J, Czakó M, Mikó A, Hadzsiev K. Case Report of Suspected Gonadal Mosaicism in FOXP1-Related Neurodevelopmental Disorder. Int J Mol Sci 2024; 25:5709. [PMID: 38891897 PMCID: PMC11171548 DOI: 10.3390/ijms25115709] [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: 04/27/2024] [Revised: 05/20/2024] [Accepted: 05/22/2024] [Indexed: 06/21/2024] Open
Abstract
Heterozygous mutations in the FOXP1 gene (OMIM#605515) are responsible for a well-characterized neurodevelopmental syndrome known as "intellectual developmental disorder with language impairment with or without autistic features" (OMIM#613670) or FOXP1 syndrome for short. The main features of the condition are global developmental delay/intellectual disability; speech impairment in all individuals, regardless of their level of cognitive abilities; behavioral abnormalities; congenital anomalies, including subtle dysmorphic features; and strabismus, brain, cardiac, and urogenital abnormalities. Here, we present two siblings with a de novo heterozygous FOXP1 variant, namely, a four-year-old boy and 14-month-old girl. Both children have significantly delayed early psychomotor development, hypotonia, and very similar, slightly dysmorphic facial features. A lack of expressive speech was the leading symptom in the case of the four-year-old boy. We performed whole-exome sequencing on the male patient, which identified a pathogenic heterozygous c.1541G>A (p.Arg514His) FOXP1 mutation. His sister's targeted mutation analysis also showed the same heterozygous FOXP1 variant. Segregation analysis revealed the de novo origin of the mutation, suggesting the presence of parental gonadal mosaicism. To the best of our knowledge, this is the first report of gonadal mosaicism in FOXP1-related neurodevelopmental disorders in the medical literature.
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Affiliation(s)
- Anna Zsigmond
- Department of Medical Genetics, Medical School, University of Pécs, H-7623 Pécs, Hungary; (A.Z.); (Á.T.); (J.B.); (M.C.); (A.M.)
| | - Ágnes Till
- Department of Medical Genetics, Medical School, University of Pécs, H-7623 Pécs, Hungary; (A.Z.); (Á.T.); (J.B.); (M.C.); (A.M.)
| | - Judit Bene
- Department of Medical Genetics, Medical School, University of Pécs, H-7623 Pécs, Hungary; (A.Z.); (Á.T.); (J.B.); (M.C.); (A.M.)
| | - Márta Czakó
- Department of Medical Genetics, Medical School, University of Pécs, H-7623 Pécs, Hungary; (A.Z.); (Á.T.); (J.B.); (M.C.); (A.M.)
| | - Alexandra Mikó
- Department of Medical Genetics, Medical School, University of Pécs, H-7623 Pécs, Hungary; (A.Z.); (Á.T.); (J.B.); (M.C.); (A.M.)
- Institute for Translational Medicine, Medical School, University of Pécs, H-7624 Pécs, Hungary
| | - Kinga Hadzsiev
- Department of Medical Genetics, Medical School, University of Pécs, H-7623 Pécs, Hungary; (A.Z.); (Á.T.); (J.B.); (M.C.); (A.M.)
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3
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Veltra D, Theodorou V, Katsalouli M, Vorgia P, Niotakis G, Tsaprouni T, Pons R, Kosma K, Kampouraki A, Tsoutsou I, Makrythanasis P, Kekou K, Traeger-Synodinos J, Sofocleous C. SCN1A Channels a Wide Range of Epileptic Phenotypes: Report of Novel and Known Variants with Variable Presentations. Int J Mol Sci 2024; 25:5644. [PMID: 38891831 PMCID: PMC11171476 DOI: 10.3390/ijms25115644] [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: 04/03/2024] [Revised: 05/15/2024] [Accepted: 05/18/2024] [Indexed: 06/21/2024] Open
Abstract
SCN1A, the gene encoding for the Nav1.1 channel, exhibits dominant interneuron-specific expression, whereby variants disrupting the channel's function affect the initiation and propagation of action potentials and neuronal excitability causing various types of epilepsy. Dravet syndrome (DS), the first described clinical presentation of SCN1A channelopathy, is characterized by severe myoclonic epilepsy in infancy (SMEI). Variants' characteristics and other genetic or epigenetic factors lead to extreme clinical heterogeneity, ranging from non-epileptic conditions to developmental and epileptic encephalopathy (DEE). This current study reports on findings from 343 patients referred by physicians in hospitals and tertiary care centers in Greece between 2017 and 2023. Positive family history for specific neurologic disorders was disclosed in 89 cases and the one common clinical feature was the onset of seizures, at a mean age of 17 months (range from birth to 15 years old). Most patients were specifically referred for SCN1A investigation (Sanger Sequencing and MLPA) and only five for next generation sequencing. Twenty-six SCN1A variants were detected, including nine novel causative variants (c.4567A>Τ, c.5564C>A, c.2176+2T>C, c.3646G>C, c.4331C>A, c.1130_1131delGAinsAC, c.1574_1580delCTGAGGA, c.4620A>G and c.5462A>C), and are herein presented, along with subsequent genotype-phenotype associations. The identification of novel variants complements SCN1A databases extending our expertise on genetic counseling and patient and family management including gene-based personalized interventions.
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Affiliation(s)
- Danai Veltra
- Laboratory of Medical Genetics, Medical School, National and Kapodistrian University of Athens, St. Sophia’s Children’s Hospital, 11527 Athens, Greece; (D.V.); (K.K.); (A.K.); (I.T.); (P.M.); (K.K.); (J.T.-S.)
- Research University Institute for the Study and Prevention of Genetic and Malignant Disease of Childhood, National and Kapodistrian University of Athens, St. Sophia’s Children’s Hospital, 11527 Athens, Greece
| | - Virginia Theodorou
- Pediatric Neurology Department, St. Sophia’s Children’s Hospital, 11527 Athens, Greece; (V.T.); (M.K.)
| | - Marina Katsalouli
- Pediatric Neurology Department, St. Sophia’s Children’s Hospital, 11527 Athens, Greece; (V.T.); (M.K.)
| | - Pelagia Vorgia
- Agrifood and Life Sciences Institute, Hellenic Mediterranean University, 71410 Heraklion, Greece;
| | - Georgios Niotakis
- Pediatric Neurology Department, Venizelion Hospital, 71409 Heraklion, Greece;
| | | | - Roser Pons
- First Department of Pediatrics, Medical School, National and Kapodistrian University of Athens, St. Sophia’s Children’s Hospital, 11527 Athens, Greece;
| | - Konstantina Kosma
- Laboratory of Medical Genetics, Medical School, National and Kapodistrian University of Athens, St. Sophia’s Children’s Hospital, 11527 Athens, Greece; (D.V.); (K.K.); (A.K.); (I.T.); (P.M.); (K.K.); (J.T.-S.)
| | - Afroditi Kampouraki
- Laboratory of Medical Genetics, Medical School, National and Kapodistrian University of Athens, St. Sophia’s Children’s Hospital, 11527 Athens, Greece; (D.V.); (K.K.); (A.K.); (I.T.); (P.M.); (K.K.); (J.T.-S.)
| | - Irene Tsoutsou
- Laboratory of Medical Genetics, Medical School, National and Kapodistrian University of Athens, St. Sophia’s Children’s Hospital, 11527 Athens, Greece; (D.V.); (K.K.); (A.K.); (I.T.); (P.M.); (K.K.); (J.T.-S.)
| | - Periklis Makrythanasis
- Laboratory of Medical Genetics, Medical School, National and Kapodistrian University of Athens, St. Sophia’s Children’s Hospital, 11527 Athens, Greece; (D.V.); (K.K.); (A.K.); (I.T.); (P.M.); (K.K.); (J.T.-S.)
- Department of Genetic Medicine and Development, Medical School, University of Geneva, 1211 Geneva, Switzerland
- Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
| | - Kyriaki Kekou
- Laboratory of Medical Genetics, Medical School, National and Kapodistrian University of Athens, St. Sophia’s Children’s Hospital, 11527 Athens, Greece; (D.V.); (K.K.); (A.K.); (I.T.); (P.M.); (K.K.); (J.T.-S.)
| | - Joanne Traeger-Synodinos
- Laboratory of Medical Genetics, Medical School, National and Kapodistrian University of Athens, St. Sophia’s Children’s Hospital, 11527 Athens, Greece; (D.V.); (K.K.); (A.K.); (I.T.); (P.M.); (K.K.); (J.T.-S.)
| | - Christalena Sofocleous
- Laboratory of Medical Genetics, Medical School, National and Kapodistrian University of Athens, St. Sophia’s Children’s Hospital, 11527 Athens, Greece; (D.V.); (K.K.); (A.K.); (I.T.); (P.M.); (K.K.); (J.T.-S.)
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杨 晓. [Sperm Mosaic Variants and Their Influence on the Offspring]. SICHUAN DA XUE XUE BAO. YI XUE BAN = JOURNAL OF SICHUAN UNIVERSITY. MEDICAL SCIENCE EDITION 2024; 55:535-541. [PMID: 38948294 PMCID: PMC11211766 DOI: 10.12182/20240560507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Indexed: 07/02/2024]
Abstract
Genomic mosaicism arising from mosaic variants is a phenomenon that describes the presence of a cell or cell populations with different genome compositions from the germline cells of an individual. It comprises all types of genetic variants. A large proportion of childhood genetic disorders are defined as being de novo, meaning that the disease-causing mutations are only detected in the proband, not in any of the parents. Population studies show that 80% of the de novo mutations arise from the paternal haplotype, that is, from paternal sperm mosaicism. This review provides a summary of the types and detection strategies of sperm mosaicism. In addition, it provides discussions on how recent studies demonstrated that genomic mosaic mutations in parents, especially those in the paternal sperms, could be inherited by the offspring and cause childhood disorders. According to the previous findings of the author's research team, sperm mosaicism derived from early embryogenesis and primordial germ cell stages can explain 5% to 20% of the de novo mutations related to clinical phenotypes and can serve as an important predictor of both rare and complex disorders. Sperm mosaicism shows great potential for clinical genetic diagnosis and consultations. Based on the published literature, the author suggests that, large-scale screening for de novo sperm mosaic mutations and population-based genetic screening should be conducted in future studies, which will greatly enhance the risk assessment in the offspring and effectively improve the genetic health at the population level. Implementation of direct sperm detection for de novo mutations will significantly increase the efficiency of the stratification of patient cohorts and improve recurrence risk assessment for future births. Future research in the field should be focused on the impact of environmental and lifestyle factors on the health of the offspring through sperms and their modeling of mutation signatures. In addition, targeted in vitro modeling of sperm mutations will also be a promising direction.
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Affiliation(s)
- 晓旭 杨
- 犹他大学 (盐湖城 UT 84112)University of Utah, Salt Lake City, UT 84112, USA
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Lecoquierre F, Cassinari K, Drouot N, May A, Fourneaux S, Charbonnier F, Derambure C, Coutant S, Saugier-Veber P, Hoischen A, Charbonnier C, Nicolas G. Assessment of parental mosaicism rates in neurodevelopmental disorders caused by apparent de novo pathogenic variants using deep sequencing. Sci Rep 2024; 14:5289. [PMID: 38438430 PMCID: PMC10912112 DOI: 10.1038/s41598-024-53358-9] [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: 11/28/2023] [Accepted: 01/31/2024] [Indexed: 03/06/2024] Open
Abstract
While de novo variants (DNV) are overall at low risk of recurrence in subsequent pregnancies, a subset is at high risk due to parental mosaicism. Accurately identifying cases of parental mosaicism is therefore important for genetic counseling in clinical care. Some studies have investigated the rate of parental mosaics, but most were either limited by the sensitivity of the techniques (i.e. exome or genome sequencing), or focused on specific types of disease such as epileptic syndromes. This study aimed to determine the proportion of parental mosaicism among the DNV causing neurodevelopmental disorders (NDDs) in a series not enriched in epilepsy syndromes. We collected 189 patients with NDD-associated DNV. We applied a smMIP enrichment method and sequenced parental blood DNA samples to an average depth of 7000x. Power simulation indicated that mosaicism with an allelic fraction of 0.5% would have been detected for 87% of positions with 90% power. We observed seven parental mosaic variants (3.7% of families), of which four (2.1% of families) had an allelic fraction of less than 1%. In total, our study identifies a relatively low proportion of parental mosaicism in NDD-associated DNVs and raises the question of a biological mechanism behind the higher rates of parental mosaicism detected in other studies, particularly those focusing on epileptic syndromes.
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Affiliation(s)
- François Lecoquierre
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, F-76000, Rouen, France.
- Centre de Ressources Biologiques institutionnel du CHU de Rouen - Biothèque filière génétique, Rouen, France.
| | - Kévin Cassinari
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, F-76000, Rouen, France
| | - Nathalie Drouot
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, F-76000, Rouen, France
| | - Angèle May
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, F-76000, Rouen, France
| | - Steeve Fourneaux
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, F-76000, Rouen, France
| | - Francoise Charbonnier
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, F-76000, Rouen, France
| | - Celine Derambure
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, F-76000, Rouen, France
| | - Sophie Coutant
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, F-76000, Rouen, France
| | - Pascale Saugier-Veber
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, F-76000, Rouen, France
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, 6525 GA, Nijmegen, The Netherlands
| | - Camille Charbonnier
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, F-76000, Rouen, France
| | - Gaël Nicolas
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, F-76000, Rouen, France
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Xu N, Shi W, Cao X, Zhou X, Jin L, Huang HF, Chen S, Xu C. Parental mosaicism detection and preimplantation genetic testing in families with multiple transmissions of de novo mutations. J Med Genet 2023; 60:910-917. [PMID: 36707240 PMCID: PMC10447385 DOI: 10.1136/jmg-2022-108920] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 01/14/2023] [Indexed: 01/28/2023]
Abstract
BACKGROUND De novo mutations (DNMs) are linked with many severe early-onset disorders ranging from rare congenital malformation to intellectual disability. Conventionally, DNMs are considered to have an estimated recurrence rate of 1%. Recently, studies have revealed a higher prevalence of parental mosaicism, leading to a greater recurrence risk, resulting in a second child harbouring the same DNM as a previous child. METHODS In this study, we included 10 families with DNMs leading to adverse pregnancy outcomes. DNA was extracted from tissue samples, including parental peripheral blood, parental saliva and paternal sperm. High-throughput sequencing was used to screen for parental mosaicism with a depth of more than 5000× on average and a variant allele fraction (VAF) detection limit of 0.5%. RESULTS The presence of mosaicism was detected in sperms in two families, with VAFs of 2.8% and 2.5%, respectively. Both families have a history of multiple adverse pregnancies and DNMs shared by siblings. Preimplantation genetic testing (PGT) and prenatal diagnosis were performed in one family, thereby preventing the reoccurrence of DNMs. CONCLUSION This study is the first to report the successful implementation of PGT for monogenic/single gene defects in the parental mosaicism family. Our study suggests that mosaic detection of paternal sperm is warranted in families with recurrent DNMs leading to adverse pregnancy outcomes, and PGT can effectively block the transmission of the pathogenic mutation.
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Affiliation(s)
- Naixin Xu
- International Peace Maternity and Child Health Hospital, Shanghai, China
- Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China
| | - Weihui Shi
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Xianling Cao
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Xuanyou Zhou
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Li Jin
- International Peace Maternity and Child Health Hospital, Shanghai, China
- Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - He-Feng Huang
- International Peace Maternity and Child Health Hospital, Shanghai, China
- Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
- Research Units of Embryo Original Diseases, Chinese Academy of Medical Sciences (No. 2019RU056), Shanghai, China
| | - Songchang Chen
- International Peace Maternity and Child Health Hospital, Shanghai, China
- Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Chenming Xu
- International Peace Maternity and Child Health Hospital, Shanghai, China
- Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
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Boßelmann CM, Leu C, Lal D. Technological and computational approaches to detect somatic mosaicism in epilepsy. Neurobiol Dis 2023:106208. [PMID: 37343892 DOI: 10.1016/j.nbd.2023.106208] [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: 03/05/2023] [Revised: 06/03/2023] [Accepted: 06/16/2023] [Indexed: 06/23/2023] Open
Abstract
Lesional epilepsy is a common and severe disease commonly associated with malformations of cortical development, including focal cortical dysplasia and hemimegalencephaly. Recent advances in sequencing and variant calling technologies have identified several genetic causes, including both short/single nucleotide and structural somatic variation. In this review, we aim to provide a comprehensive overview of the methodological advancements in this field while highlighting the unresolved technological and computational challenges that persist, including ultra-low variant allele fractions in bulk tissue, low availability of paired control samples, spatial variability of mutational burden within the lesion, and the issue of false-positive calls and validation procedures. Information from genetic testing in focal epilepsy may be integrated into clinical care to inform histopathological diagnosis, postoperative prognosis, and candidate precision therapies.
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Affiliation(s)
- Christian M Boßelmann
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA; Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Costin Leu
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA; Department of Clinical and Experimental Epilepsy, Institute of Neurology, University College London, London, UK.
| | - Dennis Lal
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA; Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, OH, USA; Stanley Center for Psychiatric Research, Broad Institute of Harvard and M.I.T., Cambridge, MA, USA; Cologne Center for Genomics (CCG), University of Cologne, Cologne, DE, USA
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Li F, Li R, Zhang Y, Jing X, Liao C. Germline mosaicism for a disease-causing mutation in the ATP1A3 gene in a Chinese family. Neurol Sci 2023; 44:1451-1453. [PMID: 36538131 DOI: 10.1007/s10072-022-06535-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 11/27/2022] [Indexed: 12/24/2022]
Affiliation(s)
- Fucheng Li
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, No. 9 Jinsui Road, Guangzhou, 510623, Guangdong, China
| | - Ru Li
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, No. 9 Jinsui Road, Guangzhou, 510623, Guangdong, China
| | - Yongling Zhang
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, No. 9 Jinsui Road, Guangzhou, 510623, Guangdong, China
| | - Xiangyi Jing
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, No. 9 Jinsui Road, Guangzhou, 510623, Guangdong, China
| | - Can Liao
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, No. 9 Jinsui Road, Guangzhou, 510623, Guangdong, China.
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Odgis JA, Gallagher KM, Rehman AU, Marathe P, Bonini KE, Sebastin M, Di Biase M, Brown K, Kelly NR, Ramos MA, Thomas-Wilson A, Guha S, Okur V, Ganapathi M, Elkhoury L, Edelmann L, Zinberg RE, Abul-Husn NS, Diaz GA, Greally JM, Suckiel SA, Jobanputra V, Horowitz CR, Kenny EE, Wasserstein MP, Gelb BD. Detection of mosaic variants using genome sequencing in a large pediatric cohort. Am J Med Genet A 2023; 191:699-710. [PMID: 36563179 PMCID: PMC10266700 DOI: 10.1002/ajmg.a.63062] [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: 05/03/2022] [Revised: 11/07/2022] [Accepted: 11/18/2022] [Indexed: 12/24/2022]
Abstract
The increased use of next-generation sequencing has expanded our understanding of the involvement and prevalence of mosaicism in genetic disorders. We describe a total of eleven cases: nine in which mosaic variants detected by genome sequencing (GS) and/or targeted gene panels (TGPs) were considered to be causative for the proband's phenotype, and two of apparent parental mosaicism. Variants were identified in the following genes: PHACTR1, SCN8A, KCNT1, CDKL5, NEXMIF, CUX1, TSC2, GABRB2, and SMARCB1. In addition, we identified one large duplication including three genes, UBE3A, GABRB3, and MAGEL2, and one large deletion including deletion of ARFGAP1, EEF1A2, CHRNA4, and KCNQ2. All patients were enrolled in the NYCKidSeq study, a research program studying the communication of genomic information in clinical care, as well as the clinical utility and diagnostic yield of GS for children with suspected genetic disorders in diverse populations in New York City. We observed variability in the correlation between reported variant allele fraction and the severity of the patient's phenotype, although we were not able to determine the mosaicism percentage in clinically relevant tissue(s). Although our study was not sufficiently powered to assess differences in mosaicism detection between the two testing modalities, we saw a trend toward better detection by GS as compared with TGP testing. This case series supports the importance of mosaicism in childhood-onset genetic conditions and informs guidelines for laboratory and clinical interpretation of mosaic variants detected by GS.
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Affiliation(s)
- Jacqueline A. Odgis
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Katie M. Gallagher
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children’s Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, USA
| | - Atteeq U. Rehman
- Molecular Diagnostics, New York Genome Center, New York, NY, USA
| | - Priya Marathe
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Katherine E. Bonini
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Monisha Sebastin
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children’s Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, USA
| | - Miranda Di Biase
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children’s Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, USA
| | - Kaitlyn Brown
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children’s Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, USA
| | - Nicole R. Kelly
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children’s Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, USA
| | - Michelle A. Ramos
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Institute for Health Equity Research, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Saurav Guha
- Molecular Diagnostics, New York Genome Center, New York, NY, USA
| | - Volkan Okur
- Molecular Diagnostics, New York Genome Center, New York, NY, USA
| | | | | | | | - Randi E. Zinberg
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Noura S. Abul-Husn
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - George A. Diaz
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - John M. Greally
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children’s Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, USA
| | - Sabrina A. Suckiel
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Vaidehi Jobanputra
- Molecular Diagnostics, New York Genome Center, New York, NY, USA
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Carol R. Horowitz
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Institute for Health Equity Research, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eimear E. Kenny
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Melissa P. Wasserstein
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children’s Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, USA
| | - Bruce D. Gelb
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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10
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Bernkopf M, Abdullah UB, Bush SJ, Wood KA, Ghaffari S, Giannoulatou E, Koelling N, Maher GJ, Thibaut LM, Williams J, Blair EM, Kelly FB, Bloss A, Burkitt-Wright E, Canham N, Deng AT, Dixit A, Eason J, Elmslie F, Gardham A, Hay E, Holder M, Homfray T, Hurst JA, Johnson D, Jones WD, Kini U, Kivuva E, Kumar A, Lees MM, Leitch HG, Morton JEV, Németh AH, Ramachandrappa S, Saunders K, Shears DJ, Side L, Splitt M, Stewart A, Stewart H, Suri M, Clouston P, Davies RW, Wilkie AOM, Goriely A. Personalized recurrence risk assessment following the birth of a child with a pathogenic de novo mutation. Nat Commun 2023; 14:853. [PMID: 36792598 PMCID: PMC9932158 DOI: 10.1038/s41467-023-36606-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 02/03/2023] [Indexed: 02/17/2023] Open
Abstract
Following the diagnosis of a paediatric disorder caused by an apparently de novo mutation, a recurrence risk of 1-2% is frequently quoted due to the possibility of parental germline mosaicism; but for any specific couple, this figure is usually incorrect. We present a systematic approach to providing individualized recurrence risk. By combining locus-specific sequencing of multiple tissues to detect occult mosaicism with long-read sequencing to determine the parent-of-origin of the mutation, we show that we can stratify the majority of couples into one of seven discrete categories associated with substantially different risks to future offspring. Among 58 families with a single affected offspring (representing 59 de novo mutations in 49 genes), the recurrence risk for 35 (59%) was decreased below 0.1%, but increased owing to parental mixed mosaicism for 5 (9%)-that could be quantified in semen for paternal cases (recurrence risks of 5.6-12.1%). Implementation of this strategy offers the prospect of driving a major transformation in the practice of genetic counselling.
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Affiliation(s)
- Marie Bernkopf
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Ummi B Abdullah
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Stephen J Bush
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Katherine A Wood
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Sahar Ghaffari
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | | | - Nils Koelling
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Geoffrey J Maher
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Loïc M Thibaut
- Centre for Population Genomics, Garvan Institute of Medical Research, UNSW Sydney, Sydney, NSW, Australia
| | - Jonathan Williams
- Oxford Genetics Laboratories, Churchill Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Edward M Blair
- NIHR Oxford Biomedical Research Centre, Oxford, UK
- Oxford Centre for Genomic Medicine, Nuffield Orthopaedic Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Fiona Blanco Kelly
- Oxford Centre for Genomic Medicine, Nuffield Orthopaedic Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Angela Bloss
- Oxford Centre for Genomic Medicine, Nuffield Orthopaedic Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Emma Burkitt-Wright
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, UK
- Division of Evolution and Genomic Sciences, University of Manchester, Manchester, UK
| | - Natalie Canham
- Department of Clinical Genetics, Liverpool Women's NHS Foundation Trust, Liverpool, UK
| | - Alexander T Deng
- Clinical Genetics Department, Guy's Hospital, Guy's & St Thomas' NHS Foundation Trust, London, UK
| | - Abhijit Dixit
- Nottingham Regional Genetics Service, City Hospital Campus, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Jacqueline Eason
- Nottingham Regional Genetics Service, City Hospital Campus, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Frances Elmslie
- South West Thames Regional Genetics Service, St George's University Hospitals NHS Foundation Trust, London, UK
| | - Alice Gardham
- North West Thames Regional Genetics Service, London North West University Healthcare NHS Trust, Northwick Park Hospital, Harrow, UK
| | - Eleanor Hay
- North East Thames Regional Genetics Service, Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Muriel Holder
- Clinical Genetics Department, Guy's Hospital, Guy's & St Thomas' NHS Foundation Trust, London, UK
| | - Tessa Homfray
- South West Thames Regional Genetics Service, St George's University Hospitals NHS Foundation Trust, London, UK
| | - Jane A Hurst
- North East Thames Regional Genetics Service, Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Diana Johnson
- Sheffield Clinical Genetics Service, Sheffield Children's NHS Foundation Trust, Sheffield, UK
| | - Wendy D Jones
- North East Thames Regional Genetics Service, Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Usha Kini
- NIHR Oxford Biomedical Research Centre, Oxford, UK
- Oxford Centre for Genomic Medicine, Nuffield Orthopaedic Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Emma Kivuva
- Clinical Genetics, Royal Devon & Exeter Hospital (Heavitree), Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
| | - Ajith Kumar
- North East Thames Regional Genetics Service, Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Melissa M Lees
- North East Thames Regional Genetics Service, Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Harry G Leitch
- Nottingham Regional Genetics Service, City Hospital Campus, Nottingham University Hospitals NHS Trust, Nottingham, UK
- MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Jenny E V Morton
- West Midlands Regional Clinical Genetics Service and Birmingham Health Partners, Birmingham Women's and Children's Hospitals NHS Foundation Trust, Birmingham, UK
| | - Andrea H Németh
- Oxford Centre for Genomic Medicine, Nuffield Orthopaedic Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Shwetha Ramachandrappa
- Clinical Genetics Department, Guy's Hospital, Guy's & St Thomas' NHS Foundation Trust, London, UK
| | - Katherine Saunders
- Oxford Centre for Genomic Medicine, Nuffield Orthopaedic Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Deborah J Shears
- Oxford Centre for Genomic Medicine, Nuffield Orthopaedic Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Lucy Side
- Wessex Clinical Genetics Service, University Hospital Southampton, Princess Anne Hospital, Southampton, UK
| | - Miranda Splitt
- Northern Genetics Service, The Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle, UK
| | - Alison Stewart
- Sheffield Clinical Genetics Service, Sheffield Children's NHS Foundation Trust, Sheffield, UK
| | - Helen Stewart
- Oxford Centre for Genomic Medicine, Nuffield Orthopaedic Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Mohnish Suri
- Nottingham Regional Genetics Service, City Hospital Campus, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Penny Clouston
- Oxford Genetics Laboratories, Churchill Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | | | - Andrew O M Wilkie
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Anne Goriely
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
- NIHR Oxford Biomedical Research Centre, Oxford, UK.
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11
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Chen J, Chen Y, Yang Y, Niu X, Zhang J, Zeng Q, Liu A, Xu X, Yang X, Li S, Yang X, Wang Y, Zhang Y. Detecting genomic mosaicism in "de novo" genetic epilepsy by amplicon-based deep sequencing. J Hum Genet 2023; 68:73-80. [PMID: 36482122 DOI: 10.1038/s10038-022-01103-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 11/28/2022] [Accepted: 11/29/2022] [Indexed: 12/13/2022]
Abstract
AIM To investigate the occurrence of mosaicism in epilepsy probands and their parents using amplicon-based deep sequencing (ADS). METHODS Patients were recruited from the outpatient of Peking University First Hospital. Two hundred and sixty-four probands with pathogenic variants tested by next-generation sequencing (NGS) were enrolled. RESULTS Mosaic variants were detected in seventeen disease-associated genes from 20 probands, 5 paternal, and 6 maternal parents. The frequency of mosaicism was 11.74% (31/264). Mosaicism in 11 genes was identified from 20 probands with the mutant allelic fractions (MAFs) of 12.95-38.00% in autosomal dominant genes. Five paternal mosaicisms were identified in genes with a MAF of 6.30-20.99%, and six maternal mosaic individuals with a MAF of 2.07-21.90%. Only four mosaic parents had milder seizure history. The affected sibling had the same phenotype consistent with that of the proband, who inherited the variant of SLC1A2 or STXBP1 from their unaffected mosaic mothers, respectively. INTERPRETATION Mosaic phenomenon is not rare in families with epilepsy. Phenotypes of mosaic parents were milder or normal. Mosaicism detection is helpful to identify the mutation origin and it provides a theoretical basis for prenatal diagnosis of family reproduction. ADS is a reliable way of mosaicism detection for clinical application.
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Affiliation(s)
- Jiaoyang Chen
- Department of Pediatrics and Pediatric Epilepsy Center, Peking University First Hospital, Beijing, 100034, China
| | - Yi Chen
- Department of Pediatrics and Pediatric Epilepsy Center, Peking University First Hospital, Beijing, 100034, China
| | - Ying Yang
- Department of Pediatrics and Pediatric Epilepsy Center, Peking University First Hospital, Beijing, 100034, China
| | - Xueyang Niu
- Department of Pediatrics and Pediatric Epilepsy Center, Peking University First Hospital, Beijing, 100034, China
| | - Jing Zhang
- Department of Pediatrics and Pediatric Epilepsy Center, Peking University First Hospital, Beijing, 100034, China
| | - Qi Zeng
- Department of Pediatrics and Pediatric Epilepsy Center, Peking University First Hospital, Beijing, 100034, China
| | - Aijie Liu
- Department of Pediatrics and Pediatric Epilepsy Center, Peking University First Hospital, Beijing, 100034, China
| | - Xiaojing Xu
- Department of Pediatrics and Pediatric Epilepsy Center, Peking University First Hospital, Beijing, 100034, China
| | - Xiaoxu Yang
- Center for Bioinformatics, Peking University, Beijing, 100871, China
| | - Shupin Li
- Department of Pediatrics and Pediatric Epilepsy Center, Peking University First Hospital, Beijing, 100034, China
| | - Xiaoling Yang
- Department of Pediatrics and Pediatric Epilepsy Center, Peking University First Hospital, Beijing, 100034, China
| | - Yi Wang
- Department of Neurology, National Epilepsy Center, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, 201102, China
| | - Yuehua Zhang
- Department of Pediatrics and Pediatric Epilepsy Center, Peking University First Hospital, Beijing, 100034, China.
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12
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Chung C, Yang X, Bae T, Vong KI, Mittal S, Donkels C, Westley Phillips H, Li Z, Marsh APL, Breuss MW, Ball LL, Garcia CAB, George RD, Gu J, Xu M, Barrows C, James KN, Stanley V, Nidhiry AS, Khoury S, Howe G, Riley E, Xu X, Copeland B, Wang Y, Kim SH, Kang HC, Schulze-Bonhage A, Haas CA, Urbach H, Prinz M, Limbrick DD, Gurnett CA, Smyth MD, Sattar S, Nespeca M, Gonda DD, Imai K, Takahashi Y, Chen HH, Tsai JW, Conti V, Guerrini R, Devinsky O, Silva WA, Machado HR, Mathern GW, Abyzov A, Baldassari S, Baulac S, Gleeson JG. Comprehensive multi-omic profiling of somatic mutations in malformations of cortical development. Nat Genet 2023; 55:209-220. [PMID: 36635388 PMCID: PMC9961399 DOI: 10.1038/s41588-022-01276-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 11/30/2022] [Indexed: 01/14/2023]
Abstract
Malformations of cortical development (MCD) are neurological conditions involving focal disruptions of cortical architecture and cellular organization that arise during embryogenesis, largely from somatic mosaic mutations, and cause intractable epilepsy. Identifying the genetic causes of MCD has been a challenge, as mutations remain at low allelic fractions in brain tissue resected to treat condition-related epilepsy. Here we report a genetic landscape from 283 brain resections, identifying 69 mutated genes through intensive profiling of somatic mutations, combining whole-exome and targeted-amplicon sequencing with functional validation including in utero electroporation of mice and single-nucleus RNA sequencing. Genotype-phenotype correlation analysis elucidated specific MCD gene sets associated with distinct pathophysiological and clinical phenotypes. The unique single-cell level spatiotemporal expression patterns of mutated genes in control and patient brains indicate critical roles in excitatory neurogenic pools during brain development and in promoting neuronal hyperexcitability after birth.
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Affiliation(s)
- Changuk Chung
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Xiaoxu Yang
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Taejeong Bae
- Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Keng Ioi Vong
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Swapnil Mittal
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Catharina Donkels
- Department of Neurosurgery, Experimental Epilepsy Research, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - H Westley Phillips
- Department of Neurosurgery, University of California at Los Angeles, Los Angeles, CA, USA
| | - Zhen Li
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Ashley P L Marsh
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Martin W Breuss
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado Aurora, Aurora, CO, USA
| | - Laurel L Ball
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Camila Araújo Bernardino Garcia
- Laboratory of Pediatric Neurosurgery and Developmental Neuropathology, Department of Surgery and Anatomy, University of São Paulo, Ribeirão Preto, Brazil
| | - Renee D George
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Jing Gu
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Mingchu Xu
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Chelsea Barrows
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Kiely N James
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Valentina Stanley
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Anna S Nidhiry
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Sami Khoury
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Gabrielle Howe
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Emily Riley
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Xin Xu
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Brett Copeland
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Yifan Wang
- Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Se Hoon Kim
- Department of Pathology, Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
| | - Hoon-Chul Kang
- Division of Pediatric Neurology, Department of Pediatrics, Severance Children's Hospital, Yonsei University College of Medicine, Seoul, South Korea
| | - Andreas Schulze-Bonhage
- Center for Basics in NeuroModulation, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Carola A Haas
- Department of Neurosurgery, Experimental Epilepsy Research, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Center for Basics in NeuroModulation, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Horst Urbach
- Department of Neuroradiology, Medical Center-University of Freiburg, Faculty of Medicine, Freiburg, Germany
| | - Marco Prinz
- Center for Basics in NeuroModulation, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Institute of Neuropathology, Medical Center-University of Freiburg, Faculty of Medicine, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - David D Limbrick
- Department of Neurology, St. Louis Children's Hospital, Washington University St Louis, Washington, MO, USA
| | - Christina A Gurnett
- Department of Neurology, St. Louis Children's Hospital, Washington University St Louis, Washington, MO, USA
| | - Matthew D Smyth
- Department of Neurosurgery, St. Louis Children's Hospital, Washington University St Louis, Washington, MO, USA
| | - Shifteh Sattar
- Epilepsy Center, Rady Children's Hospital, San Diego, CA, USA
| | - Mark Nespeca
- Epilepsy Center, Rady Children's Hospital, San Diego, CA, USA
| | - David D Gonda
- Epilepsy Center, Rady Children's Hospital, San Diego, CA, USA
| | - Katsumi Imai
- National Epilepsy Center, NHO Shizuoka Institute of Epilepsy and Neurological Disorders, Shizuoka, Japan
| | - Yukitoshi Takahashi
- National Epilepsy Center, NHO Shizuoka Institute of Epilepsy and Neurological Disorders, Shizuoka, Japan
| | - Hsin-Hung Chen
- Division of Pediatric Neurosurgery, The Neurological Institute, Taipei Veterans General Hospital, Taipei City, Taiwan
| | - Jin-Wu Tsai
- Institute of Brain Science, Brain Research Center, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Valerio Conti
- Pediatric Neurology Unit and Laboratories, IRCCS Meyer Children's Hospital University of Florence, Firenze, Italy
| | - Renzo Guerrini
- Pediatric Neurology Unit and Laboratories, IRCCS Meyer Children's Hospital University of Florence, Firenze, Italy
| | - Orrin Devinsky
- Comprehensive Epilepsy Center, Department of Neurology, New York University Langone Health, New York, NY, USA
| | - Wilson A Silva
- Department of Genetics, Center for Cell-Based Therapy, Center for Integrative Systems Biology, University of São Paulo, Ribeirão Preto, Brazil
| | - Helio R Machado
- Laboratory of Pediatric Neurosurgery and Developmental Neuropathology, Department of Surgery and Anatomy, University of São Paulo, Ribeirão Preto, Brazil
| | - Gary W Mathern
- Department of Neurosurgery, University of California at Los Angeles, Los Angeles, CA, USA
| | - Alexej Abyzov
- Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Sara Baldassari
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, Hôpital de la Pitié Salpêtrière, Paris, France
| | - Stéphanie Baulac
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, Hôpital de la Pitié Salpêtrière, Paris, France
| | - Joseph G Gleeson
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA.
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA.
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13
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Pan J, Li J, Chen S, Xu C, Huang H, Jin L. Living birth following preimplantation genetic testing for monogenic disorders to prevent low-level germline mosaicism related Nicolaides–Baraitser syndrome. Front Genet 2022; 13:989041. [PMID: 36160002 PMCID: PMC9500527 DOI: 10.3389/fgene.2022.989041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 08/22/2022] [Indexed: 11/13/2022] Open
Abstract
Objective: Paternal sperm mosaicism has few consequences for fathers for mutations being restricted to sperm. However, it could potentially underlie severe sporadic disease in their offspring. Here, we present a live birth of a female infant from a father with low-level sperm DNA mosaicism achieved via preimplantation genetic testing for monogenic disorders (PGT-M).Methods: A couple with the father carrying sperm DNA mosaicism received standard in vitro fertilization treatment, with intracytoplasmic sperm injection, embryo biopsy, polymerase chain reaction, and DNA analysis. Only one unaffected embryo was transferred to the uterine cavity. Amniocentesis was performed at the 16th week of gestation by copy-number variation-sequencing, karyotyping, and Sanger sequencing.Results: Eight surviving embryos were biopsied during the blastocyst stage. Karyomapping and Sanger sequencing were applied to detect the euploidy and paternal mutation. After performing PGT-M, followed by successful pregnancy, the prenatal genetic diagnoses revealed that the fetus was unaffected, and one healthy girl was born.Conclusion: This is the first reported live birth with unaffected children achieved via PGT for a low-level germline mosaicism father. It not only opens the possibility of preventing the recurrent monogenic disease of children among gonadal mosaicism families but also alerts clinicians to consider gonadal mosaicism as the source of DMNs.
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Affiliation(s)
- Jiexue Pan
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China
- Shanghai Ji Ai Genetics and IVF Institute, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China
- Research Units of Embryo Original Diseases, Chinese Academy of Medical Sciences, Shanghai, China
| | - Jie Li
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China
- Shanghai Ji Ai Genetics and IVF Institute, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Songchang Chen
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China
- Shanghai Ji Ai Genetics and IVF Institute, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Chenming Xu
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China
- Shanghai Ji Ai Genetics and IVF Institute, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Hefeng Huang
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China
- Research Units of Embryo Original Diseases, Chinese Academy of Medical Sciences, Shanghai, China
- *Correspondence: Hefeng Huang, ; Li Jin,
| | - Li Jin
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China
- Shanghai Ji Ai Genetics and IVF Institute, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
- *Correspondence: Hefeng Huang, ; Li Jin,
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14
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Deng H, Zhang Y, Ding J, Wang F. Detection of Very Low-Level Somatic Mosaic COL4A5 Splicing Variant in Asymptomatic Female Using Droplet Digital PCR. Front Med (Lausanne) 2022; 9:847056. [PMID: 35360741 PMCID: PMC8963732 DOI: 10.3389/fmed.2022.847056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Accepted: 02/09/2022] [Indexed: 12/02/2022] Open
Abstract
Background Alport syndrome is a hereditary glomerulopathy featured by haematuria, proteinuria, and progressive renal failure. X-linked Alport syndrome (XLAS) due to COL4A5 disease-causing variants is the most common form. In the case of XLAS resulting from 10–18% presumed de novo COL4A5 disease-causing variants, there are only a few studies for mosaicism in the probands or parents. Very low-level (<1.0%) somatic mosaicism for COL4A5 disease-causing variants has not been published. Materials and Methods Chinese XLAS families with suspected parental mosaicism were enrolled in the present study to evaluate the forms of mosaicism, to offer more appropriate genetic counseling. PCR and direct sequencing were used to detect COL4A5 disease-causing variants harbored by the affected probands in parental multi-tissue DNAs (peripheral blood, urine sediments, saliva, hair), and droplet digital PCR (ddPCR) was used to quantify the mutant COL4A5 allelic fractions in parental different samples such as peripheral blood, saliva, and urine sediments. Results A Chinese asymptomatic female with suspected somatic and germline mosaicism was enrolled in the present study. She gave birth to two boys with XLAS caused by a hemizygous disease-causing variant c. 2245-1G>A in COL4A5 (NM_033380) intron 28, whereas this disease-causing variant was not detected in genomic DNA extracted from peripheral blood leukocytes in the woman using Sanger sequencing. She had multiple normal urine test results, and continuous linear immunofluorescence staining of α2 (IV) and α5 (IV) chains of skin tissue. Sanger sequencing demonstrated that COL4A5 disease-causing variant c. 2245-1G>A was not detected in her genomic DNAs isolated from urine sediments, saliva, and hair roots. Using ddPCR, the wild-type and mutant-type (c.2245-1G>A) COL4A5 was identified in the female's genomic DNAs isolated from peripheral blood, saliva, and urine sediments. The mutant allelic fractions in these tissues were 0.26% (peripheral blood), 0.73% (saliva), and 1.39% (urine), respectively. Conclusions Germline and very low-level somatic mosaicism for a COL4A5 splicing variant was detected in an asymptomatic female, which highlights that parental mosaicism should be excluded when a COL4A5 presumed de novo disease-causing variant is detected.
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15
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Frisk S, Wachtmeister A, Laurell T, Lindstrand A, Jäntti N, Malmgren H, Lagerstedt-Robinson K, Tesi B, Taylan F, Nordgren A. Detection of germline mosaicism in fathers of children with intellectual disability syndromes caused by de novo variants. Mol Genet Genomic Med 2022; 10:e1880. [PMID: 35118825 PMCID: PMC9000944 DOI: 10.1002/mgg3.1880] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 12/21/2021] [Accepted: 01/14/2022] [Indexed: 12/03/2022] Open
Abstract
Background De novo variants are a common cause to rare intellectual disability syndromes, associated with low recurrence risk. However, when such variants occur pre‐zygotically in parental germ cells, the recurrence risk might be higher. Still, the recurrence risk estimates are mainly based on empirical data and the prevalence of germline mosaicism is often unknown. Methods To establish the prevalence of mosaicism in parents of children with intellectual disability syndromes caused by de novo variants, we performed droplet digital PCR on DNA extracted from blood (43 trios), and sperm (31 fathers). Results We detected low‐level mosaicism in sperm‐derived DNA but not in blood in the father of a child with Kleefstra syndrome caused by an EHMT1 variant. Additionally, we found a higher level of paternal mosaicism in sperm compared to blood in the father of a child with Gillespie syndrome caused by an ITPR1 variant. Conclusion By employing droplet digital PCR, we detected paternal germline mosaicism in two intellectual disability syndromes. In both cases, the mosaicism level was higher in sperm than blood, indicating that analysis of blood alone may underestimate germline mosaicism. Therefore, sperm analysis can be clinically useful to establish the recurrence risk for parents and improve genetic counselling.
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Affiliation(s)
- Sofia Frisk
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Alexandra Wachtmeister
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Tobias Laurell
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Hand Surgery, Södersjukhuset, Stockholm, Sweden
| | - Anna Lindstrand
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Nina Jäntti
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Helena Malmgren
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Kristina Lagerstedt-Robinson
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Bianca Tesi
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Fulya Taylan
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Ann Nordgren
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
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16
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Rydzanicz M, Glinkowski W, Walczak A, Koppolu A, Kostrzewa G, Gasperowicz P, Pollak A, Stawiński P, Płoski R. Postzygotic mosaicism of a novel PTPN11 mutation in monozygotic twins discordant for metachondromatosis. Am J Med Genet A 2022; 188:1482-1487. [PMID: 35112464 DOI: 10.1002/ajmg.a.62670] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 12/16/2021] [Accepted: 01/11/2022] [Indexed: 01/05/2023]
Abstract
Genetic mosaicism caused by postzygotic mutations is of a great interest due to its role in human disease. Monozygotic twins arising from a single zygote are considered as genetically identical, and any differences likely to be caused by postzygotic events. Thus, phenotypically discordant monozygotic twins offer a unique opportunity to study genotype-phenotype correlation. Here, we present a three-generation family starting from a pair of monozygotic twins discordant for metachondromatosis due to postzygotic p.(Gln175His) variant in the PTPN11 gene. Both phenotypically discordant monozygotic twins harbor p.(Gln175His), however significant differences in mosaic ratio is observed not only between twins, but also within different tissue types within one individual. Phenotypic manifestation of p.(Gln175His) in examined family clearly depends on allele variant fraction (VAF). Individuals harboring constitutional mutation (VAF 50%) present typical metachondromatosis. Milder phenotype is observed in twin harboring high-level mosaicism in the tissue of ectodermal origin (VAF 45%), but not in a blood (VAF 5%). Finally, her twin sister harboring low-level mosaicism in blood (VAF 2%) and nonblood (VAF 12%) tissues is phenotypically normal. Our results provide insights into biological role of mosaicism in disease and further support the usefulness of nonblood tissues as an optimal source of DNA for the identification of postzygotic mutations in phenotypically discordant monozygotic twins.
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Affiliation(s)
| | - Wojciech Glinkowski
- Center of Excellence "TeleOrto" for Telediagnostics and Treatment of Disorders and Injuries of the Locomotor System, Department of Medical Informatics and Telemedicine, Medical University of Warsaw, Warsaw, Poland
| | - Anna Walczak
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Agnieszka Koppolu
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland.,Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Grażyna Kostrzewa
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Piotr Gasperowicz
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Agnieszka Pollak
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Piotr Stawiński
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Rafał Płoski
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
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17
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Çitli Ş, Serdaroglu E. Maternal Germline Mosaicism of a de Novo TUBB2B Mutation Leads to Complex Cortical Dysplasia in Two Siblings. Fetal Pediatr Pathol 2022; 41:155-165. [PMID: 32281916 DOI: 10.1080/15513815.2020.1753270] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Introduction: Complex cortical dysplasia with other brain malformations-7 (a.k.a. polymicrogyria) caused by mutations in TUBB2B gene is a clinically heterogeneous condition. Case report: We report two siblings with polymicrogyria. Brain MRI showed polymicrogyria, small brainstem, thin corpus callosum and fused basal ganglia. Karyotypes and chromosomal microarray analysis were normal. By whole exome sequencing, there were a de novo variant of c.728C > T (p.P243L) in both siblings and a common single nucleotide polymorphism (SNP) (c.718C > T) in both siblings and the mother. Seminal DNA analysis obtained from father was normal. Conclusion: Maternal germline mosaicism was considered because the sequencing result of the father's sperm was normal, two siblings had the same disease, and both patients and mother had the same SNP.
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Affiliation(s)
- Şenol Çitli
- Medical Genetics, Gaziosmanpasa University Medical Faculty, Tokat, Turkey
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18
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Cook CB, Armstrong L, Boerkoel CF, Clarke LA, du Souich C, Demos MK, Gibson WT, Gill H, Lopez E, Patel MS, Selby K, Abu-Sharar Z, Elliott AM, Friedman JM. Somatic mosaicism detected by genome-wide sequencing in 500 parent-child trios with suspected genetic disease: clinical and genetic counseling implications. Cold Spring Harb Mol Case Stud 2021; 7:mcs.a006125. [PMID: 34697084 PMCID: PMC8751411 DOI: 10.1101/mcs.a006125] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 10/13/2021] [Indexed: 01/28/2023] Open
Abstract
Identifying genetic mosaicism is important in establishing a diagnosis, assessing recurrence risk, and providing accurate genetic counseling. Next-generation sequencing has allowed for the identification of mosaicism at levels below those detectable by conventional Sanger sequencing or chromosomal microarray analysis. The CAUSES Clinic was a pediatric translational trio-based genome-wide (exome or genome) sequencing study of 500 families (531 children) with suspected genetic disease at BC Children's and Women's Hospitals. Here we present 12 cases of apparent mosaicism identified in the CAUSES cohort: nine cases of parental mosaicism for a disease-causing variant found in a child and three cases of mosaicism in the proband for a de novo variant. In six of these cases, there was no evidence of mosaicism on Sanger sequencing—the variant was not detected on Sanger sequencing in three cases, and it appeared to be heterozygous in three others. These cases are examples of six clinical manifestations of mosaicism: a proband with classical clinical features of mosaicism (e.g., segmental abnormalities of skin pigmentation or asymmetrical growth of bilateral body parts), a proband with unusually mild manifestations of a disease, a mosaic proband who is clinically indistinguishable from the constitutive phenotype, a mosaic parent with no clinical features of the disease, a mosaic parent with mild manifestations of the disease, and a family in which both parents are unaffected and two siblings have the same disease-causing constitutional mutation. Our data demonstrate the importance of considering the possibility of mosaicism whenever exome or genome sequencing is performed and that its detection via genome-wide sequencing can permit more accurate genetic counseling.
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Affiliation(s)
- Courtney B Cook
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada V6H 3N1
| | - Linlea Armstrong
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada V6H 3N1.,BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada V5Z 4H4
| | - Cornelius F Boerkoel
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada V6H 3N1
| | - Lorne A Clarke
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada V6H 3N1
| | - Christèle du Souich
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada V6H 3N1.,BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada V5Z 4H4
| | - Michelle K Demos
- Division of Neurology, Department of Pediatrics, BC Children's Hospital, Vancouver, British Columbia, Canada V6H 0B3
| | - William T Gibson
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada V6H 3N1.,BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada V5Z 4H4
| | - Harinder Gill
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada V6H 3N1
| | - Elena Lopez
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada V6H 3N1
| | - Millan S Patel
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada V6H 3N1
| | - Kathryn Selby
- Division of Neurology, Department of Pediatrics, BC Children's Hospital, Vancouver, British Columbia, Canada V6H 0B3
| | - Ziad Abu-Sharar
- Division of Neurology, Department of Pediatrics, BC Children's Hospital, Vancouver, British Columbia, Canada V6H 0B3
| | | | - Alison M Elliott
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada V6H 3N1.,BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada V5Z 4H4.,Women's Health Research Institute, Vancouver, British Columbia, Canada V6H 2N9
| | - Jan M Friedman
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada V6H 3N1.,BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada V5Z 4H4
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19
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Breuss MW, Yang X, Gleeson JG. Sperm mosaicism: implications for genomic diversity and disease. Trends Genet 2021; 37:890-902. [PMID: 34158173 PMCID: PMC9484299 DOI: 10.1016/j.tig.2021.05.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/26/2021] [Accepted: 05/27/2021] [Indexed: 12/18/2022]
Abstract
While sperm mosaicism has few consequences for men, the offspring and future generations are unwitting recipients of gonadal cell mutations, often yielding severe disease. Recent studies, fueled by emergent technologies, show that sperm mosaicism is a common source of de novo mutations (DNMs) that underlie severe pediatric disease as well as human genetic diversity. Sperm mosaicism can be divided into three types: Type I arises during sperm meiosis and is non-age dependent; Type II arises in spermatogonia and increases as men age; and Type III arises during paternal embryogenesis, spreads throughout the body, and contributes stably to sperm throughout life. Where Types I and II confer little risk of recurrence, Type III may confer identifiable risk to future offspring. These mutations are likely to be the single largest contributor to human genetic diversity. New sequencing approaches may leverage this framework to evaluate and reduce disease risk for future generations.
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Affiliation(s)
- Martin W Breuss
- Department of Pediatrics, Section of Genetics and Metabolism, University of Colorado School of Medicine, Aurora, CO, USA
| | - Xiaoxu Yang
- Rady Children's Institute for Genomic Medicine, Department of Neurosciences, University of California, San Diego, CA, USA
| | - Joseph G Gleeson
- Rady Children's Institute for Genomic Medicine, Department of Neurosciences, University of California, San Diego, CA, USA.
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20
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Yang X, Breuss MW, Xu X, Antaki D, James KN, Stanley V, Ball LL, George RD, Wirth SA, Cao B, Nguyen A, McEvoy-Venneri J, Chai G, Nahas S, Van Der Kraan L, Ding Y, Sebat J, Gleeson JG. Developmental and temporal characteristics of clonal sperm mosaicism. Cell 2021; 184:4772-4783.e15. [PMID: 34388390 PMCID: PMC8496133 DOI: 10.1016/j.cell.2021.07.024] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 05/12/2021] [Accepted: 07/14/2021] [Indexed: 01/07/2023]
Abstract
Throughout development and aging, human cells accumulate mutations resulting in genomic mosaicism and genetic diversity at the cellular level. Mosaic mutations present in the gonads can affect both the individual and the offspring and subsequent generations. Here, we explore patterns and temporal stability of clonal mosaic mutations in male gonads by sequencing ejaculated sperm. Through 300× whole-genome sequencing of blood and sperm from healthy men, we find each ejaculate carries on average 33.3 ± 12.1 (mean ± SD) clonal mosaic variants, nearly all of which are detected in serial sampling, with the majority absent from sampled somal tissues. Their temporal stability and mutational signature suggest origins during embryonic development from a largely immutable stem cell niche. Clonal mosaicism likely contributes a transmissible, predicted pathogenic exonic variant for 1 in 15 men, representing a life-long threat of transmission for these individuals and a significant burden on human population health.
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Affiliation(s)
- Xiaoxu Yang
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Martin W Breuss
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Xin Xu
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Danny Antaki
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Kiely N James
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Valentina Stanley
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Laurel L Ball
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Renee D George
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Sara A Wirth
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Beibei Cao
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - An Nguyen
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Jennifer McEvoy-Venneri
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Guoliang Chai
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Shareef Nahas
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | | | - Yan Ding
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Jonathan Sebat
- Beyster Center for Genomics of Psychiatric Diseases, University of California, San Diego, La Jolla, CA 92093, USA; Department of Psychiatry, University of California, San Diego, La Jolla, CA 92093, USA; Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Joseph G Gleeson
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA.
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21
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Jukkarwala A, Menon RN, Sunesh ER, Radhakrishnan A. Electroclinical Phenotype-Genotype Homogeneity in Drug-Resistant "Generalized" Tonic-Clonic Seizures of Early Childhood. Clin EEG Neurosci 2021; 52:371-375. [PMID: 32880473 DOI: 10.1177/1550059420953735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
PURPOSE Children with refractory focal to bilateral tonic-clonic seizures, despite normal high-resolution imaging, are often not subjected to genetic tests due to the costs involved and instead undergo multimodality presurgical evaluation targeted at delineating a focal onset. The objective of this study was to ascertain genotype-phenotype correlations in this group of patients. METHOD An online hospital database search was conducted for children who presented in 2019 with drug-resistant epilepsy dominated by nonlateralizing focal-onset/rapid generalized (bilateral) tonic-clonic seizures (GTCS), subjected to presurgical evaluation and subsequent genetic testing due to absence of a clear focus hypothesis. RESULTS Phenotypic homogeneity was apparent in 3 children who had onset in infancy with drug-resistant GTCS (predominantly unprovoked and occasionally fever provoked) and subsequent delayed development. 3-Tesla magnetic resonance imaging (MRI) scans were negative and video EEG documented a homogeneous pattern of multifocal and/or generalized epileptiform discharges with phenomenology favoring probable focal-onset/generalized-onset bilateral tonic-clonic seizures. All 3 tested positive for SCN1A gene variants (heterozygous missense substitution variants in 2 children, one of which was novel and a novel duplication in one that led to frameshift and premature truncation of the protein), suggestive of SCN1A-mediated epilepsy. This electroclinical profile constituted 3 out of 25 patients with SCN1A-epilepsy phenotypes at our center. CONCLUSIONS These cases suggest that children with early-onset drug-resistant "generalized" epilepsy are likely to have a genetic basis although the presentation may not be typical of Dravet syndrome. Hence, genetic testing for SCN1A variants is recommended in children with drug-resistant MRI negative focal-onset/generalized-onset bilateral tonic-clonic seizures before subjecting them to exhaustive presurgical workup and to guide appropriate treatment and prognostication.
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Affiliation(s)
- Anis Jukkarwala
- Geetanjali Medical College & Hospital, Udaipur, Rajasthan, India
| | - Ramshekhar N Menon
- Sree Chitra Tirunal Institute for Medical Sciences & Technology, Trivandrum, Kerala, India
| | - E R Sunesh
- Sree Chitra Tirunal Institute for Medical Sciences & Technology, Trivandrum, Kerala, India
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22
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Xi N, Song X, Wang XY, Qin SF, He GN, Sun LL, Chen XM. 2+0 CYP21A2 deletion carrier — a limitation of the genetic testing and counseling: A case report. World J Clin Cases 2021; 9:6789-6797. [PMID: 34447826 PMCID: PMC8362542 DOI: 10.12998/wjcc.v9.i23.6789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 03/04/2021] [Accepted: 06/28/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND CYP21A2 gene mutations may all cause reduction or loss of 21-hydroxylase activity, leading to development of congenital adrenal hyperplasia (CAH) with different clinical phenotypes. For families with CAH children, genetic testing of the parents and genetic counseling are recommended to assess the risk of recurrence.
CASE SUMMARY We report a case of CAH with a high suspicion before delivery. The risk of the child suffering from CAH during the pregnancy had been underestimated due to the deviation of genetic counseling and genetic testing results. Our report confirmed a CYP21A2 homozygous deletion in this case, CYP21A2 heterozygous deletion in the mother, and a rare 2+0 CYP21A2 deletion in the father.
CONCLUSION It is important to analyze the distribution of CYP21A2 gene in the two alleles of parents of children with CAH.
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Affiliation(s)
- Na Xi
- Department of Medical Genetics and Prenatal Diagnosis, Sichuan Provincial Hospital for Women and Children, Chengdu 610045, Sichuan Province, China
| | - Xiao Song
- Department of Medical Genetics and Prenatal Diagnosis, Sichuan Provincial Hospital for Women and Children, Chengdu 610045, Sichuan Province, China
| | - Xue-Yan Wang
- Department of Medical Genetics and Prenatal Diagnosis, Sichuan Provincial Hospital for Women and Children, Chengdu 610045, Sichuan Province, China
| | - Sheng-Fang Qin
- Department of Medical Genetics and Prenatal Diagnosis, Sichuan Provincial Hospital for Women and Children, Chengdu 610045, Sichuan Province, China
| | - Guan-Nan He
- Department of Ultrasound, Sichuan Provincial Hospital for Women and Children, Chengdu 610045, Sichuan Province, China
| | - Ling-Ling Sun
- Department of Medical Genetics and Prenatal Diagnosis, Sichuan Provincial Hospital for Women and Children, Chengdu 610045, Sichuan Province, China
| | - Xi-Min Chen
- Department of Medical Genetics and Prenatal Diagnosis, Sichuan Provincial Hospital for Women and Children, Chengdu 610045, Sichuan Province, China
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23
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Pan N, Chen S, Cai X, Li J, Yu T, Huang HF, Zhang J, Xu C. Low-level germline mosaicism of a novel SMARCA2 missense variant: Expanding the phenotypic spectrum and mode of genetic transmission. Mol Genet Genomic Med 2021; 9:e1763. [PMID: 34296532 PMCID: PMC8457699 DOI: 10.1002/mgg3.1763] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 07/06/2021] [Accepted: 07/08/2021] [Indexed: 12/02/2022] Open
Abstract
Background Nicolaides–Baraitser syndrome (NCBRS) is a severe neurodevelopmental disorder with multiple abnormalities. To date, all pathogenic variants in SMARCA2 causing NCBRS are de novo and most are missense variants located in the ATPase domain of SMARCA2 protein. Methods In this study, a familial trio whole‐exome sequencing was performed on the proband presenting with intellectual disability, early‐onset epilepsy, and autistic features. A novel missense variant c.553C>G (p.Gln185Glu) in SMARCA2 was identified, which is located in the QLQ domain. The same variant was subsequently also found in the mother's ongoing pregnancy. Samples from accessible tissues such as saliva and sperm other than blood were collected from the parents, and the detection of the target variant was performed by amplicon‐based deep sequencing. Results Low‐level mosaicism of the target variant c.553C>G (p.Gln185Glu) was detected in the father's sperm with allele fraction of 2.8% by amplicon‐based deep sequencing, which was not detected in either parents’ blood or saliva specimens. Heterozygosity of this variant was confirmed in the proband. Conclusion This is the first report of paternal germline mosaicism for a SMARCA2 disease‐causing variant. In addition, the missense variant c.553C>G (p.Gln185Glu) in the QLQ domain causes mainly neurological and developmental phenotypes with unremarkable characteristic facial features and limb abnormalities. Our findings expand the phenotypic spectrum and mode of genetic transmission associated with the SMARCA2 variants.
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Affiliation(s)
- Nina Pan
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China
| | - Songchang Chen
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China.,State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, China
| | - Xiaoqiang Cai
- Beijing BioBiggen Technology Co., Ltd.,, Beijing, China
| | - Jianli Li
- Beijing BioBiggen Technology Co., Ltd.,, Beijing, China
| | - Tao Yu
- Beijing BioBiggen Technology Co., Ltd.,, Beijing, China
| | - He-Feng Huang
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China.,Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China.,Clinical Research Center for Birth Defects and Rare Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Key Laboratory of Reproductive Genetics, Ministry of Education, Zhejiang University, Hangzhou, China.,Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Jinglan Zhang
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China.,Beijing BioBiggen Technology Co., Ltd.,, Beijing, China.,Clinical Research Center for Birth Defects and Rare Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Chenming Xu
- Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China.,Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China
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24
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Shu L, Zhang Q, Tian Q, Yang S, Peng X, Mao X, Yang L, Du J, Wang H. Parental mosaicism in de novo neurodevelopmental diseases. Am J Med Genet A 2021; 185:2119-2125. [PMID: 33851778 DOI: 10.1002/ajmg.a.62174] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 01/28/2021] [Accepted: 02/26/2021] [Indexed: 11/12/2022]
Abstract
Neurodevelopmental diseases are increasingly recognized to be caused by "de novo" variants with the expanding use of next-generation sequencing. The apparent de novo variants may actually be low-level hereditary parental mosaic variants, which could increase the recurrence risk of disease by >50% and is thought to be an underappreciated cause of neurodevelopmental diseases. Our study aimed to investigate the frequency of parental mosaicism in "de novo" neurodevelopmental diseases. A total of 237 patients (and parents) with neurodevelopmental diseases carrying apparent de novo pathogenic or likely pathogenic variants were recruited consecutively. Deep next-generation sequencing was performed on parental samples to identify parental mosaicism. Fourteen parental disease-causing mosaicism variants (3.0%) in 11 genes were detected with alternate allele frequency (AAF) 0.22%-34%. Three parents showed milder clinical phenotypes than their offspring with relatively high AAF (23.33%, 25%, 34% separately). One recurrent variant was identified prenatally. A review of cohort study on parental mosaicism in neurodevelopmental diseases was performed. Our study highlights that identifying the parental mosaic disease-causing variants especially the low-level mosaicism will contribute to improving the accuracy of genetic counseling and prenatal diagnosis for reproductive risks.
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Affiliation(s)
- Li Shu
- Department of Medical Genetics, Maternal and Child Health Hospital of Hunan Province, Changsha, China.,National Health Commission Key Laboratory of Birth Defects Research, Prevention and Treatment, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, China.,Department of School of Life Sciences, Central South University, Changsha, China
| | - Qianjun Zhang
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China.,Department of Medical Genetics, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China.,NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Central South University, Changsha, China
| | - Qi Tian
- Department of Medical Genetics, Maternal and Child Health Hospital of Hunan Province, Changsha, China.,National Health Commission Key Laboratory of Birth Defects Research, Prevention and Treatment, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, China
| | - Sai Yang
- Department of Neurology, Children's Hospital of Hunan Province, Changsha, China
| | - Xingwang Peng
- Marketing Management Center, AmCare Genomics Laboratory, Guangzhou, China
| | - Xiao Mao
- Department of Medical Genetics, Maternal and Child Health Hospital of Hunan Province, Changsha, China.,National Health Commission Key Laboratory of Birth Defects Research, Prevention and Treatment, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, China
| | - Liming Yang
- Department of Neurology, Children's Hospital of Hunan Province, Changsha, China
| | - Juan Du
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China.,Department of Medical Genetics, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China.,NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Central South University, Changsha, China
| | - Hua Wang
- Department of Medical Genetics, Maternal and Child Health Hospital of Hunan Province, Changsha, China.,National Health Commission Key Laboratory of Birth Defects Research, Prevention and Treatment, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, China
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25
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Wang Y, Bae T, Thorpe J, Sherman MA, Jones AG, Cho S, Daily K, Dou Y, Ganz J, Galor A, Lobon I, Pattni R, Rosenbluh C, Tomasi S, Tomasini L, Yang X, Zhou B, Akbarian S, Ball LL, Bizzotto S, Emery SB, Doan R, Fasching L, Jang Y, Juan D, Lizano E, Luquette LJ, Moldovan JB, Narurkar R, Oetjens MT, Rodin RE, Sekar S, Shin JH, Soriano E, Straub RE, Zhou W, Chess A, Gleeson JG, Marquès-Bonet T, Park PJ, Peters MA, Pevsner J, Walsh CA, Weinberger DR, Vaccarino FM, Moran JV, Urban AE, Kidd JM, Mills RE, Abyzov A. Comprehensive identification of somatic nucleotide variants in human brain tissue. Genome Biol 2021; 22:92. [PMID: 33781308 PMCID: PMC8006362 DOI: 10.1186/s13059-021-02285-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 02/01/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Post-zygotic mutations incurred during DNA replication, DNA repair, and other cellular processes lead to somatic mosaicism. Somatic mosaicism is an established cause of various diseases, including cancers. However, detecting mosaic variants in DNA from non-cancerous somatic tissues poses significant challenges, particularly if the variants only are present in a small fraction of cells. RESULTS Here, the Brain Somatic Mosaicism Network conducts a coordinated, multi-institutional study to examine the ability of existing methods to detect simulated somatic single-nucleotide variants (SNVs) in DNA mixing experiments, generate multiple replicates of whole-genome sequencing data from the dorsolateral prefrontal cortex, other brain regions, dura mater, and dural fibroblasts of a single neurotypical individual, devise strategies to discover somatic SNVs, and apply various approaches to validate somatic SNVs. These efforts lead to the identification of 43 bona fide somatic SNVs that range in variant allele fractions from ~ 0.005 to ~ 0.28. Guided by these results, we devise best practices for calling mosaic SNVs from 250× whole-genome sequencing data in the accessible portion of the human genome that achieve 90% specificity and sensitivity. Finally, we demonstrate that analysis of multiple bulk DNA samples from a single individual allows the reconstruction of early developmental cell lineage trees. CONCLUSIONS This study provides a unified set of best practices to detect somatic SNVs in non-cancerous tissues. The data and methods are freely available to the scientific community and should serve as a guide to assess the contributions of somatic SNVs to neuropsychiatric diseases.
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Affiliation(s)
- Yifan Wang
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Avenue, Ann Arbor, MI, 48109, USA
| | - Taejeong Bae
- Department of Health Sciences Research, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA
| | - Jeremy Thorpe
- Program in Biochemistry, Cellular and Molecular Biology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Maxwell A Sherman
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- MIT Department of Electrical Engineering and Computer Science, Cambridge, MA, USA
| | - Attila G Jones
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Sean Cho
- Department of Neurology, Kennedy Krieger Institute, Baltimore, MD, 21205, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- Present Address: Arcus Biosciences, Hayward, CA, 94545, USA
| | | | - Yanmei Dou
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Javier Ganz
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, 02115, USA
- Departments of Neurology and Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Alon Galor
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Irene Lobon
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), PRBB, 08003, Barcelona, Catalonia, Spain
- Department of Cell Biology, Physiology and Immunology, and Institute of Neurosciences, University of Barcelona, 08028, Barcelona, Spain
| | - Reenal Pattni
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Chaggai Rosenbluh
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Simone Tomasi
- Child Study Center, Yale University, New Haven, CT, 06520, USA
| | - Livia Tomasini
- Child Study Center, Yale University, New Haven, CT, 06520, USA
| | - Xiaoxu Yang
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Bo Zhou
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Schahram Akbarian
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Laurel L Ball
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Sara Bizzotto
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, 02115, USA
- Departments of Neurology and Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Sarah B Emery
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Ryan Doan
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, 02115, USA
- Departments of Neurology and Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Liana Fasching
- Child Study Center, Yale University, New Haven, CT, 06520, USA
| | - Yeongjun Jang
- Department of Health Sciences Research, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA
| | - David Juan
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), PRBB, 08003, Barcelona, Catalonia, Spain
| | - Esther Lizano
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), PRBB, 08003, Barcelona, Catalonia, Spain
| | - Lovelace J Luquette
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - John B Moldovan
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Rujuta Narurkar
- Lieber Institute for Brain Development, Baltimore, MD, 21205, USA
| | - Matthew T Oetjens
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Rachel E Rodin
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, 02115, USA
- Departments of Neurology and Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Shobana Sekar
- Department of Health Sciences Research, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA
| | - Joo Heon Shin
- Lieber Institute for Brain Development, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Eduardo Soriano
- Department of Cell Biology, Physiology and Immunology, and Institute of Neurosciences, University of Barcelona, 08028, Barcelona, Spain
- Vall d'Hebron Institut de Recerca, 08035, Barcelona, Spain
- Centro de Investigación en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 28031, Madrid, Spain
- ICREA Academia, 08010 Barcelona, Spain
| | - Richard E Straub
- Lieber Institute for Brain Development, Baltimore, MD, 21205, USA
| | - Weichen Zhou
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Avenue, Ann Arbor, MI, 48109, USA
| | - Andrew Chess
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technologies, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joseph G Gleeson
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Tomas Marquès-Bonet
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), PRBB, 08003, Barcelona, Catalonia, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), 08010, Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), 08036, Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, 08193, Cerdanyola del Vallès, Barcelona, Spain
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | | | - Jonathan Pevsner
- Department of Neurology, Kennedy Krieger Institute, Baltimore, MD, 21205, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Christopher A Walsh
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, 02115, USA
- Departments of Neurology and Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Daniel R Weinberger
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- Lieber Institute for Brain Development, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Flora M Vaccarino
- Child Study Center, Yale University, New Haven, CT, 06520, USA
- Department of Neuroscience, Yale University, New Haven, 06520, CT, USA
| | - John V Moran
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Alexander E Urban
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Tashia and John Morgridge Faculty Scholar, Stanford Child Health Research Institute, Stanford, CA, 94305, USA
| | - Jeffrey M Kidd
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Avenue, Ann Arbor, MI, 48109, USA
| | - Ryan E Mills
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Avenue, Ann Arbor, MI, 48109, USA
| | - Alexej Abyzov
- Department of Health Sciences Research, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA.
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26
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Chalas C, Receveur A, Frydman N, Massin N, Tachdjian G, Drouineaud V, Benachi A, Patrat C, Petit FM. A case of germline mosaicism for a 7q32.1q33 deletion in a sperm donor: consequences on pregnancy follow-up and recommendations. Basic Clin Androl 2020; 30:14. [PMID: 33024563 PMCID: PMC7532087 DOI: 10.1186/s12610-020-00113-5] [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: 05/20/2020] [Accepted: 08/24/2020] [Indexed: 01/23/2023] Open
Abstract
Background Germline mosaicism is considered to be a rare event. However, its occurrence is underestimated due to the limited availability of germ cells. The genomic variations that underlie this phenomenon comprise single nucleotide polymorphism (SNPs), copy number variations (CNVs) and aneuploidies. In the case of CNVs, deletions are more frequent in the paternal germline while duplications are more commonly maternal in origin. Germline mosaicism increases with paternal age as the risk of SNPs increase with the number of germ cell divisions. We here report a case of germline mosaicism in the spermatozoa of a donor that resulted in one pathological pregnancy. Results Straws from the same sperm donor were provided to seven recipient couples, resulting in four pregnancies. Second trimester ultrasound analysis revealed bilateral talipes equinovarus associated with growth retardation in one of these pregnancies. Array-comparative genomic hybridization (CGH) carried out after amniocentesis revealed a 4 Mb deletion in the 7q32.1q33 region. The blood karyotypes and array-CGHs were normal in the mother, as well as in the donor. However, the microsatellite profile indicated a paternal origin. Fluorescent in situ hybridization (FISH) analysis of the donor’s spermatozoa revealed the same chromosomal rearrangements in 12% of the spermatozoa population. Due to the documented risk of mental retardation associated with genomic rearrangements in the same region, the couple decided to terminate the pregnancy. Amniocentesis was performed in the other couples, which yielded normal FISH analysis results. Conclusions Several cases of germline mosaicism have been reported to date, but their frequency is probably underestimated. Moreover, it is important to note that germline mosaicism cannot be ruled out by conventional cytogenetic screening of blood cells. This case highlights the need for close follow-up of every pregnancy obtained through gamete donation, given that the occurrence of germline mosaicism may have major consequences when multiple pregnancies are obtained concomitantly.
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Affiliation(s)
- Celine Chalas
- Laboratoire d'Histologie-Embryologie-Biologie de la Reproduction - CECOS, Hôpital Cochin, AP-HP, Centre Université de Paris, F-75014 Paris, France
| | - Aline Receveur
- Laboratoire de cytogénomique, Hôpital Antoine Béclère, AP-HP, Université Paris Saclay, cedex, F-92141 Clamart, France
| | - Nelly Frydman
- Laboratoire d'Histologie-Embryologie-Cytogenetique- CECOS, Hôpital Antoine Béclère, AP-HP, Université Paris Saclay, cedex, F-92141 Clamart, France.,Faculté de médecine de Bicêtre, Université Paris-Saclay, F-94270 Le Kremlin Bicêtre, France
| | - Nathalie Massin
- Service de gynécologie et obstétrique, Centre Hospitalier Intercommunal, F-94010 Créteil, France
| | - Gerard Tachdjian
- Laboratoire de cytogénomique, Hôpital Antoine Béclère, AP-HP, Université Paris Saclay, cedex, F-92141 Clamart, France.,Laboratoire d'Histologie-Embryologie-Cytogenetique- CECOS, Hôpital Antoine Béclère, AP-HP, Université Paris Saclay, cedex, F-92141 Clamart, France.,Faculté de médecine de Bicêtre, Université Paris-Saclay, F-94270 Le Kremlin Bicêtre, France
| | - Veronique Drouineaud
- Laboratoire d'Histologie-Embryologie-Biologie de la Reproduction - CECOS, Hôpital Cochin, AP-HP, Centre Université de Paris, F-75014 Paris, France
| | - Alexandra Benachi
- Faculté de médecine de Bicêtre, Université Paris-Saclay, F-94270 Le Kremlin Bicêtre, France.,Service de gynécologie et obstétrique, Hôpital Antoine Béclère, AP-HP, Université Paris Saclay, cedex, F-92141 Clamart, France
| | - Catherine Patrat
- Laboratoire d'Histologie-Embryologie-Biologie de la Reproduction - CECOS, Hôpital Cochin, AP-HP, Centre Université de Paris, F-75014 Paris, France.,Université de Paris, U 1016, Institut Cochin, F-75014 Paris, France
| | - Francois Michael Petit
- Laboratoire de génétique moléculaire, Hôpital Antoine Béclère, AP-HP, Université Paris Saclay, cedex, F-92141 Clamart, France
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27
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Gong P, Jiao X, Zhang Y, Yang Z. Complex Mosaicism of Two Distinct Mutations in a Female Patient With KCNA2-Related Encephalopathy: A Case Report. Front Genet 2020; 11:911. [PMID: 32903602 PMCID: PMC7438874 DOI: 10.3389/fgene.2020.00911] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 07/22/2020] [Indexed: 12/29/2022] Open
Abstract
KCNA2 gene mutations were described to cause a new molecular entity within the developmental and epileptic or epileptic encephalopathies. Here, we firstly reported a patient with an unusual mosaicism for KCNA2, presenting two distinct mosaic missense mutations at the same loci. Clinical trio-based whole-exome sequencing using next-generation sequencing (NGS) revealed two novel mutations in KCNA2: c.1225A > T [p.(Ile409Phe)] and c.1225A > C [p.(Ile409Leu)]. Both missense mutations were in mosaic status and Sanger sequencing confirmed them as de novo. The affected 5-year-old girl presented as seizures with fever sensitivity, and mild cognitive and behavioral disorders. EEG showed focal centrotemporal epileptiform discharges accompanied by nocturnal focal seizures at the age of slightly older than 5 years, more likely carrying a loss-of-function mutation of KCNA2-related phenotype. Further NGS with a mean coverage of 6950 × showed 26% (mosaic mutation reads/total reads) of the c.1225A > T mutation and 23% of the c.1225A > C mutation. The sum of their allele fractions was close to 50%, approximately equal to a heterozygous variant. The patient had no seizures for 8 months on combination of levetiracetam (18.75 mg/kg/d) and valproate (20 mg/kg/d) till the last follow-up at the age of 5 years and 11 months. Our findings highlighted the two mosaic mutations responsible for the pathogenesis of KCNA2-related encephalopathy. The patient expanded the mutational spectrum of KCNA2-related encephalopathy and provided new insight into the complex genetic disorder.
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Affiliation(s)
- Pan Gong
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Xianru Jiao
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Yuehua Zhang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Zhixian Yang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
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28
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MosaicBase: A Knowledgebase of Postzygotic Mosaic Variants in Noncancer Disease-related and Healthy Human Individuals. GENOMICS PROTEOMICS & BIOINFORMATICS 2020; 18:140-149. [PMID: 32911083 PMCID: PMC7646124 DOI: 10.1016/j.gpb.2020.05.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Revised: 03/18/2020] [Accepted: 05/31/2020] [Indexed: 12/14/2022]
Abstract
Mosaic variants resulting from postzygotic mutations are prevalent in the human genome and play important roles in human diseases. However, except for cancer-related variants, there is no collection of postzygotic mosaic variants in noncancer disease-related and healthy individuals. Here, we present MosaicBase, a comprehensive database that includes 6698 mosaic variants related to 266 noncancer diseases and 27,991 mosaic variants identified in 422 healthy individuals. Genomic and phenotypic information of each variant was manually extracted and curated from 383 publications. MosaicBase supports the query of variants with Online Mendelian Inheritance in Man (OMIM) entries, genomic coordinates, gene symbols, or Entrez IDs. We also provide an integrated genome browser for users to easily access mosaic variants and their related annotations for any genomic region. By analyzing the variants collected in MosaicBase, we find that mosaic variants that directly contribute to disease phenotype show features distinct from those of variants in individuals with mild or no phenotypes, in terms of their genomic distribution, mutation signatures, and fraction of mutant cells. MosaicBase will not only assist clinicians in genetic counseling and diagnosis but also provide a useful resource to understand the genomic baseline of postzygotic mutations in the general human population. MosaicBase is publicly available at http://mosaicbase.com/ or http://49.4.21.8:8000.
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29
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Menezes LFS, Sabiá Júnior EF, Tibery DV, Carneiro LDA, Schwartz EF. Epilepsy-Related Voltage-Gated Sodium Channelopathies: A Review. Front Pharmacol 2020; 11:1276. [PMID: 33013363 PMCID: PMC7461817 DOI: 10.3389/fphar.2020.01276] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 07/31/2020] [Indexed: 12/29/2022] Open
Abstract
Epilepsy is a disease characterized by abnormal brain activity and a predisposition to generate epileptic seizures, leading to neurobiological, cognitive, psychological, social, and economic impacts for the patient. There are several known causes for epilepsy; one of them is the malfunction of ion channels, resulting from mutations. Voltage-gated sodium channels (NaV) play an essential role in the generation and propagation of action potential, and malfunction caused by mutations can induce irregular neuronal activity. That said, several genetic variations in NaV channels have been described and associated with epilepsy. These mutations can affect channel kinetics, modifying channel activation, inactivation, recovery from inactivation, and/or the current window. Among the NaV subtypes related to epilepsy, NaV1.1 is doubtless the most relevant, with more than 1500 mutations described. Truncation and missense mutations are the most observed alterations. In addition, several studies have already related mutated NaV channels with the electrophysiological functioning of the channel, aiming to correlate with the epilepsy phenotype. The present review provides an overview of studies on epilepsy-associated mutated human NaV1.1, NaV1.2, NaV1.3, NaV1.6, and NaV1.7.
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Affiliation(s)
- Luis Felipe Santos Menezes
- Laboratório de Neurofarmacologia, Departamento de Ciências Fisiológicas, Universidade de Brasília, Brasília, Brazil
| | - Elias Ferreira Sabiá Júnior
- Laboratório de Neurofarmacologia, Departamento de Ciências Fisiológicas, Universidade de Brasília, Brasília, Brazil
| | - Diogo Vieira Tibery
- Laboratório de Neurofarmacologia, Departamento de Ciências Fisiológicas, Universidade de Brasília, Brasília, Brazil
| | - Lilian Dos Anjos Carneiro
- Faculdade de Medicina, Centro Universitário Euro Americano, Brasília, Brazil.,Faculdade de Medicina, Centro Universitário do Planalto Central, Brasília, Brazil
| | - Elisabeth Ferroni Schwartz
- Laboratório de Neurofarmacologia, Departamento de Ciências Fisiológicas, Universidade de Brasília, Brasília, Brazil
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30
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Gambin T, Liu Q, Karolak JA, Grochowski CM, Xie NG, Wu LR, Yan YH, Cao Y, Coban Akdemir ZH, Wilson TA, Jhangiani SN, Chen E, Eng CM, Muzny D, Posey JE, Yang Y, Zhang DY, Shaw C, Liu P, Lupski JR, Stankiewicz P. Low-level parental somatic mosaic SNVs in exomes from a large cohort of trios with diverse suspected Mendelian conditions. Genet Med 2020; 22:1768-1776. [PMID: 32655138 PMCID: PMC7606563 DOI: 10.1038/s41436-020-0897-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 06/25/2020] [Accepted: 06/25/2020] [Indexed: 02/06/2023] Open
Abstract
Purpose: The goal of this study was to assess the scale of low-level parental mosaicism in exome sequencing (ES) databases. Methods: We analyzed approximately 2000 family trio ES datasets from the Baylor-Hopkins Center for Mendelian Genomics (BHCMG) and Baylor Genetics (BG). Among apparent de novo single nucleotide variants (SNVs) identified in the affected probands, we selected rare unique variants with variant allele fraction (VAF) between 30-70% in the probands and lower than 10% in one of the parents. Results: Out of 102 candidate mosaic variants validated using amplicon-based NGS, droplet digital PCR, or blocker displacement amplification, 27 (26.4%) were confirmed to be low- (VAF between 1-10%) or very low- (VAF <1%) level mosaic. Detection precision in parental samples with two or more alternate reads was 63.6% (BHCMG) and 43.6% (BG). In nine investigated individuals, we observed variability of mosaic ratios among blood, saliva, fibroblast, buccal, hair, and urine samples. Conclusion: Our computational pipeline enables robust discrimination between true and false positive candidate mosaic variants and efficient detection of low-level mosaicism in ES samples. We confirm that the presence of two or more alternate reads in the parental sample is a reliable predictor of low-level parental somatic mosaicism.
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Affiliation(s)
- Tomasz Gambin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Institute of Computer Science, Warsaw University of Technology, Warsaw, Poland.,Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | - Qian Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Justyna A Karolak
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland
| | | | - Nina G Xie
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Lucia R Wu
- Department of Bioengineering, Rice University, Houston, TX, USA
| | | | - Ye Cao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA.,Department of Obstetrics and Gynecology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Zeynep H Coban Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Theresa A Wilson
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Ed Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Christine M Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA
| | - Donna Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA
| | - David Y Zhang
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Chad Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA.,Department of Statistics, Rice University, Houston, TX, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA.,Texas Children's Hospital, Houston, TX, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Paweł Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA. .,Baylor Genetics, Houston, TX, USA.
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31
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Liu Q, Karolak JA, Grochowski CM, Wilson TA, Rosenfeld JA, Bacino CA, Lalani SR, Patel A, Breman A, Smith JL, Cheung SW, Lupski JR, Bi W, Stankiewicz P. Parental somatic mosaicism for CNV deletions - A need for more sensitive and precise detection methods in clinical diagnostics settings. Genomics 2020; 112:2937-2941. [PMID: 32387503 DOI: 10.1016/j.ygeno.2020.05.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/22/2020] [Accepted: 05/04/2020] [Indexed: 10/25/2022]
Abstract
To further assess the scale and level of parental somatic mosaicism, we queried the CMA database at Baylor Genetics. We selected 50 unrelated families where clinically relevant apparent de novo CNV-deletions were found in the affected probands. Parental blood samples screening using deletion junction-specific PCR revealed four parents with somatic mosaicism. Droplet digital PCR (ddPCR), qPCR, and amplicon-based next-generation sequencing (NGS) were applied to validate these findings. Using ddPCR levels of mosaicism ranged from undetectable to 18.5%. Amplicon-based NGS and qPCR for the father with undetectable mosaicism was able to detect mosaicism at 0.39%. In one mother, ddPCR analysis revealed 15.6%, 10.6%, 8.2%, and undetectable levels of mosaicism in her blood, buccal cells, saliva, and urine samples, respectively. Our data suggest that more sensitive and precise methods, e.g. CNV junction-specific LR-PCR, ddPCR, or qPCR may allow for a more refined assessment of the potential disease recurrence risk for an identified variant.
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Affiliation(s)
- Qian Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Justyna A Karolak
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, 60-781 Poznan, Poland
| | | | - Theresa A Wilson
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | - Carlos A Bacino
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA; Texas Children's Hospital, Houston, TX 77030, USA
| | - Seema R Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | - Ankita Patel
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | - Amy Breman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | - Janice L Smith
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | - Sau Wai Cheung
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | - Pawel Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
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32
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Highly Sensitive Blocker Displacement Amplification and Droplet Digital PCR Reveal Low-Level Parental FOXF1 Somatic Mosaicism in Families with Alveolar Capillary Dysplasia with Misalignment of Pulmonary Veins. J Mol Diagn 2020; 22:447-456. [PMID: 32036090 DOI: 10.1016/j.jmoldx.2019.12.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 10/30/2019] [Accepted: 12/11/2019] [Indexed: 12/20/2022] Open
Abstract
Detection of low-level somatic mosaicism [alternate allele fraction (AAF) ≤ 10%] in parents of affected individuals with the apparent de novo pathogenic variants enables more accurate estimate of recurrence risk. To date, only a few systematic analyses of low-level parental somatic mosaicism have been performed. Herein, highly sensitive blocker displacement amplification, droplet digital PCR, quantitative PCR, long-range PCR, and array comparative genomic hybridization were applied in families with alveolar capillary dysplasia with misalignment of pulmonary veins. We screened 18 unrelated families with the FOXF1 variant previously determined to be apparent de novo (n = 14), of unknown parental origin (n = 1), or inherited from a parent suspected to be somatic and/or germline mosaic (n = 3). We identified four (22%) families with FOXF1 parental somatic mosaic single-nucleotide variants (n = 3) and copy number variant deletion (n = 1) detected in parental blood samples and an AAF ranging between 0.03% and 19%. In one family, mosaic allele ratio in tissues originating from three germ layers ranged between <0.03% and 0.65%. Because the ratio of parental somatic mosaicism have significant implications for the recurrence risk, this study further implies the importance of a systematic screening of parental samples for low-level and very-low-level (AAF ≤ 1%) somatic mosaicism using methods that are more sensitive than those routinely applied in diagnostics.
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33
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Accurate detection of mosaic variants in sequencing data without matched controls. Nat Biotechnol 2020; 38:314-319. [PMID: 31907404 PMCID: PMC7065972 DOI: 10.1038/s41587-019-0368-8] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 11/23/2019] [Indexed: 02/07/2023]
Abstract
Detection of mosaic mutations that arise in normal development is challenging, as such mutations are typically present in only a minute fraction of cells and there is no clear matched control for removing germline variants and systematic artifacts. We present MosaicForecast, a machine-learning method that leverages read-based phasing and read-level features to accurately detect mosaic single-nucleotide variants (SNVs) and indels, achieving a multifold increase in specificity compared to existing algorithms. Using single-cell sequencing and targeted sequencing, we validated 80–90% of the mosaic SNVs and 60–80% indels detected in human brain whole-genome sequencing data. Our method should help elucidate the contribution of mosaic somatic mutations to the origin and development of disease.
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34
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Breuss MW, Antaki D, George RD, Kleiber M, James KN, Ball LL, Hong O, Mitra I, Yang X, Wirth SA, Gu J, Garcia CAB, Gujral M, Brandler WM, Musaev D, Nguyen A, McEvoy-Venneri J, Knox R, Sticca E, Botello MCC, Uribe Fenner J, Pérez MC, Arranz M, Moffitt AB, Wang Z, Hervás A, Devinsky O, Gymrek M, Sebat J, Gleeson JG. Autism risk in offspring can be assessed through quantification of male sperm mosaicism. Nat Med 2020; 26:143-150. [PMID: 31873310 PMCID: PMC7032648 DOI: 10.1038/s41591-019-0711-0] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 11/21/2019] [Indexed: 01/28/2023]
Abstract
De novo mutations arising on the paternal chromosome make the largest known contribution to autism risk, and correlate with paternal age at the time of conception. The recurrence risk for autism spectrum disorders is substantial, leading many families to decline future pregnancies, but the potential impact of assessing parental gonadal mosaicism has not been considered. We measured sperm mosaicism using deep-whole-genome sequencing, for variants both present in an offspring and evident only in father's sperm, and identified single-nucleotide, structural and short tandem-repeat variants. We found that mosaicism quantification can stratify autism spectrum disorders recurrence risk due to de novo mutations into a vast majority with near 0% recurrence and a small fraction with a substantially higher and quantifiable risk, and we identify novel mosaic variants at risk for transmission to a future offspring. This suggests, therefore, that genetic counseling would benefit from the addition of sperm mosaicism assessment.
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Affiliation(s)
- Martin W Breuss
- Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Danny Antaki
- Beyster Center for Genomics of Psychiatric Diseases, University of California, San Diego, La Jolla, CA, USA
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Renee D George
- Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Morgan Kleiber
- Beyster Center for Genomics of Psychiatric Diseases, University of California, San Diego, La Jolla, CA, USA
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Kiely N James
- Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Laurel L Ball
- Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Oanh Hong
- Beyster Center for Genomics of Psychiatric Diseases, University of California, San Diego, La Jolla, CA, USA
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Ileena Mitra
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Xiaoxu Yang
- Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Sara A Wirth
- Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Jing Gu
- Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Camila A B Garcia
- Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Madhusudan Gujral
- Beyster Center for Genomics of Psychiatric Diseases, University of California, San Diego, La Jolla, CA, USA
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - William M Brandler
- Beyster Center for Genomics of Psychiatric Diseases, University of California, San Diego, La Jolla, CA, USA
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Damir Musaev
- Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - An Nguyen
- Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Jennifer McEvoy-Venneri
- Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Renatta Knox
- Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
- Department of Child Neurology, Weill Cornell Medical College, New York, NY, USA
| | - Evan Sticca
- Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | | | - Javiera Uribe Fenner
- Child and Adolescent Mental Health Unit, Hospital Universitari Mútua de Terrassa, Barcelona, Spain
| | | | - Maria Arranz
- Fundació Docència i Recerca Mútua Terrassa, Barcelona, Spain
| | - Andrea B Moffitt
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Zihua Wang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Amaia Hervás
- Research Laboratory Unit, Fundació Docencia i Recerca Mútua Terrassa, Barcelona, Spain
| | - Orrin Devinsky
- Department of Neurology, Epilepsy Division, New York University School of Medicine, New York, NY, USA
| | - Melissa Gymrek
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Jonathan Sebat
- Beyster Center for Genomics of Psychiatric Diseases, University of California, San Diego, La Jolla, CA, USA.
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA.
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
| | - Joseph G Gleeson
- Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA, USA.
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA.
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35
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Pelorosso C, Watrin F, Conti V, Buhler E, Gelot A, Yang X, Mei D, McEvoy-Venneri J, Manent JB, Cetica V, Ball LL, Buccoliero AM, Vinck A, Barba C, Gleeson JG, Guerrini R, Represa A. Somatic double-hit in MTOR and RPS6 in hemimegalencephaly with intractable epilepsy. Hum Mol Genet 2019; 28:3755-3765. [PMID: 31411685 PMCID: PMC6935386 DOI: 10.1093/hmg/ddz194] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/30/2019] [Accepted: 07/31/2019] [Indexed: 01/19/2023] Open
Abstract
Single germline or somatic activating mutations of mammalian target of rapamycin (mTOR) pathway genes are emerging as a major cause of type II focal cortical dysplasia (FCD), hemimegalencephaly (HME) and tuberous sclerosis complex (TSC). A double-hit mechanism, based on a primary germline mutation in one allele and a secondary somatic hit affecting the other allele of the same gene in a small number of cells, has been documented in some patients with TSC or FCD. In a patient with HME, severe intellectual disability, intractable seizures and hypochromic skin patches, we identified the ribosomal protein S6 (RPS6) p.R232H variant, present as somatic mosaicism at ~15.1% in dysplastic brain tissue and ~11% in blood, and the MTOR p.S2215F variant, detected as ~8.8% mosaicism in brain tissue, but not in blood. Overexpressing the two variants independently in animal models, we demonstrated that MTOR p.S2215F caused neuronal migration delay and cytomegaly, while RPS6 p.R232H prompted increased cell proliferation. Double mutants exhibited a more severe phenotype, with increased proliferation and migration defects at embryonic stage and, at postnatal stage, cytomegalic cells exhibiting eccentric nuclei and binucleation, which are typical features of balloon cells. These findings suggest a synergistic effect of the two variants. This study indicates that, in addition to single activating mutations and double-hit inactivating mutations in mTOR pathway genes, severe forms of cortical dysplasia can also result from activating mutations affecting different genes in this pathway. RPS6 is a potential novel disease-related gene.
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Affiliation(s)
- Cristiana Pelorosso
- Paediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, Children’s Hospital A. Meyer, University of Florence, Florence 50139, Italy
| | - Françoise Watrin
- INMED, Aix-Marseille University, INSERM UMR1249, Marseille 13009, France
| | - Valerio Conti
- Paediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, Children’s Hospital A. Meyer, University of Florence, Florence 50139, Italy
| | - Emmanuelle Buhler
- INMED, Aix-Marseille University, INSERM UMR1249, Marseille 13009, France
| | - Antoinette Gelot
- Service d'Anatomie Pathologique, Hôpital Trousseau, Hôpitaux Universitaires de l'Est Parisien, Université Pierre et Marie Curie, Paris 75012, France
| | - Xiaoxu Yang
- Department of Neuroscience, Howard Hughes Medical Institute, Rady Children’s Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Davide Mei
- Paediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, Children’s Hospital A. Meyer, University of Florence, Florence 50139, Italy
| | - Jennifer McEvoy-Venneri
- Department of Neuroscience, Howard Hughes Medical Institute, Rady Children’s Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | | | - Valentina Cetica
- Paediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, Children’s Hospital A. Meyer, University of Florence, Florence 50139, Italy
| | - Laurel L Ball
- Department of Neuroscience, Howard Hughes Medical Institute, Rady Children’s Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Anna Maria Buccoliero
- Pathology Unit, Children’s Hospital A. Meyer, University of Florence, Florence 50139, Italy
| | - Antonin Vinck
- INMED, Aix-Marseille University, INSERM UMR1249, Marseille 13009, France
| | - Carmen Barba
- Paediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, Children’s Hospital A. Meyer, University of Florence, Florence 50139, Italy
| | - Joseph G Gleeson
- Department of Neuroscience, Howard Hughes Medical Institute, Rady Children’s Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Renzo Guerrini
- Paediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, Children’s Hospital A. Meyer, University of Florence, Florence 50139, Italy
- IRCCS Fondazione Stella Maris, Pisa 56126, Italy
| | - Alfonso Represa
- INMED, Aix-Marseille University, INSERM UMR1249, Marseille 13009, France
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36
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Goldmann JM, Veltman JA, Gilissen C. De Novo Mutations Reflect Development and Aging of the Human Germline. Trends Genet 2019; 35:828-839. [PMID: 31610893 DOI: 10.1016/j.tig.2019.08.005] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 08/15/2019] [Accepted: 08/28/2019] [Indexed: 01/19/2023]
Abstract
Human germline de novo mutations (DNMs) are both a driver of evolution and an important cause of genetic diseases. In the past few years, whole-genome sequencing (WGS) of parent-offspring trios has facilitated the large-scale detection and study of human DNMs, which has led to exciting discoveries. The overarching theme of all of these studies is that the DNMs of an individual are a complex mixture of mutations that arise through different biological processes acting at different times during human development and life.
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Affiliation(s)
- J M Goldmann
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA Nijmegen, The Netherlands
| | - J A Veltman
- Institute of Genetic Medicine, International Centre for Life, Newcastle University, Newcastle upon Tyne, UK; Department of Human Genetics, Donders Centre for Neuroscience, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA Nijmegen, The Netherlands
| | - C Gilissen
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA Nijmegen, The Netherlands.
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37
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Clinically-relevant postzygotic mosaicism in parents and children with developmental disorders in trio exome sequencing data. Nat Commun 2019; 10:2985. [PMID: 31278258 PMCID: PMC6611863 DOI: 10.1038/s41467-019-11059-2] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 06/12/2019] [Indexed: 12/22/2022] Open
Abstract
Mosaic genetic variants can have major clinical impact. We systematically analyse trio exome sequence data from 4,293 probands from the DDD Study with severe developmental disorders for pathogenic postzygotic mosaicism (PZM) in the child or a clinically-unaffected parent, and use ultrahigh-depth sequencing to validate candidate mosaic variants. We observe that levels of mosaicism for small genetic variants are usually equivalent in both saliva and blood and ~3% of causative de novo mutations exhibit PZM; this is an important observation, as the sibling recurrence risk is extremely low. We identify parental PZM in 21 trios (0.5% of trios), resulting in a substantially increased sibling recurrence risk in future pregnancies. Together, these forms of mosaicism account for 40 (1%) diagnoses in our cohort. Likely child-PZM mutations occur equally on both parental haplotypes, and the penetrance of detectable mosaic pathogenic variants overall is likely to be less than half that of constitutive variants.
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38
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Møller RS, Liebmann N, Larsen LHG, Stiller M, Hentschel J, Kako N, Abdin D, Di Donato N, Pal DK, Zacher P, Syrbe S, Dahl HA, Lemke JR. Parental mosaicism in epilepsies due to alleged de novo variants. Epilepsia 2019; 60:e63-e66. [PMID: 31077350 DOI: 10.1111/epi.15187] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 04/02/2019] [Accepted: 04/15/2019] [Indexed: 02/03/2023]
Abstract
Severe early onset epilepsies are often caused by de novo pathogenic variants. Few studies have reported the frequency of somatic mosaicism in parents of children with severe epileptic encephalopathies. Here we aim to investigate the frequency of mosaicism in the parents of children with epilepsy caused by alleged de novo variants. We tested parental genomic DNA derived from different tissues for 75 cases using targeted next-generation sequencing. Five parents (6.6%) showed mosaicism at minor allele frequencies of 0.8%-29% for the pathogenic variant detected in their offspring. Parental mosaicism was observed in the following genes: SCN1A, SCN2A, SCN8A, and STXBP1. One of the identified parents had epilepsy himself. Our results show that de novo events can occur already in parental tissue and in some cases can be detected in peripheral blood. Consequently, parents affected by low-grade mosaicism are faced with an increased recurrence risk for transmitting the pathogenic variant, compared to the overall recurrence risk for a second affected child estimated at approximately 1%. However, testing for parental somatic mosaicism will help identifying those parents who truly are at higher risk and will significantly improve genetic counseling in the respective families.
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Affiliation(s)
- Rikke S Møller
- Danish Epilepsy Centre, Dianalund, Denmark
- Institute of Regional Health Research, University of Southern Denmark, Odense, Denmark
| | - Nora Liebmann
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | | | - Mathias Stiller
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Julia Hentschel
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | | | - Dalia Abdin
- Institute for Clinical Genetics, TU Dresden, Dresden, Germany
| | | | - Deb K Pal
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- MRC Centre for Neurodevelopmental Disorders, King's College London, London, UK
- King's College Hospital, London, UK
- Evelina London Children's Hospital, London, UK
| | - Pia Zacher
- The Saxon Epilepsy Center Kleinwachau, Radeberg, Germany
| | - Steffen Syrbe
- Department of General Paediatrics, Division of Child Neurology and Inherited Metabolic Diseases, Centre for Paediatrics and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | | | - Johannes R Lemke
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
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39
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Yang X, Yang X, Chen J, Li S, Zeng Q, Huang AY, Ye AY, Yu Z, Wang S, Jiang Y, Wu X, Wu Q, Wei L, Zhang Y. ATP1A3 mosaicism in families with alternating hemiplegia of childhood. Clin Genet 2019; 96:43-52. [PMID: 30891744 PMCID: PMC6850116 DOI: 10.1111/cge.13539] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 03/10/2019] [Accepted: 03/15/2019] [Indexed: 01/17/2023]
Abstract
Alternating hemiplegia of childhood (AHC) is a rare and severe neurodevelopmental disorder characterized by recurrent hemiplegic episodes. Most AHC cases are sporadic and caused by de novo ATP1A3 pathogenic variants. In this study, the aim was to identify the origin of ATP1A3 pathogenic variants in a Chinese cohort. In 105 probands including 101 sporadic and 4 familial cases, 98 patients with ATP1A3 pathogenic variants were identified, and 96.8% were confirmed as de novo. Micro-droplet digital polymerase chain reaction was applied for detecting ATP1A3 mosaicism in 80 available families. In blood samples, four asymptomatic parents, including two paternal and two maternal, and one proband with a milder phenotype were identified as mosaicism. Six (7.5%) parental mosaicisms were identified in multiple tissues, including four previously identified in blood and two additional cases identified from paternal sperms. Mosaicism was identified in multiple tissues with varied mutant allele fractions (MAFs, 0.03%-33.03%). The results suggested that MAF of mosaicism may be related to phenotype severity. This is the first systematic report of ATP1A3 mosaicism in AHC and showed mosaicism as an unrecognized source of previously considered "de novo" AHC. Identifying ATP1A3 mosaicism provides more evidence for estimating recurrence risk and has implications in genetic counseling of AHC.
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Affiliation(s)
- Xiaoling Yang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Xiaoxu Yang
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Jiaoyang Chen
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Shupin Li
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Qi Zeng
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - August Y Huang
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Adam Y Ye
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China.,Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Zhe Yu
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Sheng Wang
- Dr Liping Wei's lab, National Institute of Biological Sciences, Beijing, China.,College of Biological Sciences, China Agricultural University, Beijing, China
| | - Yuwu Jiang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Xiru Wu
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Qixi Wu
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.,Human Genetic Resources Core Facility, School of Life Sciences, Peking University, Beijing, China
| | - Liping Wei
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Yuehua Zhang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
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40
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Genomic mosaicism in the pathogenesis and inheritance of a Rett syndrome cohort. Genet Med 2018; 21:1330-1338. [PMID: 30405208 PMCID: PMC6752670 DOI: 10.1038/s41436-018-0348-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Accepted: 10/17/2018] [Indexed: 01/01/2023] Open
Abstract
PURPOSE To determine the role of mosaicism in the pathogenesis and inheritance of Rett and Rett-like disorders. METHODS We recruited 471 Rett and Rett-like patients. Panel-sequencing targeting MECP2, CDKL5, and FOXG1 was performed. Mosaicism was quantified in 147 patients by a Bayesian genotyper. Candidates were validated by amplicon sequencing and digital PCR. Germline mosaicism of 21 fathers with daughters carrying pathogenic MECP2 variants was further quantified. RESULTS Pathogenic variants of MECP2/CDKL5/FOXG1 were found in 324/471 (68.7%) patients. Somatic MECP2 mosaicism was confirmed in 5/471 (1.1%) patients, including 3/18 males (16.7%) and 2/453 females (0.4%). Three of the five patients with somatic MECP2 mosaicism had mosaicism at MECP2-Arg106. Germline MECP2 mosaicism was detected in 5/21 (23.8%) fathers. CONCLUSION This is the first systematic screening of somatic and paternal germline MECP2 mosaicism at a cohort level. Our findings indicate that somatic MECP2 mosaicism contributes directly to the pathogenicity of Rett syndrome, especially in male patients. MECP2-Arg106 might be a mosaic hotspot. The high proportion of paternal germline MECP2 mosaicism indicates an underestimated mechanism underlying the paternal origin bias of MECP2 variants. Finally, this study provides an empirical foundation for future studies of genetic disorders caused by de novo variations of strong paternal origin.
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41
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Hu P, Martinez AF, Kruszka P, Berger S, Roessler E, Muenke M. Low-level parental mosaicism affects the recurrence risk of holoprosencephaly. Genet Med 2018; 21:1015-1020. [DOI: 10.1038/s41436-018-0261-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 07/26/2018] [Indexed: 11/09/2022] Open
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42
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Myers KA, Johnstone DL, Dyment DA. Epilepsy genetics: Current knowledge, applications, and future directions. Clin Genet 2018; 95:95-111. [PMID: 29992546 DOI: 10.1111/cge.13414] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Revised: 07/03/2018] [Accepted: 07/06/2018] [Indexed: 12/12/2022]
Abstract
The rapid pace of disease gene discovery has resulted in tremendous advances in the field of epilepsy genetics. Clinical testing with comprehensive gene panels, exomes, and genomes are now available and have led to higher diagnostic rates and insights into the underlying disease processes. As such, the contribution to the care of patients by medical geneticists, neurogeneticists and genetic counselors are significant; the dysmorphic examination, the necessary pre- and post-test counseling, the selection of the appropriate next-generation sequencing-based test(s), and the interpretation of sequencing results require a care provider to have a comprehensive working knowledge of the strengths and limitations of the available testing technologies. As the underlying mechanisms of the encephalopathies and epilepsies are better understood, there may be opportunities for the development of novel therapies based on an individual's own specific genotype. Drug screening with in vitro and in vivo models of epilepsy can potentially facilitate new treatment strategies. The future of epilepsy genetics will also probably include other-omic approaches such as transcriptomes, metabolomes, and the expanded use of whole genome sequencing to further improve our understanding of epilepsy and provide better care for those with the disease.
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Affiliation(s)
- K A Myers
- Department of Pediatrics, University of McGill, Montreal, Canada.,Research Institute of the McGill University Health Centre, Montreal, Canada
| | - D L Johnstone
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - D A Dyment
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada.,Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Canada
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43
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Ye AY, Dou Y, Yang X, Wang S, Huang AY, Wei L. A model for postzygotic mosaicisms quantifies the allele fraction drift, mutation rate, and contribution to de novo mutations. Genome Res 2018; 28:943-951. [PMID: 29875290 PMCID: PMC6028137 DOI: 10.1101/gr.230003.117] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 05/02/2018] [Indexed: 12/14/2022]
Abstract
The allele fraction (AF) distribution, occurrence rate, and evolutionary contribution of postzygotic single-nucleotide mosaicisms (pSNMs) remain largely unknown. In this study, we developed a mathematical model to describe the accumulation and AF drift of pSNMs during the development of multicellular organisms. By applying the model, we quantitatively analyzed two large-scale data sets of pSNMs identified from human genomes. We found that the postzygotic mutation rate per cell division during early embryogenesis, especially during the first cell division, was higher than the average mutation rate in either male or female gametes. We estimated that the stochastic cell death rate per cell cleavage during human embryogenesis was ∼5%, and parental pSNMs occurring during the first three cell divisions contributed to ∼10% of the de novo mutations observed in children. We further demonstrated that the genomic profiles of pSNMs could be used to measure the divergence distance between tissues. Our results highlight the importance of pSNMs in estimating recurrence risk and clarified the quantitative relationship between postzygotic and de novo mutations.
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Affiliation(s)
- Adam Yongxin Ye
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, People's Republic of China.,Peking-Tsinghua Center for Life Sciences, Beijing 100871, People's Republic of China.,Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, People's Republic of China
| | - Yanmei Dou
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, People's Republic of China.,National Institute of Biological Sciences, Beijing 102206, People's Republic of China
| | - Xiaoxu Yang
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, People's Republic of China
| | - Sheng Wang
- National Institute of Biological Sciences, Beijing 102206, People's Republic of China.,College of Biological Sciences, China Agricultural University, Beijing 100094, People's Republic of China
| | - August Yue Huang
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, People's Republic of China
| | - Liping Wei
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, People's Republic of China
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44
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Huang AY, Yang X, Wang S, Zheng X, Wu Q, Ye AY, Wei L. Distinctive types of postzygotic single-nucleotide mosaicisms in healthy individuals revealed by genome-wide profiling of multiple organs. PLoS Genet 2018; 14:e1007395. [PMID: 29763432 PMCID: PMC5969758 DOI: 10.1371/journal.pgen.1007395] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Revised: 05/25/2018] [Accepted: 05/04/2018] [Indexed: 12/26/2022] Open
Abstract
Postzygotic single-nucleotide mosaicisms (pSNMs) have been extensively studied in tumors and are known to play critical roles in tumorigenesis. However, the patterns and origin of pSNMs in normal organs of healthy humans remain largely unknown. Using whole-genome sequencing and ultra-deep amplicon re-sequencing, we identified and validated 164 pSNMs from 27 postmortem organ samples obtained from five healthy donors. The mutant allele fractions ranged from 1.0% to 29.7%. Inter- and intra-organ comparison revealed two distinctive types of pSNMs, with about half originating during early embryogenesis (embryonic pSNMs) and the remaining more likely to result from clonal expansion events that had occurred more recently (clonal expansion pSNMs). Compared to clonal expansion pSNMs, embryonic pSNMs had higher proportion of C>T mutations with elevated mutation rate at CpG sites. We observed differences in replication timing between these two types of pSNMs, with embryonic and clonal expansion pSNMs enriched in early- and late-replicating regions, respectively. An increased number of embryonic pSNMs were located in open chromatin states and topologically associating domains that transcribed embryonically. Our findings provide new insights into the origin and spatial distribution of postzygotic mosaicism during normal human development. Genomic mosaicism led by postzygotic mutation is the major cause of cancers and many non-cancer developmental disorders. Theoretically, postzygotic mutations should be accumulated during the developmental process of healthy individuals, but the genome-wide characterization of postzygotic mosaicisms across many organ types of the same individual remained limited. In this study, we identified and validated two types of postzygotic mosaicism from the whole-genomes of 27 organs obtained from five healthy donors. We further found that the postzygotic mosaicisms arising during early embryogenesis and later clonal expansion events show distinct genomic patterns in mutation spectrum, replication timing, and chromatin status.
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Affiliation(s)
- August Yue Huang
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
- * E-mail: (LW); (AYH)
| | - Xiaoxu Yang
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Sheng Wang
- National Institute of Biological Sciences, Beijing, China
- College of Biological Sciences, China Agricultural University, Beijing, China
| | - Xianing Zheng
- National Institute of Biological Sciences, Beijing, China
| | - Qixi Wu
- Peking-Tsinghua Center for Life Sciences, Beijing, China
- Human Genetics Resources Core Facility, School of Life Sciences, Peking University, Beijing, China
| | - Adam Yongxin Ye
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Beijing, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Liping Wei
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
- * E-mail: (LW); (AYH)
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