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Rodrigues B, Sousa V, Yrigollen CM, Tassone F, Villate O, Allen EG, Glicksman A, Tortora N, Nolin SL, Nogueira AJA, Jorge P. FMR1 allelic complexity in premutation carriers provides no evidence for a correlation with age at amenorrhea. Reprod Biol Endocrinol 2024; 22:71. [PMID: 38907244 PMCID: PMC11191145 DOI: 10.1186/s12958-024-01227-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 05/09/2024] [Indexed: 06/23/2024] Open
Abstract
BACKGROUND Premutations in the Fragile X Messenger Ribonucleoprotein 1 (FMR1) gene, defined as between 55 and 200 CGGs, have been implicated in fragile X-associated primary ovarian insufficiency (FXPOI). Only 20% of female premutation carriers develop early ovulatory dysfunction, the reason for this incomplete penetrance is unknown. This study validated the mathematical model in premutation alleles, after assigning each allele a score representing allelic complexity. Subsequently, allelic scores were used to investigate the impact of allele complexity on age at amenorrhea for 58 premutation cases (116 alleles) previously published. METHODS The allelic score was determined using a formula previously described by our group. The impact of each allelic score on age at amenorrhea was analyzed using Pearson's test and a contour plot generated to visualize the effect. RESULTS Correlation of allelic score revealed two distinct complexity behaviors in premutation alleles. No significant correlation was observed between the allelic score of premutation alleles and age at amenorrhea. The same lack of significant correlation was observed regarding normal-sized alleles, despite a nearly significant trend. CONCLUSIONS Our results suggest that the use of allelic scores combination have the potential to explain female infertility, namely the development of FXPOI, or ovarian dysfunction, despite the lack of correlation with age at amenorrhea. Such a finding is of great clinical significance for early identification of females at risk of ovulatory dysfunction, enhancement of fertility preservation techniques, and increasing the probability for a successful pregnancy in females with premutations. Additional investigation is necessary to validate this hypothesis.
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Affiliation(s)
- Bárbara Rodrigues
- Molecular Genetics Laboratory, Laboratory Genetics Service, Genetics and Pathology Clinic, Unidade Local de Saúde de Santo António (ULSSA), Porto, Portugal
- UMIB - Unit for Multidisciplinary Research in Biomedicine, ICBAS - School of Medicine and Biomedical Sciences, UPorto - University of Porto, Porto, Portugal
- ITR - Laboratory for Integrative and Translational Research in Population Health, Porto, Portugal
| | - Vanessa Sousa
- Molecular Genetics Laboratory, Laboratory Genetics Service, Genetics and Pathology Clinic, Unidade Local de Saúde de Santo António (ULSSA), Porto, Portugal
- UMIB - Unit for Multidisciplinary Research in Biomedicine, ICBAS - School of Medicine and Biomedical Sciences, UPorto - University of Porto, Porto, Portugal
- ITR - Laboratory for Integrative and Translational Research in Population Health, Porto, Portugal
- Cytogenetics Laboratory, Department of Microscopy, ICBAS - School of Medicine and Biomedical Sciences, UPorto - University of Porto, Porto, Portugal
| | - Carolyn M Yrigollen
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA, USA
| | - Flora Tassone
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California, Davis, Stockton Blvd, USA
- MIND Institute, School of Medicine, University of California, Davis, CA, USA
| | - Olatz Villate
- Pediatric Oncology Group, Biocruces Bizkaia Health Research Institute, Barakaldo, Biscay, Basque Country, Spain
| | - Emily G Allen
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Anne Glicksman
- New York State Institute for Basic Research in Developmental Disabilities, New York, NY, USA
| | - Nicole Tortora
- New York State Institute for Basic Research in Developmental Disabilities, New York, NY, USA
| | - Sarah L Nolin
- New York State Institute for Basic Research in Developmental Disabilities, New York, NY, USA
| | - António J A Nogueira
- CESAM - Center for Environmental and Marine Studies, Department of Biology, University of Aveiro, Aveiro, Portugal
| | - Paula Jorge
- Molecular Genetics Laboratory, Laboratory Genetics Service, Genetics and Pathology Clinic, Unidade Local de Saúde de Santo António (ULSSA), Porto, Portugal.
- UMIB - Unit for Multidisciplinary Research in Biomedicine, ICBAS - School of Medicine and Biomedical Sciences, UPorto - University of Porto, Porto, Portugal.
- ITR - Laboratory for Integrative and Translational Research in Population Health, Porto, Portugal.
- Cytogenetics Laboratory, Department of Microscopy, ICBAS - School of Medicine and Biomedical Sciences, UPorto - University of Porto, Porto, Portugal.
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Rajagopal S, Donaldson J, Flower M, Hensman Moss DJ, Tabrizi SJ. Genetic modifiers of repeat expansion disorders. Emerg Top Life Sci 2023; 7:325-337. [PMID: 37861103 PMCID: PMC10754329 DOI: 10.1042/etls20230015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 09/20/2023] [Accepted: 10/09/2023] [Indexed: 10/21/2023]
Abstract
Repeat expansion disorders (REDs) are monogenic diseases caused by a sequence of repetitive DNA expanding above a pathogenic threshold. A common feature of the REDs is a strong genotype-phenotype correlation in which a major determinant of age at onset (AAO) and disease progression is the length of the inherited repeat tract. Over a disease-gene carrier's life, the length of the repeat can expand in somatic cells, through the process of somatic expansion which is hypothesised to drive disease progression. Despite being monogenic, individual REDs are phenotypically variable, and exploring what genetic modifying factors drive this phenotypic variability has illuminated key pathogenic mechanisms that are common to this group of diseases. Disease phenotypes are affected by the cognate gene in which the expansion is found, the location of the repeat sequence in coding or non-coding regions and by the presence of repeat sequence interruptions. Human genetic data, mouse models and in vitro models have implicated the disease-modifying effect of DNA repair pathways via the mechanisms of somatic mutation of the repeat tract. As such, developing an understanding of these pathways in the context of expanded repeats could lead to future disease-modifying therapies for REDs.
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Affiliation(s)
- Sangeerthana Rajagopal
- UCL Huntington's Disease Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, U.K
- UK Dementia Research Institute, University College London, London WCC1N 3BG, U.K
| | - Jasmine Donaldson
- UCL Huntington's Disease Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, U.K
- UK Dementia Research Institute, University College London, London WCC1N 3BG, U.K
| | - Michael Flower
- UCL Huntington's Disease Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, U.K
- UK Dementia Research Institute, University College London, London WCC1N 3BG, U.K
| | - Davina J Hensman Moss
- UCL Huntington's Disease Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, U.K
- UK Dementia Research Institute, University College London, London WCC1N 3BG, U.K
- St George's University of London, London SW17 0RE, U.K
| | - Sarah J Tabrizi
- UCL Huntington's Disease Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, U.K
- UK Dementia Research Institute, University College London, London WCC1N 3BG, U.K
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3
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Aishworiya R, Hwang YH, Santos E, Hayward B, Usdin K, Durbin-Johnson B, Hagerman R, Tassone F. Clinical implications of somatic allele expansion in female FMR1 premutation carriers. Sci Rep 2023; 13:7050. [PMID: 37120588 PMCID: PMC10148869 DOI: 10.1038/s41598-023-33528-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 04/14/2023] [Indexed: 05/01/2023] Open
Abstract
Carriers of a premutation allele (PM) in the FMR1 gene are at risk of developing a number of Fragile X premutation asssociated disorders (FXPAC), including Fragile X-associated Tremor/Ataxia Syndrome (FXTAS), Fragile X-associated Primary Ovarian Insufficiency (FXPOI), and Fragile X-associated neuropsychiatric disorders (FXAND). We have recently reported somatic CGG allele expansion in female PM; however, its clinical significance remains unclear. The aim of this study was to examine the potential clinical association between somatic FMR1 allele instability and PM associated disorders. Participants comprised of 424 female PM carriers age 0.3- 90 years. FMR1 molecular measures and clinical information on the presence of medical conditions, were determined for all subjects for primary analysis. Two sub-groups of participants (age ≥ 25, N = 377 and age ≥ 50, N = 134) were used in the analysis related to presence of FXPOI and FXTAS, respectively. Among all participants (N = 424), the degree of instability (expansion) was significantly higher (median 2.5 vs 2.0, P = 0.026) in participants with a diagnosis of attention deficit hyperactivity disorder (ADHD) compared to those without. FMR1 mRNA expression was significantly higher in subjects with any psychiatric disorder diagnosis (P = 0.0017); specifically, in those with ADHD (P = 0.009), and with depression (P = 0.025). Somatic FMR1 expansion was associated with the presence of ADHD in female PM and FMR1 mRNA levels were associated with the presence of mental health disorders. The findings of our research are innovative as they suggest a potential role of the CGG expansion in the clinical phenotype of PM and may potentially guide clinical prognosis and management.
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Affiliation(s)
- Ramkumar Aishworiya
- Medical Investigation of Neurodevelopmental Disorders (MIND) Institute, University of California Davis, 2825 50Th Street, Sacramento, CA, 95817, USA
- Khoo Teck Puat-National University Children's Medical Institute, National University Health System, 5 Lower Kent Ridge Road, Singapore, 119074, Singapore
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, 10 Medical Drive, Singapore, 117597, Singapore
| | - Ye Hyun Hwang
- Department of Biochemistry and Molecular Medicine, University of California Davis, School of Medicine, 4610 X St, Sacramento, CA, 95817, USA
| | - Ellery Santos
- Medical Investigation of Neurodevelopmental Disorders (MIND) Institute, University of California Davis, 2825 50Th Street, Sacramento, CA, 95817, USA
- Department of Pediatrics, University of California Davis, School of Medicine, 4610 X St, Sacramento, CA, 95817, USA
| | - Bruce Hayward
- Laboratory of Cell and Molecular Biology, Digestive and Kidney Diseases, National Institute of Diabetes, 9000 Rockville Pike, Bethesda, MD, 20892, USA
| | - Karen Usdin
- Laboratory of Cell and Molecular Biology, Digestive and Kidney Diseases, National Institute of Diabetes, 9000 Rockville Pike, Bethesda, MD, 20892, USA
| | - Blythe Durbin-Johnson
- Department of Public Health Sciences, University of California, Davis, School of Medicine, 4610 X St, Sacramento, CA, 95817, USA
| | - Randi Hagerman
- Medical Investigation of Neurodevelopmental Disorders (MIND) Institute, University of California Davis, 2825 50Th Street, Sacramento, CA, 95817, USA
- Department of Pediatrics, University of California Davis, School of Medicine, 4610 X St, Sacramento, CA, 95817, USA
| | - Flora Tassone
- Medical Investigation of Neurodevelopmental Disorders (MIND) Institute, University of California Davis, 2825 50Th Street, Sacramento, CA, 95817, USA.
- Department of Biochemistry and Molecular Medicine, University of California Davis, School of Medicine, 4610 X St, Sacramento, CA, 95817, USA.
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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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ATTCT and ATTCC repeat expansions in the ATXN10 gene affect disease penetrance of spinocerebellar ataxia type 10. HGG ADVANCES 2022; 3:100137. [PMID: 36092952 PMCID: PMC9460507 DOI: 10.1016/j.xhgg.2022.100137] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 08/11/2022] [Indexed: 11/21/2022] Open
Abstract
Spinocerebellar ataxia type 10 (SCA10) is an autosomal-dominant disorder caused by an expanded pentanucleotide repeat in the ATXN10 gene. This repeat expansion, when fully penetrant, has a size of 850–4,500 repeats. It has been shown that the repeat composition can be a modifier of disease, e.g., seizures. Here, we describe a Mexican kindred in which we identified both pure (ATTCT)n and mixed (ATTCT)n-(ATTCC)n expansions in the same family. We used amplification-free targeted sequencing and optical genome mapping to decipher the composition of these repeat expansions. We found a considerable degree of mosaicism of the repeat expansion. This mosaicism was confirmed in skin fibroblasts from individuals with ATXN10 expansions with RNAScope in situ hybridization. All affected family members with the mixed ATXN10 repeat expansion showed typical clinical signs of spinocerebellar ataxia and epilepsy. In contrast, individuals with the pure ATXN10 expansion present with Parkinson's disease or are unaffected, even in individuals more than 20 years older than the average age at onset for SCA10. Our findings suggest that the pure (ATTCT)n expansion is non-pathogenic, while repeat interruptions, e.g., (ATTCC)n, are necessary to cause SCA10. This mechanism has been recently described for several other repeat expansions including SCA31 (BEAN1), SCA37 (DAB1), and three loci for benign adult familial myoclonic epilepsy BAFME (SAMD12, TNRC6A, RAPGEF2). Therefore, long-read sequencing and optical genome mapping of the entire genomic structure of repeat expansions are critical for clinical practice and genetic counseling, as variations in the repeat can affect disease penetrance, symptoms, and disease trajectory.
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Baud A, Derbis M, Tutak K, Sobczak K. Partners in crime: Proteins implicated in
RNA
repeat expansion diseases. WIRES RNA 2022; 13:e1709. [PMID: 35229468 PMCID: PMC9539487 DOI: 10.1002/wrna.1709] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 12/07/2021] [Accepted: 12/08/2021] [Indexed: 11/06/2022]
Affiliation(s)
- Anna Baud
- Department of Gene Expression Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University Poznan Poland
| | - Magdalena Derbis
- Department of Gene Expression Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University Poznan Poland
| | - Katarzyna Tutak
- Department of Gene Expression Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University Poznan Poland
| | - Krzysztof Sobczak
- Department of Gene Expression Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University Poznan Poland
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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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Chiu R, Rajan-Babu IS, Friedman JM, Birol I. Straglr: discovering and genotyping tandem repeat expansions using whole genome long-read sequences. Genome Biol 2021; 22:224. [PMID: 34389037 PMCID: PMC8361843 DOI: 10.1186/s13059-021-02447-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 07/26/2021] [Indexed: 12/11/2022] Open
Abstract
Tandem repeat (TR) expansion is the underlying cause of over 40 neurological disorders. Long-read sequencing offers an exciting avenue over conventional technologies for detecting TR expansions. Here, we present Straglr, a robust software tool for both targeted genotyping and novel expansion detection from long-read alignments. We benchmark Straglr using various simulations, targeted genotyping data of cell lines carrying expansions of known diseases, and whole genome sequencing data with chromosome-scale assembly. Our results suggest that Straglr may be useful for investigating disease-associated TR expansions using long-read sequencing.
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Affiliation(s)
- Readman Chiu
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, V5Z 4S6, Canada
| | - Indhu-Shree Rajan-Babu
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
- BC Children's Hospital Research Institute, Vancouver, BC, V5Z 4H4, Canada
- Department of Medical and Molecular Genetics, King's College London, Strand, London, WC2R 2LS, UK
| | - Jan M Friedman
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
- BC Children's Hospital Research Institute, Vancouver, BC, V5Z 4H4, Canada
| | - Inanc Birol
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, V5Z 4S6, Canada.
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada.
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Berry-Kravis E, Zhou L, Jackson J, Tassone F. Diagnostic profile of the AmplideX Fragile X Dx and Carrier Screen Kit for diagnosis and screening of fragile X syndrome and other FMR1-related disorders. Expert Rev Mol Diagn 2021; 21:255-267. [PMID: 33666525 DOI: 10.1080/14737159.2021.1899812] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Introduction: In 2009, a novel, CGG repeat primed FMR1 PCR assay was designed with primers flanking the triplet repeat region, as well as a third chimeric primer complementary to the (CGG)n repeat, that was capable of amplifying alleles throughout the repeat range. This assay for the first time allowed consistent detection of large full mutation alleles with PCR, resolution of heterozygosity in females and mapping of AGG interspersions.Areas Covered: The AmplideX Fragile X Dx and Carrier Screen Kit (Asuragen, Inc.) represents a refined assay that underwent validation with sensitivity analyses for FDA approval. Single-site precision, analytical sensitivity and specificity, limit of detection and diagnostic performance were assessed in comparison to reference methods at three independent sites. Single-site precision across all genotype categories showed 100% agreement at 20 ng input across multiple operators, days, instruments and kit lots. Compared to Southern Blot analysis, the overall percent agreement was over 98% for all expanded alleles.Expert Opinion: Limitations include no methylation assessment and hard to see full mutation peaks in some mosaic samples, but overall the assay is considered a highly accurate and time-efficient assay for FMR1 allele size determination.
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Affiliation(s)
- Elizabeth Berry-Kravis
- Department of Pediatrics, Rush University Medical Center, Chicago, IL, USA.,Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA.,Department of Biochemistry, Rush University Medical Center, Chicago, IL, USA
| | - Lili Zhou
- Department of Pediatrics, Rush University Medical Center, Chicago, IL, USA.,Department of Pathology, Rush University Medical Center, Chicago, IL, USA
| | - Jonathan Jackson
- Department of Pediatrics, Rush University Medical Center, Chicago, IL, USA
| | - Flora Tassone
- Department of Biochemistry and Molecular Medicine, University of California Davis, School of Medicine, Sacramento, CA, USA.,MIND Institute, University of California Davis Medical Center, Sacramento, CA, USA
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'Essential Tremor' Phenotype in FMR1 Premutation/Gray Zone Sibling Series: Exploring Possible Genetic Modifiers. Twin Res Hum Genet 2021; 24:95-102. [PMID: 33757613 DOI: 10.1017/thg.2021.10] [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] [Indexed: 12/20/2022]
Abstract
Fragile X-associated tremor/ataxia syndrome (FXTAS) occurs in carriers of fragile X mental retardation 1 (FMR1) X-linked small CGG expansion (gray zone [GZ] and premutation [PM]) alleles, containing 41-200 repeats. Major features comprise kinetic tremor, gait ataxia, cognitive decline and cerebellar peduncular white matter lesions, but atypical/incomplete FXTAS may occur. We explored the possibility of polygenic effects modifying the FXTAS spectrum phenotypes. We used three motor scales and selected cognitive tests in a series of three males and three females from a single sibship carrying PM or GZ alleles (44 to 75 repeats). The molecular profiles from these siblings were determined by genomewide association study with single-nucleotide polymorphism (SNP) genotyping by Illumina Global Screening Array. Nonparametric linkage analysis was applied and Parkinson's disease (PD) polygenic risk scores (PRSs) were calculated for all the siblings, based on 107 known risk variants. All male and female siblings manifested similar kinetic tremor phenotypes. In contrast to FXTAS, they showed negligible gait ataxia, and few white matter lesions on MRI. Cognitive functioning was unaffected. Suggestive evidence of linkage to a broad region of the short arm of chromosome 10 was obtained, and median PD PRS for the sibship fell within the top 30% of a sample of over 500,000 UK and Australian controls. The genomewide study results are suggestive of modifying effects of genetic risk loci linked to PD, on the neurological phenotype of FMR1-CGG small expansion carriers, resulting in an oligosymptomatic kinetic tremor seen in FXTAS spectrum, but also consistent with essential tremor.
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