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Nelson N, Feurstein S, Niaz A, Truong J, Holien JK, Lucas S, Fairfax K, Dickinson J, Bryan TM. Functional genomics for curation of variants in telomere biology disorder associated genes: A systematic review. Genet Med 2023; 25:100354. [PMID: 36496180 DOI: 10.1016/j.gim.2022.11.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 11/28/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022] Open
Abstract
PURPOSE Patients with an underlying telomere biology disorder (TBD) have variable clinical presentations, and they can be challenging to diagnose clinically. A genomic diagnosis for patients presenting with TBD is vital for optimal treatment. Unfortunately, many variants identified during diagnostic testing are variants of uncertain significance. This complicates management decisions, delays treatment, and risks nonuptake of potentially curative therapies. Improved application of functional genomic evidence may reduce variants of uncertain significance classifications. METHODS We systematically searched the literature for published functional assays interrogating TBD gene variants. When possible, established likely benign/benign and likely pathogenic/pathogenic variants were used to estimate the assay sensitivity, specificity, positive predictive value, negative predictive value, and odds of pathogenicity. RESULTS In total, 3131 articles were screened and 151 met inclusion criteria. Sufficient data to enable a PS3/BS3 recommendation were available for TERT variants only. We recommend that PS3 and BS3 can be applied at a moderate and supportive level, respectively. PS3/BS3 application was limited by a lack of assay standardization and limited inclusion of benign variants. CONCLUSION Further assay standardization and assessment of benign variants are required for optimal use of the PS3/BS3 criterion for TBD gene variant classification.
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Affiliation(s)
- Niles Nelson
- The Menzies Institute for Medical Research, College of Health and Medicine, The University of Tasmania, Hobart, Tasmania, Australia; Department of Molecular Medicine, The Royal Hobart Hospital, Hobart, Tasmania, Australia; Department of Molecular Haematology, The Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.
| | - Simone Feurstein
- Section of Hematology, Oncology, and Rheumatology, Department of Internal Medicine, Heidelberg University Hospital, Heidelberg, Germany
| | - Aram Niaz
- Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, New South Wales, Australia
| | - Jia Truong
- School of Science, STEM College, RMIT University, Bundoora, Victoria, Australia
| | - Jessica K Holien
- School of Science, STEM College, RMIT University, Bundoora, Victoria, Australia
| | - Sionne Lucas
- The Menzies Institute for Medical Research, College of Health and Medicine, The University of Tasmania, Hobart, Tasmania, Australia
| | - Kirsten Fairfax
- The Menzies Institute for Medical Research, College of Health and Medicine, The University of Tasmania, Hobart, Tasmania, Australia
| | - Joanne Dickinson
- The Menzies Institute for Medical Research, College of Health and Medicine, The University of Tasmania, Hobart, Tasmania, Australia
| | - Tracy M Bryan
- Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, New South Wales, Australia
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Janczar S, Kirschner M, Beier F, Brümmendorf TH, Ussowicz M, Babol-Pokora K, Oszer A, Yoshimi A, Kalwak K, Mlynarski W. Challenges in the interpretation of a germline TERT variant in a patient with juvenile myelomonocytic leukemia. Pediatr Blood Cancer 2022; 69:e29909. [PMID: 35927969 DOI: 10.1002/pbc.29909] [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] [Received: 05/17/2022] [Revised: 07/01/2022] [Accepted: 07/13/2022] [Indexed: 11/08/2022]
Abstract
Dyskeratosis congenita (DC) is a bone marrow failure syndrome with extrahematopoietic abnormalities. DC is a paradigmatic telomere biology disorder (TBD) caused by germline mutations in genes responsible for telomere maintenance including TERT. Cryptic TBD is a bone marrow failure syndrome due to premature telomere shortening but without additional symptoms, frequently clinically indistinguishable from severe aplastic anemia (SAA) or hypoplastic myelodysplastic syndrome. We present the complex diagnostic pathway in a boy with a rare germline p.Thr726Met TERT variant with previous reports of SAA association and compromised enzymatic function who presented with juvenile myelomonocytic leukemia, which is a rare myelodysplastic/myeloproliferative neoplasm of childhood.
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Affiliation(s)
- Szymon Janczar
- Department of Pediatrics, Oncology and Haematology, Medical University of Lodz, Lodz, Poland
| | - Martin Kirschner
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, RWTH Aachen University, Aachen, Germany.,Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Aachen, Germany
| | - Fabian Beier
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, RWTH Aachen University, Aachen, Germany.,Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Aachen, Germany
| | - Tim H Brümmendorf
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, RWTH Aachen University, Aachen, Germany.,Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Aachen, Germany
| | - Marek Ussowicz
- Department of Paediatric Bone Marrow Transplantation, Oncology and Hematology, Wroclaw Medical University, Wrocław, Poland
| | - Katarzyna Babol-Pokora
- Department of Pediatrics, Oncology and Haematology, Medical University of Lodz, Lodz, Poland
| | - Aleksandra Oszer
- Department of Pediatrics, Oncology and Haematology, Medical University of Lodz, Lodz, Poland
| | - Ayami Yoshimi
- Division of Pediatric Hematology and Oncology, Medical Center, Faculty of Medicine, Department of Pediatrics and Adolescent Medicine, University of Freiburg, Freiburg, Germany
| | - Krzysztof Kalwak
- Department of Paediatric Bone Marrow Transplantation, Oncology and Hematology, Wroclaw Medical University, Wrocław, Poland
| | - Wojciech Mlynarski
- Department of Pediatrics, Oncology and Haematology, Medical University of Lodz, Lodz, Poland
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Liutkeviciene R, Mikalauskaite R, Gedvilaite G, Glebauskiene B, Kriauciuniene L, Žemaitienė R. Relative Leukocyte Telomere Length and Telomerase Complex Regulatory Markers Association with Leber's Hereditary Optic Neuropathy. MEDICINA (KAUNAS, LITHUANIA) 2022; 58:medicina58091240. [PMID: 36143917 PMCID: PMC9504758 DOI: 10.3390/medicina58091240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 08/21/2022] [Accepted: 09/05/2022] [Indexed: 11/30/2022]
Abstract
Background and Objectives: To evaluate the association of relative leukocyte telomere length (RLTL) and telomerase complex regulatory markers with Leber’s hereditary optic neuropathy (LHON). Material and Methods: A case-control study was performed in patients with LHON (≥18 years) and healthy subjects. The diagnosis of LHON was based on a genetic blood test (next-generation sequencing with Illumina MiSeq, computer analysis: BWA2.1 Illumina BaseSpace, Alamut, and mtDNA Variant analyzer 1000 were performed) and diagnostic criteria approved by the LHON disease protocol. Statistical analysis was performed using the standard statistical software package, IBM SPSS Statistics 27. Statistically significant results were considered when p < 0.05. Results: Significantly longer RLTL was observed in LHON patients than in healthy controls (p < 0.001). RLTL was significantly longer in women and men with LOHN than in healthy women and men in the control group (p < 0.001 and p = 0.003, respectively). In the elderly group (>32 years), RLTL was statistically significantly longer in LHON patients compared with healthy subjects (p < 0.001). The GG genotype of the TERC rs12696304 polymorphism was found to be statistically significantly higher in the LHON group (p = 0.041), and the C allele in the TERC rs12696304 polymorphism was found to be statistically significantly less common in the LHON group (p < 0.001). The RLTL of LHON patients was found to be statistically significantly longer in the TERC rs12696304 polymorphism in all tested genotypes (CC, p = 0.005; CG, p = 0.008; GG, p = 0.025), TEP1 rs1760904 polymorphism in the GA genotype (p < 0.001), and TEP1 gene rs1713418 in the AA and AG genotypes (p = 0.011 and p < 0.001, respectively). Conclusions: The RLTL in LHON patients was found to be longer than in healthy subjects regardless of treatment with idebenone. The TERC rs12696304 polymorphism, of all studied polymorphisms, was the most significantly associated with changes in LHON and telomere length.
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Affiliation(s)
- Rasa Liutkeviciene
- Department of Ophthalmology, Lithuanian University of Health Sciences, 44307 Kaunas, Lithuania
- Neuroscience Institute, Lithuanian University of Health Sciences, 44307 Kaunas, Lithuania
| | - Rasa Mikalauskaite
- Department of Ophthalmology, Lithuanian University of Health Sciences, 44307 Kaunas, Lithuania
| | - Greta Gedvilaite
- Neuroscience Institute, Lithuanian University of Health Sciences, 44307 Kaunas, Lithuania
- Correspondence:
| | - Brigita Glebauskiene
- Department of Ophthalmology, Lithuanian University of Health Sciences, 44307 Kaunas, Lithuania
| | - Loresa Kriauciuniene
- Department of Ophthalmology, Lithuanian University of Health Sciences, 44307 Kaunas, Lithuania
- Neuroscience Institute, Lithuanian University of Health Sciences, 44307 Kaunas, Lithuania
| | - Reda Žemaitienė
- Department of Ophthalmology, Lithuanian University of Health Sciences, 44307 Kaunas, Lithuania
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