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Alshawsh M, Wake M, Gecz J, Corbett M, Saffery R, Pitt J, Greaves R, Williams K, Field M, Cheong J, Bui M, Arora S, Sadedin S, Lunke S, Wall M, Amor DJ, Godler DE. Epigenomic newborn screening for conditions with intellectual disability and autistic features in Australian newborns. Epigenomics 2024; 16:1203-1214. [PMID: 39365098 PMCID: PMC11487350 DOI: 10.1080/17501911.2024.2402681] [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: 05/12/2024] [Accepted: 09/06/2024] [Indexed: 10/05/2024] Open
Abstract
This study describes a protocol to assess a novel workflow called Epi-Genomic Newborn Screening (EpiGNs) on 100,000 infants from the state of Victoria, Australia. The workflow uses a first-tier screening approach called methylation-specific quantitative melt analysis (MS-QMA), followed by second and third tier testing including targeted methylation and copy number variation analyzes with droplet digital PCR, EpiTYPER system and low-coverage whole genome sequencing. EpiGNs utilizes only two 3.2 mm newborn blood spot punches to screen for genetic conditions, including fragile X syndrome, Prader-Willi syndrome, Angelman syndrome, Dup15q syndrome and sex chromosome aneuploidies. The program aims to: identify clinically actionable methylation screening thresholds for the first-tier screen and estimate prevalence for the conditions screened.
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Affiliation(s)
- Mohammed Alshawsh
- Department of Paediatrics, Monash University, Melbourne, VIC, 3168, Australia
- Murdoch Children's Research Institute, Parkville, VIC, 3052Australia
| | - Melissa Wake
- Murdoch Children's Research Institute, Parkville, VIC, 3052Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
| | - Jozef Gecz
- Robinson Research Institute & Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, Australia
| | - Mark Corbett
- Robinson Research Institute & Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, Australia
| | - Richard Saffery
- Murdoch Children's Research Institute, Parkville, VIC, 3052Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
| | - James Pitt
- Murdoch Children's Research Institute, Parkville, VIC, 3052Australia
| | - Ronda Greaves
- Murdoch Children's Research Institute, Parkville, VIC, 3052Australia
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Katrina Williams
- Department of Paediatrics, Monash University, Melbourne, VIC, 3168, Australia
- Murdoch Children's Research Institute, Parkville, VIC, 3052Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
| | - Michael Field
- Genetics of Learning Disability Service, Hunter Genetics, Waratah, New South Wales, Australia
| | - Jeanie Cheong
- Murdoch Children's Research Institute, Parkville, VIC, 3052Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
- Department of Obstetrics, Gynaecology & Newborn Health, The Royal Women's Hospital, Melbourne, Australia
| | - Minh Bui
- Centre for Epidemiology & Biostatistics, Melbourne School of Population & Global Health, University of Melbourne, Carlton, Australia
| | - Sheena Arora
- Centre for Health Economics Research & Evaluation, University of Technology Sydney, Broadway, NSW, Australia
| | - Simon Sadedin
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Sebastian Lunke
- Murdoch Children's Research Institute, Parkville, VIC, 3052Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Meg Wall
- Murdoch Children's Research Institute, Parkville, VIC, 3052Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - David J Amor
- Murdoch Children's Research Institute, Parkville, VIC, 3052Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
| | - David E Godler
- Murdoch Children's Research Institute, Parkville, VIC, 3052Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
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Howell S, Davis SM, Carstens B, Haag M, Ross JL, Tartaglia NR. Discordant Prenatal Cell-Free DNA Screening vs. Diagnostic Results of Sex Chromosome Aneuploidies: Implications for Newborn Screening and Genetic Counseling. Int J Neonatal Screen 2024; 10:48. [PMID: 39051404 PMCID: PMC11270358 DOI: 10.3390/ijns10030048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 06/08/2024] [Accepted: 07/04/2024] [Indexed: 07/27/2024] Open
Abstract
Sex chromosome aneuploidies (SCAs) collectively occur in 1 in 500 livebirths, and diagnoses in the neonatal period are increasing with advancements in prenatal and early genetic testing. Inevitably, SCA will be identified on either routine prenatal or newborn screening in the near future. Tetrasomy SCAs are rare, manifesting more significant phenotypes compared to trisomies. Prenatal cell-free DNA (cfDNA) screening has been demonstrated to have relatively poor positive predictive values (PPV) in SCAs, directing genetic counseling discussions towards false-positive likelihood rather than thoroughly addressing all possible outcomes and phenotypes, respectively. The eXtraordinarY Babies study is a natural history study of children prenatally identified with SCAs, and it developed a longitudinal data resource and common data elements with the Newborn Screening Translational Research Network (NBSTRN). A review of cfDNA and diagnostic reports from participants identified a higher than anticipated rate of discordance. The aims of this project are to (1) compare our findings to outcomes from a regional clinical cytogenetic laboratory and (2) describe discordant outcomes from both samples. Twenty-one (10%), and seven (8.3%) cases were found to be discordant between cfDNA (result or indication reported to lab) and diagnosis for the Babies Study and regional laboratory, respectively. Discordant results represented six distinct discordance categories when comparing cfDNA to diagnostic results, with the largest groups being Trisomy cfDNA vs. Tetrasomy diagnosis (66.7% of discordance in eXtraordinarY Babies study) and Mosaicism (57.1% in regional laboratory). Traditional genetic counseling for SCA-related cfDNA results is inadequate given a high degree of discordance that jeopardizes the accuracy of the information discussed and informed decision making following prenatal genetic counseling.
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Affiliation(s)
- Susan Howell
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO 80045, USA; (S.M.D.); (N.R.T.)
- eXtraOrdinarY Kids Clinic and Research Program, Children’s Hospital Colorado, Aurora, CO 80045, USA
| | - Shanlee M. Davis
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO 80045, USA; (S.M.D.); (N.R.T.)
- eXtraOrdinarY Kids Clinic and Research Program, Children’s Hospital Colorado, Aurora, CO 80045, USA
| | - Billie Carstens
- Department of Pathology, University of Colorado School of Medicine, Aurora, CO 80045, USA; (B.C.); (M.H.)
| | - Mary Haag
- Department of Pathology, University of Colorado School of Medicine, Aurora, CO 80045, USA; (B.C.); (M.H.)
| | - Judith L. Ross
- Department of Pediatrics, Nemours Children’s Hospital-DE and Thomas Jefferson University, Wilmington, DE 19803, USA;
| | - Nicole R. Tartaglia
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO 80045, USA; (S.M.D.); (N.R.T.)
- eXtraOrdinarY Kids Clinic and Research Program, Children’s Hospital Colorado, Aurora, CO 80045, USA
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O'Connor M, Qiao H, Odamah K, Cerdeira PC, Man HY. Heterozygous Nexmif female mice demonstrate mosaic NEXMIF expression, autism-like behaviors, and abnormalities in dendritic arborization and synaptogenesis. Heliyon 2024; 10:e24703. [PMID: 38322873 PMCID: PMC10844029 DOI: 10.1016/j.heliyon.2024.e24703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 11/28/2023] [Accepted: 01/12/2024] [Indexed: 02/08/2024] Open
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental disorder with a strong genetic basis. ASDs are commonly characterized by impairments in language, restrictive and repetitive behaviors, and deficits in social interactions. Although ASD is a highly heterogeneous disease with many different genes implicated in its etiology, many ASD-associated genes converge on common cellular defects, such as aberrant neuronal morphology and synapse dysregulation. Our previous work revealed that, in mice, complete loss of the ASD-associated X-linked gene NEXMIF results in a reduction in dendritic complexity, a decrease in spine and synapse density, altered synaptic transmission, and ASD-like behaviors. Interestingly, human females of NEXMIF haploinsufficiency have recently been reported to demonstrate autistic features; however, the cellular and molecular basis for this haploinsufficiency-caused ASD remains unclear. Here we report that in the brains of Nexmif± female mice, NEXMIF shows a mosaic pattern in its expression in neurons. Heterozygous female mice demonstrate behavioral impairments similar to those of knockout male mice. In the mosaic mixture of neurons from Nexmif± mice, cells that lack NEXMIF have impairments in dendritic arborization and spine development. Remarkably, the NEXMIF-expressing neurons from Nexmif± mice also demonstrate similar defects in dendritic growth and spine formation. These findings establish a novel mouse model of NEXMIF haploinsufficiency and provide new insights into the pathogenesis of NEXMIF-dependent ASD.
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Affiliation(s)
- Margaret O'Connor
- Department of Biology, Boston University, 5 Cummington Mall, Boston, MA 02215, USA
| | - Hui Qiao
- Department of Biology, Boston University, 5 Cummington Mall, Boston, MA 02215, USA
| | - KathrynAnn Odamah
- Department of Biology, Boston University, 5 Cummington Mall, Boston, MA 02215, USA
| | | | - Heng-Ye Man
- Department of Biology, Boston University, 5 Cummington Mall, Boston, MA 02215, USA
- Department of Pharmacology, Physiology & Biophysics, Boston University School of Medicine, 72 East Concord St., Boston, MA 02118, USA
- Center for Systems Neuroscience, Boston University, 610 Commonwealth Ave, Boston, MA 02215, USA
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Detection of Cryptic Fragile X Full Mutation Alleles by Southern Blot in a Female and Her Foetal DNA via Chorionic Villus Sampling, Complicated by Mosaicism for 45,X0/46,XX/47,XXX. Genes (Basel) 2021; 12:genes12060798. [PMID: 34073864 PMCID: PMC8225079 DOI: 10.3390/genes12060798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/08/2021] [Accepted: 05/18/2021] [Indexed: 11/23/2022] Open
Abstract
We describe a female with a 72 CGG FMR1 premutation (PM) (CGG 55–199) and family history of fragile X syndrome (FXS), referred for prenatal testing. The proband had a high risk of having an affected pregnancy with a full mutation allele (FM) (CGG > 200), that causes FXS through hypermethylation of the FMR1 promoter. The CGG sizing analysis in this study used AmplideX triplet repeat primed polymerase chain reaction (TP-PCR) and long-range methylation sensitive PCR (mPCR). These methods detected a 73 CGG PM allele in the proband’s blood, and a 164 CGG PM allele in her male cultured chorionic villus sample (CVS). In contrast, the Southern blot analysis showed mosaicism for: (i) a PM (71 CGG) and an FM (285–768 CGG) in the proband’s blood, and (ii) a PM (165 CGG) and an FM (408–625 CGG) in the male CVS. The FMR1 methylation analysis, using an EpiTYPER system in the proband, showed levels in the range observed for mosaic Turner syndrome. This was confirmed by molecular and cytogenetic karyotyping, identifying 45,X0/46,XX/47,XXX lines. In conclusion, this case highlights the importance of Southern blot in pre- and postnatal testing for presence of an FM, which was not detected using AmplideX TP-PCR or mPCR in the proband and her CVS.
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Kraan CM, Baker EK, Arpone M, Bui M, Ling L, Gamage D, Bretherton L, Rogers C, Field MJ, Wotton TL, Francis D, Hunter MF, Cohen J, Amor DJ, Godler DE. DNA Methylation at Birth Predicts Intellectual Functioning and Autism Features in Children with Fragile X Syndrome. Int J Mol Sci 2020; 21:ijms21207735. [PMID: 33086711 PMCID: PMC7589848 DOI: 10.3390/ijms21207735] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/15/2020] [Accepted: 10/16/2020] [Indexed: 12/12/2022] Open
Abstract
Fragile X syndrome (FXS) is a leading single-gene cause of intellectual disability (ID) with autism features. This study analysed diagnostic and prognostic utility of the Fragile X-Related Epigenetic Element 2 DNA methylation (FREE2m) assessed by Methylation Specific-Quantitative Melt Analysis and the EpiTYPER system, in retrospectively retrieved newborn blood spots (NBS) and newly created dried blood spots (DBS) from 65 children with FXS (~2–17 years). A further 168 NBS from infants from the general population were used to establish control reference ranges, in both sexes. FREE2m analysis showed sensitivity and specificity approaching 100%. In FXS males, NBS FREE2m strongly correlated with intellectual functioning and autism features, however associations were not as strong for FXS females. Fragile X mental retardation 1 gene (FMR1) mRNA levels in blood were correlated with FREE2m in both NBS and DBS, for both sexes. In females, DNAm was significantly increased at birth with a decrease in childhood. The findings support the use of FREE2m analysis in newborns for screening, diagnostic and prognostic testing in FXS.
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Affiliation(s)
- Claudine M Kraan
- Diagnosis and Development, Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne VIC 3052, Australia; (C.M.K.); (E.K.B.); (M.A.); (L.L.); (D.G.); (L.B.); (D.J.A.)
- Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville VIC 3052, Australia
| | - Emma K Baker
- Diagnosis and Development, Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne VIC 3052, Australia; (C.M.K.); (E.K.B.); (M.A.); (L.L.); (D.G.); (L.B.); (D.J.A.)
- Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville VIC 3052, Australia
- School of Psychology and Public Health, La Trobe University, Bundoora VIC 3086, Australia
| | - Marta Arpone
- Diagnosis and Development, Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne VIC 3052, Australia; (C.M.K.); (E.K.B.); (M.A.); (L.L.); (D.G.); (L.B.); (D.J.A.)
- Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville VIC 3052, Australia
- Brain and Mind, Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville VIC 3052, Australia
| | - Minh Bui
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne VIC 3052, Australia;
| | - Ling Ling
- Diagnosis and Development, Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne VIC 3052, Australia; (C.M.K.); (E.K.B.); (M.A.); (L.L.); (D.G.); (L.B.); (D.J.A.)
| | - Dinusha Gamage
- Diagnosis and Development, Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne VIC 3052, Australia; (C.M.K.); (E.K.B.); (M.A.); (L.L.); (D.G.); (L.B.); (D.J.A.)
| | - Lesley Bretherton
- Diagnosis and Development, Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne VIC 3052, Australia; (C.M.K.); (E.K.B.); (M.A.); (L.L.); (D.G.); (L.B.); (D.J.A.)
| | - Carolyn Rogers
- Genetics of Learning Disability Service (GOLD service), Hunter Genetics, Newcastle NSW 2298, Australia; (C.R.); (M.J.F.)
| | - Michael J Field
- Genetics of Learning Disability Service (GOLD service), Hunter Genetics, Newcastle NSW 2298, Australia; (C.R.); (M.J.F.)
| | - Tiffany L Wotton
- New South Wales Newborn Screening Program, Children’s Hospital at Westmead, Sydney NSW 2145, Australia;
| | - David Francis
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne VIC 3052, Australia;
| | - Matt F Hunter
- Monash Genetics, Monash Health, Clayton, VIC 3168, Australia;
| | - Jonathan Cohen
- Centre for Developmental Disability Health Victoria, Monash University, Doveton VIC 3177, Australia;
- Fragile X Alliance Inc., North Caulfield VIC 3161, Australia
| | - David J Amor
- Diagnosis and Development, Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne VIC 3052, Australia; (C.M.K.); (E.K.B.); (M.A.); (L.L.); (D.G.); (L.B.); (D.J.A.)
- Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville VIC 3052, Australia
| | - David E Godler
- Diagnosis and Development, Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne VIC 3052, Australia; (C.M.K.); (E.K.B.); (M.A.); (L.L.); (D.G.); (L.B.); (D.J.A.)
- Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville VIC 3052, Australia
- Correspondence: ; Tel.: +613-8341-6496
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Early Diagnosis in Prader-Willi Syndrome Reduces Obesity and Associated Co-Morbidities. Genes (Basel) 2019; 10:genes10110898. [PMID: 31698873 PMCID: PMC6896038 DOI: 10.3390/genes10110898] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 11/01/2019] [Accepted: 11/04/2019] [Indexed: 02/07/2023] Open
Abstract
Prader–Willi syndrome (PWS) is an imprinting genetic disorder characterized by lack of expression of genes on the paternal chromosome 15q11–q13 region. Growth hormone (GH) replacement positively influences stature and body composition in PWS. Our hypothesis was that early diagnosis delays onset of obesity in PWS. We studied 352 subjects with PWS, recruited from the NIH Rare Disease Clinical Research Network, to determine if age at diagnosis, ethnicity, gender, and PWS molecular class influenced the age they first become heavy, as determined by their primary care providers, and the age they first developed an increased appetite and began seeking food. The median ages that children with PWS became heavy were 10 years, 6 years and 4 years for age at diagnosis < 1 year, between 1 and 3 years, and greater than 3 years of age, respectively. The age of diagnosis and ethnicity were significant factors influencing when PWS children first became heavy (p < 0.01), however gender and the PWS molecular class had no influence. Early diagnosis delayed the onset of becoming heavy in individuals with PWS, permitting early GH and other treatment, thus reducing the risk of obesity-associated co-morbidities. Non-white individuals had an earlier onset of becoming heavy.
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Hensel CH, Vanzo RJ, Martin MM, Ling L, Aliaga SM, Bui M, Francis DI, Twede H, Field MH, Morison JW, Amor DJ, Godler DE. Abnormally Methylated FMR1 in Absence of a Detectable Full Mutation in a U.S.A Patient Cohort Referred for Fragile X Testing. Sci Rep 2019; 9:15315. [PMID: 31653898 PMCID: PMC6814816 DOI: 10.1038/s41598-019-51618-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 09/30/2019] [Indexed: 12/11/2022] Open
Abstract
In 2016, Methylation-Specific Quantitative Melt Analysis (MS-QMA) on 3,340 male probands increased diagnostic yield from 1.60% to 1.84% for fragile X syndrome (FXS) using a pooling approach. In this study probands from Lineagen (UT, U.S.A.) of both sexes were screened using MS-QMA without sample pooling. The cohorts included: (i) 279 probands with no FXS full mutation (FM: CGG > 200) detected by AmplideX CGG sizing; (ii) 374 negative and 47 positive controls. MS-QMA sensitivity and specificity in controls approached 100% for both sexes. For male probands with no FM detected by standard testing (n = 189), MS-QMA identified abnormal DNA methylation (mDNA) in 4% normal size (NS: < 44 CGGs), 6% grey zone (CGG 45–54) and 12% premutation (CGG 54–199) alleles. The abnormal mDNA was confirmed by AmplideX methylation sensitive (m)PCR and EpiTYPER tests. In contrast, no abnormal mDNA was detected in 89 males with NS alleles from the general population. For females, 11% of 43 probands with NS alleles by the AmplideX sizing assay had abnormal mDNA by MS-QMA, with FM / NS mosaicism confirmed by AmplideX mPCR. FMR1 MS-QMA analysis can cost-effectively screen probands of both sexes for methylation and FM mosaicism that may be missed by standard testing.
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Affiliation(s)
| | - Rena J Vanzo
- Lineagen, Inc., Salt Lake City, UT, United States of America
| | - Megan M Martin
- Lineagen, Inc., Salt Lake City, UT, United States of America
| | - Ling Ling
- Diagnosis and Development, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC, Australia
| | - Solange M Aliaga
- Diagnosis and Development, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC, Australia
| | - Minh Bui
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, VIC, Australia
| | - David I Francis
- Victorian Clinical Genetics Services and Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC, Australia
| | - Hope Twede
- Lineagen, Inc., Salt Lake City, UT, United States of America
| | - Michael H Field
- Genetics of Learning Disability Service (GOLD service), Hunter Genetics, Newcastle, NSW, Australia
| | - Jonathon W Morison
- Business Development and Legal Office, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC, Australia
| | - David J Amor
- Faculty of Medicine, Dentistry and Health Sciences, Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia.,Neurodisability and Rehabilitation Research Group, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC, Australia
| | - David E Godler
- Diagnosis and Development, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC, Australia. .,Faculty of Medicine, Dentistry and Health Sciences, Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia.
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8
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Significantly Elevated FMR1 mRNA and Mosaicism for Methylated Premutation and Full Mutation Alleles in Two Brothers with Autism Features Referred for Fragile X Testing. Int J Mol Sci 2019; 20:ijms20163907. [PMID: 31405222 PMCID: PMC6721168 DOI: 10.3390/ijms20163907] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 08/04/2019] [Accepted: 08/07/2019] [Indexed: 11/26/2022] Open
Abstract
Although fragile X syndrome (FXS) is caused by a hypermethylated full mutation (FM) expansion with ≥200 cytosine-guanine-guanine (CGG) repeats, and a decrease in FMR1 mRNA and its protein (FMRP), incomplete silencing has been associated with more severe autism features in FXS males. This study reports on brothers (B1 and B2), aged 5 and 2 years, with autistic features and language delay, but a higher non-verbal IQ in comparison to typical FXS. CGG sizing using AmplideX PCR only identified premutation (PM: 55–199 CGGs) alleles in blood. Similarly, follow-up in B1 only revealed PM alleles in saliva and skin fibroblasts; whereas, an FM expansion was detected in both saliva and buccal DNA of B2. While Southern blot analysis of blood detected an unmethylated FM, methylation analysis with a more sensitive methodology showed that B1 had partially methylated PM alleles in blood and fibroblasts, which were completely unmethylated in buccal and saliva cells. In contrast, B2 was partially methylated in all tested tissues. Moreover, both brothers had FMR1 mRNA ~5 fold higher values than those of controls, FXS and PM cohorts. In conclusion, the presence of unmethylated FM and/or PM in both brothers may lead to an overexpression of toxic expanded mRNA in some cells, which may contribute to neurodevelopmental problems, including elevated autism features.
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9
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Clinical and Molecular Differences between 4-Year-Old Monozygous Male Twins Mosaic for Normal, Premutation and Fragile X Full Mutation Alleles. Genes (Basel) 2019; 10:genes10040279. [PMID: 30959842 PMCID: PMC6523498 DOI: 10.3390/genes10040279] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 04/01/2019] [Accepted: 04/01/2019] [Indexed: 01/04/2023] Open
Abstract
This study describes monozygotic (MZ) male twins with fragile X syndrome (FXS), mosaic for normal size (NS: <44 CGGs), premutation (PM: 55–199 CGG) and full mutation (FM alleles ≥ 200) alleles, with autism. At 4 years of age chromosomal microarray confirmed monozygosity with both twins showing an XY sex complement. Normal size (30 CGG), PM (99 CGG) and FM (388–1632 CGGs) alleles were detected in Twin 1 (T1) by standard polymerase chain reaction (PCR) and Southern blot testing, while only PM (99 CGG) and FM (672–1025) alleles were identified in Twin 2 (T2). At ~5 years, T2 had greater intellectual impairments with a full scale IQ (FSIQ) of 55 and verbal IQ (VIQ) of 59, compared to FSIQ of 62 and VIQ of 78 for T1. This was consistent with the quantitative FMR1 methylation testing, revealing 10% higher methylation at 80% for T2; suggesting that less active unmethylated alleles were present in T2 as compared to T1. AmplideX methylation PCR also identified partial methylation, including an unmethylated NS allele in T2, undetected by standard testing. In conclusion, this report demonstrates significant differences in intellectual functioning between the MZ twins mosaic for NS, PM and FM alleles with partial FMR1 promoter methylation.
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10
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Kraan CM, Godler DE, Amor DJ. Epigenetics of fragile X syndrome and fragile X-related disorders. Dev Med Child Neurol 2019; 61:121-127. [PMID: 30084485 DOI: 10.1111/dmcn.13985] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/13/2018] [Indexed: 12/31/2022]
Abstract
The fragile X mental retardation 1 gene (FMR1)-related disorder fragile X syndrome (FXS) is the most common heritable form of cognitive impairment and the second most common cause of comorbid autism. FXS usually results when a premutation trinucleotide CGG repeat in the 5' untranslated region of the FMR1 gene (CGG 55-200) expands over generations to a full mutation allele (CGG >200). This expansion is associated with silencing of the FMR1 promoter via an epigenetic mechanism that involves DNA methylation of the CGG repeat and the surrounding regulatory regions. Decrease in FMR1 transcription is associated with loss of the FMR1 protein that is needed for typical brain development. The past decade has seen major advances in our understanding of the genetic and epigenetic processes that underlie FXS. Here we review these advances and their implications for diagnosis and treatment for individuals who have FMR1-related disorders. WHAT THIS PAPER ADDS: Improved analysis of DNA methylation allows better epigenetic evaluation of the fragile X gene. New testing techniques have unmasked interindividual variation among children with fragile X syndrome. New testing methods have also detected additional cases of fragile X.
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Affiliation(s)
- Claudine M Kraan
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
| | - David E Godler
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
| | - David J Amor
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
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Miao Z, Liu X, Li W, He Q, Liu X. Assessment of efficacy of prenatal genetic diagnosis for fragile X syndrome using nested PCR. Exp Ther Med 2018; 15:5107-5112. [PMID: 29844802 DOI: 10.3892/etm.2018.6060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 11/01/2017] [Indexed: 11/06/2022] Open
Abstract
Fragile X syndrome (FXS) is the most common inherited cause of intellectual disability and the leading monogenic cause of autism spectrum disorder. It has previously been demonstrated that prenatal genetic diagnosis is efficient for the diagnosis of FXS. The present study investigated the diagnostic effects of nested polymerase chain reaction (PCR) for fragile X mental retardation 1 (FMR1) and expanded CGG repeats. It was demonstrated that the nested PCR assay rapidly measured the multi-copies of the FMR1 gene in individual samples. The nested PCR assay detected normal CGG repeat lengths and expanded CGG repeat lengths with a low occurrence of false positives. In addition, the nested PCR assay resulted in increased sensitivity and specificity for patients with FXS. Furthermore, the nested PCR assay identified the mutation and generated conclusive cases for FXS, indicating that this assay is beneficial for the diagnosis of FXS patients. In conclusion, these outcomes indicate that nested PCR assay is a reliable and easier method for diagnosis of FXS, which may be used for the diagnosis of FXS patients.
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Affiliation(s)
- Zhengyou Miao
- Jiaxing Maternity and Child Health Care Hospital, Jiaxing, Zhejiang 314000, P.R. China.,Hangzhou Bio-San Biochemical Technologies Co. Ltd., Hangzhou, Zhejiang 310007, P.R. China
| | - Xiaodan Liu
- Jiaxing Maternity and Child Health Care Hospital, Jiaxing, Zhejiang 314000, P.R. China.,Hangzhou Bio-San Biochemical Technologies Co. Ltd., Hangzhou, Zhejiang 310007, P.R. China
| | - Weiwei Li
- Jiaxing Maternity and Child Health Care Hospital, Jiaxing, Zhejiang 314000, P.R. China.,Hangzhou Bio-San Biochemical Technologies Co. Ltd., Hangzhou, Zhejiang 310007, P.R. China
| | - Qunyan He
- Jiaxing Maternity and Child Health Care Hospital, Jiaxing, Zhejiang 314000, P.R. China.,Hangzhou Bio-San Biochemical Technologies Co. Ltd., Hangzhou, Zhejiang 310007, P.R. China
| | - Xia Liu
- Jiaxing Maternity and Child Health Care Hospital, Jiaxing, Zhejiang 314000, P.R. China.,Hangzhou Bio-San Biochemical Technologies Co. Ltd., Hangzhou, Zhejiang 310007, P.R. China
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12
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Jorge P, Garcia E, Gonçalves A, Marques I, Maia N, Rodrigues B, Santos H, Fonseca J, Soares G, Correia C, Reis-Lima M, Cirigliano V, Santos R. Classical fragile-X phenotype in a female infant disclosed by comprehensive genomic studies. BMC MEDICAL GENETICS 2018; 19:74. [PMID: 29747568 PMCID: PMC5946481 DOI: 10.1186/s12881-018-0589-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 04/19/2018] [Indexed: 11/23/2022]
Abstract
Background We describe a female infant with Fragile-X syndrome, with a fully expanded FMR1 allele and preferential inactivation of the homologous X-chromosome carrying a de novo deletion. This unusual and rare case demonstrates the importance of a detailed genomic approach, the absence of which could be misguiding, and calls for reflection on the current clinical and diagnostic workup for developmental disabilities. Case presentation We present a female infant, referred for genetic testing due to psychomotor developmental delay without specific dysmorphic features or relevant family history. FMR1 mutation screening revealed a methylated full mutation and a normal but inactive FMR1 allele, which led to further investigation. Complete skewing of X-chromosome inactivation towards the paternally-inherited normal-sized FMR1 allele was found. No pathogenic variants were identified in the XIST promoter. Microarray analysis revealed a 439 kb deletion at Xq28, in a region known to be associated with extreme skewing of X-chromosome inactivation. Conclusions Overall results enable us to conclude that the developmental delay is the cumulative result of a methylated FMR1 full mutation on the active X-chromosome and the inactivation of the other homologue carrying the de novo 439 kb deletion. Our findings should be taken into consideration in future guidelines for the diagnostic workup on the diagnosis of intellectual disabilities, particularly in female infant cases.
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Affiliation(s)
- Paula Jorge
- Centro de Genética Médica Jacinto de Magalhães (CGMJM), Centro Hospitalar do Porto, CHP, E.P.E., Praça Pedro Nunes, 88 4099-028, Porto, Portugal. .,Unit for Multidisciplinary Research in Biomedicine, Abel Salazar Institute of Biomedical Sciences, University of Porto - UMIB-ICBAS-UP, Porto, Portugal.
| | - Elsa Garcia
- GDPN - Labco diagnostics, Synlab Group, Genética e Diagnóstico Pré-natal, Porto, Portugal
| | - Ana Gonçalves
- Unit for Multidisciplinary Research in Biomedicine, Abel Salazar Institute of Biomedical Sciences, University of Porto - UMIB-ICBAS-UP, Porto, Portugal.,Unidade de genética molecular, Centro de Genética Médica Jacinto de Magalhães, Centro Hospitalar do Porto, CHP, E.P.E, Porto, Portugal
| | - Isabel Marques
- Unit for Multidisciplinary Research in Biomedicine, Abel Salazar Institute of Biomedical Sciences, University of Porto - UMIB-ICBAS-UP, Porto, Portugal.,Unidade de genética molecular, Centro de Genética Médica Jacinto de Magalhães, Centro Hospitalar do Porto, CHP, E.P.E, Porto, Portugal
| | - Nuno Maia
- Unit for Multidisciplinary Research in Biomedicine, Abel Salazar Institute of Biomedical Sciences, University of Porto - UMIB-ICBAS-UP, Porto, Portugal.,Unidade de genética molecular, Centro de Genética Médica Jacinto de Magalhães, Centro Hospitalar do Porto, CHP, E.P.E, Porto, Portugal
| | - Bárbara Rodrigues
- Mestranda Biologia Molecular e Celular Universidade de Aveiro, Unidade de Genética Molecular, Centro de Genética Médica Jacinto de Magalhães, Centro Hospitalar do Porto, CHP, E.P.E, Porto, Portugal
| | - Helena Santos
- Unidade de Neurociências da criança e adolescente, Serviço de Pediatria, Centro Hospitalar de Vila Nova de Gaia/Espinho (C.H.V.N.Gaia/Espinho), E.P.E, Vila Nova de Gaia, Portugal
| | - Jacinta Fonseca
- Unidade de Neurociências da criança e adolescente, Serviço de Pediatria, Centro Hospitalar de Vila Nova de Gaia/Espinho (C.H.V.N.Gaia/Espinho), E.P.E, Vila Nova de Gaia, Portugal
| | - Gabriela Soares
- Unidade de genética médica, Centro de Genética Médica Jacinto de Magalhães, Centro Hospitalar do Porto, CHP, E.P.E, Porto, Portugal
| | - Cecília Correia
- GDPN- Labco diagnostics, Synlab Group, Genética e Diagnóstico Pré-natal, Porto, Portugal
| | - Margarida Reis-Lima
- GDPN- Labco diagnostics, Synlab Group, Genética e Diagnóstico Pré-natal, Porto, Portugal
| | - Vincenzo Cirigliano
- Department of Molecular Genetics, Labco diagnostics, Synlab Group, Esplugues de Llobregat, Barcelona, Spain
| | - Rosário Santos
- Unit for Multidisciplinary Research in Biomedicine, Abel Salazar Institute of Biomedical Sciences, University of Porto - UMIB-ICBAS-UP, Porto, Portugal.,Unidade de genética molecular, Centro de Genética Médica Jacinto de Magalhães, Centro Hospitalar do Porto, CHP, E.P.E, Porto, Portugal.,UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
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13
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Developmental Emergence of Phenotypes in the Auditory Brainstem Nuclei of Fmr1 Knockout Mice. eNeuro 2017; 4:eN-NWR-0264-17. [PMID: 29291238 PMCID: PMC5744645 DOI: 10.1523/eneuro.0264-17.2017] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 11/14/2017] [Accepted: 12/05/2017] [Indexed: 01/21/2023] Open
Abstract
Fragile X syndrome (FXS), the most common monogenic cause of autism, is often associated with hypersensitivity to sound. Several studies have shown abnormalities in the auditory brainstem in FXS; however, the emergence of these auditory phenotypes during development has not been described. Here, we investigated the development of phenotypes in FXS model [Fmr1 knockout (KO)] mice in the ventral cochlear nucleus (VCN), medial nucleus of the trapezoid body (MNTB), and lateral superior olive (LSO). We studied features of the brainstem known to be altered in FXS or Fmr1 KO mice, including cell size and expression of markers for excitatory (VGLUT) and inhibitory (VGAT) synapses. We found that cell size was reduced in the nuclei with different time courses. VCN cell size is normal until after hearing onset, while MNTB and LSO show decreases earlier. VGAT expression was elevated relative to VGLUT in the Fmr1 KO mouse MNTB by P6, before hearing onset. Because glial cells influence development and are altered in FXS, we investigated their emergence in the developing Fmr1 KO brainstem. The number of microglia developed normally in all three nuclei in Fmr1 KO mice, but we found elevated numbers of astrocytes in Fmr1 KO in VCN and LSO at P14. The results indicate that some phenotypes are evident before spontaneous or auditory activity, while others emerge later, and suggest that Fmr1 acts at multiple sites and time points in auditory system development.
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14
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Schenkel LC, Schwartz C, Skinner C, Rodenhiser DI, Ainsworth PJ, Pare G, Sadikovic B. Clinical Validation of Fragile X Syndrome Screening by DNA Methylation Array. J Mol Diagn 2016; 18:834-841. [PMID: 27585064 DOI: 10.1016/j.jmoldx.2016.06.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 06/14/2016] [Accepted: 06/21/2016] [Indexed: 01/11/2023] Open
Abstract
Fragile X syndrome (FXS) is the most common inherited cause of intellectual disability. It is most frequently caused by an abnormal expansion of the CGG trinucleotide repeat (>200 repeats) located in the promoter of the fragile X mental retardation gene (FMR1), resulting in promoter DNA hypermethylation and gene silencing. Current clinical tests for FXS are technically challenging and labor intensive, and may involve use of hazardous chemicals or radioisotopes. We clinically validated the Illumina Infinium HumanMethylation450 DNA methylation array for FXS screening. We assessed genome-wide and FMR1-specific DNA methylation in 32 males previously diagnosed with FXS, including nine with mosaicism, as well as five females with full mutation, and premutation carrier males (n = 11) and females (n = 11), who were compared to 300 normal control DNA samples. Our findings demonstrate 100% sensitivity and specificity for detection of FXS in male patients, as well as the ability to differentiate patients with mosaic methylation defects. Full mutation and premutation carrier females did not show FMR1 methylation changes. We have clinically validated this genome-wide DNA methylation assay as a cost- and labor-effective alternative for sensitive and specific screening for FXS, while ruling out the most common differential diagnoses of FXS, Prader-Willi syndrome, and Sotos syndrome in the same assay.
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Affiliation(s)
- Laila C Schenkel
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
| | - Charles Schwartz
- Center for Molecular Studies, J.C. Self Research Institute of Human Genetics, Greenwood Genetic Center, Greenwood, South Carolina
| | - Cindy Skinner
- Center for Molecular Studies, J.C. Self Research Institute of Human Genetics, Greenwood Genetic Center, Greenwood, South Carolina
| | - David I Rodenhiser
- Department of Biochemistry, Oncology and Paediatrics, Western University, London, Ontario, Canada; London Regional Cancer Program, London Health Sciences Center, London, Ontario, Canada; Children's Health Research Institute, London Health Sciences Center, London, Ontario, Canada
| | - Peter J Ainsworth
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada; Department of Biochemistry, Oncology and Paediatrics, Western University, London, Ontario, Canada; London Regional Cancer Program, London Health Sciences Center, London, Ontario, Canada; Children's Health Research Institute, London Health Sciences Center, London, Ontario, Canada; Molecular Genetics Laboratory, London Health Sciences Center, London, Ontario, Canada
| | - Guillaume Pare
- Departments of Pathology and Molecular Medicine and Clinical Epidemiology and Biostatistics, McMaster University, Hamilton, Ontario, Canada
| | - Bekim Sadikovic
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada; London Regional Cancer Program, London Health Sciences Center, London, Ontario, Canada; Children's Health Research Institute, London Health Sciences Center, London, Ontario, Canada; Molecular Genetics Laboratory, London Health Sciences Center, London, Ontario, Canada.
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