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Schuermans VNE, van de Goor A, Broen MPG, Boselie TFM. Mother and daughter with a SMARCE1 mutation resulting in a cervical clear cell meningioma at an identical location: illustrative cases. JOURNAL OF NEUROSURGERY. CASE LESSONS 2023; 5:CASE22466. [PMID: 36593672 PMCID: PMC9811575 DOI: 10.3171/case22466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 11/29/2022] [Indexed: 01/04/2023]
Abstract
BACKGROUND A rare meningioma subtype is a clear cell (CC) meningioma, which can be associated with a SMARCE1 gene mutation. Manifestation of a CC meningioma in the cervical spine is unusual. In the current case, both mother and daughter present with a CC meningioma at an identical cervical location. OBSERVATIONS A 67-year-old patient with an intradural extramedullary mass at the level of C5 presented with progressive myelopathy. The mass was resected through a ventral approach by a two-level corpectomy with an expandable cage and instrumentation. The daughter of this patient appeared to have had an intradural extramedullary mass at C5 at the age of 20, which was resected through a posterior approach. Pathological investigation of both tumors revealed CC meningioma. Genetic testing of the daughter revealed a SMARCE1 mutation. LESSONS It is of major importance to consider a SMARCE1 mutation in elderly presenting with a CC meningioma, which is still uncommon in current practice. This could lead to timely diagnostics in the succeeding generation. Complete resection of a CC meningioma is important because of the high recurrence rate. Routine follow-up should therefore be performed in the postoperative period. An anterior approach should be considered for a ventral cervical CC meningioma.
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Affiliation(s)
- Valérie N. E. Schuermans
- Department of Neurosurgery, Zuyderland Medical Center, Heerlen, The Netherlands; ,Departments of Neurosurgery and ,CAPHRI Care and Public Health Research Institute, Maastricht University, Maastricht, The Netherlands
| | - Ank van de Goor
- Departments of Neurosurgery and ,Maastricht University, Maastricht, The Netherlands; and
| | - Martinus P. G. Broen
- Neurology, Maastricht University Medical Center, Maastricht, The Netherlands,GROW, Schoolfor Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
| | - Toon F. M. Boselie
- Department of Neurosurgery, Zuyderland Medical Center, Heerlen, The Netherlands; ,Departments of Neurosurgery and ,CAPHRI Care and Public Health Research Institute, Maastricht University, Maastricht, The Netherlands
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Kingdom R, Wright CF. Incomplete Penetrance and Variable Expressivity: From Clinical Studies to Population Cohorts. Front Genet 2022; 13:920390. [PMID: 35983412 PMCID: PMC9380816 DOI: 10.3389/fgene.2022.920390] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 06/09/2022] [Indexed: 12/20/2022] Open
Abstract
The same genetic variant found in different individuals can cause a range of diverse phenotypes, from no discernible clinical phenotype to severe disease, even among related individuals. Such variants can be said to display incomplete penetrance, a binary phenomenon where the genotype either causes the expected clinical phenotype or it does not, or they can be said to display variable expressivity, in which the same genotype can cause a wide range of clinical symptoms across a spectrum. Both incomplete penetrance and variable expressivity are thought to be caused by a range of factors, including common variants, variants in regulatory regions, epigenetics, environmental factors, and lifestyle. Many thousands of genetic variants have been identified as the cause of monogenic disorders, mostly determined through small clinical studies, and thus, the penetrance and expressivity of these variants may be overestimated when compared to their effect on the general population. With the wealth of population cohort data currently available, the penetrance and expressivity of such genetic variants can be investigated across a much wider contingent, potentially helping to reclassify variants that were previously thought to be completely penetrant. Research into the penetrance and expressivity of such genetic variants is important for clinical classification, both for determining causative mechanisms of disease in the affected population and for providing accurate risk information through genetic counseling. A genotype-based definition of the causes of rare diseases incorporating information from population cohorts and clinical studies is critical for our understanding of incomplete penetrance and variable expressivity. This review examines our current knowledge of the penetrance and expressivity of genetic variants in rare disease and across populations, as well as looking into the potential causes of the variation seen, including genetic modifiers, mosaicism, and polygenic factors, among others. We also considered the challenges that come with investigating penetrance and expressivity.
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Affiliation(s)
- Rebecca Kingdom
- Institute of Biomedical and Clinical Science, Royal Devon & Exeter Hospital, University of Exeter Medical School, Exeter, United Kingdom
| | - Caroline F Wright
- Institute of Biomedical and Clinical Science, Royal Devon & Exeter Hospital, University of Exeter Medical School, Exeter, United Kingdom
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Roman TS, Crowley SB, Roche MI, Foreman AKM, O'Daniel JM, Seifert BA, Lee K, Brandt A, Gustafson C, DeCristo DM, Strande NT, Ramkissoon L, Milko LV, Owen P, Roy S, Xiong M, Paquin RS, Butterfield RM, Lewis MA, Souris KJ, Bailey DB, Rini C, Booker JK, Powell BC, Weck KE, Powell CM, Berg JS. Genomic Sequencing for Newborn Screening: Results of the NC NEXUS Project. Am J Hum Genet 2020; 107:596-611. [PMID: 32853555 PMCID: PMC7536575 DOI: 10.1016/j.ajhg.2020.08.001] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 07/24/2020] [Indexed: 02/08/2023] Open
Abstract
Newborn screening (NBS) was established as a public health program in the 1960s and is crucial for facilitating detection of certain medical conditions in which early intervention can prevent serious, life-threatening health problems. Genomic sequencing can potentially expand the screening for rare hereditary disorders, but many questions surround its possible use for this purpose. We examined the use of exome sequencing (ES) for NBS in the North Carolina Newborn Exome Sequencing for Universal Screening (NC NEXUS) project, comparing the yield from ES used in a screening versus a diagnostic context. We enrolled healthy newborns and children with metabolic diseases or hearing loss (106 participants total). ES confirmed the participant's underlying diagnosis in 15 out of 17 (88%) children with metabolic disorders and in 5 out of 28 (∼18%) children with hearing loss. We discovered actionable findings in four participants that would not have been detected by standard NBS. A subset of parents was eligible to receive additional information for their child about childhood-onset conditions with low or no clinical actionability, clinically actionable adult-onset conditions, and carrier status for autosomal-recessive conditions. We found pathogenic variants associated with hereditary breast and/or ovarian cancer in two children, a likely pathogenic variant in the gene associated with Lowe syndrome in one child, and an average of 1.8 reportable variants per child for carrier results. These results highlight the benefits and limitations of using genomic sequencing for NBS and the challenges of using such technology in future precision medicine approaches.
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Affiliation(s)
- Tamara S Roman
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Stephanie B Crowley
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Myra I Roche
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Pediatrics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Ann Katherine M Foreman
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Julianne M O'Daniel
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Bryce A Seifert
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kristy Lee
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Alicia Brandt
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Chelsea Gustafson
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Daniela M DeCristo
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Natasha T Strande
- Department of Pathology and Laboratory Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Lori Ramkissoon
- Department of Pathology and Laboratory Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Laura V Milko
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Phillips Owen
- Renaissance Computing Institute, Chapel Hill, NC 27517, USA
| | - Sayanty Roy
- Department of Pathology and Laboratory Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Mai Xiong
- Department of Pathology and Laboratory Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ryan S Paquin
- Center for Communication Science, RTI International, Research Triangle Park, NC 27709, USA
| | - Rita M Butterfield
- Department of Family Medicine and Community Health, Duke University School of Medicine, Durham, NC 27705, USA
| | - Megan A Lewis
- Center for Communication Science, RTI International, Research Triangle Park, NC 27709, USA
| | - Katherine J Souris
- Department of Health Behavior, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Donald B Bailey
- Genomics, Bioinformatics and Translational Research Center, RTI International, Research Triangle Park, NC 27709, USA
| | - Christine Rini
- Feinberg School of Medicine, Department of Medical Social Sciences, and the Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
| | - Jessica K Booker
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Pathology and Laboratory Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Bradford C Powell
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Karen E Weck
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Pathology and Laboratory Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Cynthia M Powell
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Pediatrics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Jonathan S Berg
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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Tang C, He Z, Liu H, Xu Y, Huang H, Yang G, Xiao Z, Li S, Liu H, Deng Y, Chen Z, Chen H, He N. Application of magnetic nanoparticles in nucleic acid detection. J Nanobiotechnology 2020; 18:62. [PMID: 32316985 PMCID: PMC7171821 DOI: 10.1186/s12951-020-00613-6] [Citation(s) in RCA: 92] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 03/25/2020] [Indexed: 12/16/2022] Open
Abstract
Nucleic acid is the main material for storing, copying, and transmitting genetic information. Gene sequencing is of great significance in DNA damage research, gene therapy, mutation analysis, bacterial infection, drug development, and clinical diagnosis. Gene detection has a wide range of applications, such as environmental, biomedical, pharmaceutical, agriculture and forensic medicine to name a few. Compared with Sanger sequencing, high-throughput sequencing technology has the advantages of larger output, high resolution, and low cost which greatly promotes the application of sequencing technology in life science research. Magnetic nanoparticles, as an important part of nanomaterials, have been widely used in various applications because of their good dispersion, high surface area, low cost, easy separation in buffer systems and signal detection. Based on the above, the application of magnetic nanoparticles in nucleic acid detection was reviewed.
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Affiliation(s)
- Congli Tang
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Ziyu He
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Hongmei Liu
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Yuyue Xu
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Hao Huang
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Gaojian Yang
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Ziqi Xiao
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Song Li
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Hongna Liu
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Yan Deng
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing, 210096 China
| | - Zhu Chen
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Hui Chen
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Nongyue He
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing, 210096 China
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Green RM, Leach CL, Diewert VM, Aponte JD, Schmidt EJ, Cheverud JM, Roseman CC, Young NM, Marcucio RS, Hallgrimsson B. Nonlinear gene expression-phenotype relationships contribute to variation and clefting in the A/WySn mouse. Dev Dyn 2019; 248:1232-1242. [PMID: 31469941 DOI: 10.1002/dvdy.110] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 08/21/2019] [Accepted: 08/27/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Cleft lip and palate is one of the most common human birth defects, but the underlying etiology is poorly understood. The A/WySn mouse is a spontaneously occurring model of multigenic clefting in which 20% to 30% of individuals develop an orofacial cleft. Recent work has shown altered methylation at a specific retrotransposon insertion downstream of the Wnt9b locus in clefting animals, which results in decreased Wnt9b expression. RESULTS Using a newly developed protocol that allows us to measure morphology, gene expression, and DNA methylation in the same embryo, we relate gene expression in an individual embryo directly to its three-dimensional morphology for the first time. We find that methylation at the retrotransposon relates to Wnt9b expression and morphology. IAP methylation relates to shape of the nasal process in a manner consistent with clefting. Embryos with low IAP methylation exhibit increased among-individual variance in facial shape. CONCLUSIONS Methylation and gene expression relate nonlinearly to nasal process morphology. Individuals at one end of a continuum of phenotypic states display a clinical phenotype and increased phenotypic variation. Variable penetrance and expressivity in this model is likely determined both by among-individual variation in methylation and changes in phenotypic robustness along the underlying liability distribution for orofacial clefting.
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Affiliation(s)
- Rebecca M Green
- Department of Cell Biology and Anatomy, Alberta Children's Hospital Research Institute and McCaig Institute for Bone and Joint Health, University of Calgary, Calgary, Alberta, Canada
| | - Courtney L Leach
- Department of Cell Biology and Anatomy, Alberta Children's Hospital Research Institute and McCaig Institute for Bone and Joint Health, University of Calgary, Calgary, Alberta, Canada
| | - Virginia M Diewert
- Faculty of Dentistry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jose David Aponte
- Department of Cell Biology and Anatomy, Alberta Children's Hospital Research Institute and McCaig Institute for Bone and Joint Health, University of Calgary, Calgary, Alberta, Canada
| | - Eric J Schmidt
- School of PA Medicine, University of Lynchburg, Lynchburg, Virginia
| | - James M Cheverud
- Department of Biology, Loyola University Chicago, Chicago, Illinois
| | - Charles C Roseman
- Department of Animal Biology, University of Illinois Urbana Champaign, Champaign, Illinois
| | - Nathan M Young
- Department of Orthopedics, University of California San Francisco, San Francisco, California
| | - Ralph S Marcucio
- Department of Orthopedics, University of California San Francisco, San Francisco, California
| | - Benedikt Hallgrimsson
- Department of Cell Biology and Anatomy, Alberta Children's Hospital Research Institute and McCaig Institute for Bone and Joint Health, University of Calgary, Calgary, Alberta, Canada
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