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Rajan-Babu IS, Dolzhenko E, Eberle MA, Friedman JM. Sequence composition changes in short tandem repeats: heterogeneity, detection, mechanisms and clinical implications. Nat Rev Genet 2024; 25:476-499. [PMID: 38467784 DOI: 10.1038/s41576-024-00696-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/19/2024] [Indexed: 03/13/2024]
Abstract
Short tandem repeats (STRs) are a class of repetitive elements, composed of tandem arrays of 1-6 base pair sequence motifs, that comprise a substantial fraction of the human genome. STR expansions can cause a wide range of neurological and neuromuscular conditions, known as repeat expansion disorders, whose age of onset, severity, penetrance and/or clinical phenotype are influenced by the length of the repeats and their sequence composition. The presence of non-canonical motifs, depending on the type, frequency and position within the repeat tract, can alter clinical outcomes by modifying somatic and intergenerational repeat stability, gene expression and mutant transcript-mediated and/or protein-mediated toxicities. Here, we review the diverse structural conformations of repeat expansions, technological advances for the characterization of changes in sequence composition, their clinical correlations and the impact on disease mechanisms.
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Affiliation(s)
- Indhu-Shree Rajan-Babu
- Department of Medical Genetics, The University of British Columbia, and Children's & Women's Hospital, Vancouver, British Columbia, Canada.
| | | | | | - Jan M Friedman
- Department of Medical Genetics, The University of British Columbia, and Children's & Women's Hospital, Vancouver, British Columbia, Canada
- BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada
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2
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Dolzhenko E, English A, Dashnow H, De Sena Brandine G, Mokveld T, Rowell WJ, Karniski C, Kronenberg Z, Danzi MC, Cheung WA, Bi C, Farrow E, Wenger A, Chua KP, Martínez-Cerdeño V, Bartley TD, Jin P, Nelson DL, Zuchner S, Pastinen T, Quinlan AR, Sedlazeck FJ, Eberle MA. Characterization and visualization of tandem repeats at genome scale. Nat Biotechnol 2024:10.1038/s41587-023-02057-3. [PMID: 38168995 DOI: 10.1038/s41587-023-02057-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 11/06/2023] [Indexed: 01/05/2024]
Abstract
Tandem repeat (TR) variation is associated with gene expression changes and numerous rare monogenic diseases. Although long-read sequencing provides accurate full-length sequences and methylation of TRs, there is still a need for computational methods to profile TRs across the genome. Here we introduce the Tandem Repeat Genotyping Tool (TRGT) and an accompanying TR database. TRGT determines the consensus sequences and methylation levels of specified TRs from PacBio HiFi sequencing data. It also reports reads that support each repeat allele. These reads can be subsequently visualized with a companion TR visualization tool. Assessing 937,122 TRs, TRGT showed a Mendelian concordance of 98.38%, allowing a single repeat unit difference. In six samples with known repeat expansions, TRGT detected all expansions while also identifying methylation signals and mosaicism and providing finer repeat length resolution than existing methods. Additionally, we released a database with allele sequences and methylation levels for 937,122 TRs across 100 genomes.
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Affiliation(s)
| | - Adam English
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Harriet Dashnow
- Departments of Human Genetics and Biomedical Informatics, University of Utah, Salt Lake City, UT, USA
| | | | - Tom Mokveld
- Pacific Biosciences of California, Menlo Park, CA, USA
| | | | | | | | - Matt C Danzi
- Dr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Warren A Cheung
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Chengpeng Bi
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Emily Farrow
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Aaron Wenger
- Pacific Biosciences of California, Menlo Park, CA, USA
| | - Khi Pin Chua
- Pacific Biosciences of California, Menlo Park, CA, USA
| | - Verónica Martínez-Cerdeño
- Institute for Pediatric Regenerative Medicine, Shriner's Hospital for Children and UC Davis School of Medicine, Sacramento, CA, USA
- Department of Pathology & Laboratory Medicine, UC Davis School of Medicine, Sacramento, CA, USA
- MIND Institute, UC Davis School of Medicine, Sacramento, CA, USA
| | - Trevor D Bartley
- Institute for Pediatric Regenerative Medicine, Shriner's Hospital for Children and UC Davis School of Medicine, Sacramento, CA, USA
- Department of Pathology & Laboratory Medicine, UC Davis School of Medicine, Sacramento, CA, USA
| | - Peng Jin
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - David L Nelson
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Stephan Zuchner
- Dr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Tomi Pastinen
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Aaron R Quinlan
- Departments of Human Genetics and Biomedical Informatics, University of Utah, Salt Lake City, UT, USA
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Department of Computer Science, Rice University, Houston, TX, USA
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3
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Lian M, Zhao M, Phang GP, Rajan-Babu IS, Chong SS. Triplet-primed PCR and Melting Curve Analysis for Rapid Molecular Screening of Spinocerebellar Ataxia Types 1, 2, and 3. Bio Protoc 2023; 13:e4704. [PMID: 37397792 PMCID: PMC10308190 DOI: 10.21769/bioprotoc.4704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 02/27/2023] [Accepted: 04/14/2023] [Indexed: 07/04/2023] Open
Abstract
There are more than 40 types of spinocerebellar ataxia (SCA), most of which are caused by abnormal expansion of short tandem repeats at various gene loci. These phenotypically similar disorders require molecular testing at multiple loci by fluorescent PCR and capillary electrophoresis to identify the causative repeat expansion. We describe a simple strategy to screen for the more common SCA1, SCA2, and SCA3 by rapidly detecting the abnormal CAG repeat expansion at the ATXN1, ATXN2, and ATXN3 loci using melting curve analysis of triplet-primed PCR products. Each of the three separate assays employs a plasmid DNA carrying a known repeat size to generate a threshold melt peak temperature, which effectively distinguishes expansion-positive samples from those without a repeat expansion. Samples that are screened positive based on their melt peak profiles are subjected to capillary electrophoresis for repeat sizing and genotype confirmation. These screening assays are robust and provide accurate detection of the repeat expansion while eliminating the need for fluorescent PCR and capillary electrophoresis for every sample.
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Affiliation(s)
- Mulias Lian
- Department of Obstetrics and Gynecology, National University Hospital, Singapore, Singapore
| | - Mingjue Zhao
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Gui-Ping Phang
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Indhu-Shree Rajan-Babu
- Department of Medical Genetics, University of British Columbia, and Children’s & Women’s Hospital, Vancouver, British Columbia, Canada
| | - Samuel S. Chong
- Department of Laboratory Medicine, National University Hospital, Singapore, Singapore
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4
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Dolzhenko E, Weisburd B, Ibañez K, Rajan-Babu IS, Anyansi C, Bennett MF, Billingsley K, Carroll A, Clamons S, Danzi MC, Deshpande V, Ding J, Fazal S, Halman A, Jadhav B, Qiu Y, Richmond PA, Saunders CT, Scheffler K, van Vugt JJFA, Zwamborn RRAJ, Chong SS, Friedman JM, Tucci A, Rehm HL, Eberle MA. REViewer: haplotype-resolved visualization of read alignments in and around tandem repeats. Genome Med 2022; 14:84. [PMID: 35948990 PMCID: PMC9367089 DOI: 10.1186/s13073-022-01085-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 07/11/2022] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Expansions of short tandem repeats are the cause of many neurogenetic disorders including familial amyotrophic lateral sclerosis, Huntington disease, and many others. Multiple methods have been recently developed that can identify repeat expansions in whole genome or exome sequencing data. Despite the widely recognized need for visual assessment of variant calls in clinical settings, current computational tools lack the ability to produce such visualizations for repeat expansions. Expanded repeats are difficult to visualize because they correspond to large insertions relative to the reference genome and involve many misaligning and ambiguously aligning reads. RESULTS We implemented REViewer, a computational method for visualization of sequencing data in genomic regions containing long repeat expansions and FlipBook, a companion image viewer designed for manual curation of large collections of REViewer images. To generate a read pileup, REViewer reconstructs local haplotype sequences and distributes reads to these haplotypes in a way that is most consistent with the fragment lengths and evenness of read coverage. To create appropriate training materials for onboarding new users, we performed a concordance study involving 12 scientists involved in short tandem repeat research. We used the results of this study to create a user guide that describes the basic principles of using REViewer as well as a guide to the typical features of read pileups that correspond to low confidence repeat genotype calls. Additionally, we demonstrated that REViewer can be used to annotate clinically relevant repeat interruptions by comparing visual assessment results of 44 FMR1 repeat alleles with the results of triplet repeat primed PCR. For 38 of these alleles, the results of visual assessment were consistent with triplet repeat primed PCR. CONCLUSIONS Read pileup plots generated by REViewer offer an intuitive way to visualize sequencing data in regions containing long repeat expansions. Laboratories can use REViewer and FlipBook to assess the quality of repeat genotype calls as well as to visually detect interruptions or other imperfections in the repeat sequence and the surrounding flanking regions. REViewer and FlipBook are available under open-source licenses at https://github.com/illumina/REViewer and https://github.com/broadinstitute/flipbook respectively.
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Affiliation(s)
- Egor Dolzhenko
- grid.185669.50000 0004 0507 3954Illumina Inc., San Diego, CA 92122 USA
| | - Ben Weisburd
- grid.66859.340000 0004 0546 1623Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, USA ,grid.32224.350000 0004 0386 9924Center for Genomic Medicine, Massachusetts General Hospital, Boston, USA
| | - Kristina Ibañez
- grid.4868.20000 0001 2171 1133William Harvey Research Institute, Queen Mary University of London, London, EC1M 6BQ UK
| | - Indhu-Shree Rajan-Babu
- grid.17091.3e0000 0001 2288 9830Department of Medical Genetics, University of British Columbia and Children’s & Women’s Hospital, Vancouver, BC V6H3N1 Canada ,grid.13097.3c0000 0001 2322 6764Department of Medical and Molecular Genetics, King’s College London, Strand, London, WC2R 2LS UK
| | - Christine Anyansi
- grid.185669.50000 0004 0507 3954Illumina Inc., San Diego, CA 92122 USA
| | - Mark F. Bennett
- grid.1042.70000 0004 0432 4889Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052 Australia ,grid.1008.90000 0001 2179 088XDepartment of Medical Biology, University of Melbourne, Parkville, VIC 3052 Australia ,grid.410678.c0000 0000 9374 3516Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Heidelberg, VIC 3084 Australia
| | - Kimberley Billingsley
- grid.419475.a0000 0000 9372 4913Center for Alzheimer’s and Related Dementias, National Institute on Aging, Bethesda, MD USA ,grid.419475.a0000 0000 9372 4913Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD USA
| | - Ashley Carroll
- grid.185669.50000 0004 0507 3954Illumina Inc., San Diego, CA 92122 USA
| | - Samuel Clamons
- grid.185669.50000 0004 0507 3954Illumina Inc., San Diego, CA 92122 USA
| | - Matt C. Danzi
- grid.26790.3a0000 0004 1936 8606Dr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL 33136 USA
| | - Viraj Deshpande
- grid.185669.50000 0004 0507 3954Illumina Inc., San Diego, CA 92122 USA
| | - Jinhui Ding
- grid.419475.a0000 0000 9372 4913Computational Biology Group, Laboratory of Neurogenetics, National Institute on Aging, NIH, Bethesda, MD 20892 USA
| | - Sarah Fazal
- grid.26790.3a0000 0004 1936 8606Dr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL 33136 USA
| | - Andreas Halman
- grid.1055.10000000403978434Peter MacCallum Cancer Centre, Melbourne, VIC 3000 Australia ,grid.1008.90000 0001 2179 088XSir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010 Australia
| | - Bharati Jadhav
- grid.59734.3c0000 0001 0670 2351Department of Genetics and Genomic Sciences and Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Yunjiang Qiu
- grid.185669.50000 0004 0507 3954Illumina Inc., San Diego, CA 92122 USA
| | - Phillip A. Richmond
- grid.414137.40000 0001 0684 7788BC Children’s Hospital Research Institute, Vancouver, BC V5Z 4H4 Canada
| | | | - Konrad Scheffler
- grid.185669.50000 0004 0507 3954Illumina Inc., San Diego, CA 92122 USA
| | - Joke J. F. A. van Vugt
- grid.5477.10000000120346234Department of Neurology, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | - Ramona R. A. J. Zwamborn
- grid.5477.10000000120346234Department of Neurology, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | | | - Samuel S. Chong
- grid.4280.e0000 0001 2180 6431Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228 Singapore ,grid.4280.e0000 0001 2180 6431Department of Obstetrics and Gynecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228 Singapore ,grid.412106.00000 0004 0621 9599Department of Laboratory Medicine, National University Hospital, Singapore, 119074 Singapore
| | - Jan M. Friedman
- grid.17091.3e0000 0001 2288 9830Department of Medical Genetics, University of British Columbia and Children’s & Women’s Hospital, Vancouver, BC V6H3N1 Canada
| | - Arianna Tucci
- grid.4868.20000 0001 2171 1133William Harvey Research Institute, Queen Mary University of London, London, EC1M 6BQ UK
| | - Heidi L. Rehm
- grid.66859.340000 0004 0546 1623Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, USA ,grid.32224.350000 0004 0386 9924Center for Genomic Medicine, Massachusetts General Hospital, Boston, USA
| | - Michael A. Eberle
- grid.185669.50000 0004 0507 3954Illumina Inc., San Diego, CA 92122 USA
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5
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Rajan-Babu IS, Lian M, Chong SS. Triplet-Primed PCR Assays for Accurate Screening of FMR1 CGG Repeat Expansion and Genotype Verification. Curr Protoc 2022; 2:e427. [PMID: 35609145 DOI: 10.1002/cpz1.427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Fragile X syndrome and other fragile X-associated disorders are caused by the full-mutation (>200 copies) and premutation (55 to 200 copies) expansion, respectively, of the CGG short tandem repeat in the fragile X messenger ribonucleoprotein 1 (FMR1) gene. Clinical diagnostic laboratories use Southern blot analysis and polymerase chain reaction (PCR)-based tests to detect and/or size the FMR1 CGG repeats. The development of sensitive and high-throughput triplet-primed PCR (TP-PCR) assays has diminished the need to subject all samples to Southern blot analysis, which is both labor- and time-intensive. In this article, we describe two direct TP-PCR (dTP-PCR) assays for the detection of FMR1 CGG repeat expansions. We outline a protocol that is based on melting curve analysis of dTP-PCR amplicons for a rapid and cost-effective first-tier screening and identification of individuals with premutation and full-mutation expansions. We also describe a protocol that employs capillary electrophoresis to resolve the dTP-PCR amplicon fragments and to estimate the repeat sizes of normal (5 to 44 copies), intermediate (45 to 54 copies), and premutation alleles, as well as to detect full mutations and determine the structure of the FMR1 alleles. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Direct triplet-primed PCR master mix preparation and amplification of the FMR1 CGG repeat locus for melting curve analysis Basic Protocol 2: Melting curve analysis of direct triplet-primed PCR amplicons on the Rotor-Gene Q MD × 5plex high-resolution melt platform Alternate Protocol: Melting curve analysis of direct triplet-primed PCR amplicons on the LightCycler 480 system Basic Protocol 3: Generation of direct triplet-primed PCR melting curve analysis profiles Basic Protocol 4: Direct triplet-primed PCR master mix preparation and amplification of the FMR1 CGG repeat locus for capillary electrophoresis Basic Protocol 5: Generation of control FMR1 plasmids for direct triplet-primed PCR melting curve analysis Basic Protocol 6: Sanger sequencing assay to verify FMR1 CGG repeat size and structure of plasmid DNA controls.
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Affiliation(s)
- Indhu-Shree Rajan-Babu
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada.,Children's & Women's Hospital, Vancouver, British Columbia, Canada
| | - Mulias Lian
- Khoo Teck Puat-National University Children's Medical Institute, National University Hospital, Singapore, Singapore
| | - Samuel S Chong
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Department of Obstetrics and Gynecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Department of Laboratory Medicine, National University Hospital, Singapore, Singapore
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Rajan-Babu IS, Phang GP, Law HY, Lee CG, Chong SS. High-Throughput Methylation-Specific Triplet-Primed PCR and Melting Curve Analysis for Selective and Reliable Identification of Actionable FMR1 Genotypes. J Mol Diagn 2022; 24:241-252. [PMID: 35038595 DOI: 10.1016/j.jmoldx.2021.11.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 10/26/2021] [Accepted: 11/23/2021] [Indexed: 11/17/2022] Open
Abstract
Methylated FMR1 full-mutation expansions cause fragile X syndrome. FMR1 premutation carriers are susceptible to other late-onset conditions, and women with premutation are at risk of transmitting a fully expanded FMR1 allele to offspring. Identification of individuals with actionable FMR1 genotypes (full-mutation males and females, and premutation females at risk for primary ovarian insufficiency and/or having fragile X-affected offspring) can enable timely access to intervention services and genetic counseling. This study presents a rapid, first-tier test based on melting curve analysis of methylation-specific triplet-primed PCR amplicons (msTP-PCR MCA) for concurrent detection of FMR1 CGG-repeat expansions and their methylation status. The msTP-PCR MCA assay was optimized on 20 fragile X reference samples, and its performance was evaluated on 111 peripheral blood-derived DNA samples from patients who have undergone prior molecular testing with PCR and/or Southern blot analysis. The msTP-PCR MCA assay detected all samples with a methylated FMR1 CGG-repeat expansion, and had sensitivity, specificity, positive predictive value, and negative predictive values of 100%, 92.06%, 91.1%, and 100%, respectively. The msTP-PCR MCA assay identified premutation/full-mutation mosaicism down to 1%, detected skewed inactivation in females with FMR1 expansions, and enabled selective identification of all individuals with an actionable FMR1 genotype. The msTP-PCR MCA assay may aid in fragile X screening of at-risk populations and newborns and voluntary carrier screening of women of reproductive age.
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Affiliation(s)
- Indhu-Shree Rajan-Babu
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Department of Medical Genetics, University of British Columbia, and Children's and Women's Hospital, Vancouver, British Columbia, Canada.
| | - Gui-Ping Phang
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Hai-Yang Law
- Department of Pediatric Medicine, KK Women's and Children's Hospital, Singapore
| | - Caroline G Lee
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Division of Cellular and Molecular Research, Humphrey Oei Institute of Cancer Research, National Cancer Centre Singapore, Singapore; Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Samuel S Chong
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Department of Obstetrics and Gynecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Department of Laboratory Medicine, National University Hospital, Singapore.
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Beltrán-Corbellini Á, Aledo-Serrano Á, Møller RS, Pérez-Palma E, García-Morales I, Toledano R, Gil-Nagel A. Epilepsy Genetics and Precision Medicine in Adults: A New Landscape for Developmental and Epileptic Encephalopathies. Front Neurol 2022; 13:777115. [PMID: 35250806 PMCID: PMC8891166 DOI: 10.3389/fneur.2022.777115] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 01/27/2022] [Indexed: 12/14/2022] Open
Abstract
This review aims to provide an updated perspective of epilepsy genetics and precision medicine in adult patients, with special focus on developmental and epileptic encephalopathies (DEEs), covering relevant and controversial issues, such as defining candidates for genetic testing, which genetic tests to request and how to interpret them. A literature review was conducted, including findings in the discussion and recommendations. DEEs are wide and phenotypically heterogeneous electroclinical syndromes. They generally have a pediatric presentation, but patients frequently reach adulthood still undiagnosed. Identifying the etiology is essential, because there lies the key for precision medicine. Phenotypes modify according to age, and although deep phenotyping has allowed to outline certain entities, genotype-phenotype correlations are still poor, commonly leading to long-lasting diagnostic odysseys and ineffective therapies. Recent adult series show that the target patients to be identified for genetic testing are those with epilepsy and different risk factors. The clinician should take active part in the assessment of the pathogenicity of the variants detected, especially concerning variants of uncertain significance. An accurate diagnosis implies precision medicine, meaning genetic counseling, prognosis, possible future therapies, and a reduction of iatrogeny. Up to date, there are a few tens of gene mutations with additional concrete treatments, including those with restrictive/substitutive therapies, those with therapies modifying signaling pathways, and channelopathies, that are worth to be assessed in adults. Further research is needed regarding phenotyping of adult syndromes, early diagnosis, and the development of targeted therapies.
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Affiliation(s)
| | - Ángel Aledo-Serrano
- Epilepsy Program, Neurology Department, Hospital Ruber Internacional, Madrid, Spain
- *Correspondence: Ángel Aledo-Serrano
| | - Rikke S. Møller
- Department of Epilepsy Genetics and Personalized Treatment, The Danish Epilepsy Centre, Dianalund, Denmark
| | - Eduardo Pérez-Palma
- Universidad del Desarrollo, Centro de Genética y Genómica, Facultad de Medicina Clínica Alemana, Santiago, Chile
| | - Irene García-Morales
- Epilepsy Program, Neurology Department, Hospital Ruber Internacional, Madrid, Spain
- Epilepsy Unit, Neurology Department, Clínico San Carlos University Hospital, Madrid, Spain
| | - Rafael Toledano
- Epilepsy Program, Neurology Department, Hospital Ruber Internacional, Madrid, Spain
- Epilepsy Unit, Neurology Department, Ramón y Cajal University Hospital, Madrid, Spain
| | - Antonio Gil-Nagel
- Epilepsy Program, Neurology Department, Hospital Ruber Internacional, Madrid, Spain
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Simultaneous Screening of the FRAXA and FRAXE Loci for Rapid Detection of FMR1 CGG and/or AFF2 CCG Repeat Expansions by Triplet-Primed PCR. J Mol Diagn 2021; 23:941-951. [PMID: 34111553 DOI: 10.1016/j.jmoldx.2021.04.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 03/29/2021] [Accepted: 04/29/2021] [Indexed: 11/22/2022] Open
Abstract
Moderate to hyper-expansion of trinucleotide repeats at the FRAXA and FRAXE fragile sites, with or without concurrent hypermethylation, has been associated with intellectual disability and other conditions. Unlike molecular diagnosis of FMR1 CGG repeat expansions in FRAXA, current detection of AFF2 CCG repeat expansions in FRAXE relies on low-throughput and otherwise inefficient techniques combining Southern blot analysis and PCR. A novel triplet-primed PCR assay was developed for simultaneous screening for trinucleotide repeat expansions at the FRAXA and FRAXE fragile sites, and was validated using archived clinical samples of known FMR1 and AFF2 genotypes. Population samples and FRAXE-affected samples were sequenced for the evaluation of variations in the AFF2 CCG repeat structure. The duplex assay accurately identified expansions at the FMR1 and AFF2 trinucleotide repeat loci. On Sanger sequencing of the AFF2 CCG repeat, the single-nucleotide polymorphism variant rs868914124(C) that effectively adds two CCG repeats at the 5'-end, was enriched in the Malay population and with short repeats (<11 CCGs), and was present in all six expanded AFF2 alleles of this study. All expanded AFF2 alleles contained multiple non-CCG interruptions toward the 5'-end of the repeat. A sensitive, robust, and rapid assay has been developed for the simultaneous detection of expansion mutations at the FMR1 and AFF2 trinucleotide repeat loci, simplifying screening for FRAXA- and FRAXE-associated disorders.
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9
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Lian M, Zhao M, Phang GP, Soong YT, Yoon CS, Lee CG, Law HY, Chong SS. Rapid Molecular Screen of Spinocerebellar Ataxia Types 1, 2, and 3 by Triplet-Primed PCR and Melting Curve Analysis. J Mol Diagn 2021; 23:565-576. [PMID: 33618058 DOI: 10.1016/j.jmoldx.2021.01.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 12/02/2020] [Accepted: 01/12/2021] [Indexed: 11/16/2022] Open
Abstract
The autosomal dominantly inherited spinocerebellar ataxias (SCAs) can be caused by dynamic mutations of short tandem repeats within various genes. Because of the significant clinical overlap among the various SCA types, molecular screening of multiple genetic loci by fluorescent PCR and capillary electrophoresis is necessary to identify the causative repeat expansion. We describe a simple, rapid, and inexpensive strategy to screen for CAG repeat expansion mutations at the ATXN1, ATXN2, and ATXN3 loci using melting curve analysis of triplet-primed PCR products. Plasmid DNAs of known repeat sizes were used to generate threshold melt peak temperatures, which rapidly and effectively distinguish samples carrying an expanded allele from those carrying nonexpanded alleles. Melting curve analysis-positive samples were confirmed by capillary electrophoresis sizing of the triplet-primed PCR products. All three assays achieved 100% sensitivity, with 95% CIs of 67.86% to 100% (SCA1), 74.65% to 100% (SCA2), and 91.58% to 100% (SCA3). The SCA1 assay also achieved 100% specificity (95% CI, 97.52%-100%), whereas the SCA2 and SCA3 assays achieved specificity of 99.46% (95% CI, 96.56%-99.97%) and 99.32% (95% CI, 95.70%-99.96%), respectively. These screening assays provide robust and highly accurate detection of expanded alleles and are amenable to large-scale screening while minimizing the need for capillary electrophoresis sizing for every sample.
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Affiliation(s)
- Mulias Lian
- Khoo Teck Puat-National University Children's Medical Institute, National University Health System, Singapore
| | - Mingjue Zhao
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Gui-Ping Phang
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Yun-Ting Soong
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Chui-Sheun Yoon
- Department of Pediatric Medicine, KK Women's and Children's Hospital, Singapore
| | - Caroline G Lee
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Cancer and Stem Cell Biology Program, Duke-NUS Graduate Medical School, Singapore; Division of Medical Sciences, National Cancer Center Singapore, Singapore
| | - Hai-Yang Law
- Department of Pediatric Medicine, KK Women's and Children's Hospital, Singapore; Pediatrics Academic Clinical Program, Duke-NUS Graduate Medical School, Singapore
| | - Samuel S Chong
- Khoo Teck Puat-National University Children's Medical Institute, National University Health System, Singapore; Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Department of Laboratory Medicine, National University Hospital, Singapore.
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10
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Lian DS, Chen XY, Zeng HS, Wang YY. Capillary electrophoresis based on nucleic acid analysis for diagnosing inherited diseases. Clin Chem Lab Med 2020; 59:249-266. [PMID: 32374277 DOI: 10.1515/cclm-2020-0186] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 04/04/2020] [Indexed: 11/15/2022]
Abstract
Most hereditary diseases are incurable, but their deterioration could be delayed or stopped if diagnosed timely. It is thus imperative to explore the state-of-the-art and high-efficient diagnostic techniques for precise analysis of the symptoms or early diagnosis of pre-symptoms. Diagnostics based on clinical presentations, hard to distinguish different phenotypes of the same genotype, or different genotypes displaying similar phenotypes, are incapable of pre-warning the disease status. Molecular diagnosis is ahead of harmful phenotype exhibition. However, conventional gold-standard molecular classifications, such as karyotype analysis, Southern blotting (SB) and sequencing, suffer drawbacks like low automation, low throughput, prolonged duration, being labor intensive and high cost. Also, deficiency in flexibility and diversity is observed to accommodate the development of precise and individualized diagnostics. The aforementioned pitfalls make them unadaptable to the increasing clinical demand for detecting and interpreting numerous samples in a rapid, accurate, high-throughput and cost-effective manner. Nevertheless, capillary electrophoresis based on genetic information analysis, with advantages of automation, high speed, high throughput, high efficiency, high resolution, digitization, versatility, miniature and cost-efficiency, coupled with flexible-designed PCR strategies in sample preparation (PCR-CE), exhibit an excellent power in deciphering cryptic molecular information of superficial symptoms of genetic diseases, and can analyze in parallel a large number of samples in a single PCR-CE, thereby providing an alternative, accurate, customized and timely diagnostic tool for routine screening of clinical samples on a large scale. Thus, the present study focuses on CE-based nucleic acid analysis used for inherited disease diagnosis. Also, the limitations and challenges of this PCR-CE for diagnosing hereditary diseases are discussed.
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Affiliation(s)
- Dong-Sheng Lian
- Guangzhou Women and Children's Medical Center of Guangzhou Medical University, NO. 9 at Jinsui Rd., Tianhe District, Guangzhou, Guangdong, P.R. China.,Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, P.R. China
| | - Xiang-Yuan Chen
- Guangzhou Women and Children's Medical Center of Guangzhou Medical University, NO. 9 at Jinsui Rd., Tianhe District, Guangzhou, Guangdong, P.R. China
| | - Hua-Song Zeng
- Guangzhou Women and Children's Medical Center of Guangzhou Medical University, NO. 9 at Jinsui Rd., Tianhe District, Guangzhou, Guangdong, P.R. China
| | - Yan-Yi Wang
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, P.R. China
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11
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Rajan-Babu IS, Chong SS. Triplet-Repeat Primed PCR and Capillary Electrophoresis for Characterizing the Fragile X Mental Retardation 1 CGG Repeat Hyperexpansions. Methods Mol Biol 2019; 1972:199-210. [PMID: 30847793 DOI: 10.1007/978-1-4939-9213-3_14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Fragile X mental retardation 1 (FMR1) CGG repeat expansions cause fragile X syndrome-the leading monogenic form of intellectual disability-and increase the risk for fragile X-associated tremor ataxia syndrome and fragile X-associated primary ovarian insufficiency. Southern blot (SB) analysis is the current gold standard test for FMR1 molecular diagnosis. Several polymerase chain reaction (PCR)-based methods are now available for sizing FMR1 CGG repeat expansions. These methods offer higher diagnostic sensitivity and specificity compared to SB analysis, significantly reduce the turnaround time and increase throughput. In this chapter, we describe a triplet-repeat primed PCR protocol that employs capillary electrophoresis to resolve the derived amplicon products, enabling precise determination of the FMR1 genotypes in both males and females and characterization of the CGG repeat structure.
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Affiliation(s)
- Indhu-Shree Rajan-Babu
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Department of Medical Genetics, The University of British Columbia, Vancouver, BC, Canada
| | - Samuel S Chong
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore. .,Khoo Teck Puat-National University Children's Medical Institute, National University Health System, Singapore, Singapore. .,Department of Laboratory Medicine, National University Hospital, Singapore, Singapore.
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12
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Tan VJ, Lian M, Faradz SMH, Winarni TI, Chong SS. A Single Common Assay for Robust and Rapid Fragile X Mental Retardation Syndrome Screening From Dried Blood Spots. Front Genet 2018; 9:582. [PMID: 30538724 PMCID: PMC6277581 DOI: 10.3389/fgene.2018.00582] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 11/08/2018] [Indexed: 12/24/2022] Open
Abstract
Background:FMR1 CGG trinucleotide repeat hyper-expansions are observed in 99% of individuals with fragile X mental retardation syndrome (FXS). We evaluated the reliability of a rapid single-step gender-neutral molecular screen for FXS when performed on DNA isolated from dried blood spots. Methods: DNA was extracted from dried blood spots of 151 individuals with intellectual disability or autism spectrum disorder, whose FMR1 repeat genotypes are known. Dried blood spots were blinded prior to DNA extraction and analysis by triplet primed PCR (TP-PCR) and melt curve analysis (MCA). All expansion-positive and representative expansion-negative samples were also genotyped by fluorescent TP-PCR and capillary electrophoresis (CE) to confirm repeat expansion status. Results: Three males and 12 females were classified as expanded by TP-PCR MCA, and were subsequently sized by fluorescent TP-PCR CE. Two males and four females carried premutations, while one male and eight females carried full mutations. All 19 non-expanded samples that were sized were confirmed as carrying only normal alleles. Replicate analysis of representative expansion-positive samples yielded reproducible melt peak profiles. TP-PCR MCA classifications were completely concordant with FMR1 CGG repeat genotypes. Conclusion: TP-PCR MCA of dried blood spot DNA accurately and reliably identifies presence/absence of FMR1 CGG repeat expansions in both genders simultaneously. This strategy may be suitable for rapid high-throughput first-tier screening for fragile X syndrome.
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Affiliation(s)
- Vivienne J Tan
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Mulias Lian
- Khoo Teck Puat - National University Children's Medical Institute, National University Health System, Singapore, Singapore
| | - Sultana M H Faradz
- Division of Human Genetics, Center for Biomedical Research, Faculty of Medicine, Diponegoro University, Semarang, Indonesia
| | - Tri I Winarni
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Khoo Teck Puat - National University Children's Medical Institute, National University Health System, Singapore, Singapore.,Division of Human Genetics, Center for Biomedical Research, Faculty of Medicine, Diponegoro University, Semarang, Indonesia.,Department of Laboratory Medicine, National University Hospital, National University Health System, Singapore, Singapore
| | - Samuel S Chong
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Khoo Teck Puat - National University Children's Medical Institute, National University Health System, Singapore, Singapore.,Department of Laboratory Medicine, National University Hospital, National University Health System, Singapore, Singapore
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13
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Miao Z, Liu X, Li W, He Q, Liu X. Assessment of efficacy of prenatal genetic diagnosis for fragile X syndrome using nested PCR. Exp Ther Med 2018; 15:5107-5112. [PMID: 29844802 DOI: 10.3892/etm.2018.6060] [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: 07/03/2017] [Accepted: 11/01/2017] [Indexed: 11/06/2022] Open
Abstract
Fragile X syndrome (FXS) is the most common inherited cause of intellectual disability and the leading monogenic cause of autism spectrum disorder. It has previously been demonstrated that prenatal genetic diagnosis is efficient for the diagnosis of FXS. The present study investigated the diagnostic effects of nested polymerase chain reaction (PCR) for fragile X mental retardation 1 (FMR1) and expanded CGG repeats. It was demonstrated that the nested PCR assay rapidly measured the multi-copies of the FMR1 gene in individual samples. The nested PCR assay detected normal CGG repeat lengths and expanded CGG repeat lengths with a low occurrence of false positives. In addition, the nested PCR assay resulted in increased sensitivity and specificity for patients with FXS. Furthermore, the nested PCR assay identified the mutation and generated conclusive cases for FXS, indicating that this assay is beneficial for the diagnosis of FXS patients. In conclusion, these outcomes indicate that nested PCR assay is a reliable and easier method for diagnosis of FXS, which may be used for the diagnosis of FXS patients.
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Affiliation(s)
- Zhengyou Miao
- Jiaxing Maternity and Child Health Care Hospital, Jiaxing, Zhejiang 314000, P.R. China.,Hangzhou Bio-San Biochemical Technologies Co. Ltd., Hangzhou, Zhejiang 310007, P.R. China
| | - Xiaodan Liu
- Jiaxing Maternity and Child Health Care Hospital, Jiaxing, Zhejiang 314000, P.R. China.,Hangzhou Bio-San Biochemical Technologies Co. Ltd., Hangzhou, Zhejiang 310007, P.R. China
| | - Weiwei Li
- Jiaxing Maternity and Child Health Care Hospital, Jiaxing, Zhejiang 314000, P.R. China.,Hangzhou Bio-San Biochemical Technologies Co. Ltd., Hangzhou, Zhejiang 310007, P.R. China
| | - Qunyan He
- Jiaxing Maternity and Child Health Care Hospital, Jiaxing, Zhejiang 314000, P.R. China.,Hangzhou Bio-San Biochemical Technologies Co. Ltd., Hangzhou, Zhejiang 310007, P.R. China
| | - Xia Liu
- Jiaxing Maternity and Child Health Care Hospital, Jiaxing, Zhejiang 314000, P.R. China.,Hangzhou Bio-San Biochemical Technologies Co. Ltd., Hangzhou, Zhejiang 310007, P.R. China
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14
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Landowska A, Rzońca S, Bal J, Gos M. [Fragile X syndrome and FMR1-dependent diseases - diagnostic scheme based on own experience .]. DEVELOPMENTAL PERIOD MEDICINE 2018; 22. [PMID: 29641418 PMCID: PMC8522923 DOI: 10.34763/devperiodmed.20182201.2232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The presence of dynamic mutation in the FMR1 gene localized on the X chromosome (Xq28) is the major cause of Fragile X syndrome. As this syndrome is quite frequently diagnosed in patients with intellectual disability and autism spectrum disorders, the genetic testing of the FMR1 gene is a routine procedure performed in these patients. Molecular methods based on the PCR technique are used commonly, as they allow to identify normal (up to 54 CGG repeats, including grey zone alleles - 45-54 CGG repeats), premutation (55-200 CGG repeats) and full mutation (>200 CGG repeats) alleles.The article presents the basic methods used in the molecular diagnosis of Fragile X syndrome and other FMR1-related disorders. The following methods are presented: a screening test with GeneScan analysis, TP-PCR based tests and methods used for methylation analysis. Their pros and cons, as well as the resulting interpretation are discussed. Moreover, there is a presentation of the molecular diagnostic scheme following European Molecular Genetics Quality Network guidelines used in the Department of Medical Genetics.
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Affiliation(s)
- Aleksandra Landowska
- Zakład Genetyki Medycznej, Instytut Matki i Dziecka, Warszawa, Polska,Aleksandra LandowskaZakład Genetyki Medycznej, Instytut Matki i Dzieckaul. Kasprzaka 17a, 01-211 Warszawatel. (+48 22) 327-71-76
| | - Sylwia Rzońca
- Zakład Genetyki Medycznej, Instytut Matki i Dziecka, Warszawa, Polska
| | - Jerzy Bal
- Zakład Genetyki Medycznej, Instytut Matki i Dziecka, Warszawa, Polska
| | - Monika Gos
- Zakład Genetyki Medycznej, Instytut Matki i Dziecka, Warszawa, Polska
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15
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Hayward BE, Kumari D, Usdin K. Recent advances in assays for the fragile X-related disorders. Hum Genet 2017; 136:1313-1327. [PMID: 28866801 DOI: 10.1007/s00439-017-1840-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 08/24/2017] [Indexed: 12/17/2022]
Abstract
The fragile X-related disorders are a group of three clinical conditions resulting from the instability of a CGG-repeat tract at the 5' end of the FMR1 transcript. Fragile X-associated tremor/ataxia syndrome (FXTAS) and fragile X-associated primary ovarian insufficiency (FXPOI) are disorders seen in carriers of FMR1 alleles with 55-200 repeats. Female carriers of these premutation (PM) alleles are also at risk of having a child who has an FMR1 allele with >200 repeats. Most of these full mutation (FM) alleles are epigenetically silenced resulting in a deficit of the FMR1 gene product, FMRP. This results in fragile X Syndrome (FXS), the most common heritable cause of intellectual disability and autism. The diagnosis and study of these disorders is challenging, in part because the detection of alleles with large repeat numbers has, until recently, been either time-consuming or unreliable. This problem is compounded by the mosaicism for repeat length and/or DNA methylation that is frequently seen in PM and FM carriers. Furthermore, since AGG interruptions in the repeat tract affect the risk that a FM allele will be maternally transmitted, the ability to accurately detect these interruptions in female PM carriers is an additional challenge that must be met. This review will discuss some of the pros and cons of some recently described assays for these disorders, including those that detect FMRP levels directly, as well as emerging technologies that promise to improve the diagnosis of these conditions and to be useful in both basic and translational research settings.
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Affiliation(s)
- Bruce E Hayward
- Section on Gene Structure and Disease, Laboratory of Cell and Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, Building 8, Room 2A19, National Institutes of Health, 8 Center Drive MSC 0830, Bethesda, MD, 20892, USA
| | - Daman Kumari
- Section on Gene Structure and Disease, Laboratory of Cell and Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, Building 8, Room 2A19, National Institutes of Health, 8 Center Drive MSC 0830, Bethesda, MD, 20892, USA
| | - Karen Usdin
- Section on Gene Structure and Disease, Laboratory of Cell and Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, Building 8, Room 2A19, National Institutes of Health, 8 Center Drive MSC 0830, Bethesda, MD, 20892, USA.
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16
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FMR1 CGG repeat expansion mutation detection and linked haplotype analysis for reliable and accurate preimplantation genetic diagnosis of fragile X syndrome. Expert Rev Mol Med 2017; 19:e10. [PMID: 28720156 PMCID: PMC5733830 DOI: 10.1017/erm.2017.10] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Fragile X mental retardation 1 (FMR1) full-mutation expansion causes fragile X syndrome. Trans-generational fragile X syndrome transmission can be avoided by preimplantation genetic diagnosis (PGD). We describe a robust PGD strategy that can be applied to virtually any couple at risk of transmitting fragile X syndrome. This novel strategy utilises whole-genome amplification, followed by triplet-primed polymerase chain reaction (TP-PCR) for robust detection of expanded FMR1 alleles, in parallel with linked multi-marker haplotype analysis of 13 highly polymorphic microsatellite markers located within 1 Mb of the FMR1 CGG repeat, and the AMELX/Y dimorphism for gender identification. The assay was optimised and validated on single lymphoblasts isolated from fragile X reference cell lines, and applied to a simulated PGD case and a clinical in vitro fertilisation (IVF)-PGD case. In the simulated PGD case, definitive diagnosis of the expected results was achieved for all ‘embryos’. In the clinical IVF-PGD case, delivery of a healthy baby girl was achieved after transfer of an expansion-negative blastocyst. FMR1 TP-PCR reliably detects presence of expansion mutations and obviates reliance on informative normal alleles for determining expansion status in female embryos. Together with multi-marker haplotyping and gender determination, misdiagnosis and diagnostic ambiguity due to allele dropout is minimised, and couple-specific assay customisation can be avoided.
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17
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Lim GXY, Yeo M, Koh YY, Winarni TI, Rajan-Babu IS, Chong SS, Faradz SMH, Guan M. Validation of a commercially available test that enables the quantification of the numbers of CGG trinucleotide repeat expansion in FMR1 gene. PLoS One 2017; 12:e0173279. [PMID: 28278294 PMCID: PMC5344422 DOI: 10.1371/journal.pone.0173279] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 02/13/2017] [Indexed: 11/26/2022] Open
Abstract
In the present study, we evaluated a commercially available TP-PCR-based assay, the FastFraXTMFMR1 Sizing kit, as a test in quantifying the number of CGG repeats in the FMR1 gene. Based on testing with well characterized DNA samples from Coriell, the kit yielded size results within 3 repeats of those obtained by common consensus (n = 14), with the exception of one allele. Furthermore, based on data obtained using all Coriell samples with or without common consensus (n = 29), the Sizing kit was 97.5% in agreement with existing approaches. Additionally, the kit generated consistent size information in repeatability and reproducibility studies (CV 0.39% to 3.42%). Clinical performance was established with 198 archived clinical samples, yielding results of 100% sensitivity (95% CI, 91.03% to 100%) and 100% specificity (95% CI, 97.64% to 100%) in categorizing patient samples into the respective normal, intermediate, premutation and full mutation genotypes.
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Affiliation(s)
| | - Minli Yeo
- The BioFactory Pte Ltd, Singapore, Singapore
| | | | - Tri Indah Winarni
- Division of Human Genetics, Center for Biomedical Research, Faculty of Medicine, Diponegoro University, Semarang, Indonesia
| | - Indhu-Shree Rajan-Babu
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Samuel S. Chong
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Khoo Teck Puat–National University Children’s Medical Institute, National University Health System, Singapore, Singapore
- Department of Laboratory Medicine, National University Hospital, Singapore, Singapore
| | - Sultana M. H. Faradz
- Division of Human Genetics, Center for Biomedical Research, Faculty of Medicine, Diponegoro University, Semarang, Indonesia
| | - Ming Guan
- The BioFactory Pte Ltd, Singapore, Singapore
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18
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Molecular Correlates and Recent Advancements in the Diagnosis and Screening of FMR1-Related Disorders. Genes (Basel) 2016; 7:genes7100087. [PMID: 27754417 PMCID: PMC5083926 DOI: 10.3390/genes7100087] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 10/06/2016] [Accepted: 10/08/2016] [Indexed: 12/12/2022] Open
Abstract
Fragile X syndrome (FXS) is the most common monogenic cause of intellectual disability and autism. Molecular diagnostic testing of FXS and related disorders (fragile X-associated primary ovarian insufficiency (FXPOI) and fragile X-associated tremor/ataxia syndrome (FXTAS)) relies on a combination of polymerase chain reaction (PCR) and Southern blot (SB) for the fragile X mental retardation 1 (FMR1) CGG-repeat expansion and methylation analyses. Recent advancements in PCR-based technologies have enabled the characterization of the complete spectrum of CGG-repeat mutation, with or without methylation assessment, and, as a result, have reduced our reliance on the labor- and time-intensive SB, which is the gold standard FXS diagnostic test. The newer and more robust triplet-primed PCR or TP-PCR assays allow the mapping of AGG interruptions and enable the predictive analysis of the risks of unstable CGG expansion during mother-to-child transmission. In this review, we have summarized the correlation between several molecular elements, including CGG-repeat size, methylation, mosaicism and skewed X-chromosome inactivation, and the extent of clinical involvement in patients with FMR1-related disorders, and reviewed key developments in PCR-based methodologies for the molecular diagnosis of FXS, FXTAS and FXPOI, and large-scale (CGG)n expansion screening in newborns, women of reproductive age and high-risk populations.
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19
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Rajan-Babu IS, Lian M, Tran AH, Dang TT, Le HTM, Thanh MN, Lee CG, Chong SS. Defining the Performance Parameters of a Rapid Screening Tool for FMR1 CGG-Repeat Expansions Based on Direct Triplet-Primed PCR and Melt Curve Analysis. J Mol Diagn 2016; 18:719-730. [DOI: 10.1016/j.jmoldx.2016.05.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 04/01/2016] [Accepted: 05/02/2016] [Indexed: 12/12/2022] Open
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20
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Schenkel LC, Schwartz C, Skinner C, Rodenhiser DI, Ainsworth PJ, Pare G, Sadikovic B. Clinical Validation of Fragile X Syndrome Screening by DNA Methylation Array. J Mol Diagn 2016; 18:834-841. [PMID: 27585064 DOI: 10.1016/j.jmoldx.2016.06.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 06/14/2016] [Accepted: 06/21/2016] [Indexed: 01/11/2023] Open
Abstract
Fragile X syndrome (FXS) is the most common inherited cause of intellectual disability. It is most frequently caused by an abnormal expansion of the CGG trinucleotide repeat (>200 repeats) located in the promoter of the fragile X mental retardation gene (FMR1), resulting in promoter DNA hypermethylation and gene silencing. Current clinical tests for FXS are technically challenging and labor intensive, and may involve use of hazardous chemicals or radioisotopes. We clinically validated the Illumina Infinium HumanMethylation450 DNA methylation array for FXS screening. We assessed genome-wide and FMR1-specific DNA methylation in 32 males previously diagnosed with FXS, including nine with mosaicism, as well as five females with full mutation, and premutation carrier males (n = 11) and females (n = 11), who were compared to 300 normal control DNA samples. Our findings demonstrate 100% sensitivity and specificity for detection of FXS in male patients, as well as the ability to differentiate patients with mosaic methylation defects. Full mutation and premutation carrier females did not show FMR1 methylation changes. We have clinically validated this genome-wide DNA methylation assay as a cost- and labor-effective alternative for sensitive and specific screening for FXS, while ruling out the most common differential diagnoses of FXS, Prader-Willi syndrome, and Sotos syndrome in the same assay.
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Affiliation(s)
- Laila C Schenkel
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
| | - Charles Schwartz
- Center for Molecular Studies, J.C. Self Research Institute of Human Genetics, Greenwood Genetic Center, Greenwood, South Carolina
| | - Cindy Skinner
- Center for Molecular Studies, J.C. Self Research Institute of Human Genetics, Greenwood Genetic Center, Greenwood, South Carolina
| | - David I Rodenhiser
- Department of Biochemistry, Oncology and Paediatrics, Western University, London, Ontario, Canada; London Regional Cancer Program, London Health Sciences Center, London, Ontario, Canada; Children's Health Research Institute, London Health Sciences Center, London, Ontario, Canada
| | - Peter J Ainsworth
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada; Department of Biochemistry, Oncology and Paediatrics, Western University, London, Ontario, Canada; London Regional Cancer Program, London Health Sciences Center, London, Ontario, Canada; Children's Health Research Institute, London Health Sciences Center, London, Ontario, Canada; Molecular Genetics Laboratory, London Health Sciences Center, London, Ontario, Canada
| | - Guillaume Pare
- Departments of Pathology and Molecular Medicine and Clinical Epidemiology and Biostatistics, McMaster University, Hamilton, Ontario, Canada
| | - Bekim Sadikovic
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada; London Regional Cancer Program, London Health Sciences Center, London, Ontario, Canada; Children's Health Research Institute, London Health Sciences Center, London, Ontario, Canada; Molecular Genetics Laboratory, London Health Sciences Center, London, Ontario, Canada.
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21
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Hayward BE, Zhou Y, Kumari D, Usdin K. A Set of Assays for the Comprehensive Analysis of FMR1 Alleles in the Fragile X-Related Disorders. J Mol Diagn 2016; 18:762-774. [PMID: 27528259 DOI: 10.1016/j.jmoldx.2016.06.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 05/24/2016] [Accepted: 06/01/2016] [Indexed: 12/16/2022] Open
Abstract
The diagnosis and study of the fragile X-related disorders is complicated by the difficulty of amplifying the long CGG/CCG-repeat tracts that are responsible for disease pathology, the potential presence of AGG interruptions within the repeat tract that can ameliorate expansion risk, the occurrence of variable DNA methylation that modulates disease severity, and the high frequency of mosaicism for both repeat number and methylation status. These factors complicate patient risk assessment. In addition, the variability in these parameters that is seen when patient cells are grown in culture requires their frequent monitoring to ensure reproducible results in a research setting. Many existing assays have the limited ability to amplify long alleles, particularly in a mixture of different allele sizes. Others are better at this, but are too expensive for routine use in most laboratories or for newborn screening programs and use reagents that are proprietary. We describe herein a set of assays to routinely evaluate all of these important parameters in a time- and cost-effective way.
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Affiliation(s)
- Bruce E Hayward
- Section on Gene Structure and Disease, Laboratory of Cell and Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
| | - Yifan Zhou
- Section on Gene Structure and Disease, Laboratory of Cell and Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
| | - Daman Kumari
- Section on Gene Structure and Disease, Laboratory of Cell and Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
| | - Karen Usdin
- Section on Gene Structure and Disease, Laboratory of Cell and Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland.
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