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Levy B, Liu J, Iqbal MA, DuPont B, Sahajpal N, Ho M, Yu J, Brody SJ, Ganapathi M, Rajkovic A, Smolarek TA, Boyar F, Bui P, Dubuc AM, Kolhe R, Stevenson RE. Multisite Evaluation and Validation of Optical Genome Mapping for Prenatal Genetic Testing. J Mol Diagn 2024; 26:906-916. [PMID: 39032820 DOI: 10.1016/j.jmoldx.2024.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 05/07/2024] [Accepted: 06/26/2024] [Indexed: 07/23/2024] Open
Abstract
Prenatal diagnostic testing of amniotic fluid, chorionic villi, or more rarely, fetal cord blood is recommended following a positive or unreportable noninvasive cell-free fetal DNA test, abnormal maternal biochemical serum screen, abnormal ultrasound, or increased genetic risk for a cytogenomic abnormality based on family history. Although chromosomal microarray is recommended as the first-tier prenatal diagnostic test, in practice, multiple assays are often assessed in concert to achieve a final diagnostic result. The use of multiple methodologies is costly, time consuming, and labor intensive. Optical genome mapping (OGM) is an emerging technique with application for prenatal diagnosis because of its ability to detect and resolve, in a single assay, all classes of pathogenic cytogenomic aberrations. In an effort to characterize the potential of OGM as a novel alternative to traditional standard of care (SOC) testing of prenatal samples, OGM was performed on a total of 200 samples representing 123 unique cases, which were previously tested with SOC methods (92/123 = 74.7% cases tested with at least two SOCs). OGM demonstrated an overall accuracy of 99.6% when compared with SOC methods, a positive predictive value of 100%, and 100% reproducibility between sites, operators, and instruments. The standardized workflow, cost-effectiveness, and high-resolution cytogenomic analysis demonstrate the potential of OGM to serve as a first-tier test for prenatal diagnosis.
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Affiliation(s)
- Brynn Levy
- Columbia University Irving Medical Center, New York, New York
| | - Jie Liu
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio; Department of Pediatrics, University of Cincinnati, Cincinnati, Ohio
| | - M Anwar Iqbal
- University of Rochester Medical Center, Rochester, New York
| | | | | | - Monique Ho
- University of Rochester Medical Center, Rochester, New York
| | - Jingwei Yu
- University of California San Francisco, San Francisco, California
| | - Sam J Brody
- Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | | | | | - Teresa A Smolarek
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio; Department of Pediatrics, University of Cincinnati, Cincinnati, Ohio
| | - Fatih Boyar
- Quest Diagnostics Nichols Institute, San Juan Capistrano, California
| | - Peter Bui
- Quest Diagnostics Nichols Institute, San Juan Capistrano, California
| | - Adrian M Dubuc
- Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Ravindra Kolhe
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, Georgia.
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Xue J, Zhu Y, Pan Y, Huang H, Wei L, Peng Y, Xi H, Zhou S, Wu H, Gu Z, Huang W, Wang H, Duan R. Strategic Implementation of Fragile X Carrier Screening in China: A Focused Pilot Study. J Mol Diagn 2024; 26:897-905. [PMID: 39032823 DOI: 10.1016/j.jmoldx.2024.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Revised: 06/20/2024] [Accepted: 06/25/2024] [Indexed: 07/23/2024] Open
Abstract
Fragile X syndrome is the leading genetic cause of intellectual disability and autism spectrum disorders. Female premutation carriers exhibit no obvious symptoms during reproductive age, but the premutation allele can expand to full mutation when transmitted to the fetus. Given the relatively low prevalence but large population, the distinct health care system, the middle-income economic status, and low awareness among public and medical professionals, the optimal genetic screening strategy remains unknown. We conducted a pilot study of Fragile X carrier screening in China, involving 22,245 pregnant women and women with childbearing intentions, divided into control and pilot groups. The prevalence of Fragile X carriers in the control group was 1 of 850, similar to East Asian populations. Strikingly, the prevalence of Fragile X carriers in the pilot group was 1 of 356, which can be attributed to extensive medical training, participant education, and rigorous genetic counseling and testing protocols. Cost-effectiveness analyses of four strategies-no screening, population-based screening, targeted screening, and our pilot screening-indicated that our pilot screening was the most cost-effective option. A follow-up survey revealed that 55% of respondents reported undergoing screening because of their family history. We have successfully established a standardized system, addressing the challenges of low prevalence, limited awareness, and genetic testing complexities. Our study provides practical recommendations for implementing Fragile X carrier screening in China.
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Affiliation(s)
- Jin Xue
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China; Department of Medical Genetics, Hunan Children's Hospital, The Affiliated Children's Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Yingbao Zhu
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Yi Pan
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Hongjing Huang
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Liyi Wei
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Ying Peng
- Prenatal Diagnosis Center, National Health Commission Key Laboratory of Birth Defects for Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, China
| | - Hui Xi
- Prenatal Diagnosis Center, National Health Commission Key Laboratory of Birth Defects for Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, China
| | - Shihao Zhou
- Hunan Provincial Key Laboratory of Regional Hereditary Birth Defects Prevention and Control, Changsha Hospital for Maternal and Child Health Care Affiliated to Hunan Normal University, Changsha, China
| | - Hongliang Wu
- Yueyang Maternal and Child Health Hospital, Yueyang, China
| | - Zhenxiang Gu
- Huaihua Hospital for Maternal and Child Health Care, Huaihua, China
| | - Wen Huang
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Hua Wang
- Department of Medical Genetics, Hunan Children's Hospital, The Affiliated Children's Hospital of Xiangya School of Medicine, Central South University, Changsha, China.
| | - Ranhui Duan
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China; Hunan Key Laboratory of Medical Genetics, Central South University, Changsha, China; Hunan Key Laboratory of Animal Models for Human Diseases, Central South University, Changsha, China.
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3
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Jin X, Zeng W, Xu Y, Jin P, Dong M. Cytosine-guanine-guanine repeats of FMR1 gene negatively affect ovarian reserve and response in Chinese women. Reprod Biomed Online 2024; 49:103779. [PMID: 38678742 DOI: 10.1016/j.rbmo.2023.103779] [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: 10/13/2023] [Revised: 12/13/2023] [Accepted: 12/20/2023] [Indexed: 05/01/2024]
Abstract
RESEARCH QUESTION Do cytosine-guanine-guanine (CGG) repeats of the FMR1 gene affect ovarian function, ovarian response and assisted reproductive technology (ART) outcomes in Chinese women? DESIGN A retrospective cohort study of 5869 women who underwent 8932 ART cycles at Women's Hospital, School of Medicine, Zhejiang University between January 2018 and June 2021. Basic hormone level, oocyte yield, embryo quality and the rate of live birth were considered as main outcome measures to evaluate the effects of CGG repeats on ovarian function, ovarian response and ART outcomes. RESULTS The CGG repeats were negatively related to serum anti-Müllerian hormone (AMH), oestradiol, antral follicle count (AFC) and oocyte yield. A significant association was found between serum AMH, oestradiol and AFC even after age was controlled for. No statistically significant association, however, was found between CGG repeats and embryo quality or live birth rate. Ovarian function mediated the association between CGG repeats and ovarian response. CONCLUSION Increased CGG repeats on the FMR1 gene were associated with diminished ovarian function and poor ovarian response, and ovarian function played an intermediary role in the relationship between CGG repeats and ovarian response.
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Affiliation(s)
- Xinyang Jin
- Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Wenshan Zeng
- Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yanfei Xu
- Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Pengzhen Jin
- Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China; Key Laboratory of Reproductive Genetics, Ministry of Education (Zhejiang University), Hangzhou, China
| | - Minyue Dong
- Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China; Key Laboratory of Reproductive Genetics, Ministry of Education (Zhejiang University), Hangzhou, China.
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Guha S, Reddi HV, Aarabi M, DiStefano M, Wakeling E, Dungan JS, Gregg AR. Laboratory testing for preconception/prenatal carrier screening: A technical standard of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2024; 26:101137. [PMID: 38814327 DOI: 10.1016/j.gim.2024.101137] [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: 03/29/2024] [Accepted: 04/01/2024] [Indexed: 05/31/2024] Open
Abstract
Carrier screening has historically assessed a relatively small number of autosomal recessive and X-linked conditions selected based on frequency in a specific subpopulation and association with severe morbidity or mortality. Advances in genomic technologies enable simultaneous screening of individuals for several conditions. The American College of Medical Genetics and Genomics recently published a clinical practice resource that presents a framework when offering screening for autosomal recessive and X-linked conditions during pregnancy and preconception and recommends a tier-based approach when considering the number of conditions to screen for and their frequency within the US population in general. This laboratory technical standard aims to complement the practice resource and to put forth considerations for clinical laboratories and clinicians who offer preconception/prenatal carrier screening.
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Affiliation(s)
| | - Honey V Reddi
- Department of Pathology and Laboratory Medicine, Medical College of Wisconsin, Milwaukee, WI
| | - Mahmoud Aarabi
- UPMC Medical Genetics and Genomics Laboratories, UPMC Magee-Womens Hospital, Pittsburgh, PA; Departments of Pathology and Obstetrics, Gynecology, and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | | | | | - Jeffrey S Dungan
- Department of Obstetrics and Gynecology, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Anthony R Gregg
- Department of Obstetrics and Gynecology, Prisma Health, Columbia, SC
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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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Zhu Y, Li J, Pan Y, Huang W, Xi H, Duan R. Attitudes of medical professionals toward fragile X carrier screening and genetic counseling in China. J Community Genet 2024; 15:177-185. [PMID: 38277068 PMCID: PMC11031535 DOI: 10.1007/s12687-024-00696-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 01/05/2024] [Indexed: 01/27/2024] Open
Abstract
Fragile X syndrome is the most common inherited cause of intellectual disability. Considering China's low prevalence, distinct healthcare system, middle-income economic status, and unique culture, China cannot simply replicate the screening systems in European and American countries. In this study, we investigated the attitudes of 450 Chinese medical professionals who received fragile X training on fragile X carrier screening and genetic counseling. Before the training, 57.6% of the respondents were unfamiliar with FXS. After the training, 7.3% of participants are unable to fully master the knowledge. Furthermore, 71.8% believe that the absence of phenotypes during the reproductive age and the availability of simple and feasible testing methods are prerequisites for screening. The presence of the phenotype would still require screening. Regarding the target population, over 90% of the participants support fragile X carrier screening in high-risk pregnant women. As for influencing factors, they consider cost as the most influential factor in pregnant women's decision to undergo screening. The acceptable price range for screening is determined to be ¥200-1000 ($30-150). In terms of the issues and challenges of screening, most medical professionals support the need for genetic counseling for intermediate alleles and 55-60 repeat premutation results. Additionally, some respondents believe that informing patients' family members of positive screening results is necessary. It is also recognized that positive results may lead to anxiety for patients. The findings of this study will provide valuable information for the establishment of fragile X carrier screening system, particularly for low-prevalence or middle-income countries.
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Affiliation(s)
- Yingbao Zhu
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Jia Li
- Xiangxi Autonomous Prefecture People's Hospital, The First Affiliated Hospital of Jishou University, Jishou, Hunan, China
| | - Yi Pan
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Wen Huang
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Hui Xi
- Department of Medical Genetics & the Prenatal Diagnosis Center of Hunan Province, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, Hunan, China.
| | - Ranhui Duan
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China.
- Hunan Key Laboratory of Medical Genetics, Central South University, Changsha, China.
- Hunan Key Laboratory of Animal Models for Human Diseases, Central South University, Changsha, China.
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Hnoonual A, Plong-On O, Worachotekamjorn J, Charalsawadi C, Limprasert P. Clinical and molecular characteristics of FMR1 microdeletion in patient with fragile X syndrome and review of the literature. Clin Chim Acta 2024; 553:117728. [PMID: 38142803 DOI: 10.1016/j.cca.2023.117728] [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: 09/18/2023] [Revised: 12/09/2023] [Accepted: 12/16/2023] [Indexed: 12/26/2023]
Abstract
BACKGROUND Fragile X syndrome (FXS) is mainly caused by FMR1 CGG repeat expansions. Other types of mutations, particularly deletions, are also responsible for FXS phenotypes, however these mutations are often missed by routine clinical testing. MATERIALS AND METHODS Molecular diagnosis in cases of suspected FXS was a combination of PCR and Southern blot. Measurement of the FMRP protein level was useful for detecting potentially deleterious impact. RESULTS PCR analysis and Southern blot revealed a case with premutation and suspected deletion alleles. Sanger sequencing showed that the deletion involved 313 bp upstream of repeats and some parts of CGG repeat tract, leaving transcription start site. FMRP was detected in 5.5 % of blood lymphocytes. CONCLUSION According to our review of case reports, most patients carrying microdeletion and full mutation had typical features of FXS. To our knowledge, our case is the first to describe mosaicism of a premutation and microdeletion in the FMR1 gene. The patient was probably protected from the effects of the deletion by mosaicism with premutation allele, leading to milder phenotype. It is thus important to consider appropriate techniques for detecting FMR1 variants other than repeat expansions which cannot be detected by routine FXS diagnosis.
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Affiliation(s)
- Areerat Hnoonual
- Department of Pathology, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand; Genomic Medicine Center, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
| | - Oradawan Plong-On
- Department of Pathology, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
| | | | - Chariyawan Charalsawadi
- Department of Pathology, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand; Genomic Medicine Center, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
| | - Pornprot Limprasert
- Department of Pathology, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand; Genomic Medicine Center, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand.
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Yu SY, Xi YL, Xu FQ, Zhang J, Liu YS. Application of long read sequencing in rare diseases: The longer, the better? Eur J Med Genet 2023; 66:104871. [PMID: 38832911 DOI: 10.1016/j.ejmg.2023.104871] [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: 08/18/2023] [Revised: 10/11/2023] [Accepted: 10/22/2023] [Indexed: 06/06/2024]
Abstract
Rare diseases encompass a diverse group of genetic disorders that affect a small proportion of the population. Identifying the underlying genetic causes of these conditions presents significant challenges due to their genetic heterogeneity and complexity. Conventional short-read sequencing (SRS) techniques have been widely used in diagnosing and investigating of rare diseases, with limitations due to the nature of short-read lengths. In recent years, long read sequencing (LRS) technologies have emerged as a valuable tool in overcoming these limitations. This minireview provides a concise overview of the applications of LRS in rare disease research and diagnosis, including the identification of disease-causing tandem repeat expansions, structural variations, and comprehensive analysis of pathogenic variants with LRS.
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Affiliation(s)
- Si-Yan Yu
- Department of Pediatric Laboratory, Affiliated Children's Hospital of Jiangnan University (Wuxi Children's Hospital), Wuxi, Jiangsu, China; The First School of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yu-Lin Xi
- Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
| | - Fu-Qiang Xu
- Department of Gynecology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Jian Zhang
- Department of Medical Laboratory, Affiliated Children's Hospital of Jiangnan University (Wuxi Children's Hospital), Wuxi, Jiangsu, China.
| | - Yan-Shan Liu
- Department of Pediatric Laboratory, Affiliated Children's Hospital of Jiangnan University (Wuxi Children's Hospital), Wuxi, Jiangsu, China; Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China.
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9
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Tassone F, Protic D, Allen EG, Archibald AD, Baud A, Brown TW, Budimirovic DB, Cohen J, Dufour B, Eiges R, Elvassore N, Gabis LV, Grudzien SJ, Hall DA, Hessl D, Hogan A, Hunter JE, Jin P, Jiraanont P, Klusek J, Kooy RF, Kraan CM, Laterza C, Lee A, Lipworth K, Losh M, Loesch D, Lozano R, Mailick MR, Manolopoulos A, Martinez-Cerdeno V, McLennan Y, Miller RM, Montanaro FAM, Mosconi MW, Potter SN, Raspa M, Rivera SM, Shelly K, Todd PK, Tutak K, Wang JY, Wheeler A, Winarni TI, Zafarullah M, Hagerman RJ. Insight and Recommendations for Fragile X-Premutation-Associated Conditions from the Fifth International Conference on FMR1 Premutation. Cells 2023; 12:2330. [PMID: 37759552 PMCID: PMC10529056 DOI: 10.3390/cells12182330] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 09/09/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
The premutation of the fragile X messenger ribonucleoprotein 1 (FMR1) gene is characterized by an expansion of the CGG trinucleotide repeats (55 to 200 CGGs) in the 5' untranslated region and increased levels of FMR1 mRNA. Molecular mechanisms leading to fragile X-premutation-associated conditions (FXPAC) include cotranscriptional R-loop formations, FMR1 mRNA toxicity through both RNA gelation into nuclear foci and sequestration of various CGG-repeat-binding proteins, and the repeat-associated non-AUG (RAN)-initiated translation of potentially toxic proteins. Such molecular mechanisms contribute to subsequent consequences, including mitochondrial dysfunction and neuronal death. Clinically, premutation carriers may exhibit a wide range of symptoms and phenotypes. Any of the problems associated with the premutation can appropriately be called FXPAC. Fragile X-associated tremor/ataxia syndrome (FXTAS), fragile X-associated primary ovarian insufficiency (FXPOI), and fragile X-associated neuropsychiatric disorders (FXAND) can fall under FXPAC. Understanding the molecular and clinical aspects of the premutation of the FMR1 gene is crucial for the accurate diagnosis, genetic counseling, and appropriate management of affected individuals and families. This paper summarizes all the known problems associated with the premutation and documents the presentations and discussions that occurred at the International Premutation Conference, which took place in New Zealand in 2023.
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Affiliation(s)
- Flora Tassone
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California Davis, Sacramento, CA 95817, USA;
- MIND Institute, University of California Davis, Davis, CA 95817, USA; (B.D.); (D.H.); (V.M.-C.)
| | - Dragana Protic
- Department of Pharmacology, Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Belgrade, 11129 Belgrade, Serbia;
- Fragile X Clinic, Special Hospital for Cerebral Palsy and Developmental Neurology, 11040 Belgrade, Serbia
| | - Emily Graves Allen
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA; (E.G.A.); (P.J.); (K.S.)
| | - Alison D. Archibald
- Victorian Clinical Genetics Services, Royal Children’s Hospital, Melbourne, VIC 3052, Australia;
- Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3052, Australia;
- Genomics in Society Group, Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne, VIC 3052, Australia
| | - Anna Baud
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614 Poznan, Poland; (A.B.); (K.T.)
| | - Ted W. Brown
- Central Clinical School, University of Sydney, Sydney, NSW 2006, Australia;
- Fragile X Association of Australia, Brookvale, NSW 2100, Australia;
- NYS Institute for Basic Research in Developmental Disabilities, New York, NY 10314, USA
| | - Dejan B. Budimirovic
- Department of Psychiatry, Fragile X Clinic, Kennedy Krieger Institute, Baltimore, MD 21205, USA;
- Department of Psychiatry & Behavioral Sciences-Child Psychiatry, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Jonathan Cohen
- Fragile X Alliance Clinic, Melbourne, VIC 3161, Australia;
| | - Brett Dufour
- MIND Institute, University of California Davis, Davis, CA 95817, USA; (B.D.); (D.H.); (V.M.-C.)
- Department of Pathology and Laboratory Medicine, Institute for Pediatric Regenerative Medicine, Shriners Hospitals for Children of Northern California, School of Medicine, University of California Davis, Sacramento, CA 95817, USA;
| | - Rachel Eiges
- Stem Cell Research Laboratory, Medical Genetics Institute, Shaare Zedek Medical Center Affiliated with the Hebrew University School of Medicine, Jerusalem 91031, Israel;
| | - Nicola Elvassore
- Veneto Institute of Molecular Medicine (VIMM), 35129 Padova, Italy; (N.E.); (C.L.)
- Department of Industrial Engineering, University of Padova, 35131 Padova, Italy
| | - Lidia V. Gabis
- Keshet Autism Center Maccabi Wolfson, Holon 5822012, Israel;
- Faculty of Medicine, Tel-Aviv University, Tel Aviv 6997801, Israel
| | - Samantha J. Grudzien
- Department of Neurology, University of Michigan, 4148 BSRB, 109 Zina Pitcher Place, Ann Arbor, MI 48109, USA; (S.J.G.); (P.K.T.)
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Deborah A. Hall
- Department of Neurological Sciences, Rush University, Chicago, IL 60612, USA;
| | - David Hessl
- MIND Institute, University of California Davis, Davis, CA 95817, USA; (B.D.); (D.H.); (V.M.-C.)
- Department of Psychiatry and Behavioral Sciences, School of Medicine, University of California Davis, Sacramento, CA 95817, USA
| | - Abigail Hogan
- Department of Communication Sciences and Disorders, Arnold School of Public Health, University of South Carolina, Columbia, SC 29208, USA; (A.H.); (J.K.)
| | - Jessica Ezzell Hunter
- RTI International, Research Triangle Park, NC 27709, USA; (J.E.H.); (S.N.P.); (M.R.); (A.W.)
| | - Peng Jin
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA; (E.G.A.); (P.J.); (K.S.)
| | - Poonnada Jiraanont
- Faculty of Medicine, King Mongkut’s Institute of Technology Ladkrabang, Bangkok 10520, Thailand;
| | - Jessica Klusek
- Department of Communication Sciences and Disorders, Arnold School of Public Health, University of South Carolina, Columbia, SC 29208, USA; (A.H.); (J.K.)
| | - R. Frank Kooy
- Department of Medical Genetics, University of Antwerp, 2000 Antwerp, Belgium;
| | - Claudine M. Kraan
- Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3052, Australia;
- Diagnosis and Development, Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia
| | - Cecilia Laterza
- Veneto Institute of Molecular Medicine (VIMM), 35129 Padova, Italy; (N.E.); (C.L.)
- Department of Industrial Engineering, University of Padova, 35131 Padova, Italy
| | - Andrea Lee
- Fragile X New Zealand, Nelson 7040, New Zealand;
| | - Karen Lipworth
- Fragile X Association of Australia, Brookvale, NSW 2100, Australia;
| | - Molly Losh
- Roxelyn and Richard Pepper Department of Communication Sciences and Disorders, Northwestern University, Evanston, IL 60201, USA;
| | - Danuta Loesch
- School of Psychology and Public Health, La Trobe University, Melbourne, VIC 3086, Australia;
| | - Reymundo Lozano
- Departments of Genetics and Genomic Sciences and Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
| | - Marsha R. Mailick
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA;
| | - Apostolos Manolopoulos
- Intramural Research Program, Laboratory of Clinical Investigation, National Institute on Aging, Baltimore, MD 21224, USA;
| | - Veronica Martinez-Cerdeno
- MIND Institute, University of California Davis, Davis, CA 95817, USA; (B.D.); (D.H.); (V.M.-C.)
- Department of Pathology and Laboratory Medicine, Institute for Pediatric Regenerative Medicine, Shriners Hospitals for Children of Northern California, School of Medicine, University of California Davis, Sacramento, CA 95817, USA;
| | - Yingratana McLennan
- Department of Pathology and Laboratory Medicine, Institute for Pediatric Regenerative Medicine, Shriners Hospitals for Children of Northern California, School of Medicine, University of California Davis, Sacramento, CA 95817, USA;
| | | | - Federica Alice Maria Montanaro
- Child and Adolescent Neuropsychiatry Unit, Department of Neuroscience, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy;
- Department of Education, Psychology, Communication, University of Bari Aldo Moro, 70121 Bari, Italy
| | - Matthew W. Mosconi
- Schiefelbusch Institute for Life Span Studies, University of Kansas, Lawrence, KS 66045, USA;
- Clinical Child Psychology Program, University of Kansas, Lawrence, KS 66045, USA
- Kansas Center for Autism Research and Training (K-CART), University of Kansas, Lawrence, KS 66045, USA
| | - Sarah Nelson Potter
- RTI International, Research Triangle Park, NC 27709, USA; (J.E.H.); (S.N.P.); (M.R.); (A.W.)
| | - Melissa Raspa
- RTI International, Research Triangle Park, NC 27709, USA; (J.E.H.); (S.N.P.); (M.R.); (A.W.)
| | - Susan M. Rivera
- Department of Psychology, University of Maryland, College Park, MD 20742, USA;
| | - Katharine Shelly
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA; (E.G.A.); (P.J.); (K.S.)
| | - Peter K. Todd
- Department of Neurology, University of Michigan, 4148 BSRB, 109 Zina Pitcher Place, Ann Arbor, MI 48109, USA; (S.J.G.); (P.K.T.)
- Ann Arbor Veterans Administration Healthcare, Ann Arbor, MI 48105, USA
| | - Katarzyna Tutak
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614 Poznan, Poland; (A.B.); (K.T.)
| | - Jun Yi Wang
- Center for Mind and Brain, University of California Davis, Davis, CA 95618, USA;
| | - Anne Wheeler
- RTI International, Research Triangle Park, NC 27709, USA; (J.E.H.); (S.N.P.); (M.R.); (A.W.)
| | - Tri Indah Winarni
- Center for Biomedical Research (CEBIOR), Faculty of Medicine, Universitas Diponegoro, Semarang 502754, Central Java, Indonesia;
| | - Marwa Zafarullah
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California Davis, Sacramento, CA 95817, USA;
| | - Randi J. Hagerman
- MIND Institute, University of California Davis, Davis, CA 95817, USA; (B.D.); (D.H.); (V.M.-C.)
- Department of Pediatrics, School of Medicine, University of California Davis, Sacramento, CA 95817, USA
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10
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Friedman L, Lauber M, Behroozmand R, Fogerty D, Kunecki D, Berry-Kravis E, Klusek J. Atypical vocal quality in women with the FMR1 premutation: an indicator of impaired sensorimotor control. Exp Brain Res 2023; 241:1975-1987. [PMID: 37347418 PMCID: PMC10863608 DOI: 10.1007/s00221-023-06653-2] [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: 02/07/2023] [Accepted: 06/13/2023] [Indexed: 06/23/2023]
Abstract
Women with the FMR1 premutation are susceptible to motor involvement related to atypical cerebellar function, including risk for developing fragile X tremor ataxia syndrome. Vocal quality analyses are sensitive to subtle differences in motor skills but have not yet been applied to the FMR1 premutation. This study examined whether women with the FMR1 premutation demonstrate differences in vocal quality, and whether such differences relate to FMR1 genetic, executive, motor, or health features of the FMR1 premutation. Participants included 35 women with the FMR1 premutation and 45 age-matched women without the FMR1 premutation who served as a comparison group. Three sustained /a/ vowels were analyzed for pitch (mean F0), variability of pitch (standard deviation of F0), and overall vocal quality (jitter, shimmer, and harmonics-to-noise ratio). Executive, motor, and health indices were obtained from direct and self-report measures and genetic samples were analyzed for FMR1 CGG repeat length and activation ratio. Women with the FMR1 premutation had a lower pitch, larger pitch variability, and poorer vocal quality than the comparison group. Working memory was related to harmonics-to-noise ratio and shimmer in women with the FMR1 premutation. Vocal quality abnormalities differentiated women with the FMR1 premutation from the comparison group and were evident even in the absence of other clinically evident motor deficits. This study supports vocal quality analyses as a tool that may prove useful in the detection of early signs of motor involvement in this population.
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Affiliation(s)
- Laura Friedman
- Department of Communication Sciences and Disorders, University of South Carolina, Columbia, USA
| | - Meagan Lauber
- Department of Communication Sciences and Disorders, University of South Carolina, Columbia, USA
| | - Roozbeh Behroozmand
- Department of Communication Sciences and Disorders, University of South Carolina, Columbia, USA
| | - Daniel Fogerty
- Department of Speech and Hearing Science, University of Illinois Urbana-Champaign, Champaign, USA
| | - Dariusz Kunecki
- Department of Pediatrics, Rush University Medical Center, Chicago, USA
| | | | - Jessica Klusek
- Department of Communication Sciences and Disorders, University of South Carolina, Columbia, USA.
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11
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Ciobanu CG, Nucă I, Popescu R, Antoci LM, Caba L, Ivanov AV, Cojocaru KA, Rusu C, Mihai CT, Pânzaru MC. Narrative Review: Update on the Molecular Diagnosis of Fragile X Syndrome. Int J Mol Sci 2023; 24:9206. [PMID: 37298158 PMCID: PMC10252420 DOI: 10.3390/ijms24119206] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 04/30/2023] [Accepted: 05/20/2023] [Indexed: 06/12/2023] Open
Abstract
The diagnosis and management of fragile X syndrome (FXS) have significantly improved in the last three decades, although the current diagnostic techniques are not yet able to precisely identify the number of repeats, methylation status, level of mosaicism, and/or the presence of AGG interruptions. A high number of repeats (>200) in the fragile X messenger ribonucleoprotein 1 gene (FMR1) results in hypermethylation of promoter and gene silencing. The actual molecular diagnosis is performed using a Southern blot, TP-PCR (Triplet-Repeat PCR), MS-PCR (Methylation-Specific PCR), and MS-MLPA (Methylation-Specific MLPA) with some limitations, with multiple assays being necessary to completely characterise a patient with FXS. The actual gold standard diagnosis uses Southern blot; however, it cannot accurately characterise all cases. Optical genome mapping is a new technology that has also been developed to approach the diagnosis of fragile X syndrome. Long-range sequencing represented by PacBio and Oxford Nanopore has the potential to replace the actual diagnosis and offers a complete characterization of molecular profiles in a single test. The new technologies have improved the diagnosis of fragile X syndrome and revealed unknown aberrations, but they are a long way from being used routinely in clinical practice.
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Affiliation(s)
- Cristian-Gabriel Ciobanu
- Medical Genetics Department, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, University Street No 16, 700115 Iasi, Romania; (C.-G.C.)
| | - Irina Nucă
- Medical Genetics Department, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, University Street No 16, 700115 Iasi, Romania; (C.-G.C.)
- Investigatii Medicale Praxis, St. Moara de Vant No 35, 700376 Iasi, Romania
| | - Roxana Popescu
- Medical Genetics Department, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, University Street No 16, 700115 Iasi, Romania; (C.-G.C.)
- Medical Genetics Department, “Saint Mary” Emergency Children’s Hospital, St. Vasile Lupu No 62, 700309 Iasi, Romania
| | - Lucian-Mihai Antoci
- Medical Genetics Department, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, University Street No 16, 700115 Iasi, Romania; (C.-G.C.)
| | - Lavinia Caba
- Medical Genetics Department, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, University Street No 16, 700115 Iasi, Romania; (C.-G.C.)
| | - Anca Viorica Ivanov
- Pediatrics Department, “Grigore T. Popa” University of Medicine and Pharmacy, University Street No 16, 700115 Iasi, Romania
| | - Karina-Alexandra Cojocaru
- Department of Biochemistry, Faculty of Dental Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, University Street No 16, 700115 Iasi, Romania
| | - Cristina Rusu
- Medical Genetics Department, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, University Street No 16, 700115 Iasi, Romania; (C.-G.C.)
- Medical Genetics Department, “Saint Mary” Emergency Children’s Hospital, St. Vasile Lupu No 62, 700309 Iasi, Romania
| | | | - Monica-Cristina Pânzaru
- Medical Genetics Department, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, University Street No 16, 700115 Iasi, Romania; (C.-G.C.)
- Medical Genetics Department, “Saint Mary” Emergency Children’s Hospital, St. Vasile Lupu No 62, 700309 Iasi, Romania
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12
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Straub D, Schmitt LM, Boggs AE, Horn PS, Dominick KC, Gross C, Erickson CA. A sensitive and reproducible qRT-PCR assay detects physiological relevant trace levels of FMR1 mRNA in individuals with Fragile X syndrome. Sci Rep 2023; 13:3808. [PMID: 36882476 PMCID: PMC9992378 DOI: 10.1038/s41598-023-29786-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 02/10/2023] [Indexed: 03/09/2023] Open
Abstract
Fragile X syndrome (FXS) is the most common inherited intellectual disability. FXS is caused by a trinucleotide repeat expansion in the 5' untranslated region of the FMR1 gene, which leads to gene methylation, transcriptional silencing, and lack of expression of Fragile X Messenger Riboprotein (FMRP). Currently available FXS therapies are inefficient, and the disease severity is highly variable, making it difficult to predict disease trajectory and treatment response. We and others have recently shown that a subset of full-mutation, fully-methylated (FM-FM) males with FXS express low amounts of FMRP which could contribute to phenotypic variability. To better understand the underlying mechanisms, we developed a sensitive qRT-PCR assay to detect FMR1 mRNA in blood. This assay reproducibly detects trace amounts of FMR1 mRNA in a subset of FM-FM males, suggesting that current Southern Blot and PCR determination of FM-FM status is not always associated with complete transcriptional silencing. The functional relevance of trace-level FMR1 mRNA is confirmed by showing a positive correlation with cognitive function; however, phenotypic variability is not fully explained by FMR1 expression. These results corroborate the need for better molecular assays for FXS diagnosis and encourage studies to elucidate the factors contributing to the phenotypic variability of FXS.
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Affiliation(s)
- Devan Straub
- Division of Child and Adolescent Psychiatry, Cincinnati Children's Hospital Medical Center, 3333 Burnet Ave., Cincinnati, OH, 45229-3039, USA
| | - Lauren M Schmitt
- Division of Behavioral Medicine and Clinical Psychology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Ave., Cincinnati, OH, 45229-3039, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, 3333 Burnet Ave., Cincinnati, OH, 45229-3039, USA
| | - Anna E Boggs
- Division of Child and Adolescent Psychiatry, Cincinnati Children's Hospital Medical Center, 3333 Burnet Ave., Cincinnati, OH, 45229-3039, USA
| | - Paul S Horn
- Department of Pediatrics, University of Cincinnati College of Medicine, 3333 Burnet Ave., Cincinnati, OH, 45229-3039, USA
- Division of Neurology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Ave, Cincinnati, OH, 45229-3039, USA
| | - Kelli C Dominick
- Division of Child and Adolescent Psychiatry, Cincinnati Children's Hospital Medical Center, 3333 Burnet Ave., Cincinnati, OH, 45229-3039, USA
- Department of Psychiatry and Behavioral Neuroscience, University of Cincinnati College of Medicine, Stetson Building Suite 3200, 260 Stetson Street, Cincinnati, OH, 45267-0559, USA
| | - Christina Gross
- Department of Pediatrics, University of Cincinnati College of Medicine, 3333 Burnet Ave., Cincinnati, OH, 45229-3039, USA
- Division of Neurology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Ave, Cincinnati, OH, 45229-3039, USA
| | - Craig A Erickson
- Division of Child and Adolescent Psychiatry, Cincinnati Children's Hospital Medical Center, 3333 Burnet Ave., Cincinnati, OH, 45229-3039, USA.
- Department of Psychiatry and Behavioral Neuroscience, University of Cincinnati College of Medicine, Stetson Building Suite 3200, 260 Stetson Street, Cincinnati, OH, 45267-0559, USA.
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13
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Chen M, Jiang H, Zhang C. Selected Genetic Factors Associated with Primary Ovarian Insufficiency. Int J Mol Sci 2023; 24:ijms24054423. [PMID: 36901862 PMCID: PMC10002966 DOI: 10.3390/ijms24054423] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 02/14/2023] [Accepted: 02/14/2023] [Indexed: 03/12/2023] Open
Abstract
Primary ovarian insufficiency (POI) is a heterogeneous disease resulting from non-functional ovaries in women before the age of 40. It is characterized by primary amenorrhea or secondary amenorrhea. As regards its etiology, although many POI cases are idiopathic, menopausal age is a heritable trait and genetic factors play an important role in all POI cases with known causes, accounting for approximately 20% to 25% of cases. This paper reviews the selected genetic causes implicated in POI and examines their pathogenic mechanisms to show the crucial role of genetic effects on POI. The genetic factors that can be found in POI cases include chromosomal abnormalities (e.g., X chromosomal aneuploidies, structural X chromosomal abnormalities, X-autosome translocations, and autosomal variations), single gene mutations (e.g., newborn ovary homeobox gene (NOBOX), folliculogenesis specific bHLH transcription factor (FIGLA), follicle-stimulating hormone receptor (FSHR), forkhead box L2 (FOXL2), bone morphogenetic protein 15 (BMP15), etc., as well as defects in mitochondrial functions and non-coding RNAs (small ncRNAs and long ncRNAs). These findings are beneficial for doctors to diagnose idiopathic POI cases and predict the risk of POI in women.
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Affiliation(s)
- Mengchi Chen
- Queen Mary School, Nanchang University, Nanchang 330006, China
| | - Haotian Jiang
- Department of Cell Biology, College of Medicine, Nanchang University, Nanchang 330006, China
| | - Chunping Zhang
- Department of Cell Biology, College of Medicine, Nanchang University, Nanchang 330006, China
- Correspondence:
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14
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Points to consider in the detection of germline structural variants using next-generation sequencing: A statement of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2023; 25:100316. [PMID: 36507974 DOI: 10.1016/j.gim.2022.09.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 09/29/2022] [Accepted: 09/30/2022] [Indexed: 12/14/2022] Open
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15
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Klusek J, Newman-Norlund R, Fairchild AJ, Newman-Norlund S, Sayers S, Stewart JC, Berry-Kravis E, Fridriksson J. Low normal FMR1 genotype in older adult women: Psychological well-being and motor function. Arch Gerontol Geriatr 2022; 103:104789. [PMID: 35981426 PMCID: PMC9464716 DOI: 10.1016/j.archger.2022.104789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 08/01/2022] [Accepted: 08/09/2022] [Indexed: 11/28/2022]
Abstract
The FMR1 gene plays a key role in adult neurogenesis and neuroplasticity, and thus may contribute to age-related health in the population. The current study focused on the "low normal" FMR1 genotype, defined by lower-than-typical numbers of FMR1 CGG repeats (<26), as a potential genetic determinant of age-related health. We characterized the effect of the low normal FMR1 genotype on psychological well-being and motor function in a racially diverse non-clinical sample of older adult women. Women with low CGG repeats were distinguished from those with CGGs falling within the mid-high end of the normal range by reduced performance on multimodal assessments of motor function and psychological well-being, with large effect sizes. Robust continuous associations were also detected between lower CGG repeat length and reduced psychological well-being, balance, and dexterity. Findings suggest that FMR1 may represent an important mediator of individual differences in age-related health; larger epidemiological studies are needed. Given that approximately 23-35% of females carry the low normal genotype, efforts to understand its clinical effects have relevance a broad swath of the aging population.
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Affiliation(s)
- Jessica Klusek
- Department of Communication Sciences and Disorders, Arnold School of Public Health, University of South Carolina, Close-Hipp Building, 1705 College Street, Columbia, SC 29208, USA.
| | - Roger Newman-Norlund
- Department of Communication Sciences and Disorders, Arnold School of Public Health, University of South Carolina, Close-Hipp Building, 1705 College Street, Columbia, SC 29208, USA; Department of Psychology, University of South Carolina, 1512 Pendleton Street, Columbia, SC 29208, USA
| | - Amanda J Fairchild
- Department of Psychology, University of South Carolina, 1512 Pendleton Street, Columbia, SC 29208, USA
| | - Sarah Newman-Norlund
- Department of Communication Sciences and Disorders, Arnold School of Public Health, University of South Carolina, Close-Hipp Building, 1705 College Street, Columbia, SC 29208, USA
| | - Sara Sayers
- Department of Communication Sciences and Disorders, Arnold School of Public Health, University of South Carolina, Close-Hipp Building, 1705 College Street, Columbia, SC 29208, USA
| | - Jill C Stewart
- Physical Therapy Program, Department of Exercise Science, Arnold School of Public Health, University of South Carolina, 921 Assembly Street, Columbia, SC 29208, USA
| | - Elizabeth Berry-Kravis
- Department of Pediatrics, Neurological Sciences and Anatomy and Cell Biology, Rush University Medical Center, 1725 West Harrison Street, Suite 718, Chicago, IL 60612, USA
| | - Julius Fridriksson
- Department of Communication Sciences and Disorders, Arnold School of Public Health, University of South Carolina, Close-Hipp Building, 1705 College Street, Columbia, SC 29208, USA
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16
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Liang Q, Liu Y, Liu Y, Duan R, Meng W, Zhan J, Xia J, Mao A, Liang D, Wu L. Comprehensive Analysis of Fragile X Syndrome: Full Characterization of the FMR1 Locus by Long-Read Sequencing. Clin Chem 2022; 68:1529-1540. [PMID: 36171182 DOI: 10.1093/clinchem/hvac154] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 07/21/2022] [Indexed: 11/14/2022]
Abstract
BACKGROUND Fragile X syndrome (FXS) is the most frequent cause of inherited X-linked intellectual disability. Conventional FXS genetic testing methods mainly focus on FMR1 CGG expansions and fail to identify AGG interruptions, rare intragenic variants, and large gene deletions. METHODS A long-range PCR and long-read sequencing-based assay termed comprehensive analysis of FXS (CAFXS) was developed and evaluated in Coriell and clinical samples by comparing to Southern blot analysis and triplet repeat-primed PCR (TP-PCR). RESULTS CAFXS accurately detected the number of CGG repeats in the range of 93 to at least 940 with mass fraction of 0.5% to 1% in the background of normal alleles, which was 2-4-fold analytically more sensitive than TP-PCR. All categories of mutations detected by control methods, including full mutations in 30 samples, were identified by CAFXS for all 62 clinical samples. CAFXS accurately determined AGG interruptions in all 133 alleles identified, even in mosaic alleles. CAFXS successfully identified 2 rare intragenic variants including the c.879A > C variant in exon 9 and a 697-bp microdeletion flanking upstream of CGG repeats, which disrupted primer annealing in TP-PCR assay. In addition, CAFXS directly determined the breakpoints of a 237.1-kb deletion and a 774.0-kb deletion encompassing the entire FMR1 gene in 2 samples. CONCLUSIONS Long-read sequencing-based CAFXS represents a comprehensive assay for identifying FMR1 CGG expansions, AGG interruptions, rare intragenic variants, and large gene deletions, which greatly improves the genetic screening and diagnosis for FXS.
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Affiliation(s)
- Qiaowei Liang
- Department of Medical Genetics, Hunan Jiahui Genetics Hospital, Changsha, Hunan, China
| | - Yingdi Liu
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Yaning Liu
- Department of Medical Genetics, Hunan Jiahui Genetics Hospital, Changsha, Hunan, China
| | - Ranhui Duan
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Wanli Meng
- Berry Genomics Corporation, Beijing, China
| | | | - Jiahui Xia
- Department of Medical Genetics, Hunan Jiahui Genetics Hospital, Changsha, Hunan, China
| | - Aiping Mao
- Berry Genomics Corporation, Beijing, China
| | - Desheng Liang
- Department of Medical Genetics, Hunan Jiahui Genetics Hospital, Changsha, Hunan, China.,Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Lingqian Wu
- Department of Medical Genetics, Hunan Jiahui Genetics Hospital, Changsha, Hunan, China.,Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
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17
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Rajan-Babu IS, Lian M, Chong SS. Triplet-Primed PCR Assays for Accurate Screening of FMR1 CGG Repeat Expansion and Genotype Verification. Curr Protoc 2022; 2:e427. [PMID: 35609145 DOI: 10.1002/cpz1.427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Fragile X syndrome and other fragile X-associated disorders are caused by the full-mutation (>200 copies) and premutation (55 to 200 copies) expansion, respectively, of the CGG short tandem repeat in the fragile X messenger ribonucleoprotein 1 (FMR1) gene. Clinical diagnostic laboratories use Southern blot analysis and polymerase chain reaction (PCR)-based tests to detect and/or size the FMR1 CGG repeats. The development of sensitive and high-throughput triplet-primed PCR (TP-PCR) assays has diminished the need to subject all samples to Southern blot analysis, which is both labor- and time-intensive. In this article, we describe two direct TP-PCR (dTP-PCR) assays for the detection of FMR1 CGG repeat expansions. We outline a protocol that is based on melting curve analysis of dTP-PCR amplicons for a rapid and cost-effective first-tier screening and identification of individuals with premutation and full-mutation expansions. We also describe a protocol that employs capillary electrophoresis to resolve the dTP-PCR amplicon fragments and to estimate the repeat sizes of normal (5 to 44 copies), intermediate (45 to 54 copies), and premutation alleles, as well as to detect full mutations and determine the structure of the FMR1 alleles. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Direct triplet-primed PCR master mix preparation and amplification of the FMR1 CGG repeat locus for melting curve analysis Basic Protocol 2: Melting curve analysis of direct triplet-primed PCR amplicons on the Rotor-Gene Q MD × 5plex high-resolution melt platform Alternate Protocol: Melting curve analysis of direct triplet-primed PCR amplicons on the LightCycler 480 system Basic Protocol 3: Generation of direct triplet-primed PCR melting curve analysis profiles Basic Protocol 4: Direct triplet-primed PCR master mix preparation and amplification of the FMR1 CGG repeat locus for capillary electrophoresis Basic Protocol 5: Generation of control FMR1 plasmids for direct triplet-primed PCR melting curve analysis Basic Protocol 6: Sanger sequencing assay to verify FMR1 CGG repeat size and structure of plasmid DNA controls.
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Affiliation(s)
- Indhu-Shree Rajan-Babu
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada.,Children's & Women's Hospital, Vancouver, British Columbia, Canada
| | - Mulias Lian
- Khoo Teck Puat-National University Children's Medical Institute, National University Hospital, Singapore, Singapore
| | - Samuel S Chong
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Department of Obstetrics and Gynecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Department of Laboratory Medicine, National University Hospital, Singapore, Singapore
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18
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Rajan-Babu IS, Phang GP, Law HY, Lee CG, Chong SS. High-Throughput Methylation-Specific Triplet-Primed PCR and Melting Curve Analysis for Selective and Reliable Identification of Actionable FMR1 Genotypes. J Mol Diagn 2022; 24:241-252. [PMID: 35038595 DOI: 10.1016/j.jmoldx.2021.11.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 10/26/2021] [Accepted: 11/23/2021] [Indexed: 11/17/2022] Open
Abstract
Methylated FMR1 full-mutation expansions cause fragile X syndrome. FMR1 premutation carriers are susceptible to other late-onset conditions, and women with premutation are at risk of transmitting a fully expanded FMR1 allele to offspring. Identification of individuals with actionable FMR1 genotypes (full-mutation males and females, and premutation females at risk for primary ovarian insufficiency and/or having fragile X-affected offspring) can enable timely access to intervention services and genetic counseling. This study presents a rapid, first-tier test based on melting curve analysis of methylation-specific triplet-primed PCR amplicons (msTP-PCR MCA) for concurrent detection of FMR1 CGG-repeat expansions and their methylation status. The msTP-PCR MCA assay was optimized on 20 fragile X reference samples, and its performance was evaluated on 111 peripheral blood-derived DNA samples from patients who have undergone prior molecular testing with PCR and/or Southern blot analysis. The msTP-PCR MCA assay detected all samples with a methylated FMR1 CGG-repeat expansion, and had sensitivity, specificity, positive predictive value, and negative predictive values of 100%, 92.06%, 91.1%, and 100%, respectively. The msTP-PCR MCA assay identified premutation/full-mutation mosaicism down to 1%, detected skewed inactivation in females with FMR1 expansions, and enabled selective identification of all individuals with an actionable FMR1 genotype. The msTP-PCR MCA assay may aid in fragile X screening of at-risk populations and newborns and voluntary carrier screening of women of reproductive age.
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Affiliation(s)
- Indhu-Shree Rajan-Babu
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Department of Medical Genetics, University of British Columbia, and Children's and Women's Hospital, Vancouver, British Columbia, Canada.
| | - Gui-Ping Phang
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Hai-Yang Law
- Department of Pediatric Medicine, KK Women's and Children's Hospital, Singapore
| | - Caroline G Lee
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Division of Cellular and Molecular Research, Humphrey Oei Institute of Cancer Research, National Cancer Centre Singapore, Singapore; Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Samuel S Chong
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Department of Obstetrics and Gynecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Department of Laboratory Medicine, National University Hospital, Singapore.
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19
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Zhang W, Li D, Pang N, Jiang L, Li B, Ye F, He F, Chen S, Liu F, Peng J, Yin J, Yin F. The second-tier status of fragile X syndrome testing for unexplained intellectual disability/global developmental delay in the era of next-generation sequencing. Front Pediatr 2022; 10:911805. [PMID: 35935362 PMCID: PMC9353215 DOI: 10.3389/fped.2022.911805] [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: 04/03/2022] [Accepted: 06/28/2022] [Indexed: 11/17/2022] Open
Abstract
OBJECTIVE Although many unexplained intellectual disability/global developmental delay (ID/GDD) individuals have benefited from the excellent detection yield of copy number variations and next-generation sequencing testing, many individuals still who suffer from ID/GDD of unexplained etiology. In this study, we investigated the applicability of fragile X syndrome (FXS) testing in unexplained ID/GDD individuals with negative or absent genetic testing. METHODS In this study, we used the triplet repeat primed polymerase chain reaction to evaluate the value and application of fragile X testing in unexplained ID/GDD individuals with negative or absent genetic testing (n = 681) from three hospitals. RESULTS Of the 681 ID/GDD individuals with negative or absent genetic testing results detected by FXS testing, 12 men and one woman were positive. This corresponded to a diagnostic yield of 1.9% for FXS testing in our cohort. All FXS individuals had either a family history of ID/GDD or suggestive clinical features. The detection yield of FXS testing in ID/GDD individuals who completed genetic testing (2.70%, 12/438) was significantly higher than in individuals without any genetic testing (0.40%, 1/243). CONCLUSIONS This is the first report of FXS testing in ID/GDD individuals who lacked previous genetic testing, which promotes standardization of the FXS diagnostic process. These results highlight the utility of FXS testing of unexplained ID/GDD individuals with negative results from standard genetic testing. In the era of next-generation sequencing, FXS testing is more suitable as a second-tier choice and provides clinicians and geneticists with auxiliary references for tracing the etiology of ID/GDD.
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Affiliation(s)
- Wen Zhang
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Pediatrics, Changsha, China.,Clinical Research Center for Children Neurodevelopmental Disabilities of Hunan Province, Xiangya Hospital, Central South University, Changsha, China
| | - Dong Li
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Pediatrics, Changsha, China.,Clinical Research Center for Children Neurodevelopmental Disabilities of Hunan Province, Xiangya Hospital, Central South University, Changsha, China
| | - Nan Pang
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Pediatrics, Changsha, China.,Clinical Research Center for Children Neurodevelopmental Disabilities of Hunan Province, Xiangya Hospital, Central South University, Changsha, China
| | - Li Jiang
- Department of Neurology, Children's Hospital Affiliated to Chongqing Medical University, Chongqing, China
| | - Baomin Li
- Department of Pediatrics, Qilu Hospital of Shandong University, Jinan, China
| | - Fanghua Ye
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China
| | - Fang He
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Pediatrics, Changsha, China.,Clinical Research Center for Children Neurodevelopmental Disabilities of Hunan Province, Xiangya Hospital, Central South University, Changsha, China
| | - Shimeng Chen
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Pediatrics, Changsha, China.,Clinical Research Center for Children Neurodevelopmental Disabilities of Hunan Province, Xiangya Hospital, Central South University, Changsha, China
| | - Fangyun Liu
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Pediatrics, Changsha, China.,Clinical Research Center for Children Neurodevelopmental Disabilities of Hunan Province, Xiangya Hospital, Central South University, Changsha, China
| | - Jing Peng
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Pediatrics, Changsha, China.,Clinical Research Center for Children Neurodevelopmental Disabilities of Hunan Province, Xiangya Hospital, Central South University, Changsha, China
| | - Jinghua Yin
- Department of Pathophysiology, Xiangya Hospital, Central South University, Changsha, China
| | - Fei Yin
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Pediatrics, Changsha, China.,Clinical Research Center for Children Neurodevelopmental Disabilities of Hunan Province, Xiangya Hospital, Central South University, Changsha, China
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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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21
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Beyond Trinucleotide Repeat Expansion in Fragile X Syndrome: Rare Coding and Noncoding Variants in FMR1 and Associated Phenotypes. Genes (Basel) 2021; 12:genes12111669. [PMID: 34828275 PMCID: PMC8623550 DOI: 10.3390/genes12111669] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/20/2021] [Accepted: 10/21/2021] [Indexed: 11/17/2022] Open
Abstract
FMR1 (FMRP translational regulator 1) variants other than repeat expansion are known to cause disease phenotypes but can be overlooked if they are not accounted for in genetic testing strategies. We collected and reanalyzed the evidence for pathogenicity of FMR1 coding, noncoding, and copy number variants published to date. There is a spectrum of disease-causing FMR1 variation, with clinical and functional evidence supporting pathogenicity of five splicing, five missense, one in-frame deletion, one nonsense, and four frameshift variants. In addition, FMR1 deletions occur in both mosaic full mutation patients and as constitutional pathogenic alleles. De novo deletions arise not only from full mutation alleles but also alleles with normal-sized CGG repeats in several patients, suggesting that the CGG repeat region may be prone to genomic instability even in the absence of repeat expansion. We conclude that clinical tests for potentially FMR1-related indications such as intellectual disability should include methods capable of detecting small coding, noncoding, and copy number variants.
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22
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Grosso V, Marcolungo L, Maestri S, Alfano M, Lavezzari D, Iadarola B, Salviati A, Mariotti B, Botta A, D’Apice MR, Novelli G, Delledonne M, Rossato M. Characterization of FMR1 Repeat Expansion and Intragenic Variants by Indirect Sequence Capture. Front Genet 2021; 12:743230. [PMID: 34646309 PMCID: PMC8504923 DOI: 10.3389/fgene.2021.743230] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 08/26/2021] [Indexed: 11/30/2022] Open
Abstract
Traditional methods for the analysis of repeat expansions, which underlie genetic disorders, such as fragile X syndrome (FXS), lack single-nucleotide resolution in repeat analysis and the ability to characterize causative variants outside the repeat array. These drawbacks can be overcome by long-read and short-read sequencing, respectively. However, the routine application of next-generation sequencing in the clinic requires target enrichment, and none of the available methods allows parallel analysis of long-DNA fragments using both sequencing technologies. In this study, we investigated the use of indirect sequence capture (Xdrop technology) coupled to Nanopore and Illumina sequencing to characterize FMR1, the gene responsible of FXS. We achieved the efficient enrichment (> 200×) of large target DNA fragments (~60-80 kbp) encompassing the entire FMR1 gene. The analysis of Xdrop-enriched samples by Nanopore long-read sequencing allowed the complete characterization of repeat lengths in samples with normal, pre-mutation, and full mutation status (> 1 kbp), and correctly identified repeat interruptions relevant for disease prognosis and transmission. Single-nucleotide variants (SNVs) and small insertions/deletions (indels) could be detected in the same samples by Illumina short-read sequencing, completing the mutational testing through the identification of pathogenic variants within the FMR1 gene, when no typical CGG repeat expansion is detected. The study successfully demonstrated the parallel analysis of repeat expansions and SNVs/indels in the FMR1 gene at single-nucleotide resolution by combining Xdrop enrichment with two next-generation sequencing approaches. With the appropriate optimization necessary for the clinical settings, the system could facilitate both the study of genotype-phenotype correlation in FXS and enable a more efficient diagnosis and genetic counseling for patients and their relatives.
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Affiliation(s)
- Valentina Grosso
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Luca Marcolungo
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Simone Maestri
- Department of Biotechnology, University of Verona, Verona, Italy
| | | | - Denise Lavezzari
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Barbara Iadarola
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Alessandro Salviati
- Department of Biotechnology, University of Verona, Verona, Italy
- GENARTIS srl, Verona, Italy
| | - Barbara Mariotti
- Department of Medicine, Section of General Pathology, University of Verona, Verona, Italy
| | - Annalisa Botta
- Department of Biomedicine and Prevention, Medical Genetics Section, University of Rome "Tor Vergata", Rome, Italy
| | | | - Giuseppe Novelli
- Department of Biomedicine and Prevention, Medical Genetics Section, University of Rome "Tor Vergata", Rome, Italy
- IRCCS Neuromed Mediterranean Neurological Institute, Pozzilli, Italy
- Department of Pharmacology, School of Medicine, University of Nevada, Reno, NV, United States
| | - Massimo Delledonne
- Department of Biotechnology, University of Verona, Verona, Italy
- GENARTIS srl, Verona, Italy
| | - Marzia Rossato
- Department of Biotechnology, University of Verona, Verona, Italy
- GENARTIS srl, Verona, Italy
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