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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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Carter MT, Srour M, Au PYB, Buhas D, Dyack S, Eaton A, Inbar-Feigenberg M, Howley H, Kawamura A, Lewis SME, McCready E, Nelson TN, Vallance H. Genetic and metabolic investigations for neurodevelopmental disorders: position statement of the Canadian College of Medical Geneticists (CCMG). J Med Genet 2023; 60:523-532. [PMID: 36822643 DOI: 10.1136/jmg-2022-108962] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 01/27/2023] [Indexed: 02/25/2023]
Abstract
PURPOSE AND SCOPE The aim of this position statement is to provide recommendations for clinicians regarding the use of genetic and metabolic investigations for patients with neurodevelopmental disorders (NDDs), specifically, patients with global developmental delay (GDD), intellectual disability (ID) and/or autism spectrum disorder (ASD). This document also provides guidance for primary care and non-genetics specialists caring for these patients while awaiting consultation with a clinical geneticist or metabolic specialist. METHODS OF STATEMENT DEVELOPMENT A multidisciplinary group reviewed existing literature and guidelines on the use of genetic and metabolic investigations for the diagnosis of NDDs and synthesised the evidence to make recommendations relevant to the Canadian context. The statement was circulated for comment to the Canadian College of Medical Geneticists (CCMG) membership-at-large and to the Canadian Pediatric Society (Mental Health and Developmental Disabilities Committee); following incorporation of feedback, it was approved by the CCMG Board of Directors on 1 September 2022. RESULTS AND CONCLUSIONS Chromosomal microarray is recommended as a first-tier test for patients with GDD, ID or ASD. Fragile X testing should also be done as a first-tier test when there are suggestive clinical features or family history. Metabolic investigations should be done if there are clinical features suggestive of an inherited metabolic disease, while the patient awaits consultation with a metabolic physician. Exome sequencing or a comprehensive gene panel is recommended as a second-tier test for patients with GDD or ID. Genetic testing is not recommended for patients with NDDs in the absence of GDD, ID or ASD, unless accompanied by clinical features suggestive of a syndromic aetiology or inherited metabolic disease.
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Affiliation(s)
| | - Myriam Srour
- Division of Neurology, McGill University Health Centre, Montreal, Québec, Canada
- Department of Pediatrics, McGill University, Montréal, QC, Canada
| | - Ping-Yee Billie Au
- Department of Medical Genetics, Alberta Children's Hospital, Calgary, Alberta, Canada
| | - Daniela Buhas
- Division of Medical Genetics, Department of Specialized Medicine, McGill University Health Centre, McGill University, Montreal, Québec, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Sarah Dyack
- Division of Medical Genetics, IWK Health Centre, Halifax, Nova Scotia, Canada
- Department of Pediatrics, Dalhousie University, Halifax, NS, Canada
| | - Alison Eaton
- Department of Medical Genetics, Stollery Children's Hospital, Edmonton, Alberta, Canada
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada
| | - Michal Inbar-Feigenberg
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Heather Howley
- Office of Research Services, CHEO Research Institute, Ottawa, Ontario, Canada
| | - Anne Kawamura
- Division of Developmental Pediatrics, Holland Bloorview Kids Rehabilitation Hospital, Toronto, Ontario, Canada
- Department of Paediatrics, University of Toronto, Toronto, ON, Canada
- Mental Health and Developmental Disability Committee, Canadian Pediatric Society, Ottawa, ON, Canada
- Canadian Paediatric Society, Toronto, Ontario, Canada
| | - Suzanne M E Lewis
- Department of Medical Genetics, BC Children's and Women's Hospital, Vancouver, British Columbia, Canada
| | - Elizabeth McCready
- Department of Pathology and Molecular Medicine, McMaster University, McMaster University, Hamilton, ON, Canada, Hamilton, Ontario, Canada
- Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences Centre, Hamilton, ON, Canada
| | - Tanya N Nelson
- Department of Pathology and Laboratory Medicine, BC Children's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
| | - Hilary Vallance
- Department of Pathology and Laboratory Medicine, BC Children's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
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Owens KM, Terhaar C, Zdrodowski J, Johnson LR, Eveleigh D. Refining reproductive risk for FMR1 premutation carriers in the general obstetric population. Am J Med Genet A 2022; 188:1476-1481. [PMID: 35129870 DOI: 10.1002/ajmg.a.62666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 08/31/2021] [Accepted: 01/06/2022] [Indexed: 11/08/2022]
Abstract
Female FMR1 premutation (FMR1 PM) carriers for fragile X syndrome (FXS) are at risk to have a child with FXS based on their CGG repeat size and AGG interruption number. Studies examining this risk in unselected populations of female PM carriers are lacking. This retrospective cohort study analyzed carrier status, CGG repeat length, AGG interruption result, and reproductive risk refinement in a population of female patients who underwent routine carrier screening for FXS. A total of 1536 PM carriers (0.43%) were identified, 95% of whom had between 55 and 90 CGG repeats. A number of 1334 carriers underwent AGG interruption testing. The majority had at least one AGG interruption and received a lower reproductive risk for FXS following AGG interruption testing (89% and 85%, respectively) as compared to their risk calculated based on CGG repeat size alone. The average change in risk across the population following AGG interruption testing was -3.4%, with a range from -50.8% to 48.9%. This article describes the range of CGG repeats and AGG interruptions in an unselected population of female PM carriers and suggests that most carriers would benefit from AGG interruption testing to refine their reproductive risk of having a child with FXS.
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Hnoonual A, Jankittunpaiboon C, Limprasert P. Screening for FMR1 CGG Repeat Expansion in Thai Patients with Autism Spectrum Disorder. BIOMED RESEARCH INTERNATIONAL 2021; 2021:4359308. [PMID: 34926684 PMCID: PMC8674057 DOI: 10.1155/2021/4359308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 11/07/2021] [Accepted: 11/26/2021] [Indexed: 11/30/2022]
Abstract
Autism spectrum disorder (ASD) is a complex disorder with a heterogeneous etiology. Fragile X syndrome (FXS) is recognized as the most common single gene mutation associated with ASD. FXS patients show some autistic behaviors and may be difficult to distinguish at a young age from autistic children. However, there have been no published reports on the prevalence of FXS in ASD patients in Thailand. In this study, we present a pilot study to analyze the CGG repeat sizes of the FMR1 gene in Thai autistic patients. We screened 202 unrelated Thai patients (168 males and 34 females) with nonsyndromic ASD and 212 normal controls using standard FXS molecular diagnosis techniques. The distributions of FMR1 CGG repeat sizes in the ASD and normal control groups were similar, with the two most common alleles having 29 and 30 CGG repeats, followed by an allele with 36 CGG repeats. No FMR1 full mutations or premutations were found in either ASD individuals or the normal controls. Interestingly, three ASD male patients with high normal CGG and intermediate CGG repeats (44, 46, and 53 CGG repeats) were identified, indicating that the prevalence of FMR1 intermediate alleles in Thai ASD patients was approximately 1% while these alleles were absent in the normal male controls. Our study indicates that CGG repeat expansions of the FMR1 gene may not be a common genetic cause of nonsyndromic ASD in Thai patients. However, further studies for mutations other than the CGG expansion in the FMR1 gene are required to get a better information on FXS prevalence in Thai ASD patients.
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Affiliation(s)
- Areerat Hnoonual
- Department of Pathology, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand
| | | | - Pornprot Limprasert
- Department of Pathology, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand
- Faculty of Medicine, Siam University, Bangkok 10160, Thailand
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Frequency of FMR1 Premutation Alleles in Patients with Undiagnosed Cerebellar Ataxia and Multiple System Atrophy in the Japanese Population. CEREBELLUM (LONDON, ENGLAND) 2021; 21:954-962. [PMID: 34845661 DOI: 10.1007/s12311-021-01329-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 09/26/2021] [Indexed: 10/19/2022]
Abstract
Fragile X-associated tremor/ataxia syndrome (FXTAS) is an adult-onset neurodegenerative disorder caused by FMR1 premutation expansion of CGG repeats. FXTAS can be misdiagnosed with many neurodegenerative disorders manifesting with cerebellar ataxias owing to their overlapping clinical and radiological features. The frequency of the FMR1 premutation allele in Japan has not been fully determined. Herein, we aimed to determine the frequency of FMR1 premutation alleles in Japanese patients with undiagnosed cerebellar ataxia and multiple system atrophy, using repeat-primed PCR in 186 patients with adult onset of undiagnosed cerebellar ataxia and 668 patients with multiple system atrophy, to identify expanded CGG repeats as well as to detect AGG interruptions within the expanded alleles. The size of expansions was estimated using fragment length analysis of PCR products obtained by conventional PCR employing a pair of unique primers flanking the repeat sequence. We identified FMR1 premutation alleles in three male patients. One patient revealed 84 repeat units with one AGG interruption and another patient showed 103 repeat units. Both had presented with sporadic cerebellar ataxia, giving an estimated frequency of 3.7% among Japanese male patients with sporadic cerebellar ataxia with age at onset above 50 years. One patient with the clinical diagnosis of multiple system atrophy harbored 60 repeat units with four AGG interruptions. FMR1 intermediate alleles were observed in two males and one female among the multiple system atrophy patients. We found that genetic tests for FMR1 premutation should be considered in Japanese male patients with cerebellar ataxia with the age at onset above 50 years.
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Marrus N, Turner TN, Forsen E, Bolster D, Marvin A, Whitehouse A, Klinger L, Gurnett CA, Constantino JN. Genetic counseling as preventive intervention: toward individual specification of transgenerational autism risk. J Neurodev Disord 2021; 13:39. [PMID: 34530736 PMCID: PMC8447585 DOI: 10.1186/s11689-021-09389-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 05/11/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Although autism spectrum disorders (ASD) are among the most heritable of all neuropsychiatric syndromes, most affected children are born to unaffected parents. Recently, we reported an average increase of 3-5% over general population risk of ASD among offspring of adults who have first-degree relatives with ASD in a large epidemiologic family sample. A next essential step is to investigate whether there are measurable characteristics of individual parents placing them at higher or lower recurrence risk, as this information could allow more personalized genetic counseling. METHODS We assembled what is to our knowledge the largest collection of data on the ability of four measurable characteristics of unaffected prospective parents to specify risk for autism among their offspring: (1) sub clinical autistic trait burden, (2) parental history of a sibling with ASD, (3) transmitted autosomal molecular genetic abnormalities, and (4) parental age. Leveraging phenotypic and genetic data in curated family cohorts, we evaluate the respective associations between these factors and child outcome when autism is present in the family in the parental generation. RESULTS All four characteristics were associated with elevation in offspring risk; however, the magnitude of their predictive power-with the exception of isolated rare inherited pathogenic variants -does not yet reach a threshold that would typically be considered actionable for reproductive decision-making. CONCLUSIONS Individual specification of risk to offspring of adults in ASD-affected families is not straightforwardly improved by ascertainment of parental phenotype, and it is not yet clear whether genomic screening of prospective parents in families affected by idiopathic ASD is warranted as a clinical standard. Systematic screening of affected family members for heritable pathogenic variants, including rare sex-linked mutations, will identify a subset of families with substantially elevated transmission risk. Polygenic risk scores are only weakly predictive at this time but steadily improving and ultimately may enable more robust prediction either singly or when combined with the risk variables examined in this study.
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Affiliation(s)
- Natasha Marrus
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave; Box 8504, St. Louis, MO, 63110, USA.
| | - Tychele N Turner
- Department of Genetics, Washington University School of Medicine, 660 S. Euclid Ave; Box 8108, St. Louis, MO, 63110, USA
| | - Elizabeth Forsen
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave; Box 8504, St. Louis, MO, 63110, USA
| | - Drew Bolster
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave; Box 8504, St. Louis, MO, 63110, USA
| | - Alison Marvin
- Maryland Center for Developmental Disabilities, Kennedy Krieger Institute, PACT Building/Office 121B; 7000 Tudsbury Road, Baltimore, MD, 21244, USA
| | - Andrew Whitehouse
- Telethon Kids Institute, Perth Children's Hospital, 15 Hospital Avenue, Nedlands, WA, 6009, USA
| | - Laura Klinger
- TEACCH Autism Program, Department of Psychiatry, University of North Carolina at Chapel Hill, Campus Box #7180, Chapel Hill, NC, 27599-7180, USA
| | - Christina A Gurnett
- Department of Neurology, Washington University School of Medicine, 660 S. Euclid Ave; Box 8111, St. Louis, MO, 63110, USA
| | - J N Constantino
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave; Box 8504, St. Louis, MO, 63110, USA
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Brand BA, Blesson AE, Smith-Hicks CL. The Impact of X-Chromosome Inactivation on Phenotypic Expression of X-Linked Neurodevelopmental Disorders. Brain Sci 2021; 11:brainsci11070904. [PMID: 34356138 PMCID: PMC8305405 DOI: 10.3390/brainsci11070904] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 06/16/2021] [Accepted: 06/20/2021] [Indexed: 12/20/2022] Open
Abstract
Nearly 20% of genes located on the X chromosome are associated with neurodevelopmental disorders (NDD) due to their expression and role in brain functioning. Given their location, several of these genes are either subject to or can escape X-chromosome inactivation (XCI). The degree to which genes are subject to XCI can influence the NDD phenotype between males and females. We provide a general review of X-linked NDD genes in the context of XCI and detailed discussion of the sex-based differences related to MECP2 and FMR1, two common X-linked causes of NDD that are subject to XCI. Understanding the effects of XCI on phenotypic expression of NDD genes may guide the development of stratification biomarkers in X-linked disorders.
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Affiliation(s)
- Boudewien A Brand
- Center for Autism and Related Disorders, Kennedy Krieger Institute, Baltimore, MD 21205, USA; (B.A.B.); (A.E.B.)
| | - Alyssa E Blesson
- Center for Autism and Related Disorders, Kennedy Krieger Institute, Baltimore, MD 21205, USA; (B.A.B.); (A.E.B.)
| | - Constance L. Smith-Hicks
- Department of Neurology and Developmental Medicine, Kennedy Krieger Institute, Baltimore, MD 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Correspondence:
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8
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Lee SH, Jeong JE, Jang YY, Kim JK. Clinical and Genetic Characteristics of Young Children with Fragile X Syndrome. ANNALS OF CHILD NEUROLOGY 2021. [DOI: 10.26815/acn.2021.00353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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9
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Assessment of FMR1 triplet repeats in patients affected with mental retardation, fragile X syndrome and primary ovarian insufficiency. J Genet 2020. [DOI: 10.1007/s12041-019-1171-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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10
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Budimirovic DB, Schlageter A, Filipovic-Sadic S, Protic DD, Bram E, Mahone EM, Nicholson K, Culp K, Javanmardi K, Kemppainen J, Hadd A, Sharp K, Adayev T, LaFauci G, Dobkin C, Zhou L, Brown WT, Berry-Kravis E, Kaufmann WE, Latham GJ. A Genotype-Phenotype Study of High-Resolution FMR1 Nucleic Acid and Protein Analyses in Fragile X Patients with Neurobehavioral Assessments. Brain Sci 2020; 10:E694. [PMID: 33008014 PMCID: PMC7601415 DOI: 10.3390/brainsci10100694] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 09/25/2020] [Accepted: 09/25/2020] [Indexed: 01/04/2023] Open
Abstract
Fragile X syndrome (FXS) is caused by silencing of the FMR1 gene, which encodes a protein with a critical role in synaptic plasticity. The molecular abnormality underlying FMR1 silencing, CGG repeat expansion, is well characterized; however, delineation of the pathway from DNA to RNA to protein using biosamples from well characterized patients with FXS is limited. Since FXS is a common and prototypical genetic disorder associated with intellectual disability (ID) and autism spectrum disorder (ASD), a comprehensive assessment of the FMR1 DNA-RNA-protein pathway and its correlations with the neurobehavioral phenotype is a priority. We applied nine sensitive and quantitative assays evaluating FMR1 DNA, RNA, and FMRP parameters to a reference set of cell lines representing the range of FMR1 expansions. We then used the most informative of these assays on blood and buccal specimens from cohorts of patients with different FMR1 expansions, with emphasis on those with FXS (N = 42 total, N = 31 with FMRP measurements). The group with FMRP data was also evaluated comprehensively in terms of its neurobehavioral profile, which allowed molecular-neurobehavioral correlations. FMR1 CGG repeat expansions, methylation levels, and FMRP levels, in both cell lines and blood samples, were consistent with findings of previous FMR1 genomic and protein studies. They also demonstrated a high level of agreement between blood and buccal specimens. These assays further corroborated previous reports of the relatively high prevalence of methylation mosaicism (slightly over 50% of the samples). Molecular-neurobehavioral correlations confirmed the inverse relationship between overall severity of the FXS phenotype and decrease in FMRP levels (N = 26 males, mean 4.2 ± 3.3 pg FMRP/ng genomic DNA). Other intriguing findings included a significant relationship between the diagnosis of FXS with ASD and two-fold lower levels of FMRP (mean 2.8 ± 1.3 pg FMRP/ng genomic DNA, p = 0.04), in particular observed in younger age- and IQ-adjusted males (mean age 6.9 ± 0.9 years with mean 3.2 ± 1.2 pg FMRP/ng genomic DNA, 57% with severe ASD), compared to FXS without ASD. Those with severe ID had even lower FMRP levels independent of ASD status in the male-only subset. The results underscore the link between FMR1 expansion, gene methylation, and FMRP deficit. The association between FMRP deficiency and overall severity of the neurobehavioral phenotype invites follow up studies in larger patient cohorts. They would be valuable to confirm and potentially extend our initial findings of the relationship between ASD and other neurobehavioral features and the magnitude of FMRP deficit. Molecular profiling of individuals with FXS may have important implications in research and clinical practice.
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Affiliation(s)
- Dejan B. Budimirovic
- Departments of Psychiatry and Neurogenetics, Fragile X Clinic, Kennedy Krieger Institute, Baltimore, MD 21205, USA;
- Department of Psychiatry & Behavioral Sciences-Child Psychiatry, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Annette Schlageter
- Asuragen, Inc., Austin, TX 78744, USA; (A.S.); (S.F.-S.); (E.B.); (K.N.); (K.C.); (K.J.); (J.K.); (A.H.)
| | - Stela Filipovic-Sadic
- Asuragen, Inc., Austin, TX 78744, USA; (A.S.); (S.F.-S.); (E.B.); (K.N.); (K.C.); (K.J.); (J.K.); (A.H.)
| | - Dragana D. Protic
- Departments of Psychiatry and Neurogenetics, Fragile X Clinic, Kennedy Krieger Institute, Baltimore, MD 21205, USA;
- School of Medicine, University of Belgrade, 11000 Belgrade, Serbia
| | - Eran Bram
- Asuragen, Inc., Austin, TX 78744, USA; (A.S.); (S.F.-S.); (E.B.); (K.N.); (K.C.); (K.J.); (J.K.); (A.H.)
| | - E. Mark Mahone
- Department of Neuropsychology, Kennedy Krieger Institute, Baltimore, MD 21205, USA;
| | - Kimberly Nicholson
- Asuragen, Inc., Austin, TX 78744, USA; (A.S.); (S.F.-S.); (E.B.); (K.N.); (K.C.); (K.J.); (J.K.); (A.H.)
| | - Kristen Culp
- Asuragen, Inc., Austin, TX 78744, USA; (A.S.); (S.F.-S.); (E.B.); (K.N.); (K.C.); (K.J.); (J.K.); (A.H.)
| | - Kamyab Javanmardi
- Asuragen, Inc., Austin, TX 78744, USA; (A.S.); (S.F.-S.); (E.B.); (K.N.); (K.C.); (K.J.); (J.K.); (A.H.)
| | - Jon Kemppainen
- Asuragen, Inc., Austin, TX 78744, USA; (A.S.); (S.F.-S.); (E.B.); (K.N.); (K.C.); (K.J.); (J.K.); (A.H.)
| | - Andrew Hadd
- Asuragen, Inc., Austin, TX 78744, USA; (A.S.); (S.F.-S.); (E.B.); (K.N.); (K.C.); (K.J.); (J.K.); (A.H.)
| | - Kevin Sharp
- Department of Pediatrics, Rush University Medical Center, Chicago, IL 60612, USA; (K.S.); (L.Z.); (E.B.-K.)
| | - Tatyana Adayev
- Institute for Basic Research in Developmental Disabilities, Staten Island, NY 10314, USA; (T.A.); (G.L.); (C.D.); (W.T.B.)
| | - Giuseppe LaFauci
- Institute for Basic Research in Developmental Disabilities, Staten Island, NY 10314, USA; (T.A.); (G.L.); (C.D.); (W.T.B.)
| | - Carl Dobkin
- Institute for Basic Research in Developmental Disabilities, Staten Island, NY 10314, USA; (T.A.); (G.L.); (C.D.); (W.T.B.)
| | - Lili Zhou
- Department of Pediatrics, Rush University Medical Center, Chicago, IL 60612, USA; (K.S.); (L.Z.); (E.B.-K.)
| | - William Ted Brown
- Institute for Basic Research in Developmental Disabilities, Staten Island, NY 10314, USA; (T.A.); (G.L.); (C.D.); (W.T.B.)
| | - Elizabeth Berry-Kravis
- Department of Pediatrics, Rush University Medical Center, Chicago, IL 60612, USA; (K.S.); (L.Z.); (E.B.-K.)
- Departments of Pediatrics, Neurological Sciences and Biochemistry, Rush University Medical Center, Chicago, IL 60612, USA
| | - Walter E. Kaufmann
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA;
- Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Gary J. Latham
- Asuragen, Inc., Austin, TX 78744, USA; (A.S.); (S.F.-S.); (E.B.); (K.N.); (K.C.); (K.J.); (J.K.); (A.H.)
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Lalonde E, Rentas S, Lin F, Dulik MC, Skraban CM, Spinner NB. Genomic Diagnosis for Pediatric Disorders: Revolution and Evolution. Front Pediatr 2020; 8:373. [PMID: 32733828 PMCID: PMC7360789 DOI: 10.3389/fped.2020.00373] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 06/02/2020] [Indexed: 12/14/2022] Open
Abstract
Powerful, recent advances in technologies to analyze the genome have had a profound impact on the practice of medical genetics, both in the laboratory and in the clinic. Increasing utilization of genome-wide testing such as chromosomal microarray analysis and exome sequencing have lead a shift toward a "genotype-first" approach. Numerous techniques are now available to diagnose a particular syndrome or phenotype, and while traditional techniques remain efficient tools in certain situations, higher-throughput technologies have become the de facto laboratory tool for diagnosis of most conditions. However, selecting the right assay or technology is challenging, and the wrong choice may lead to prolonged time to diagnosis, or even a missed diagnosis. In this review, we will discuss current core technologies for the diagnosis of classic genetic disorders to shed light on the benefits and disadvantages of these strategies, including diagnostic efficiency, variant interpretation, and secondary findings. Finally, we review upcoming technologies posed to impart further changes in the field of genetic diagnostics as we move toward "genome-first" practice.
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Affiliation(s)
- Emilie Lalonde
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, School of Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, United States
| | - Stefan Rentas
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, School of Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, United States
| | - Fumin Lin
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, School of Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, United States
| | - Matthew C. Dulik
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, School of Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, United States
| | - Cara M. Skraban
- Division of Human Genetics, Department of Pediatrics, School of Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, United States
| | - Nancy B. Spinner
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, School of Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, United States
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12
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Reversion to Normal of FMR1 Expanded Alleles: A Rare Event in Two Independent Fragile X Syndrome Families. Genes (Basel) 2020; 11:genes11030248. [PMID: 32111011 PMCID: PMC7140891 DOI: 10.3390/genes11030248] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 02/12/2020] [Accepted: 02/24/2020] [Indexed: 01/12/2023] Open
Abstract
Fragile X syndrome (FXS) is mostly due to the expansion and subsequent methylation of a polymorphic CGG repeat in the 5’ UTR of the FMR1 gene. Full mutation alleles (FM) have more than 200 repeats and result in FMR1 gene silencing and FXS. FMs arise from maternal premutations (PM) that have 56–200 CGGs; contractions of a maternal PM or FM are rare. Here, we describe two unaffected boys in two independent FXS families who inherited a non-mosaic allele in the normal and intermediate range, respectively, from their mothers who are carriers of an expanded CGG allele. The first boy inherited a 51 CGG allele (without AGG interruptions) from his mother, who carries a PM allele with 72 CGGs. The other boy inherited from his FM mother an unusual allele with 19 CGGs resulting from a deletion, removing 85 bp upstream of the CGG repeat. Given that transcription of the deleted allele was found to be preserved, we assume that the binding sites for FMR1 transcription factors are excluded from the deletion. Such unusual cases resulting in non-mosaic reduction of maternal CGG expansions may help to clarify the molecular mechanisms underlying the instability of the FMR1 gene.
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13
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Johansen Taber K, Lim-Harashima J, Naemi H, Goldberg J. Fragile X syndrome carrier screening accompanied by genetic consultation has clinical utility in populations beyond those recommended by guidelines. Mol Genet Genomic Med 2019; 7:e1024. [PMID: 31694075 PMCID: PMC6900367 DOI: 10.1002/mgg3.1024] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 08/30/2019] [Accepted: 10/01/2019] [Indexed: 01/12/2023] Open
Abstract
Background Fragile X syndrome (FXS) is the most common inherited form of intellectual disability. Many providers offer preconception or prenatal FXS carrier screening. However, guidelines recommend screening only for those with a family history or undergoing fertility evaluation. Wider screening has been resisted because of concerns about patient understanding of FXS‐associated inheritance patterns and phenotypes. Additionally, the clinical utility has been questioned. Methods We addressed these concerns by analyzing reproductive decision‐making and pregnancy management informed by post‐test genetic consultation among 122 FMR1 premutation carriers identified by expanded carrier screening. Results Sixty‐three percent of those screened met guidelines screening criteria; the remaining 37% did not. Ninety‐eight percent had undergone post‐test genetic consultation. Of respondents screened preconceptionally, 74% reported planning or pursuing actions to reduce the risk of an affected pregnancy; the extent to which couples planned/pursued these actions was not significantly different between those meeting either screening criterion (76%) versus those meeting neither criterion (55%). Of respondents screened prenatally, 41% pursued prenatal diagnostic testing; the extent to which couples pursued prenatal diagnosis was not significantly different between those who met either screening criterion (37%) versus those who met neither criterion (31%). Conclusion These results support the expansion of FXS screening criteria in guidelines.
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Affiliation(s)
| | | | | | - Jim Goldberg
- Myriad Women's Health, South San Francisco, CA, USA
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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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15
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Hayward B, Loutaev I, Ding X, Nolin SL, Thurm A, Usdin K, Smith CB. Fragile X syndrome in a male with methylated premutation alleles and no detectable methylated full mutation alleles. Am J Med Genet A 2019; 179:2132-2137. [DOI: 10.1002/ajmg.a.61286] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 06/14/2019] [Accepted: 06/23/2019] [Indexed: 12/17/2022]
Affiliation(s)
- Bruce Hayward
- Section on Gene Structure and Disease, Laboratory of Cell and Molecular BiologyNational Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health Bethesda Maryland
| | - Inna Loutaev
- Section on Neuroadaptation and Protein MetabolismNational Institute of Mental Health, National Institutes of Health Bethesda Maryland
| | - Xiaohua Ding
- Molecular Diagnostic LaboratoryNew York State Institute for Basic Research in Developmental Disabilities Staten Island New York
| | - Sarah L. Nolin
- Molecular Diagnostic LaboratoryNew York State Institute for Basic Research in Developmental Disabilities Staten Island New York
| | - Audrey Thurm
- Office of the Clinical DirectorNational Institute of Mental Health, National Institutes of Health Bethesda Maryland
| | - Karen Usdin
- Section on Gene Structure and Disease, Laboratory of Cell and Molecular BiologyNational Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health Bethesda Maryland
| | - Carolyn B. Smith
- Section on Neuroadaptation and Protein MetabolismNational Institute of Mental Health, National Institutes of Health Bethesda Maryland
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16
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Bacrot S, Monnot S, Haddad G, Barcia G, Rachid M, Boisson M, Pasquier N, Rondeau S, Munnich A, Steffann J, Bonnefont JP, Raynaud M. Prenatal diagnosis of fragile X syndrome: Small meiotic recombination events at the FMR1 locus. Prenat Diagn 2019; 39:388-393. [PMID: 30779209 DOI: 10.1002/pd.5439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 02/11/2019] [Accepted: 02/16/2019] [Indexed: 11/11/2022]
Affiliation(s)
- Séverine Bacrot
- Université Paris Descartes - Sorbonne Paris Cite, Institut Imagine UMR1163, Fédération de Génétique médicale, Hôpital universitaire Necker-Enfants Malades, AP-HP, Paris, France
| | - Sophie Monnot
- Université Paris Descartes - Sorbonne Paris Cite, Institut Imagine UMR1163, Fédération de Génétique médicale, Hôpital universitaire Necker-Enfants Malades, AP-HP, Paris, France
| | - Georges Haddad
- Service de gynécologie obstétrique, Centre hospitalier de Blois, Blois, France
| | - Giulia Barcia
- Université Paris Descartes - Sorbonne Paris Cite, Institut Imagine UMR1163, Fédération de Génétique médicale, Hôpital universitaire Necker-Enfants Malades, AP-HP, Paris, France
| | - Myriam Rachid
- Université Paris Descartes - Sorbonne Paris Cite, Institut Imagine UMR1163, Fédération de Génétique médicale, Hôpital universitaire Necker-Enfants Malades, AP-HP, Paris, France
| | - Marie Boisson
- Université Paris Descartes - Sorbonne Paris Cite, Institut Imagine UMR1163, Fédération de Génétique médicale, Hôpital universitaire Necker-Enfants Malades, AP-HP, Paris, France
| | - Nathalie Pasquier
- Service de Génétique, CHRU de Tours, UMR 1253, iBrain, Université de Tours, Inserm, Tours, France
| | - Sophie Rondeau
- Université Paris Descartes - Sorbonne Paris Cite, Institut Imagine UMR1163, Fédération de Génétique médicale, Hôpital universitaire Necker-Enfants Malades, AP-HP, Paris, France
| | - Arnold Munnich
- Université Paris Descartes - Sorbonne Paris Cite, Institut Imagine UMR1163, Fédération de Génétique médicale, Hôpital universitaire Necker-Enfants Malades, AP-HP, Paris, France
| | - Julie Steffann
- Université Paris Descartes - Sorbonne Paris Cite, Institut Imagine UMR1163, Fédération de Génétique médicale, Hôpital universitaire Necker-Enfants Malades, AP-HP, Paris, France
| | - Jean-Paul Bonnefont
- Université Paris Descartes - Sorbonne Paris Cite, Institut Imagine UMR1163, Fédération de Génétique médicale, Hôpital universitaire Necker-Enfants Malades, AP-HP, Paris, France
| | - Martine Raynaud
- Service de Génétique, CHRU de Tours, UMR 1253, iBrain, Université de Tours, Inserm, Tours, France
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Abstract
Fragile X syndrome (FXS) is one of the most common reasons for intellectual disability (ID). First described in the 1940s, it took many years to understand the disease. The awe-inspiring breakthroughs in both science and technology facilitated the recognition of the unique inheritance pattern and the genetic mechanism of fragile X. In this chapter we describe the history and evolution of our understanding of FXS as mirrored by advances in genetics.
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Affiliation(s)
- Adi Reches
- Genetic Institute and Racine IVF Unit at Lis Maternity Hospital Tel Aviv, Sackler Faculty of Medicine, Tel Aviv Sourasky Medical Center, Tel Aviv University, Tel Aviv, Israel.
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18
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Domniz N, Ries-Levavi L, Cohen Y, Marom-Haham L, Berkenstadt M, Pras E, Glicksman A, Tortora N, Latham GJ, Hadd AG, Nolin SL, Elizur SE. Absence of AGG Interruptions Is a Risk Factor for Full Mutation Expansion Among Israeli FMR1 Premutation Carriers. Front Genet 2018; 9:606. [PMID: 30619448 PMCID: PMC6300753 DOI: 10.3389/fgene.2018.00606] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 11/19/2018] [Indexed: 11/13/2022] Open
Abstract
Introduction: Fragile X syndrome (FXS) is a common form of X-linked intellectual and developmental disability with a prevalence of 1/4000-5000 in males and 1/6000-8000 in females. Most cases of the syndrome result from expansion of a premutation (55-200 CGGs) to a full mutation (>200 CGGs) repeat located in the 5' untranslated region of the fragile X mental retardation (FMR1) gene. The risk for full mutation expansions increases dramatically with increasing numbers of CGG repeats. Recent studies, however, revealed AGG interruptions within the repeat area function as a "protective factor" decreasing the risk of intergenerational expansion. Materials and Methods: This study was conducted to validate the relevance of AGG analysis for the ethnically diverse Israeli population. To increase the accuracy of our results, we combined results from Israel with those from the New York State Institute for Basic Research in Developmental Disabilities (IBR). To the best of our knowledge this is the largest cohort of different ethnicities to examine risks of unstable transmissions and full mutation expansions among FMR1 premutation carriers. Results: The combined data included 1471 transmissions of maternal premutation alleles: 369 (25.1%) stable and 1,102 (74.9%) unstable transmissions. Full mutation expansions were identified in 20.6% (303/1471) of transmissions. A total of 97.4% (388/397) of transmissions from alleles with no AGGs were unstable, 79.6% (513/644) in alleles with 1 AGG and 46.7% (201/430) in alleles with 2 or more AGGs. The same trend was seen with full mutation expansions where 40% (159/397) of alleles with no AGGs expanded to a full mutation, 20.2% (130/644) for alleles with 1 AGG and only 3.2% (14/430) in alleles with 2 AGGs or more. None of the alleles with 3 or more AGGs expanded to full mutations. Conclusion: We recommend that risk estimates for FMR1 premutation carriers be based on AGG interruptions as well as repeat size in Israel and worldwide.
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Affiliation(s)
- Noam Domniz
- IVF Unit, Sheba Medical Center, Tel Hashomer, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Liat Ries-Levavi
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Danek Genetic Institute, Sheba Medical Center, Tel Hashomer, Israel
| | - Yoram Cohen
- IVF Unit, Sheba Medical Center, Tel Hashomer, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Lilach Marom-Haham
- IVF Unit, Sheba Medical Center, Tel Hashomer, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Michal Berkenstadt
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Danek Genetic Institute, Sheba Medical Center, Tel Hashomer, Israel
| | - Elon Pras
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Danek Genetic Institute, Sheba Medical Center, Tel Hashomer, Israel
| | - Anne Glicksman
- New York State Institute for Basic Research in Developmental Disabilities, Staten Island, NY, United States
| | - Nicole Tortora
- New York State Institute for Basic Research in Developmental Disabilities, Staten Island, NY, United States
| | | | | | - Sarah L Nolin
- New York State Institute for Basic Research in Developmental Disabilities, Staten Island, NY, United States
| | - Shai E Elizur
- IVF Unit, Sheba Medical Center, Tel Hashomer, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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19
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Fink DA, Nelson LM, Pyeritz R, Johnson J, Sherman SL, Cohen Y, Elizur SE. Fragile X Associated Primary Ovarian Insufficiency (FXPOI): Case Report and Literature Review. Front Genet 2018; 9:529. [PMID: 30542367 PMCID: PMC6278244 DOI: 10.3389/fgene.2018.00529] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 10/22/2018] [Indexed: 11/29/2022] Open
Abstract
Abnormalities in the X-linked FMR1 gene are associated with a constellation of disorders, which have broad and profound implications for the person first diagnosed, and extended family members of all ages. The rare and pleiotropic nature of the associated disorders, both common and not, place great burdens on (1) the affected families, (2) their care providers and clinicians, and (3) investigators striving to conduct research on the conditions. Fragile X syndrome, occurring more severely in males, is the leading genetic cause of intellectual disability. Fragile X associated tremor and ataxia syndrome (FXTAS) is a neurodegenerative disorder seen more often in older men. Fragile X associated primary ovarian insufficiency (FXPOI) is a chronic disorder characterized by oligo/amenorrhea and hypergonadotropic hypogonadism before age 40 years. There may be significant morbidity due to: (1) depression and anxiety related to the loss of reproductive hormones and infertility; (2) reduced bone mineral density; and (3) increased risk of cardiovascular disease related to estrogen deficiency. Here we report the case of a young woman who never established regular menses and yet experienced a 5-year diagnostic odyssey before establishing a diagnosis of FXPOI despite a known family history of fragile X syndrome and early menopause. Also, despite having clearly documented FXPOI the woman conceived spontaneously and delivered two healthy children. We review the pathophysiology and management of FXPOI. As a rare disease, the diagnosis of FXPOI presents special challenges. Connecting patients and community health providers with investigators who have the requisite knowledge and expertise about the FMR1 gene and FXPOI would facilitate both patient care and research. There is a need for an international natural history study on FXPOI. The effort should be coordinated by a global virtual center, which takes full advantage of mobile device communication systems.
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Affiliation(s)
- Dorothy A Fink
- Hospital for Special Surgery, New York, NY, United States
| | | | - Reed Pyeritz
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Josh Johnson
- University of Colorado, Denver, CO, United States
| | | | - Yoram Cohen
- Sheba Medical Center, Tel Hashomer and Tel Aviv University, Tel Aviv, Israel
| | - Shai E Elizur
- Sheba Medical Center, Tel Hashomer and Tel Aviv University, Tel Aviv, Israel
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20
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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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21
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Haham LM, Avrahami I, Domniz N, Ries-Levavi L, Berkenstadt M, Orvieto R, Cohen Y, Elizur SE. Preimplantation genetic diagnosis versus prenatal diagnosis-decision-making among pregnant FMR1 premutation carriers. J Assist Reprod Genet 2018; 35:2071-2075. [PMID: 30136016 DOI: 10.1007/s10815-018-1293-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 08/16/2018] [Indexed: 12/16/2022] Open
Abstract
PURPOSE To detect which factors influence decision-making among pregnant FMR1 premutation carriers regarding the preferred mode of genetic diagnosis: IVF-PGT-M (in vitro fertilization with preimplantation genetic testing for monogenic gene diseases), or CVS (chorionic villus sampling), or AC (amniocentesis) after spontaneous conception. METHODS In Israel FMR1 premutation preconception genetic screening is offered, free of charge, to every woman in her reproductive years. FMR1 premutation carriers with ≥ 70 CGG repeats, or a history of FXS offspring, are offered IVF-PGT-M. This is a historical cohort study including all pregnant FMR1 premutation carriers who underwent prenatal diagnosis between the years 2011 and 2016 at a tertiary medical center. Data were collected from electronic charts and through phone interviews. RESULTS One hundred seventy-five women with high-risk pregnancies who were offered IVF-PGT-M were evaluated. In 37 pregnancies (21%), the women decided to undergo IVF-PGT-M. Using the generalized estimating equations (GEE) statistical method including seven parameters, we found that previous termination of pregnancy due to FXS and advanced woman's age were significantly associated with making the decision to undergo IVF-PGT-M. Previously failed IVF was the most significant parameter in a woman's decision not to undergo IVF-PGT-M. CONCLUSION The most dominant factor affecting the decision of FMR1 premutation carriers to choose spontaneous conception with prenatal diagnosis versus IVF-PGT-M is a previous experience of failed IVF treatments. Women whose IVF treatments failed in the past tended to try to conceive naturally and later, during the course of the pregnancy, perform CVS or AC. Conversely, women who previously experienced a termination of pregnancy (TOP) due to an affected fetus, and older women, preferred to undergo IVF-PGT-M procedures.
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Affiliation(s)
| | | | - Noam Domniz
- IVF Unit, Sheba Medical Center, Tel Hashomer, Israel
| | - Liat Ries-Levavi
- The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Michal Berkenstadt
- The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Raoul Orvieto
- IVF Unit, Sheba Medical Center, Tel Hashomer, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Yoram Cohen
- IVF Unit, Sheba Medical Center, Tel Hashomer, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Shai E Elizur
- IVF Unit, Sheba Medical Center, Tel Hashomer, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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22
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23
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Owens KM, Dohany L, Holland C, DaRe J, Mann T, Settler C, Longman RE. FMR1 premutation frequency in a large, ethnically diverse population referred for carrier testing. Am J Med Genet A 2018; 176:1304-1308. [PMID: 29603880 PMCID: PMC6001625 DOI: 10.1002/ajmg.a.38692] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 02/23/2018] [Accepted: 03/09/2018] [Indexed: 12/13/2022]
Abstract
Fragile X syndrome (FXS) is the most common inherited cause of intellectual disability and is caused by an expansion of cytosine‐guanine‐guanine (CGG) repeats in the FMR1 gene. Female premutation allele carriers (55–200 CGG repeats) are at risk to have an affected child. Currently, specific population‐based carrier screening for FXS is not recommended. Previous studies exploring female premutation carrier frequency have been limited by size or ethnicity. This retrospective study provides a pan‐ethnic estimate of the Fragile X premutation carrier frequency in a large, ethnically diverse population of women referred for routine carrier screening during a specified time period at Progenity, Inc. Patient ethnicity was self‐reported and categorized as: African American, Ashkenazi Jewish, Asian, Caucasian, Hispanic, Native American, Other/Mixed/Unknown, or Sephardic Jewish. FXS test results were stratified by ethnicity and repeat allele category. Total premutation carrier frequency was calculated and compared against each ethnic group. A total of 134,933 samples were included. The pan‐ethnic premutation carrier frequency was 1 in 201. Only the Asian group differed significantly from this frequency. Using the carrier frequency of 1 in 201, a conservative pan‐ethnic risk estimate for a male fetus to have FXS can be calculated as 1 in 2,412. This risk is similar to the highest ethnic‐based fetal risks for cystic fibrosis and spinal muscular atrophy, for which population‐wide screening is currently recommended. This study adds to the literature and supports further evaluation into specific population‐wide screening recommendations for FXS.
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Affiliation(s)
| | | | | | | | | | | | - Ryan E Longman
- Department of Obstetrics and Gynecology, University of Miami Miller School of Medicine, Miami, Florida
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24
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Wotton T, Wiley V, Bennetts B, Christie L, Wilcken B, Jenkins G, Rogers C, Boyle J, Field M. Are We Ready for Fragile X Newborn Screening Testing?-Lessons Learnt from a Feasibility Study. Int J Neonatal Screen 2018; 4:9. [PMID: 33072935 PMCID: PMC7548904 DOI: 10.3390/ijns4010009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 01/23/2018] [Indexed: 12/17/2022] Open
Abstract
Fragile X syndrome (FXS) is the most prevalent heritable cause of cognitive impairment but is not yet included in a newborn screening (NBS) program within Australia. This paper aims to assess the feasibility and reliability of population screening for FXS using a pilot study in one hospital. A total of 1971 mothers consented for 2000 newborns to be tested using routine NBS dried blood spot samples. DNA was extracted and a modified PCR assay with a chimeric CGG primer was used to detect fragile X alleles in both males and females in the normal, premutation, and full mutation ranges. A routine PCR-based fragile X assay was run in parallel to validate the chimeric primer assay. Babies with CGG repeat number ≥59 were referred for family studies. One thousand nine hundred and ninety NBS samples had a CGG repeat number less than 55 (1986 < 50); 10 had premutation alleles >54 CGG repeats (1/123 females and 1/507 males). There was complete concordance between the two PCR-based assays. A recent review revealed no clinically identified cases in the cohort up to 5 years later. The cost per test was $AUD19. Fragile X status can be determined on routine NBS samples using the chimeric primer assay. However, whilst this assay may not be considered cost-effective for population screening, it could be considered as a second-tier assay to a developed immunoassay for fragile X mental retardation protein (FMRP).
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Affiliation(s)
- Tiffany Wotton
- The NSW Newborn Screening Programme, The Children’s Hospital at Westmead, Westmead, NSW 2145, Australia
- Correspondence:
| | - Veronica Wiley
- The NSW Newborn Screening Programme, The Children’s Hospital at Westmead, Westmead, NSW 2145, Australia
- Disciplines of Paediatrics & Child Health and Genetic Medicine, The University of Sydney, Sydney, NSW 2006, Australia
| | - Bruce Bennetts
- Disciplines of Paediatrics & Child Health and Genetic Medicine, The University of Sydney, Sydney, NSW 2006, Australia
- Sydney Genome Diagnostics—Department of Molecular Genetics, The Children’s Hospital at Westmead, Westmead, NSW 2145, Australia
| | - Louise Christie
- Genetics of Learning Disability, Hunter Genetics, Waratah, NSW 2298, Australia
| | - Bridget Wilcken
- The NSW Newborn Screening Programme, The Children’s Hospital at Westmead, Westmead, NSW 2145, Australia
- Disciplines of Paediatrics & Child Health and Genetic Medicine, The University of Sydney, Sydney, NSW 2006, Australia
| | - Gemma Jenkins
- Sydney Genome Diagnostics—Department of Molecular Genetics, The Children’s Hospital at Westmead, Westmead, NSW 2145, Australia
| | - Carolyn Rogers
- Genetics of Learning Disability, Hunter Genetics, Waratah, NSW 2298, Australia
| | - Jackie Boyle
- Genetics of Learning Disability, Hunter Genetics, Waratah, NSW 2298, Australia
| | - Michael Field
- Genetics of Learning Disability, Hunter Genetics, Waratah, NSW 2298, Australia
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25
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Arpone M, Baker EK, Bretherton L, Bui M, Li X, Whitaker S, Dissanayake C, Cohen J, Hickerton C, Rogers C, Field M, Elliott J, Aliaga SM, Ling L, Francis D, Hearps SJC, Hunter MF, Amor DJ, Godler DE. Intragenic DNA methylation in buccal epithelial cells and intellectual functioning in a paediatric cohort of males with fragile X. Sci Rep 2018; 8:3644. [PMID: 29483611 PMCID: PMC5827525 DOI: 10.1038/s41598-018-21990-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 02/12/2018] [Indexed: 01/05/2023] Open
Abstract
Increased intragenic DNA methylation of the Fragile X Related Epigenetic Element 2 (FREE2) in blood has been correlated with lower intellectual functioning in females with fragile X syndrome (FXS). This study explored these relationships in a paediatric cohort of males with FXS using Buccal Epithelial Cells (BEC). BEC were collected from 25 males with FXS, aged 3 to 17 years and 19 age-matched male controls without FXS. Methylation of 9 CpG sites within the FREE2 region was examined using the EpiTYPER approach. Full Scale IQ (FSIQ) scores of males with FXS were corrected for floor effect using the Whitaker and Gordon (WG) extrapolation method. Compared to controls, children with FXS had significant higher methylation levels for all CpG sites examined (p < 3.3 × 10−7), and within the FXS group, lower FSIQ (WG corrected) was associated with higher levels of DNA methylation, with the strongest relationship found for CpG sites within FMR1 intron 1 (p < 5.6 × 10−5). Applying the WG method to the FXS cohort unmasked significant epi-genotype-phenotype relationships. These results extend previous evidence in blood to BEC and demonstrate FREE2 DNA methylation to be a sensitive epigenetic biomarker significantly associated with the variability in intellectual functioning in FXS.
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Affiliation(s)
- Marta Arpone
- Faculty of Medicine, Dentistry and Health Sciences, Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia. .,Cyto-Molecular Diagnostics Research, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC, Australia. .,Child Neuropsychology, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC, Australia.
| | - Emma K Baker
- Cyto-Molecular Diagnostics Research, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC, Australia
| | - Lesley Bretherton
- Faculty of Medicine, Dentistry and Health Sciences, Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia.,Child Neuropsychology, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC, Australia.,Melbourne School of Psychological Sciences, University of Melbourne, Melbourne, VIC, Australia
| | - Minh Bui
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, VIC, Australia
| | - Xin Li
- Cyto-Molecular Diagnostics Research, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC, Australia
| | - Simon Whitaker
- School of Human and Health Science, University of Huddersfield, Queensgate, Huddersfield, United Kingdom
| | - Cheryl Dissanayake
- Olga Tennison Autism Research Centre, La Trobe University, Melbourne, VIC, Australia
| | - Jonathan Cohen
- Fragile X Alliance Inc, North Caulfield, VIC, Australia and Centre for Developmental Disability Health Victoria, Monash University, Dandenong, VIC, Australia
| | - Chriselle Hickerton
- Cyto-Molecular Diagnostics Research, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC, Australia
| | - Carolyn Rogers
- Genetics of Learning Disability Service (GOLD service), Hunter Genetics, Newcastle, NSW, Australia
| | - Mike Field
- Genetics of Learning Disability Service (GOLD service), Hunter Genetics, Newcastle, NSW, Australia
| | - Justine Elliott
- Victorian Clinical Genetics Services and Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC, Australia
| | - Solange M Aliaga
- Faculty of Medicine, Dentistry and Health Sciences, Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia.,Cyto-Molecular Diagnostics Research, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC, Australia.,Centre for Diagnosis and Treatment of Fragile X Syndrome, INTA University of Chile, Santiago, Chile
| | - Ling Ling
- Cyto-Molecular Diagnostics Research, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC, Australia
| | - David Francis
- Victorian Clinical Genetics Services and Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC, Australia
| | - Stephen J C Hearps
- Child Neuropsychology, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC, Australia
| | - Matthew F Hunter
- Monash Genetics, Monash Health, Melbourne, VIC, Australia and Department of Paediatrics, Monash University, Melbourne, VIC, Australia
| | - David J Amor
- Faculty of Medicine, Dentistry and Health Sciences, Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia.,Victorian Clinical Genetics Services and Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC, Australia
| | - David E Godler
- Faculty of Medicine, Dentistry and Health Sciences, Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia.,Cyto-Molecular Diagnostics Research, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC, Australia
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Manor E, Jabareen A, Magal N, Kofman A, Hagerman RJ, Tassone F. Prenatal Diagnosis of Fragile X: Can a Full Mutation Allele in the FMR1 Gene Contract to a Normal Size? Front Genet 2017; 8:158. [PMID: 29163631 PMCID: PMC5675867 DOI: 10.3389/fgene.2017.00158] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 10/09/2017] [Indexed: 01/29/2023] Open
Abstract
Here we describe a case of a prenatal diagnosis of a male fetus that inherited the unstable allele from his full mutation mosaic mother (29, 160, >200 CGG repeats) reduced to a normal size range (19 CGG repeats). Haplotype analysis showed that the fetus 19 CGG repeats allele derived from the maternal unstable allele which was inherited from his maternal grandmother. No size mosaicism was detected by testing the DNA from in vitro cultured samples, including seventh passage culture as well as from two amniocentesis samples. Sequence analysis confirmed that the allele was 19 CGG repeats long. Methylation assay showed no methylation. Although none of the techniques used in this study can provide with absolute certainty the diagnosis, the results strongly indicate the presence in the fetus of an allele with a CGG repeat number in the normal range. Because this is a prenatal diagnosis case, the crucial question is whether the 19 CGG allele derived from the maternal unstable expanded allele, which contracted to the normal range, became a normal stable allele or a normal unstable allele which could expand in the next generation. It is also possible that allele size mosaicism of the FMR1 gene that went undetected exists. Because this is a prenatal diagnosis case, we cannot with certainty exclude the presence of an undetected expanded allele of the FMR1 gene, in addition to the 19 CGG allele derived from an unstable expanded allele, which contracted to the normal range.
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Affiliation(s)
- Esther Manor
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Beersheba, Israel.,Genetics Institute, Soroka Medical Center, Beersheba, Israel
| | - Azhar Jabareen
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Beersheba, Israel.,Genetics Institute, Soroka Medical Center, Beersheba, Israel
| | - Nurit Magal
- Department of Medical Genetics, Rabin Medical Center, Petah Tikva, Israel.,Felsenstein Medical Research Center, Rabin Medical Center, Petah Tikva, Israel
| | - Arei Kofman
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Beersheba, Israel.,Genetics Institute, Soroka Medical Center, Beersheba, Israel
| | - Randi J Hagerman
- Department of Pediatrics, MIND Institute, UC Davis Medical Center, Sacramento, CA, United States
| | - Flora Tassone
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California, Davis, Davis, CA, United States.,MIND Institute, UC Davis Medical Center, Sacramento, CA, United States
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Man L, Lekovich J, Rosenwaks Z, Gerhardt J. Fragile X-Associated Diminished Ovarian Reserve and Primary Ovarian Insufficiency from Molecular Mechanisms to Clinical Manifestations. Front Mol Neurosci 2017; 10:290. [PMID: 28955201 PMCID: PMC5600956 DOI: 10.3389/fnmol.2017.00290] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Accepted: 08/28/2017] [Indexed: 12/12/2022] Open
Abstract
Fragile X syndrome (FXS), is caused by a loss-of-function mutation in the FMR1 gene located on the X-chromosome, which leads to the most common cause of inherited intellectual disability in males and the leading single-gene defect associated with autism. A full mutation (FM) is represented by more than 200 CGG repeats within the FMR1 gene, resulting in FXS. A FM is inherited from women carrying a FM or a premutation (PM; 55–200 CGG repeats) allele. PM is associated with phenotypes distinct from those associated with FM. Some manifestations of the PM are unique; fragile-X-associated tremor/ataxia syndrome (FXTAS), and fragile-X-associated primary ovarian insufficiency (FXPOI), while others tend to be non-specific such as intellectual disability. In addition, women carrying a PM may suffer from subfertility or infertility. There is a need to elucidate whether the impairment of ovarian function found in PM carriers arises during the primordial germ cell (PGC) development stage, or due to a rapidly diminishing oocyte pool throughout life or even both. Due to the possibility of expansion into a FM in the next generation, and other ramifications, carrying a PM can have an enormous impact on one’s life; therefore, preconception counseling for couples carrying the PM is of paramount importance. In this review, we will elaborate on the clinical manifestations in female PM carriers and propose the definition of fragile-X-associated diminished ovarian reserve (FXDOR), then we will review recent scientific findings regarding possible mechanisms leading to FXDOR and FXPOI. Lastly, we will discuss counseling, preventative measures and interventions available for women carrying a PM regarding different aspects of their reproductive life, fertility treatment, pregnancy, prenatal testing, contraception and fertility preservation options.
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Affiliation(s)
- Limor Man
- The Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell MedicineNew York, NY, United States
| | - Jovana Lekovich
- The Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell MedicineNew York, NY, United States
| | - Zev Rosenwaks
- The Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell MedicineNew York, NY, United States
| | - Jeannine Gerhardt
- The Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell MedicineNew York, NY, United States
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Sherman SL, Kidd SA, Riley C, Berry-Kravis E, Andrews HF, Miller RM, Lincoln S, Swanson M, Kaufmann WE, Brown WT. FORWARD: A Registry and Longitudinal Clinical Database to Study Fragile X Syndrome. Pediatrics 2017; 139:S183-S193. [PMID: 28814539 PMCID: PMC5621599 DOI: 10.1542/peds.2016-1159e] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/24/2017] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND AND OBJECTIVE Advances in the care of patients with fragile X syndrome (FXS) have been hampered by lack of data. This deficiency has produced fragmentary knowledge regarding the natural history of this condition, healthcare needs, and the effects of the disease on caregivers. To remedy this deficiency, the Fragile X Clinic and Research Consortium was established to facilitate research. Through a collective effort, the Fragile X Clinic and Research Consortium developed the Fragile X Online Registry With Accessible Research Database (FORWARD) to facilitate multisite data collection. This report describes FORWARD and the way it can be used to improve health and quality of life of FXS patients and their relatives and caregivers. METHODS FORWARD collects demographic information on individuals with FXS and their family members (affected and unaffected) through a 1-time registry form. The longitudinal database collects clinician- and parent-reported data on individuals diagnosed with FXS, focused on those who are 0 to 24 years of age, although individuals of any age can participate. RESULTS The registry includes >2300 registrants (data collected September 7, 2009 to August 31, 2014). The longitudinal database includes data on 713 individuals diagnosed with FXS (data collected September 7, 2012 to August 31, 2014). Longitudinal data continue to be collected on enrolled patients along with baseline data on new patients. CONCLUSIONS FORWARD represents the largest resource of clinical and demographic data for the FXS population in the United States. These data can be used to advance our understanding of FXS: the impact of cooccurring conditions, the impact on the day-to-day lives of individuals living with FXS and their families, and short-term and long-term outcomes.
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Affiliation(s)
- Stephanie L. Sherman
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia;,Address correspondence to Stephanie L. Sherman, PhD, Department of Human Genetics, Emory University School of Medicine, 615 Michael St, Whitehead Building, Suite 301, Atlanta, GA 303022. E-mail:
| | - Sharon A. Kidd
- National Fragile X Foundation, Washington, District of Columbia
| | - Catharine Riley
- National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Elizabeth Berry-Kravis
- Departments of Pediatrics,,Neurological Sciences, and,Biochemistry, Rush University Medical Center, Chicago, Illinois
| | - Howard F. Andrews
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, New York
| | | | - Sharyn Lincoln
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, Massachusetts
| | - Mark Swanson
- National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Walter E. Kaufmann
- Department of Neurology, Boston Children’s Hospital, Boston Massachusetts;,Center for Translational Research, Greenwood Genetic Center, Greenwood, South Carolina; and
| | - W. Ted Brown
- Department of Human Genetics, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, New York
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29
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Ciaccio C, Fontana L, Milani D, Tabano S, Miozzo M, Esposito S. Fragile X syndrome: a review of clinical and molecular diagnoses. Ital J Pediatr 2017; 43:39. [PMID: 28420439 PMCID: PMC5395755 DOI: 10.1186/s13052-017-0355-y] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2016] [Accepted: 04/07/2017] [Indexed: 12/24/2022] Open
Abstract
Background Fragile X Syndrome (FXS) is the second cause of intellectual disability after Down syndrome and the most prevalent cause of intellectual disability in males, affecting 1:5000–7000 men and 1:4000–6000 women. It is caused by an alteration of the FMR1 gene, which maps at the Xq27.3 band: more than 99% of individuals have a CGG expansion (>200 triplets) in the 5′ UTR of the gene, and FMR1 mutations and duplication/deletion are responsible for the remaining (<1%) molecular diagnoses of FXS. The aim of this review was to gather the current clinical and molecular knowledge about FXS to provide clinicians with a tool to guide the initial assessment and follow-up of FXS and to offer to laboratory workers and researchers an update about the current diagnostic procedures. Discussion FXS is a well-known condition; however, most of the studies thus far have focused on neuropsychiatric features. Unfortunately, some of the available studies have limitations, such as the paucity of patients enrolled or bias due to the collection of the data in a single-country population, which may be not representative of the average global FXS population. In recent years, insight into the adult presentation of the disease has progressively increased. Pharmacological treatment of FXS is essentially symptom based, but the growing understanding of the molecular and biological mechanisms of the disease are paving the way to targeted therapy, which may reverse the effects of FMRP deficiency and be a real cure for the disease itself, not just its symptoms. Conclusions The clinical spectrum of FXS is wide, presenting not only as an isolated intellectual disability but as a multi-systemic condition, involving predominantly the central nervous system but potentially affecting any apparatus. Given the relative high frequency of the condition and its complex clinical management, FXS appears to have an important economic and social burden.
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Affiliation(s)
- Claudia Ciaccio
- Pediatric Highly Intensive Care Unit, Department of Pathophysiology and Transplantation, University of Milan, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via Commenda 9, 20122, Milan, Italy
| | - Laura Fontana
- Division of Pathology, Department of Pathophysiology and Transplantation, University of Milan, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Donatella Milani
- Pediatric Highly Intensive Care Unit, Department of Pathophysiology and Transplantation, University of Milan, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via Commenda 9, 20122, Milan, Italy
| | - Silvia Tabano
- Division of Pathology, Department of Pathophysiology and Transplantation, University of Milan, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Monica Miozzo
- Division of Pathology, Department of Pathophysiology and Transplantation, University of Milan, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Susanna Esposito
- Pediatric Clinic, Department of Surgical and Biomedical Sciences, Università degli Studi di Perugia, Piazza Lucio Severi 1, Loc. S. Andrea delle Fratte, 06132, Perugia, Italy.
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30
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Finucane B, Lincoln S, Bailey L, Martin CL. Prognostic dilemmas and genetic counseling for prenatally detected fragile X gene expansions. Prenat Diagn 2016; 37:37-42. [PMID: 27862088 DOI: 10.1002/pd.4963] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 10/28/2016] [Accepted: 11/01/2016] [Indexed: 12/17/2022]
Abstract
With widespread adoption of fragile X carrier screening in pregnant women, the number of expectant couples receiving news of an unanticipated Fragile X Mental Retardation 1 (FMR1) gene expansion has increased. The most common abnormal result from maternal FMR1 testing involves an intermediate allele, also known as a gray zone result, which requires genetic counseling but poses minimal risk for an adverse developmental outcome. By contrast, the finding of a maternal FMR1 premutation or full mutation during pregnancy has important implications for the woman herself, her unborn child, and her extended family. These multiple levels of impact, in addition to the complex inheritance pattern and variable expressivity of fragile X-associated disorders, cause significant stress for newly identified expectant couples and pose unique challenges for genetic counselors in the prenatal setting. © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Brenda Finucane
- Autism & Developmental Medicine Institute, Geisinger Health System, Lewisburg, PA, USA
| | - Sharyn Lincoln
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Lindsay Bailey
- Genomic Medicine Institute, Geisinger Health System, Danville, PA, USA
| | - Christa Lese Martin
- Autism & Developmental Medicine Institute, Geisinger Health System, Lewisburg, PA, USA
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31
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Contraction of fully expanded FMR1 alleles to the normal range: predisposing haplotype or rare events? J Hum Genet 2016; 62:269-275. [DOI: 10.1038/jhg.2016.122] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 09/08/2016] [Accepted: 09/09/2016] [Indexed: 12/28/2022]
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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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33
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Dean DD, Muthuswamy S, Agarwal S. Fragile X syndrome: Current insight. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2016. [DOI: 10.1016/j.ejmhg.2016.01.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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Entezari A, Khaniani MS, Bahrami T, Derakhshan SM, Darvish H. Screening for intermediate CGG alleles of FMR1 gene in male Iranian patients with Parkinsonism. Neurol Sci 2016; 38:123-128. [DOI: 10.1007/s10072-016-2723-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 09/01/2016] [Indexed: 02/01/2023]
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Ups and Downs: Mechanisms of Repeat Instability in the Fragile X-Related Disorders. Genes (Basel) 2016; 7:genes7090070. [PMID: 27657135 PMCID: PMC5042400 DOI: 10.3390/genes7090070] [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: 08/09/2016] [Revised: 08/30/2016] [Accepted: 09/13/2016] [Indexed: 02/06/2023] Open
Abstract
The Fragile X-related disorders (FXDs) are a group of clinical conditions resulting from the expansion of a CGG/CCG-repeat tract in exon 1 of the Fragile X mental retardation 1 (FMR1) gene. While expansions of the repeat tract predominate, contractions are also seen with the net result being that individuals can show extensive repeat length heterogeneity in different tissues. The mechanisms responsible for expansion and contraction are still not well understood. This review will discuss what is known about these processes and current evidence that supports a model in which expansion arises from the interaction of components of the base excision repair, mismatch repair and transcription coupled repair pathways.
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36
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Towards a Better Molecular Diagnosis of FMR1-Related Disorders-A Multiyear Experience from a Reference Lab. Genes (Basel) 2016; 7:genes7090059. [PMID: 27598204 PMCID: PMC5042390 DOI: 10.3390/genes7090059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 08/03/2016] [Accepted: 08/19/2016] [Indexed: 11/29/2022] Open
Abstract
The article summarizes over 20 years of experience of a reference lab in fragile X mental retardation 1 gene (FMR1) molecular analysis in the molecular diagnosis of fragile X spectrum disorders. This includes fragile X syndrome (FXS), fragile X-associated primary ovarian insufficiency (FXPOI) and fragile X-associated tremor/ataxia syndrome (FXTAS), which are three different clinical conditions with the same molecular background. They are all associated with an expansion of CGG repeats in the 5′UTR of FMR1 gene. Until 2016, the FMR1 gene was tested in 9185 individuals with the pre-screening PCR, supplemented with Southern blot analysis and/or Triplet Repeat Primed PCR based method. This approach allowed us to confirm the diagnosis of FXS, FXPOI FXTAS in 636/9131 (6.96%), 4/43 (9.3%) and 3/11 (27.3%) of the studied cases, respectively. Moreover, the FXS carrier status was established in 389 individuals. The technical aspect of the molecular analysis is very important in diagnosis of FXS-related disorders. The new methods were subsequently implemented in our laboratory. This allowed the significance of the Southern blot technique to be decreased until its complete withdrawal. Our experience points out the necessity of implementation of the GeneScan based methods to simplify the testing procedure as well as to obtain more information for the patient, especially if TP-PCR based methods are used.
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Banks N, Patounakis G, Devine K, DeCherney AH, Widra E, Levens ED, Whitcomb BW, Hill MJ. Is FMR1 CGG repeat length a predictor of in vitro fertilization stimulation response or outcome? Fertil Steril 2016; 105:1537-1546.e8. [PMID: 26940792 DOI: 10.1016/j.fertnstert.2016.02.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 02/03/2016] [Accepted: 02/04/2016] [Indexed: 01/24/2023]
Abstract
OBJECTIVE To study a broad range of FMR1 CGG repeat lengths and assisted reproduction technology (ART) outcomes. DESIGN Retrospective cohort study. SETTING Private ART practice. PATIENT(S) Fresh autologous ART stimulation cycles. INTERVENTION(S) None. MAIN OUTCOME MEASURE(S) Oocyte yield, live birth. RESULT(S) We screened 14,088 fresh autologous ART cycles from 2012 to 2015, of which 4,690 cycles in 3,290 patients met the inclusion criteria. The FMR1 repeat length was statistically significantly but weakly associated with oocyte yield and other markers of ovarian response. The receiver operating characteristic curve analysis suggested extremely limited predictive ability. Moreover, the FMR1 repeat length was not statistically significantly associated with outcomes in multivariable models, including other markers of ovarian reserve. The FMR1 repeat length was not associated with embryo quality or live birth. Only patient age had a strong ability to predict live birth. CONCLUSION(S) The FMR1 repeat length is associated with ART response, but only weakly. It provides no incremental predictive ability beyond the conventionally used predictors, including patient age, antimüllerian hormone concentration, antral follicle count, and follicle-stimulating hormone level. These data suggest a possible role of the FMR1 repeat length within the normal range in ovarian response but demonstrate no clinically relevant indication for testing FMR1 as a predictor of ART outcomes.
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Affiliation(s)
- Nicole Banks
- Program in Reproductive and Adult Endocrinology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| | - George Patounakis
- Program in Reproductive and Adult Endocrinology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| | - Kate Devine
- Program in Reproductive and Adult Endocrinology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland; Shady Grove Fertility Science Center, Rockville, Maryland
| | - Alan H DeCherney
- Program in Reproductive and Adult Endocrinology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| | - Eric Widra
- Shady Grove Fertility Science Center, Rockville, Maryland
| | - Eric D Levens
- Shady Grove Fertility Science Center, Rockville, Maryland
| | - Brian W Whitcomb
- Division of Biostatistics and Epidemiology, University of Massachusetts School of Public Health and Health Sciences, Amherst, Massachusetts
| | - Micah J Hill
- Program in Reproductive and Adult Endocrinology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland.
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38
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Pastore LM, Manichaikul A, Wang XQ, Finkelstein JS. FMR1 CGG Repeats: Reference Levels and Race-Ethnic Variation in Women With Normal Fertility (Study of Women's Health Across the Nation). Reprod Sci 2016; 23:1225-33. [PMID: 26905421 DOI: 10.1177/1933719116632927] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
FMR1 premutation carriers (55-199 CGG repeats), and potentially women with high normal (35-44) or low normal (<28) CGG repeats, are at risk of premature ovarian aging. The scarcity of population data on CGG repeats <45 CGG, and variation in race-ethnicity, makes it difficult to determine true associations. DNA was analyzed for FMR1 CGG repeat lengths from 803 women (386 caucasians, 219 African Americans, 102 Japanese, and 96 Chinese) from the US-based Study of Women's Health Across the Nation (SWAN). Participants had ≥1 menses in the 3 months before enrollment, ≥1 pregnancy, no history of infertility or hormonal therapy, and menopause ≥46 years. Statistical analyses used Fisher exact tests. Among these women with normal reproductive histories, significant FMR1 repeat length differences were found across race-ethnicity for both the longer (P = .0002) and the shorter (P < .0001) alleles. The trinucleotide length variance was greater for non-Asian than Asian women (P < .0001), despite identical median values. Our data indicate that short allele lengths <25 CGG on one or both alleles are more common in non-Asian than Asian women. We confirm the minor allele in the 35 to 39 CGG range among Asians as reported previously. Only 2 (0.3%) premutation carriers were identified. These data demonstrate that FMR1 distributions do vary by race-ethnicity, even within the "normal" range. This study indicates the need to control for race-ethnicity in FMR1 ovarian aging research and provides race-ethnic population data for females separated by allele.
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Affiliation(s)
- Lisa M Pastore
- Department of Obstetrics, Gynecology and Reproductive Medicine, Stony Brook Medicine, Stony Brook, NY, USA
| | - Ani Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA Division of Biostatistics and Epidemiology, Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Xin Q Wang
- Division of Biostatistics and Epidemiology, Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
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Clinical and Technical Overview of Preimplantation Genetic Diagnosis for Fragile X Syndrome: Experience at the University Hospital Virgen del Rocio in Spain. BIOMED RESEARCH INTERNATIONAL 2015; 2015:965839. [PMID: 26713318 PMCID: PMC4680048 DOI: 10.1155/2015/965839] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 11/11/2015] [Accepted: 11/18/2015] [Indexed: 01/21/2023]
Abstract
Fragile X syndrome (FXS) accounts for about one-half of cases of X-linked intellectual disability and is the most common monogenic cause of mental impairment. Reproductive options for the FXS carriers include preimplantation genetic diagnosis (PGD). However, this strategy is considered by some centers as wasteful owing to the high prevalence of premature ovarian failure in FXS carriers and the difficulties in genetic diagnosis of the embryos. Here we present the results of our PGD Program applied to FXS, at the Department of Genetics, Reproduction and Fetal Medicine of the University Hospital Virgen del Rocío in Seville. A total of 11 couples have participated in our PGD Program for FXS since 2010. Overall, 15 cycles were performed, providing a total of 43 embryos. The overall percentage of transfers per cycle was 46.67% and the live birth rate per cycle was 13.33%. As expected, these percentages are considerably lower than the ones obtained in PGD for other pathologies. Our program resulted in the birth of 3 unaffected babies of FXS for 2 of the 11 couples (18.2%) supporting that, despite the important drawbacks of PGD for FXS, efforts should be devoted in offering this reproductive option to the affected families.
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Extra alleles in FMR1 triple-primed PCR: artifact, aneuploidy, or somatic mosaicism? J Mol Diagn 2015; 16:689-96. [PMID: 25307758 DOI: 10.1016/j.jmoldx.2014.06.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 05/06/2014] [Accepted: 06/06/2014] [Indexed: 12/13/2022] Open
Abstract
Triple-primed PCR assays have become the preferred fragile X syndrome testing method. Using a commercially available assay, we detected a reproducible extra peak(s) in 0.5% of 13,161 clinical samples. The objectives of this study were to determine the cause of these extra peaks; to identify whether these peaks represent an assay specific artifact, an underlying chromosome aneuploidy, or somatic mosaicism; and to ascertain their clinical relevance. The presence of an extra allele(s) was confirmed by a laboratory-developed PCR, with sequencing of the FMR1 5' UTR or Southern blot for some samples. The laboratory-developed procedure detected the extra allele(s) in 57 of 64 samples. Thus, we confirmed an extra peak, typically of lower abundance, in approximately 0.4% of all samples. Of these samples, 5 were from males and 52 were from heterozygous or homozygous females. Six patients likely had X chromosome aneuploidies. In 82.3% of samples, the extra allele had fewer repeats than the predominant allele(s). Additional alleles detected by FMR1 triple-primed PCR are not an assay-specific artifact and are likely due to X chromosome aneuploidies or somatic repeat instability. Additional normal alleles likely have no clinical significance for fragile X syndrome carrier or affected status. Extra alleles in individuals with normal karyotypes probably represent FMR1 somatic variation.
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Huang W, Xia Q, Luo S, He H, Zhu T, Du Q, Duan R. Distribution of fragile X mental retardation 1 CGG repeat and flanking haplotypes in a large Chinese population. Mol Genet Genomic Med 2015; 3:172-81. [PMID: 26029703 PMCID: PMC4444158 DOI: 10.1002/mgg3.128] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Fragile X syndrome is mainly caused by a CGG repeat expansion within the 5' UTR of the fragile X mental retardation 1 (FMR1) gene. Previous analyses of the FMR1 CGG repeat patterns and flanking haplotypes in Caucasians and African Americans have identified several factors that may influence repeat instability. However, the CGG repeat patterns and distribution for FRAXAC2 have not yet been investigated in mainland Chinese. We surveyed the CGG repeat lengths in 1113 Han Chinese (534 males and 579 females), and the CGG repeat patterns of 534 males were determined by sequence analysis. We also explored the flanking haplotypes (DXS548-FRAXAC1-FRAXAC2) in 566 unaffected and 28 unrelated fragile X Chinese males. The most frequent alleles for DXS548 and FRAXAC1 were identical between our Chinese population and other Asian populations. We identified several low-abundance alleles for DXS548 and FRAXAC1 not found in previous studies in mainland Chinese and Taiwanese cohorts. The most frequent allele was (CGG)29 followed by (CGG)30, and the most frequent patterns were 9 + 9 + 9, 10 + 9 + 9, and 9 + 9 + 6 + 9, similar to those in Singaporeans. We identified only one premutation female carrier with 89 CGG repeats in the 1113 Han Chinese. A few associations between the CGG repeat patterns and flanking haplotypes were determined in this study. In general, the Chinese population had a smaller number of alleles and lower expected heterozygosity for all three STR markers and FRAXA locus when compared with Caucasians and African Americans. We identified a novel haplotype 7-3-5 + that is significantly associated with the full mutation.
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Affiliation(s)
- Wen Huang
- The State Key Laboratory of Medical Genetics & School of Life Sciences, Central South University Changsha, 410078, Hunan, China
| | - Qiuping Xia
- The State Key Laboratory of Medical Genetics & School of Life Sciences, Central South University Changsha, 410078, Hunan, China
| | - Shiyu Luo
- The State Key Laboratory of Medical Genetics & School of Life Sciences, Central South University Changsha, 410078, Hunan, China
| | - Hua He
- The State Key Laboratory of Medical Genetics & School of Life Sciences, Central South University Changsha, 410078, Hunan, China
| | - Ting Zhu
- The State Key Laboratory of Medical Genetics & School of Life Sciences, Central South University Changsha, 410078, Hunan, China
| | - Qian Du
- The State Key Laboratory of Medical Genetics & School of Life Sciences, Central South University Changsha, 410078, Hunan, China
| | - Ranhui Duan
- The State Key Laboratory of Medical Genetics & School of Life Sciences, Central South University Changsha, 410078, Hunan, China
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Simplified strategy for rapid first-line screening of fragile X syndrome: closed-tube triplet-primed PCR and amplicon melt peak analysis. Expert Rev Mol Med 2015; 17:e7. [PMID: 25936533 PMCID: PMC4836207 DOI: 10.1017/erm.2015.5] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Premutation and full-mutation hyperexpansion of CGG-triplets in the X-linked Fragile X Mental Retardation 1 (FMR1) gene have been implicated in fragile X-associated tremor/ataxia syndrome, fragile X-associated primary ovarian insufficiency, and fragile X syndrome (FXS), respectively. The currently available molecular diagnostic tests are either costly or labour-intensive, which prohibits their application as a first-line FMR1 test in large-scale population-based screening programs. In this study, we demonstrate the utility of a simplified closed-tube strategy for rapid first-line screening of FXS based on melt peak temperature (Tm) analysis of direct triplet-primed polymerase chain reaction amplicons (dTP-PCR MCA). In addition, we also evaluated the correlation between Tm and CGG-repeat size based on capillary electrophoresis (CE) of dTP-PCR amplicons. The assays were initially tested on 29 FMR1 reference DNA samples, followed by a blinded validation on 107 previously characterised patient DNA samples. The dTP-PCR MCA produced distinct melt profiles of higher Tm for samples carrying an expanded allele. Among the samples tested, we also observed a good correlation between Tm and CGG-repeat size. In the blinded validation study, dTP-PCR MCA accurately classified all normal and expansion carriers, and the FMR1 genotypic classification of all samples was completely concordant with the previously determined genotypes as well as the dTP-PCR CE results. This simple and cost-effective MCA-based assay may be useful as a first-line FXS screening tool that could rapidly screen out the large majority of unaffected individuals, thus minimising the number of samples that need to be analysed by Southern blot analysis.
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Tural S, Tekcan A, Kara N, Elbistan M, Güven D, Ali Tasdemir H. FMR1 gene mutation screening by TP-PCR in patients with premature ovarian failure and fragile-X. Gynecol Endocrinol 2015; 31:191-5. [PMID: 25366135 DOI: 10.3109/09513590.2014.975685] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
CGG repeat expansion in the FMR1 gene is associated with fragile X syndrome, fragile X-associated tremor/ ataxia syndrome and fragile X-associated primary ovarian insufficiency. In this study, FMR1 gene mutation screening was carried out in 50 patients. Among them, 12 (%24) were POF and 19 (%38) were Fragile-X. We also examined the parents of the Fragile-X patients. DNA was extracted from blood with kit procedure. To examine expansion of the fragile-X CGG repeat, TP-PCR assay was performed and all amplicons were evaluated on an ABI3130XL Genetic Analyzer System by Fragman analysis. The data were analyzed by Gene Mapper Program. As a result of this study, the patients were identified with the fragile-X whose FMR1 gene CGG alleles have been observed in normal range. However, in patients who were referred with premature ovarian failure, pre-mutation frequency was observed as 6.6%. Only limited study in Turkish population reported frequency of pre-mutation carrier in POF and Fragile-X. Detection of pre-mutation carrier is important for next generation to have healthy siblings. We emphasize that TP-PCR technique is clear, reliable, sensitive, easy and fast method to detect pre-mutation. However, full mutations have to be examined by the technique of Southern blot in the diagnosis of fragile-X.
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Affiliation(s)
- Sengul Tural
- Faculy of Medicine, Department of Medical Biology, Section of Medical Genetics
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Intermediate CGG repeat length at the FMR1 locus is not associated with hormonal indicators of ovarian age. Menopause 2015; 21:740-8. [PMID: 24423935 DOI: 10.1097/gme.0000000000000139] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVE Premutation and intermediate CGG repeat length at the fragile X mental retardation 1 (FMR1) locus have been associated with premature ovarian failure. We tested whether intermediate length is associated with indicators of ovarian age in a sample of fertile women. Our primary measures of ovarian age were antimüllerian hormone (AMH) and follicle-stimulating hormone (FSH) levels. METHODS The cross-sectional sample comprised 258 women with karyotyped spontaneous abortions (140 trisomic spontaneous abortions and 118 chromosomally normal spontaneous abortions or spontaneous abortions with anomalies other than trisomy) and 325 women with recent live births (LBs). We analyzed data from the total sample and data from LBs only. We defined CGG repeat length by the length (both continuous and categorical) on the longer allele. RESULTS CGG repeat length was not significantly associated with either hormone measure. A repeat length of 35 to 54 CGG, versus the modal category of 30 CGG, was associated with an approximately 7% increase in median AMH level and a 3% increase in median FSH level. Results were unaltered when analyses were limited to LBs. Analyses of hormone levels using cutpoints to define older ovarian age showed no associations with repeat length. Among 10 women with repeat lengths of 35 to 54 CGG analyzed for AGG sequences, the uninterrupted CGG length was not significantly longer among women with hormonal indicators of "old" versus "young" ovarian age. CONCLUSIONS Our data do not support an association between intermediate CGG repeat length and levels of AMH or FSH among fertile women.
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Usdin K, House NCM, Freudenreich CH. Repeat instability during DNA repair: Insights from model systems. Crit Rev Biochem Mol Biol 2015; 50:142-67. [PMID: 25608779 DOI: 10.3109/10409238.2014.999192] [Citation(s) in RCA: 127] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The expansion of repeated sequences is the cause of over 30 inherited genetic diseases, including Huntington disease, myotonic dystrophy (types 1 and 2), fragile X syndrome, many spinocerebellar ataxias, and some cases of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Repeat expansions are dynamic, and disease inheritance and progression are influenced by the size and the rate of expansion. Thus, an understanding of the various cellular mechanisms that cooperate to control or promote repeat expansions is of interest to human health. In addition, the study of repeat expansion and contraction mechanisms has provided insight into how repair pathways operate in the context of structure-forming DNA, as well as insights into non-canonical roles for repair proteins. Here we review the mechanisms of repeat instability, with a special emphasis on the knowledge gained from the various model systems that have been developed to study this topic. We cover the repair pathways and proteins that operate to maintain genome stability, or in some cases cause instability, and the cross-talk and interactions between them.
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Affiliation(s)
- Karen Usdin
- Laboratory of Cell and Molecular Biology, NIDDK, NIH , Bethesda, MD , USA
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46
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Gerhardt J, Zaninovic N, Zhan Q, Madireddy A, Nolin SL, Ersalesi N, Yan Z, Rosenwaks Z, Schildkraut CL. Cis-acting DNA sequence at a replication origin promotes repeat expansion to fragile X full mutation. ACTA ACUST UNITED AC 2014; 206:599-607. [PMID: 25179629 PMCID: PMC4151148 DOI: 10.1083/jcb.201404157] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
An SNP upstream of the CGG repeats located at a replication initiation site may contribute to origin inactivation, to altered replication fork progression through the CGG repeats, and repeat expansion to fragile X full mutation. Fragile X syndrome (FXS) is caused by CGG repeat expansion that leads to FMR1 silencing. Women with a premutation allele are at risk of having a full mutation child with FXS. To investigate the mechanism of repeat expansion, we examined the relationship between a single-nucleotide polymorphism (SNP) variant that is linked to repeat expansion in haplogroup D and a replication origin located ∼53 kb upstream of the repeats. This origin is absent in FXS human embryonic stem cells (hESCs), which have the SNP variant C, but present in the nonaffected hESCs, which have a T variant. The SNP maps directly within the replication origin. Interestingly, premutation hESCs have a replication origin and the T variant similar to nonaffected hESCs. These results suggest that a T/C SNP located at a replication origin could contribute to the inactivation of this replication origin in FXS hESCs, leading to altered replication fork progression through the repeats, which could result in repeat expansion to the FXS full mutation.
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Affiliation(s)
- Jeannine Gerhardt
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Nikica Zaninovic
- Center for Reproductive Medicine and Infertility, Weill Cornell Medical College, New York, NY 10021
| | - Qiansheng Zhan
- Center for Reproductive Medicine and Infertility, Weill Cornell Medical College, New York, NY 10021
| | - Advaitha Madireddy
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Sarah L Nolin
- New York State Institute for Basic Research in Developmental Disabilities, Staten Island, NY 10314
| | - Nicole Ersalesi
- New York State Institute for Basic Research in Developmental Disabilities, Staten Island, NY 10314
| | - Zi Yan
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Zev Rosenwaks
- Center for Reproductive Medicine and Infertility, Weill Cornell Medical College, New York, NY 10021
| | - Carl L Schildkraut
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461
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Biancalana V, Glaeser D, McQuaid S, Steinbach P. EMQN best practice guidelines for the molecular genetic testing and reporting of fragile X syndrome and other fragile X-associated disorders. Eur J Hum Genet 2014; 23:417-25. [PMID: 25227148 PMCID: PMC4666582 DOI: 10.1038/ejhg.2014.185] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 07/09/2014] [Accepted: 07/10/2014] [Indexed: 01/25/2023] Open
Abstract
Different mutations occurring in the unstable CGG repeat in 5' untranslated region of FMR1 gene are responsible for three fragile X-associated disorders. An expansion of over ∼200 CGG repeats when associated with abnormal methylation and inactivation of the promoter is the mutation termed ‘full mutation' and is responsible for fragile X syndrome (FXS), a neurodevelopmental disorder described as the most common cause of inherited intellectual impairment. The term ‘abnormal methylation' is used here to distinguish the DNA methylation induced by the expanded repeat from the ‘normal methylation' occurring on the inactive X chromosomes in females with normal, premutation, and full mutation alleles. All male and roughly half of the female full mutation carriers have FXS. Another anomaly termed ‘premutation' is characterized by the presence of 55 to ∼200 CGGs without abnormal methylation, and is the cause of two other diseases with incomplete penetrance. One is fragile X-associated primary ovarian insufficiency (FXPOI), which is characterized by a large spectrum of ovarian dysfunction phenotypes and possible early menopause as the end stage. The other is fragile X-associated tremor/ataxia syndrome (FXTAS), which is a late onset neurodegenerative disorder affecting males and females. Because of the particular pattern and transmission of the CGG repeat, appropriate molecular testing and reporting is very important for the optimal genetic counselling in the three fragile X-associated disorders. Here, we describe best practice guidelines for genetic analysis and reporting in FXS, FXPOI, and FXTAS, including carrier and prenatal testing.
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Affiliation(s)
- Valérie Biancalana
- Laboratoire Diagnostic Génétique, Faculté de Médecine-CHRU, Strasbourg, France
| | | | - Shirley McQuaid
- National Centre for Medical Genetics, Our Lady's Children's Hospital, Crumlin, Dublin, Ireland
| | - Peter Steinbach
- Institute of Human Genetics, University Hospital of Ulm, Ulm, Germany
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Fragile X full mutation expansions are inhibited by one or more AGG interruptions in premutation carriers. Genet Med 2014; 17:358-64. [PMID: 25210937 DOI: 10.1038/gim.2014.106] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 07/09/2014] [Indexed: 11/08/2022] Open
Abstract
PURPOSE Fragile X CGG repeat alleles often contain one or more AGG interruptions that influence allele stability and risk of a full mutation transmission from parent to child. We have examined transmissions of maternal and paternal alleles with 45-90 repeats to quantify the effect of AGG interruptions on fragile X repeat instability. METHODS A novel FMR1 polymerase chain reaction assay was used to determine CGG repeat length and AGG interruptions for 1,040 alleles from 705 families. RESULTS We grouped transmissions into nine categories of five repeats by parental size and found that in every size category, alleles with no AGGs had the greatest risk for instability. For maternal alleles <75 repeats, 89% (24/27) that expanded to a full mutation had no AGGs. Two contractions in maternal transmission were accompanied by loss of AGGs, suggesting a mechanism for generating alleles that lack AGG interruptions. Maternal age was examined as a factor in full mutation expansions using prenatal samples to minimize ascertainment bias, and a possible effect was observed though it was not statistically significant (P = 0.06). CONCLUSION These results strengthen the association of AGG repeats with CGG repeat stability and provide more accurate risk estimates of full mutation expansions for women with 45-90 repeat alleles.
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Yrigollen CM, Martorell L, Durbin-Johnson B, Naudo M, Genoves J, Murgia A, Polli R, Zhou L, Barbouth D, Rupchock A, Finucane B, Latham GJ, Hadd A, Berry-Kravis E, Tassone F. AGG interruptions and maternal age affect FMR1 CGG repeat allele stability during transmission. J Neurodev Disord 2014; 6:24. [PMID: 25110527 PMCID: PMC4126815 DOI: 10.1186/1866-1955-6-24] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Accepted: 01/17/2014] [Indexed: 01/25/2023] Open
Abstract
Background The presence of AGG interruptions in the CGG repeat locus of the fragile X mental retardation 1 (FMR1) gene decreases the instability of the allele during transmission from parent to child, and decreases the risk of expansion of a premutation allele to a full mutation allele (the predominant cause of fragile X syndrome) during maternal transmission. Methods To strengthen recent findings on the utility of AGG interruptions in predicting instability or expansion to a full mutation of FMR1 CGG repeat alleles, we assessed the outcomes of 108 intermediate (also named gray zone) and 710 premutation alleles that were transmitted from parent to child, and collected from four international clinical sites. We have used the results to revise our initial model that predicted the risk of a maternal premutation allele expanding to a full mutation during transmission and to test the effect of AGG interruptions on the magnitude of expanded allele instability of intermediate or premutation alleles that did not expand to a full mutation. Results Consistent with previous studies, the number of AGG triplets that interrupts the CGG repeat locus was found to influence the risk of allele instability, including expansion to a full mutation. The total length of the CGG repeat allele remains the best predictor of instability or expansion to a full mutation, but the number of AGG interruptions and, to a much lesser degree, maternal age are also factors when considering the risk of transmission of the premutation allele to a full mutation. Conclusions Our findings demonstrate that a model with total CGG length, number of AGG interruptions, and maternal age is recommended for calculating the risk of expansion to a full mutation during maternal transmission. Taken together, the results of this study provide relevant information for the genetic counseling of female premutation carriers, and improve the current predictive models which calculate risk of expansion to a full mutation using only total CGG repeat length.
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Affiliation(s)
- Carolyn M Yrigollen
- Department of Biochemistry and Molecular Medicine, University of California, Davis, School of Medicine, 2700 Stockton Blvd., Suite 2102, Sacramento, CA 95817, USA
| | - Loreto Martorell
- Molecular Genetics Section, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Blythe Durbin-Johnson
- Department of Public Health Sciences, University of California, Davis, Davis, CA, USA
| | - Montserrat Naudo
- Molecular Genetics Section, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Jordi Genoves
- Molecular Genetics Section, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Alessandra Murgia
- Laboratory of Molecular Genetics of Neurodevelopment, Department of Women's and Children's Health, University of Padova, Padova, Italy
| | - Roberta Polli
- Laboratory of Molecular Genetics of Neurodevelopment, Department of Women's and Children's Health, University of Padova, Padova, Italy
| | - Lili Zhou
- Department of Pediatrics, Neurological Sciences, and Biochemistry, Rush University Medical Center, Chicago, IL, USA
| | - Deborah Barbouth
- Dr. John T. Macdonald Foundation, Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Abigail Rupchock
- Dr. John T. Macdonald Foundation, Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Brenda Finucane
- Geisinger Autism and Developmental Medicine Institute, Lewisburg, PA, USA
| | | | | | - Elizabeth Berry-Kravis
- Department of Pediatrics, Neurological Sciences, and Biochemistry, Rush University Medical Center, Chicago, IL, USA
| | - Flora Tassone
- Department of Biochemistry and Molecular Medicine, University of California, Davis, School of Medicine, 2700 Stockton Blvd., Suite 2102, Sacramento, CA 95817, USA ; MIND Institute, University of California, Davis, School of Medicine, Davis, CA, USA
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Latham GJ, Coppinger J, Hadd AG, Nolin SL. The role of AGG interruptions in fragile X repeat expansions: a twenty-year perspective. Front Genet 2014; 5:244. [PMID: 25120560 PMCID: PMC4114290 DOI: 10.3389/fgene.2014.00244] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2014] [Accepted: 07/08/2014] [Indexed: 11/21/2022] Open
Abstract
In 1994, it was suggested that AGG interruptions affect the stability of the fragile X triplet repeat. Until recently, however, this hypothesis was not explored on a large scale due primarily to the technical difficulty of determining AGG interruption patterns of the two alleles in females. The recent development of a PCR technology that overcomes this difficulty and accurately identifies the number and position of AGGs has led to several studies that examine their influence on repeat stability. Here, we present a historical perspective of relevant studies published during the last 20 years on AGG interruptions and examine those recent publications that have refined risk estimates for repeat instability and full-mutation expansions.
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Affiliation(s)
| | | | | | - Sarah L Nolin
- Department of Human Genetics, New York State Institute for Basic Research in Developmental Disabilities Staten Island, NY, USA
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