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Shahid R, Yasin M, Rehman ZU, Jadoon H, Tahir H, Meraj N, Khan N, Zubair M, Zulfiqar I, Nowshid M, Azeem A, Jabeen M, Hameed A, Saleha S. Maternal FMR1 alleles expansion in newborns during transmission: a prospective cohort study. Pediatr Res 2023; 93:720-724. [PMID: 35681093 DOI: 10.1038/s41390-022-02128-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 04/05/2022] [Accepted: 05/17/2022] [Indexed: 11/09/2022]
Abstract
INTRODUCTION The CGG repeats in the 5' untranslated region of the fragile X mental retardation 1 gene (FMR1) gene shows increased instability upon maternal transmission. Maternal FMR1 intermediate (45-54 repeats) and premutation (PM: 55-<200 repeats) alleles usually expand to full mutation (>200 repeats) alleles in offspring and consequently, cause fragile X syndrome (FXS) in them. METHODS In a prospective cohort study, Pakistani pregnant women in prenatal care were first screened for FMR1 expanded alleles. In the follow-up, pregnancy outcomes in women carrying FMR1 expanded alleles were recorded and their newborn offspring were also screened for FXS. RESULTS In a total of 1950 pregnant women, 89 (4.6%) were detected carriers for FMR1 expanded alleles; however, rates of detection of expanded alleles were found significantly high in women with a history of FXS. In addition, miscarriages and birth of affected newborns with FXS were significantly more common in women carrying large size PM alleles and had a history of FXS (P = 0.0494 and P = 0.0494, respectively). CONCLUSIONS The current study provides the first evidence of screening Pakistani pregnant women for FMR1 expanded alleles in prenatal care. Moreover, the miscarriage was also detected as a clinical predictor for FXS. IMPACT Offspring would have a higher risk of developing FXS due to maternal FMR1 alleles expansions during transmission. This is the first prospective cohort study in Pakistan for finding FMR1 allelic status of pregnant women and their newborn offspring in follow-up. The robust offspring risk for FXS estimated in this study may be valuable information for genetic counseling of women carriers for FMR1 expanded alleles. The family history and miscarriage were detected as effective indicators for FXS carrier screening in Pakistani women.
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Affiliation(s)
- Rabia Shahid
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat, 26000, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Yasin
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat, 26000, Khyber Pakhtunkhwa, Pakistan
| | - Zia Ur Rehman
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat, 26000, Khyber Pakhtunkhwa, Pakistan
| | - Humaira Jadoon
- Department of Obstetrics & Gynecology, Ayub Medical Institute, Abbottabad, 22010, Khyber Pakhtunkhwa, Pakistan
| | - Haleema Tahir
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat, 26000, Khyber Pakhtunkhwa, Pakistan
| | - Neelam Meraj
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat, 26000, Khyber Pakhtunkhwa, Pakistan
| | - Niamat Khan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat, 26000, Khyber Pakhtunkhwa, Pakistan
| | - Maria Zubair
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat, 26000, Khyber Pakhtunkhwa, Pakistan
| | - Irba Zulfiqar
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat, 26000, Khyber Pakhtunkhwa, Pakistan
| | - Maha Nowshid
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat, 26000, Khyber Pakhtunkhwa, Pakistan
| | - Arfa Azeem
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat, 26000, Khyber Pakhtunkhwa, Pakistan
| | - Musarrat Jabeen
- Department of Obstetrics and Gynecology, Liaqat Memorial Hospital, KIMS, Kohat, 26000, Khyber Pakhtunkhwa, Pakistan
| | - Abdul Hameed
- Institute of Biomedical and Genetic Engineering (IBGE), Islamabad, 44000, Pakistan
| | - Shamim Saleha
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat, 26000, Khyber Pakhtunkhwa, Pakistan.
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Tabolacci E, Nobile V, Pucci C, Chiurazzi P. Mechanisms of the FMR1 Repeat Instability: How Does the CGG Sequence Expand? Int J Mol Sci 2022; 23:ijms23105425. [PMID: 35628235 PMCID: PMC9141726 DOI: 10.3390/ijms23105425] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 05/10/2022] [Accepted: 05/11/2022] [Indexed: 11/16/2022] Open
Abstract
A dynamic mutation in exon 1 of the FMR1 gene causes Fragile X-related Disorders (FXDs), due to the expansion of an unstable CGG repeat sequence. Based on the CGG sequence size, two types of FMR1 alleles are possible: “premutation” (PM, with 56-200 CGGs) and “full mutation” (FM, with >200 triplets). Premutated females are at risk of transmitting a FM allele that, when methylated, epigenetically silences FMR1 and causes Fragile X syndrome (FXS), a very common form of inherited intellectual disability (ID). Expansions events of the CGG sequence are predominant over contractions and are responsible for meiotic and mitotic instability. The CGG repeat usually includes one or more AGG interspersed triplets that influence allele stability and the risk of transmitting FM to children through maternal meiosis. A unique mechanism responsible for repeat instability has not been identified, but several processes are under investigations using cellular and animal models. The formation of unusual secondary DNA structures at the expanded repeats are likely to occur and contribute to the CGG expansion. This review will focus on the current knowledge about CGG repeat instability addressing the CGG sequence expands.
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Affiliation(s)
- Elisabetta Tabolacci
- Dipartimento Scienze della Vita e Sanità Pubblica, Sezione di Medicina Genomica, Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario “A. Gemelli” IRCCS, 00168 Rome, Italy; (E.T.); (V.N.); (C.P.)
| | - Veronica Nobile
- Dipartimento Scienze della Vita e Sanità Pubblica, Sezione di Medicina Genomica, Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario “A. Gemelli” IRCCS, 00168 Rome, Italy; (E.T.); (V.N.); (C.P.)
| | - Cecilia Pucci
- Dipartimento Scienze della Vita e Sanità Pubblica, Sezione di Medicina Genomica, Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario “A. Gemelli” IRCCS, 00168 Rome, Italy; (E.T.); (V.N.); (C.P.)
| | - Pietro Chiurazzi
- Dipartimento Scienze della Vita e Sanità Pubblica, Sezione di Medicina Genomica, Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario “A. Gemelli” IRCCS, 00168 Rome, Italy; (E.T.); (V.N.); (C.P.)
- UOC Genetica Medica, Fondazione Policlinico Universitario “A. Gemelli” IRCCS, 00168 Rome, Italy
- Correspondence: ; Tel.: +39-06-3015-4606
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Bartlett E, Archibald AD, Francis D, Ling L, Thomas R, Chandler G, Ward L, O'Farrell G, Pandelache A, Delatycki MB, Bennetts BH, Ho G, Fisk K, Baker EK, Amor DJ, Godler DE. Paternal retraction of a fragile X allele to normal size, showing normal function over two generations. Am J Med Genet A 2021; 188:304-309. [PMID: 34545686 DOI: 10.1002/ajmg.a.62500] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 08/09/2021] [Accepted: 08/18/2021] [Indexed: 11/09/2022]
Abstract
The FMR1 premutation (PM:55-199 CGG) is associated with fragile X-associated tremor/ataxia syndrome (FXTAS) and when maternally transmitted is at risk of expansion to a hypermethylated full mutation (FM: ≥ 200 CGG) that causes fragile X syndrome (FXS). We describe a maternally transmitted PM (77 CGG) that was passed to a son (103 CGG), and to a daughter (220-1822 CGG), who were affected with FXTAS and FXS, respectively. The male with the PM showed low-level mosaicism for normal size of 30 and 37 CGG. This male had two offspring: one female mosaic for PM and FM (56, 157, >200 CGG) and another with only a 37 CGG allele detected in multiple tissues, neither with a clinical phenotype. The female with the 37 CGG allele showed normal levels of FMR1 methylation and mRNA and passed this 37 CGG allele to one of her daughters, who was also unaffected. These findings show that post-zygotic paternal retraction can lead to low-level mosaicism for normal size alleles, with these normal alleles being functional when passed over two generations.
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Affiliation(s)
- Essra Bartlett
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Alison D Archibald
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia.,Faculty of Medicine, Dentistry and Health Sciences, Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia.,Bruce Lefroy Centre, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - David Francis
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Ling Ling
- Diagnosis and Development, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Rob Thomas
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Gabrielle Chandler
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Lisa Ward
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Gemma O'Farrell
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Alison Pandelache
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Martin B Delatycki
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia.,Faculty of Medicine, Dentistry and Health Sciences, Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia.,Bruce Lefroy Centre, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Bruce H Bennetts
- Sydney Genome Diagnostics-Molecular Genetics, Children's Hospital at Westmead, Sydney, New South Wales, Australia.,Discipline of Genetic Medicine, Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - Gladys Ho
- Sydney Genome Diagnostics-Molecular Genetics, Children's Hospital at Westmead, Sydney, New South Wales, Australia.,Discipline of Genetic Medicine, Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - Katrina Fisk
- Sydney Genome Diagnostics-Molecular Genetics, Children's Hospital at Westmead, Sydney, New South Wales, Australia
| | - Emma K Baker
- Diagnosis and Development, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia.,Faculty of Medicine, Dentistry and Health Sciences, Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia.,School of Psychology and Public Health, La Trobe University, Melbourne, Victoria, Australia
| | - David J Amor
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia.,Faculty of Medicine, Dentistry and Health Sciences, Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia.,Neurodisability and Rehabilitation, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - David E Godler
- Diagnosis and Development, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia.,Faculty of Medicine, Dentistry and Health Sciences, Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
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Laboratory testing for fragile X, 2021 revision: a technical standard of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2021; 23:799-812. [PMID: 33795824 DOI: 10.1038/s41436-021-01115-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 02/01/2021] [Accepted: 02/02/2021] [Indexed: 11/08/2022] Open
Abstract
Molecular genetic testing of the FMR1 gene is commonly performed in clinical laboratories. Pathogenic variants in the FMR1 gene are associated with fragile X syndrome, fragile X-associated tremor ataxia syndrome (FXTAS), and fragile X-associated primary ovarian insufficiency (FXPOI). This document provides updated information regarding FMR1 pathogenic variants, including prevalence, genotype-phenotype correlations, and variant nomenclature. Methodological considerations are provided for Southern blot analysis and polymerase chain reaction (PCR) amplification of FMR1, including triplet repeat-primed and methylation-specific PCR.The American College of Medical Genetics and Genomics (ACMG) Laboratory Quality Assurance Committee has the mission of maintaining high technical standards for the performance and interpretation of genetic tests. In part, this is accomplished by the publication of the document ACMG Technical Standards for Clinical Genetics Laboratories, which is now maintained online ( http://www.acmg.net ). This subcommittee also reviews the outcome of national proficiency testing in the genetics area and may choose to focus on specific diseases or methodologies in response to those results. Accordingly, the subcommittee selected fragile X syndrome to be the first topic in a series of supplemental sections, recognizing that it is one of the most frequently ordered genetic tests and that it has many alternative methods with different strengths and weaknesses. This document is the fourth update to the original standards and guidelines for fragile X testing that were published in 2001, with revisions in 2005 and 2013, respectively.This versionClarifies the clinical features associated with different FMRI variants (Section 2.3)Discusses important reporting considerations (Section 3.3.1.3)Provides updates on technology (Section 4.1).
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Kraan CM, Baker EK, Arpone M, Bui M, Ling L, Gamage D, Bretherton L, Rogers C, Field MJ, Wotton TL, Francis D, Hunter MF, Cohen J, Amor DJ, Godler DE. DNA Methylation at Birth Predicts Intellectual Functioning and Autism Features in Children with Fragile X Syndrome. Int J Mol Sci 2020; 21:ijms21207735. [PMID: 33086711 PMCID: PMC7589848 DOI: 10.3390/ijms21207735] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/15/2020] [Accepted: 10/16/2020] [Indexed: 12/12/2022] Open
Abstract
Fragile X syndrome (FXS) is a leading single-gene cause of intellectual disability (ID) with autism features. This study analysed diagnostic and prognostic utility of the Fragile X-Related Epigenetic Element 2 DNA methylation (FREE2m) assessed by Methylation Specific-Quantitative Melt Analysis and the EpiTYPER system, in retrospectively retrieved newborn blood spots (NBS) and newly created dried blood spots (DBS) from 65 children with FXS (~2–17 years). A further 168 NBS from infants from the general population were used to establish control reference ranges, in both sexes. FREE2m analysis showed sensitivity and specificity approaching 100%. In FXS males, NBS FREE2m strongly correlated with intellectual functioning and autism features, however associations were not as strong for FXS females. Fragile X mental retardation 1 gene (FMR1) mRNA levels in blood were correlated with FREE2m in both NBS and DBS, for both sexes. In females, DNAm was significantly increased at birth with a decrease in childhood. The findings support the use of FREE2m analysis in newborns for screening, diagnostic and prognostic testing in FXS.
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Affiliation(s)
- Claudine M Kraan
- Diagnosis and Development, Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne VIC 3052, Australia; (C.M.K.); (E.K.B.); (M.A.); (L.L.); (D.G.); (L.B.); (D.J.A.)
- Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville VIC 3052, Australia
| | - Emma K Baker
- Diagnosis and Development, Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne VIC 3052, Australia; (C.M.K.); (E.K.B.); (M.A.); (L.L.); (D.G.); (L.B.); (D.J.A.)
- Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville VIC 3052, Australia
- School of Psychology and Public Health, La Trobe University, Bundoora VIC 3086, Australia
| | - Marta Arpone
- Diagnosis and Development, Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne VIC 3052, Australia; (C.M.K.); (E.K.B.); (M.A.); (L.L.); (D.G.); (L.B.); (D.J.A.)
- Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville VIC 3052, Australia
- Brain and Mind, Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville VIC 3052, Australia
| | - Minh Bui
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne VIC 3052, Australia;
| | - Ling Ling
- Diagnosis and Development, Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne VIC 3052, Australia; (C.M.K.); (E.K.B.); (M.A.); (L.L.); (D.G.); (L.B.); (D.J.A.)
| | - Dinusha Gamage
- Diagnosis and Development, Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne VIC 3052, Australia; (C.M.K.); (E.K.B.); (M.A.); (L.L.); (D.G.); (L.B.); (D.J.A.)
| | - Lesley Bretherton
- Diagnosis and Development, Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne VIC 3052, Australia; (C.M.K.); (E.K.B.); (M.A.); (L.L.); (D.G.); (L.B.); (D.J.A.)
| | - Carolyn Rogers
- Genetics of Learning Disability Service (GOLD service), Hunter Genetics, Newcastle NSW 2298, Australia; (C.R.); (M.J.F.)
| | - Michael J Field
- Genetics of Learning Disability Service (GOLD service), Hunter Genetics, Newcastle NSW 2298, Australia; (C.R.); (M.J.F.)
| | - Tiffany L Wotton
- New South Wales Newborn Screening Program, Children’s Hospital at Westmead, Sydney NSW 2145, Australia;
| | - David Francis
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne VIC 3052, Australia;
| | - Matt F Hunter
- Monash Genetics, Monash Health, Clayton, VIC 3168, Australia;
| | - Jonathan Cohen
- Centre for Developmental Disability Health Victoria, Monash University, Doveton VIC 3177, Australia;
- Fragile X Alliance Inc., North Caulfield VIC 3161, Australia
| | - David J Amor
- Diagnosis and Development, Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne VIC 3052, Australia; (C.M.K.); (E.K.B.); (M.A.); (L.L.); (D.G.); (L.B.); (D.J.A.)
- Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville VIC 3052, Australia
| | - David E Godler
- Diagnosis and Development, Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne VIC 3052, Australia; (C.M.K.); (E.K.B.); (M.A.); (L.L.); (D.G.); (L.B.); (D.J.A.)
- Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville VIC 3052, Australia
- Correspondence: ; Tel.: +613-8341-6496
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Methylated premutation of the FMR1 gene in three sisters: correlating CGG expansion and epigenetic inactivation. Eur J Hum Genet 2019; 28:567-575. [PMID: 31804632 DOI: 10.1038/s41431-019-0554-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 11/07/2019] [Accepted: 11/17/2019] [Indexed: 11/08/2022] Open
Abstract
Fragile X syndrome (FXS) is a very frequent cause of inherited intellectual disability (ID) and autism. Most FXS patients have an expansion over 200 repeats of (CGG)n sequence ("full mutation" (FM)) located in the 5'UTR of the FMR1 gene, resulting in local DNA methylation (methylated "full mutation" (MFM)) and epigenetic silencing. The absence of the FMRP protein is responsible for the clinical phenotype of FXS. FM arises from a smaller maternal allele with 56-200 CGG repeats ("premutation" (PM)) during maternal meiosis. Carriers of PM alleles, which are typically unmethylated, can manifest other clinical features (primary ovarian insufficiency (POI) or FXS-associated tremor-ataxia syndrome (FXTAS)), known as fragile X-related disorders. In FXS families, rare males who have inherited an unmethylated "full mutation" (UFM) have been described. These individuals produce enough FMRP to allow normal intellectual functioning. Here we report the rare case of three sisters with a completely methylated PM of around 140 CGGs and detail their neuropsychological function. X inactivation analysis confirmed that the three sisters have a random inactivation of the X chromosome, suggesting that the PM allele is always methylated also when residing on the active X. We propose that in exceptional cases, just as the FM may be unmethylated, also a PM allele may be fully methylated. To our knowledge, females with a methylated PM allele and a mild impairment have reported only once. The study of these atypical individuals demonstrates that the size of the CGG expansion is not as tightly coupled to methylation as previously thought.
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Chiara M, Zambelli F, Picardi E, Horner DS, Pesole G. Critical assessment of bioinformatics methods for the characterization of pathological repeat expansions with single-molecule sequencing data. Brief Bioinform 2019; 21:1971-1986. [DOI: 10.1093/bib/bbz099] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 06/22/2019] [Accepted: 07/09/2019] [Indexed: 01/19/2023] Open
Abstract
Abstract
A number of studies have reported the successful application of single-molecule sequencing technologies to the determination of the size and sequence of pathological expanded microsatellite repeats over the last 5 years. However, different custom bioinformatics pipelines were employed in each study, preventing meaningful comparisons and somewhat limiting the reproducibility of the results. In this review, we provide a brief summary of state-of-the-art methods for the characterization of expanded repeats alleles, along with a detailed comparison of bioinformatics tools for the determination of repeat length and sequence, using both real and simulated data. Our reanalysis of publicly available human genome sequencing data suggests a modest, but statistically significant, increase of the error rate of single-molecule sequencing technologies at genomic regions containing short tandem repeats. However, we observe that all the methods herein tested, irrespective of the strategy used for the analysis of the data (either based on the alignment or assembly of the reads), show high levels of sensitivity in both the detection of expanded tandem repeats and the estimation of the expansion size, suggesting that approaches based on single-molecule sequencing technologies are highly effective for the detection and quantification of tandem repeat expansions and contractions.
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Affiliation(s)
- Matteo Chiara
- Department of Biosciences, University of Milan, via Celoria 26, 20133 Milan, Italy
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Via Amendola e, 70126 Bari, Italy
| | - Federico Zambelli
- Department of Biosciences, University of Milan, via Celoria 26, 20133 Milan, Italy
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Via Amendola e, 70126 Bari, Italy
| | - Ernesto Picardi
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Via Amendola e, 70126 Bari, Italy
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari “A. Moro”, Via Orabona 4, 70126 Bari, Italy
| | - David S Horner
- Department of Biosciences, University of Milan, via Celoria 26, 20133 Milan, Italy
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Via Amendola e, 70126 Bari, Italy
| | - Graziano Pesole
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Via Amendola e, 70126 Bari, Italy
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari “A. Moro”, Via Orabona 4, 70126 Bari, Italy
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Geisler D. Educational Case: Fragile X Syndrome with Size Mosaicism. Acad Pathol 2019; 6:2374289519877550. [PMID: 31633014 PMCID: PMC6769227 DOI: 10.1177/2374289519877550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 08/18/2019] [Accepted: 08/22/2019] [Indexed: 11/27/2022] Open
Abstract
The following fictional case is intended as a learning tool within the Pathology Competencies for Medical Education (PCME), a set of national standards for teaching pathology. These are divided into three basic competencies: Disease Mechanisms and Processes, Organ System Pathology, and Diagnostic Medicine and Therapeutic Pathology. For additional information, and a full list of learning objectives for all three competencies, seehttp://journals.sagepub.com/doi/10.1177/2374289517715040.
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Affiliation(s)
- Daniel Geisler
- Department of Pathology, University of Pittsburgh Medical Center, PA, USA
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Manor E, Gonen R, Sarussi B, Keidar-Friedman D, Kumar J, Tang HT, Tassone F. The role of AGG interruptions in the FMR1 gene stability: A survey in ethnic groups with low and high rate of consanguinity. Mol Genet Genomic Med 2019; 7:e00946. [PMID: 31453660 PMCID: PMC6785435 DOI: 10.1002/mgg3.946] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 07/21/2019] [Accepted: 07/26/2019] [Indexed: 11/07/2022] Open
Abstract
Background The prevalence and the role of AGG interruptions within the FMR1 gene in the normal population is unknown. In this study, we investigated the frequent of AGG loss, in one or two alleles within the normal population. The role of AGG in the FMR1 stability has been assessed by correlating AGG loss to the prevalence of premutation/full mutation in two ethnic groups differing in their consanguinity rate: high versus low consanguinity rate (HCR vs. LCR). Methods The CGG repeat allele size and AGG presence were measured in 6,865 and 6,204 females belonging to the LCR (5%) and HCR (>45%) groups, respectively, by Tripled‐Primed‐PCR technique. Results A lower prevalence of the premutation was observed in the HCR (1:158) as compared to the LCR group (1:128). No full mutation was found in the HCR females while in the LCR group the prevalence found was 1:1,149. Homozygosity rate was higher in the HCR population compared to the LCR group.The overall AGG loss was higher in the HCR population than in the LCR and increased with increased CGG repeat number in both ethnic groups. Conclusions Although we observed a significantly higher rate of homozygosity and AGG loss in the HCR group, this did not affect the prevalence of the premutation and full mutation in this population. Their prevalence was significantly lower than in the LCR population. Finally, we discuss whether the loss of AGG could be also a polymorphic event but not only a stabilizing factor.
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Affiliation(s)
- Esther Manor
- Faculty of Health Science, Ben-Gurion University of the Negev Genetic Institute, Soroka University Medical Center, Beer Sheva, Israel
| | | | | | | | - Jay Kumar
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California Davis, Sacramento, USA
| | - Hiu-Tung Tang
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California Davis, Sacramento, USA
| | - Flora Tassone
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California Davis, Sacramento, USA.,MIND Institute, Medical Center, University of California Davis, Sacramento, USA
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Nolin SL, Glicksman A, Tortora N, Allen E, Macpherson J, Mila M, Vianna‐Morgante AM, Sherman SL, Dobkin C, Latham GJ, Hadd AG. Expansions and contractions of the FMR1 CGG repeat in 5,508 transmissions of normal, intermediate, and premutation alleles. Am J Med Genet A 2019; 179:1148-1156. [PMID: 31050164 PMCID: PMC6619443 DOI: 10.1002/ajmg.a.61165] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 03/21/2019] [Accepted: 04/11/2019] [Indexed: 12/15/2022]
Abstract
Instability of the FMR1 repeat, commonly observed in transmissions of premutation alleles (55-200 repeats), is influenced by the size of the repeat, its internal structure and the sex of the transmitting parent. We assessed these three factors in unstable transmissions of 14/3,335 normal (~5 to 44 repeats), 54/293 intermediate (45-54 repeats), and 1561/1,880 premutation alleles. While most unstable transmissions led to expansions, contractions to smaller repeats were observed in all size classes. For normal alleles, instability was more frequent in paternal transmissions and in alleles with long 3' uninterrupted repeat lengths. For premutation alleles, contractions also occurred more often in paternal than maternal transmissions and the frequency of paternal contractions increased linearly with repeat size. All paternal premutation allele contractions were transmitted as premutation alleles, but maternal premutation allele contractions were transmitted as premutation, intermediate, or normal alleles. The eight losses of AGG interruptions in the FMR1 repeat occurred exclusively in contractions of maternal premutation alleles. We propose a refined model of FMR1 repeat progression from normal to premutation size and suggest that most normal alleles without AGG interruptions are derived from contractions of maternal premutation alleles.
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Affiliation(s)
- Sarah L. Nolin
- Department of Human GeneticsNew York State Institute for Basic Research in Developmental DisabilitiesStaten IslandNew York
| | - Anne Glicksman
- Department of Human GeneticsNew York State Institute for Basic Research in Developmental DisabilitiesStaten IslandNew York
| | - Nicole Tortora
- Department of Human GeneticsNew York State Institute for Basic Research in Developmental DisabilitiesStaten IslandNew York
| | - Emily Allen
- Department of Human GeneticsEmory University School of MedicineAtlantaGeorgia
| | - James Macpherson
- Wessex Regional Genetics LaboratorySalisbury NHS District HospitalSalisburyUnited Kingdom
| | - Montserrat Mila
- Biochemical and Molecular GeneticsHospital Clinic de Barcelona, IDIBAPS and CIBERERBarcelonaSpain
| | - Angela M. Vianna‐Morgante
- Department of Genetics and Evolutionary Biology, Institute of BiosciencesUniversidade de São PauloSão PauloBrazil
| | | | - Carl Dobkin
- Department of Human GeneticsNew York State Institute for Basic Research in Developmental DisabilitiesStaten IslandNew York
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Repeat Instability in the Fragile X-Related Disorders: Lessons from a Mouse Model. Brain Sci 2019; 9:brainsci9030052. [PMID: 30832215 PMCID: PMC6468611 DOI: 10.3390/brainsci9030052] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 02/21/2019] [Accepted: 02/27/2019] [Indexed: 12/21/2022] Open
Abstract
The fragile X-related disorders (FXDs) are a group of clinical conditions that result primarily from an unusual mutation, the expansion of a CGG-repeat tract in exon 1 of the FMR1 gene. Mouse models are proving useful for understanding many aspects of disease pathology in these disorders. There is also reason to think that such models may be useful for understanding the molecular basis of the unusual mutation responsible for these disorders. This review will discuss what has been learnt to date about mechanisms of repeat instability from a knock-in FXD mouse model and what the implications of these findings may be for humans carrying expansion-prone FMR1 alleles.
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FERREIRA JORGEF, BATISTA JACQUELINES, FANTIN CLEITON. Screening for FMR1 expanded alleles in patients with Autism Spectrum Disorders in Manaus, Northern Brazil. AN ACAD BRAS CIENC 2019; 91:e20180882. [DOI: 10.1590/0001-3765201920180882] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 10/04/2018] [Indexed: 11/22/2022] Open
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