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Azuelos C, Marquis MA, Laberge AM. A systematic review of the assessment of the clinical utility of genomic sequencing: Implications of the lack of standard definitions and measures of clinical utility. Eur J Med Genet 2024; 68:104925. [PMID: 38432472 DOI: 10.1016/j.ejmg.2024.104925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 12/31/2023] [Accepted: 02/11/2024] [Indexed: 03/05/2024]
Abstract
PURPOSE Exome sequencing (ES) and genome sequencing (GS) are diagnostic tests for rare genetic diseases. Studies report clinical utility of ES/GS. The goal of this systematic review is to establish how clinical utility is defined and measured in studies evaluating the impacts of ES/GS results for pediatric patients. METHODS Relevant articles were identified in PubMed, Medline, Embase, and Web of Science. Eligible studies assessed clinical utility of ES/GS for pediatric patients published before 2021. Other relevant articles were added based on articles' references. Articles were coded to assess definitions and measures of clinical utility. RESULTS Of 1346 articles, 83 articles met eligibility criteria. Clinical utility was not clearly defined in 19% of studies and 92% did not use an explicit measure of clinical utility. When present, definitions of clinical utility diverged from recommended definitions and varied greatly, from narrow (diagnostic yield of ES/GS) to broad (including decisions about withdrawal of care/palliative care and/or impacts on other family members). CONCLUSION Clinical utility is used to guide policy and practice decisions about test use. The lack of a standard definition of clinical utility of ES/GS may lead to under- or overestimations of clinical utility, complicating policymaking and raising ethical issues.
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Affiliation(s)
- Claudia Azuelos
- Medical Genetics, Dept of Pediatrics, CHU Sainte-Justine and Université de Montréal, Canada.
| | - Marc-Antoine Marquis
- Palliative Care, Dept of Pediatrics, CHU Sainte-Justine and Université de Montréal, Canada
| | - Anne-Marie Laberge
- Medical Genetics, Dept of Pediatrics, CHU Sainte-Justine and Université de Montréal, Canada.
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2
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Rowland ME, Jiang Y, Shafiq S, Ghahramani A, Pena-Ortiz MA, Dumeaux V, Bérubé NG. Systemic and intrinsic functions of ATRX in glial cell fate and CNS myelination in male mice. Nat Commun 2023; 14:7090. [PMID: 37925436 PMCID: PMC10625541 DOI: 10.1038/s41467-023-42752-y] [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: 01/17/2020] [Accepted: 10/20/2023] [Indexed: 11/06/2023] Open
Abstract
Myelin, an extension of the oligodendrocyte plasma membrane, wraps around axons to facilitate nerve conduction. Myelination is compromised in ATR-X intellectual disability syndrome patients, but the causes are unknown. We show that loss of ATRX leads to myelination deficits in male mice that are partially rectified upon systemic thyroxine administration. Targeted ATRX inactivation in either neurons or oligodendrocyte progenitor cells (OPCs) reveals OPC-intrinsic effects on myelination. OPCs lacking ATRX fail to differentiate along the oligodendrocyte lineage and acquire a more plastic state that favors astrocytic differentiation in vitro and in vivo. ATRX chromatin occupancy in OPCs greatly overlaps with that of the chromatin remodelers CHD7 and CHD8 as well as H3K27Ac, a mark of active enhancers. Overall, our data indicate that ATRX regulates the onset of myelination systemically via thyroxine, and by promoting OPC differentiation and suppressing astrogliogenesis. These functions of ATRX identified in mice could explain white matter pathogenesis observed in ATR-X syndrome patients.
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Affiliation(s)
- Megan E Rowland
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
- Children's Health Research Institute, Division of Genetics & Development, London, ON, Canada
| | - Yan Jiang
- Children's Health Research Institute, Division of Genetics & Development, London, ON, Canada
- Department of Paediatrics, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Sarfraz Shafiq
- Children's Health Research Institute, Division of Genetics & Development, London, ON, Canada
- Department of Anatomy and Cell Biology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Alireza Ghahramani
- Children's Health Research Institute, Division of Genetics & Development, London, ON, Canada
- Department of Anatomy and Cell Biology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Miguel A Pena-Ortiz
- Children's Health Research Institute, Division of Genetics & Development, London, ON, Canada
- Graduate Program in Neuroscience, Western University, London, ON, Canada
| | - Vanessa Dumeaux
- Department of Anatomy and Cell Biology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
- Department of Oncology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Nathalie G Bérubé
- Children's Health Research Institute, Division of Genetics & Development, London, ON, Canada.
- Department of Paediatrics, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada.
- Department of Anatomy and Cell Biology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada.
- Graduate Program in Neuroscience, Western University, London, ON, Canada.
- Department of Oncology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada.
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3
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Tillotson R, Yan K, Ruston J, DeYoung T, Córdova A, Turcotte-Cardin V, Yee Y, Taylor C, Visuvanathan S, Babbs C, Ivakine EA, Sled JG, Nieman BJ, Picketts DJ, Justice MJ. A new mouse model of ATR-X syndrome carrying a common patient mutation exhibits neurological and morphological defects. Hum Mol Genet 2023; 32:2485-2501. [PMID: 37171606 PMCID: PMC10360390 DOI: 10.1093/hmg/ddad075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 03/18/2023] [Accepted: 05/05/2023] [Indexed: 05/13/2023] Open
Abstract
ATRX is a chromatin remodelling ATPase that is involved in transcriptional regulation, DNA damage repair and heterochromatin maintenance. It has been widely studied for its role in ALT-positive cancers, but its role in neurological function remains elusive. Hypomorphic mutations in the X-linked ATRX gene cause a rare form of intellectual disability combined with alpha-thalassemia called ATR-X syndrome in hemizygous males. Clinical features also include facial dysmorphism, microcephaly, short stature, musculoskeletal defects and genital abnormalities. As complete deletion of ATRX in mice results in early embryonic lethality, the field has largely relied on conditional knockout models to assess the role of ATRX in multiple tissues. Given that null alleles are not found in patients, a more patient-relevant model was needed. Here, we have produced and characterized the first patient mutation knock-in model of ATR-X syndrome, carrying the most common causative mutation, R246C. This is one of a cluster of missense mutations located in the chromatin-binding domain and disrupts its function. The knock-in mice recapitulate several aspects of the patient disorder, including craniofacial defects, microcephaly, reduced body size and impaired neurological function. They provide a powerful model for understanding the molecular mechanisms underlying ATR-X syndrome and testing potential therapeutic strategies.
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Affiliation(s)
- Rebekah Tillotson
- Genetics and Genome Biology Program, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, ON M5G 0A4, Canada
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital/Headley Way, Oxford OX3 9DS, UK
| | - Keqin Yan
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
| | - Julie Ruston
- Genetics and Genome Biology Program, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, ON M5G 0A4, Canada
| | - Taylor DeYoung
- Mouse Imaging Centre, The Hospital for Sick Children, Toronto, ON M5T 3H7, Canada
| | - Alex Córdova
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
| | - Valérie Turcotte-Cardin
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
- Cellular & Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Yohan Yee
- Mouse Imaging Centre, The Hospital for Sick Children, Toronto, ON M5T 3H7, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Christine Taylor
- Genetics and Genome Biology Program, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, ON M5G 0A4, Canada
| | - Shagana Visuvanathan
- Genetics and Genome Biology Program, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, ON M5G 0A4, Canada
| | - Christian Babbs
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital/Headley Way, Oxford OX3 9DS, UK
| | - Evgueni A Ivakine
- Genetics and Genome Biology Program, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, ON M5G 0A4, Canada
- Department of Physiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - John G Sled
- Mouse Imaging Centre, The Hospital for Sick Children, Toronto, ON M5T 3H7, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
- Translational Medicine Program, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, ON M5G 0A4, Canada
| | - Brian J Nieman
- Mouse Imaging Centre, The Hospital for Sick Children, Toronto, ON M5T 3H7, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
- Translational Medicine Program, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, ON M5G 0A4, Canada
- Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada
| | - David J Picketts
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
- Cellular & Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Monica J Justice
- Genetics and Genome Biology Program, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, ON M5G 0A4, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A1, Canada
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4
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Achour A, Koopmann TT, Baas F, Harteveld CL. The Evolving Role of Next-Generation Sequencing in Screening and Diagnosis of Hemoglobinopathies. Front Physiol 2021; 12:686689. [PMID: 34385932 PMCID: PMC8353275 DOI: 10.3389/fphys.2021.686689] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 06/11/2021] [Indexed: 11/23/2022] Open
Abstract
During the last few years, next-generation sequencing (NGS) has undergone a rapid transition from a research setting to a clinical application, becoming the method of choice in many clinical genetics laboratories for the detection of disease-causing variants in a variety of genetic diseases involving multiple genes. The hemoglobinopathies are the most frequently found Mendelian inherited monogenic disease worldwide and are composed of a complex group of disorders frequently involving the inheritance of more than one abnormal gene. This review aims to present the role of NGS in both screening and pre- and post-natal diagnostics of the hemoglobinopathies, and the added value of NGS is discussed based on the results described in the literature. Overall, NGS has an added value in large-scale high throughput carrier screening and in the complex cases for which common molecular techniques have some inadequacies. It is proven that the majority of thalassemia cases and Hb variants can be diagnosed using routine analysis involving a combined approach of hematology, hemoglobin separation, and classical DNA methods; however, we conclude that NGS can be a useful addition to the existing methods in the diagnosis of these disorders.
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Affiliation(s)
- Ahlem Achour
- Department of Clinical Genetics/LDGA, Leiden University Medical Center, Leiden, Netherlands.,Department of Congenital and Hereditary Diseases, Charles Nicolle Hospital, Tunis, Tunisia
| | - Tamara T Koopmann
- Department of Clinical Genetics/LDGA, Leiden University Medical Center, Leiden, Netherlands
| | - Frank Baas
- Department of Clinical Genetics/LDGA, Leiden University Medical Center, Leiden, Netherlands
| | - Cornelis L Harteveld
- Department of Clinical Genetics/LDGA, Leiden University Medical Center, Leiden, Netherlands
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Timpano S, Picketts DJ. Neurodevelopmental Disorders Caused by Defective Chromatin Remodeling: Phenotypic Complexity Is Highlighted by a Review of ATRX Function. Front Genet 2020; 11:885. [PMID: 32849845 PMCID: PMC7432156 DOI: 10.3389/fgene.2020.00885] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Accepted: 07/20/2020] [Indexed: 12/15/2022] Open
Abstract
The ability to determine the genetic etiology of intellectual disability (ID) and neurodevelopmental disorders (NDD) has improved immensely over the last decade. One prevailing metric from these studies is the large percentage of genes encoding epigenetic regulators, including many members of the ATP-dependent chromatin remodeling enzyme family. Chromatin remodeling proteins can be subdivided into five classes that include SWI/SNF, ISWI, CHD, INO80, and ATRX. These proteins utilize the energy from ATP hydrolysis to alter nucleosome positioning and are implicated in many cellular processes. As such, defining their precise roles and contributions to brain development and disease pathogenesis has proven to be complex. In this review, we illustrate that complexity by reviewing the roles of ATRX on genome stability, replication, and transcriptional regulation and how these mechanisms provide key insight into the phenotype of ATR-X patients.
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Affiliation(s)
- Sara Timpano
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - David J. Picketts
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, ON, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
- Department of Medicine, University of Ottawa, Ottawa, ON, Canada
- University of Ottawa Brain and Mind Research Institute, Ottawa, ON, Canada
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6
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Glial ensheathment of the somatodendritic compartment regulates sensory neuron structure and activity. Proc Natl Acad Sci U S A 2019; 116:5126-5134. [PMID: 30804200 DOI: 10.1073/pnas.1814456116] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Sensory neurons perceive environmental cues and are important of organismal survival. Peripheral sensory neurons interact intimately with glial cells. While the function of axonal ensheathment by glia is well studied, less is known about the functional significance of glial interaction with the somatodendritic compartment of neurons. Herein, we show that three distinct glia cell types differentially wrap around the axonal and somatodendritic surface of the polymodal dendritic arborization (da) neuron of the Drosophila peripheral nervous system for detection of thermal, mechanical, and light stimuli. We find that glial cell-specific loss of the chromatin modifier gene dATRX in the subperineurial glial layer leads to selective elimination of somatodendritic glial ensheathment, thus allowing us to investigate the function of such ensheathment. We find that somatodendritic glial ensheathment regulates the morphology of the dendritic arbor, as well as the activity of the sensory neuron, in response to sensory stimuli. Additionally, glial ensheathment of the neuronal soma influences dendritic regeneration after injury.
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7
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Miniscule differences between sex chromosomes in the giant genome of a salamander. Sci Rep 2018; 8:17882. [PMID: 30552368 PMCID: PMC6294749 DOI: 10.1038/s41598-018-36209-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 11/12/2018] [Indexed: 11/08/2022] Open
Abstract
In the Mexican axolotl (Ambystoma mexicanum), sex is determined by a single Mendelian factor, yet its sex chromosomes do not exhibit morphological differentiation typical of many vertebrate taxa that possess a single sex-determining locus. As sex chromosomes are theorized to differentiate rapidly, species with undifferentiated sex chromosomes provide the opportunity to reconstruct early events in sex chromosome evolution. Whole genome sequencing of 48 salamanders, targeted chromosome sequencing and in situ hybridization were used to identify the homomorphic sex chromosome that carries an A. mexicanum sex-determining factor and sequences that are present only on the W chromosome. Altogether, these sequences cover ~300 kb of validated female-specific (W chromosome) sequence, representing ~1/100,000th of the 32 Gb genome. Notably, a recent duplication of ATRX, a gene associated with mammalian sex-determining pathways, is one of few functional (non-repetitive) genes identified among these W-specific sequences. This duplicated gene (ATRW) was used to develop highly predictive markers for diagnosing sex and represents a strong candidate for a recently-acquired sex determining locus (or sexually antagonistic gene) in A. mexicanum.
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8
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Li CY, Cui JY. Regulation of protein-coding gene and long noncoding RNA pairs in liver of conventional and germ-free mice following oral PBDE exposure. PLoS One 2018; 13:e0201387. [PMID: 30067809 PMCID: PMC6070246 DOI: 10.1371/journal.pone.0201387] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 07/14/2018] [Indexed: 02/07/2023] Open
Abstract
Gut microbiome communicates with the host liver to modify hepatic xenobiotic biotransformation and nutrient homeostasis. Polybrominated diphenyl ethers (PBDEs) are persistent environmental contaminants that are detected in fatty food, household dust, and human breast milk at worrisome levels. Recently, long noncoding RNAs (lncRNAs) have been recognized as novel biomarkers for toxicological responses and may regulate the transcriptional/translational output of protein-coding genes (PCGs). However, very little is known regarding to what extent the interactions between PBDEs and gut microbiome modulate hepatic lncRNAs and PCGs, and what critical signaling pathways are impacted at the transcriptomic scale. In this study, we performed RNA-Seq in livers of nine-week-old male conventional (CV) and germ-free (GF) mice orally exposed to the most prevalent PBDE congeners BDE-47 and BDE-99 (100 μmol/kg once daily for 4-days; vehicle: corn oil, 10 ml/kg), and unveiled key molecular pathways and PCG-lncRNA pairs targeted by PBDE-gut microbiome interactions. Lack of gut microbiome profoundly altered the PBDE-mediated transcriptomic response in liver, with the most prominent effect observed in BDE-99-exposed GF mice. The top pathways up-regulated by PBDEs were related to xenobiotic metabolism, whereas the top pathways down-regulated by PBDEs were in lipid metabolism and protein synthesis in both enterotypes. Genomic annotation of the differentially regulated lncRNAs revealed that majority of these lncRNAs overlapped with introns and 3'-UTRs of PCGs. Lack of gut microbiome profoundly increased the percentage of PBDE-regulated lncRNAs mapped to the 3'-UTRs of PCGs, suggesting the potential involvement of lncRNAs in increasing the translational efficiency of PCGs by preventing miRNA-3'-UTR binding, as a compensatory mechanism following toxic exposure to PBDEs. Pathway analysis of PCGs paired with lncRNAs revealed that in CV mice, BDE-47 regulated nucleic acid and retinol metabolism, as well as circadian rhythm; whereas BDE-99 regulated fatty acid metabolism. In GF mice, BDE-47 differentially regulated 19 lncRNA-PCG pairs that were associated with glutathione conjugation and transcriptional regulation. In contrast, BDE-99 up-regulated the xenobiotic-metabolizing Cyp3a genes, but down-regulated the fatty acid-metabolizing Cyp4 genes. Taken together, the present study reveals common and unique lncRNAs and PCG targets of PBDEs in mouse liver, and is among the first to show that lack of gut microbiome sensitizes the liver to toxic exposure of BDE-99 but not BDE-47. Therefore, lncRNAs may serve as specific biomarkers that differentiate various PBDE congeners as well as environmental chemical-mediated dysbiosis. Coordinate regulation of PCG-lncRNA pairs may serve as a more efficient molecular mechanism to combat against xenobiotic insult, and especially during dysbiosis-induced increase in the internal dose of toxicants.
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Affiliation(s)
- Cindy Yanfei Li
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, United States of America
| | - Julia Yue Cui
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, United States of America
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9
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Smith HS, Swint JM, Lalani SR, Yamal JM, de Oliveira Otto MC, Castellanos S, Taylor A, Lee BH, Russell HV. Clinical Application of Genome and Exome Sequencing as a Diagnostic Tool for Pediatric Patients: a Scoping Review of the Literature. Genet Med 2018; 21:3-16. [PMID: 29760485 DOI: 10.1038/s41436-018-0024-6] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 03/20/2018] [Indexed: 12/17/2022] Open
Abstract
PURPOSE Availability of clinical genomic sequencing (CGS) has generated questions about the value of genome and exome sequencing as a diagnostic tool. Analysis of reported CGS application can inform uptake and direct further research. This scoping literature review aims to synthesize evidence on the clinical and economic impact of CGS. METHODS PubMed, Embase, and Cochrane were searched for peer-reviewed articles published between 2009 and 2017 on diagnostic CGS for infant and pediatric patients. Articles were classified according to sample size and whether economic evaluation was a primary research objective. Data on patient characteristics, clinical setting, and outcomes were extracted and narratively synthesized. RESULTS Of 171 included articles, 131 were case reports, 40 were aggregate analyses, and 4 had a primary economic evaluation aim. Diagnostic yield was the only consistently reported outcome. Median diagnostic yield in aggregate analyses was 33.2% but varied by broad clinical categories and test type. CONCLUSION Reported CGS use has rapidly increased and spans diverse clinical settings and patient phenotypes. Economic evaluations support the cost-saving potential of diagnostic CGS. Multidisciplinary implementation research, including more robust outcome measurement and economic evaluation, is needed to demonstrate clinical utility and cost-effectiveness of CGS.
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Affiliation(s)
- Hadley Stevens Smith
- Baylor College of Medicine, The University of Texas School of Public Health, Houston, Texas, USA
| | - J Michael Swint
- The University of Texas School of Public Health, The Center for Clinical Research and Evidence-Based Medicine, The University of Texas McGovern Medical School, Houston, Texas, USA
| | - Seema R Lalani
- Baylor College of Medicine, Baylor Genetics Laboratory, Houston, Texas, USA
| | - Jose-Miguel Yamal
- The University of Texas School of Public Health, Houston, Texas, USA
| | | | | | - Amy Taylor
- Texas Medical Center Library, Houston, Texas, USA
| | | | - Heidi V Russell
- Texas Children's Hospital, Baylor College of Medicine, Houston, Texas, USA
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10
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Nandakumar P, Mansouri A, Das S. The Role of ATRX in Glioma Biology. Front Oncol 2017; 7:236. [PMID: 29034211 PMCID: PMC5626857 DOI: 10.3389/fonc.2017.00236] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 09/14/2017] [Indexed: 02/03/2023] Open
Abstract
The current World Health Organization classification of CNS tumors has made a tremendous leap from past editions by incorporating molecular criteria in addition to the pre-existing histological parameters. The revised version has had a particular impact on the classification of diffuse low-grade gliomas and their high-grade variants. The ATRX status is one of the critical markers that define the molecular classification of gliomas. In this review, we will first provide an overview of the role of ATRX in regular cell biology. Furthermore, the role of ATRX in tumorigenesis, specifically gliomas, is comprehensively elucidated. The possible correlation of ATRX status with other genetic/epigenetic modifications is also presented. We conclude by discussing some of the challenges associated with incorporating ATRX status assessment into routine clinical practice while also exploring opportunities for future diagnostics/therapeutics in gliomas based on ATRX status.
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Affiliation(s)
- Pravanya Nandakumar
- Division of Neurosurgery, St. Michael's Hospital, University of Toronto, Toronto, ON, Canada
| | - Alireza Mansouri
- Center for Cancer Research, Neuro-Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States.,Division of Neuro-Oncology, Johns Hopkins University, Baltimore, MD, United States
| | - Sunit Das
- Division of Neurosurgery, St. Michael's Hospital, University of Toronto, Toronto, ON, Canada.,The Arthur and Sonia Labatt Brain Tumour Centre, Hospital for Sick Kids, University of Toronto, Toronto, ON, Canada
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11
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Lee S, Choi M. Ultra-rare Disease and Genomics-Driven Precision Medicine. Genomics Inform 2016; 14:42-5. [PMID: 27445646 PMCID: PMC4951399 DOI: 10.5808/gi.2016.14.2.42] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 05/10/2016] [Accepted: 05/26/2016] [Indexed: 11/20/2022] Open
Abstract
Since next-generation sequencing (NGS) technique was adopted into clinical practices, revolutionary advances in diagnosing rare genetic diseases have been achieved through translating genomic medicine into precision or personalized management. Indeed, several successful cases of molecular diagnosis and treatment with personalized or targeted therapies of rare genetic diseases have been reported. Still, there are several obstacles to be overcome for wider application of NGS-based precision medicine, including high sequencing cost, incomplete variant sensitivity and accuracy, practical complexities, and a shortage of available treatment options.
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Affiliation(s)
- Sangmoon Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Murim Choi
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Korea
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