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Liao J, Song S, Gusscott S, Fu Z, VanderKolk I, Busscher BM, Lau KH, Brind’Amour J, Szabó PE. Establishment of paternal methylation imprint at the H19/Igf2 imprinting control region. SCIENCE ADVANCES 2023; 9:eadi2050. [PMID: 37672574 PMCID: PMC10482337 DOI: 10.1126/sciadv.adi2050] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 08/02/2023] [Indexed: 09/08/2023]
Abstract
The insulator model explains the workings of the H19 and Igf2 imprinted domain in the soma, where insulation of the Igf2 promoter from its enhancers occurs by CTCF in the maternally inherited unmethylated chromosome but not the paternally inherited methylated allele. The molecular mechanism that targets paternal methylation imprint establishment to the imprinting control region (ICR) in the male germline is unknown. We tested the function of prospermatogonia-specific broad low-level transcription in this process using mouse genetics. Paternal imprint establishment was abnormal when transcription was stopped at the entry point to the ICR. The germline epimutation persisted into the paternal allele of the soma, resulting in reduced Igf2 in fetal organs and reduced fetal growth, consistent with the insulator model and insulin-like growth factor 2 (IGF2)'s role as fetal growth factor. These results collectively support the role of broad low-level transcription through the H19/Igf2 ICR in the establishment of its paternal methylation imprint in the male germ line, with implications for Silver-Russell syndrome.
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Affiliation(s)
- Ji Liao
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Sangmin Song
- Division of Molecular and Cellular Biology, City of Hope Cancer Center, Duarte, CA 91010, USA
| | - Samuel Gusscott
- Département de Biomédecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, Quebec J2S, Canada
| | - Zhen Fu
- Bioinformatics and Biostatistics Core, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Ivan VanderKolk
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | | | - Kin H. Lau
- Bioinformatics and Biostatistics Core, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Julie Brind’Amour
- Département de Biomédecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, Quebec J2S, Canada
| | - Piroska E. Szabó
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
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Stoltze UK, Hildonen M, Hansen TVO, Foss-Skiftesvik J, Byrjalsen A, Lundsgaard M, Pignata L, Grønskov K, Tumer Z, Schmiegelow K, Brok JS, Wadt KAW. Germline (epi)genetics reveals high predisposition in females: a 5-year, nationwide, prospective Wilms tumour cohort. J Med Genet 2023; 60:842-849. [PMID: 37019617 PMCID: PMC10447365 DOI: 10.1136/jmg-2022-108982] [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: 10/18/2022] [Accepted: 03/10/2023] [Indexed: 04/07/2023]
Abstract
BACKGROUND Studies suggest that Wilms tumours (WT) are caused by underlying genetic (5%-10%) and epigenetic (2%-29%) mechanisms, yet studies covering both aspects are sparse. METHODS We performed prospective whole-genome sequencing of germline DNA in Danish children diagnosed with WT from 2016 to 2021, and linked genotypes to deep phenotypes. RESULTS Of 24 patients (58% female), 3 (13%, all female) harboured pathogenic germline variants in WT risk genes (FBXW7, WT1 and REST). Only one patient had a family history of WT (3 cases), segregating with the REST variant. Epigenetic testing revealed one (4%) additional patient (female) with uniparental disomy of chromosome 11 and Beckwith-Wiedemann syndrome (BWS). We observed a tendency of higher methylation of the BWS-related imprinting centre 1 in patients with WT than in healthy controls. Three patients (13%, all female) with bilateral tumours and/or features of BWS had higher birth weights (4780 g vs 3575 g; p=0.002). We observed more patients with macrosomia (>4250 g, n=5, all female) than expected (OR 9.98 (95% CI 2.56 to 34.66)). Genes involved in early kidney development were enriched in our constrained gene analysis, including both known (WT1, FBXW7) and candidate (CTNND1, FRMD4A) WT predisposition genes. WT predisposing variants, BWS and/or macrosomia (n=8, all female) were more common in female patients than male patients (p=0.01). CONCLUSION We find that most females (57%) and 33% of all patients with WT had either a genetic or another indicator of WT predisposition. This emphasises the need for scrutiny when diagnosing patients with WT, as early detection of underlying predisposition may impact treatment, follow-up and genetic counselling.
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Affiliation(s)
- Ulrik Kristoffer Stoltze
- Department of Clinical Genetics, Rigshospitalet, Copenhagen, Denmark
- Department of Pediatrics, Rigshospitalet, Copenhagen, Denmark
| | - Mathis Hildonen
- Department of Genetics, Kennedy Center-National Research Center on Rare Genetic Diseases, Glostrup, Denmark
| | | | | | - Anna Byrjalsen
- Department of Clinical Genetics, Rigshospitalet, Copenhagen, Denmark
| | - Malene Lundsgaard
- Department of Clinical Genetics, Aalborg University Hospital, Aalborg, North Denmark Region, Denmark
| | - Laura Pignata
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Università Degli Studi Della Campania "Luigi Vanvitelli", Caserta, Italy
| | - Karen Grønskov
- Department of Clinical Genetics, Rigshospitalet, Copenhagen, Denmark
| | - Zeynep Tumer
- Applied Human Molecular Genetics, Kennedy Center, Copenhagen University Hospital, Rigshospitalet, Glostrup, Denmark
| | | | - Jesper Sune Brok
- Department of Pediatrics and Adolescent Medicine, Rigshospitalet, Copenhagen, Denmark
| | - Karin A W Wadt
- Department of Clinical Genetics, University Hospital of Copenhagen, Copenhagen, Denmark
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Kim HY, Shin CH, Lee YA, Shin CH, Kim GH, Ko JM. Deciphering Epigenetic Backgrounds in a Korean Cohort with Beckwith-Wiedemann Syndrome. Ann Lab Med 2022; 42:668-677. [PMID: 35765875 PMCID: PMC9277041 DOI: 10.3343/alm.2022.42.6.668] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 04/07/2022] [Accepted: 06/08/2022] [Indexed: 11/22/2022] Open
Abstract
Background Beckwith–Wiedemann syndrome (BWS) is a congenital overgrowth disorder caused by genetic or epigenetic alterations at two imprinting centers (ICs) in the 11p15.5 region. Delineation of the molecular defects is important for prognosis and predicting familial recurrence. We evaluated epigenetic alterations and potential epigenotype–phenotype correlations in Korean children with BWS. Methods Forty children with BWS with proven genetic or epigenetic defects in the 11p15.5 region were included. The phenotype was scored using the BWS consensus scoring system. Methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA), bisulfite pyrosequencing, a single-nucleotide polymorphism microarray, and CDKN1C sequencing were used for confirmative diagnosis. Results Patients met the criteria for genetic testing, with a mean clinical score of 5.4±2.0. Methylation alterations were consistent between MS-MLPA and bisulfite pyrosequencing in all patients. Twenty-six patients (65.0%) had IC2 loss of methylation (IC2-LoM), 11 (27.5%) had paternal uniparental disomy (patUPD), and one (2.5%) had IC1 gain of methylation. Macroglossia and external ear anomalies were more common in IC2-LoM than in patUPD, and lateralized overgrowth was more common in patUPD than in IC2-LoM (all P<0.05). Methylation levels at IC2 were inversely correlated with birth weight standard deviation score (r=–0.476, P=0.014) and clinical score (r=–0.520, P=0.006) in the IC2-LoM group. Conclusions Comprehensive molecular analysis of the 11p15.5 region revealed epigenotype–phenotype correlations in our BWS cohort. Bisulfite pyrosequencing can help clarify epigenotypes. Methylation levels were correlated with fetal growth and clinical severity in patients with BWS.
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Affiliation(s)
- Hwa Young Kim
- Department of Pediatrics, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Choong Ho Shin
- Department of Pediatrics, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Young Ah Lee
- Department of Pediatrics, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Chang Ho Shin
- Department of Orthopaedic Surgery, Seoul National University College of Medicine, Seoul, Korea
| | - Gu-Hwan Kim
- Medical Genetics Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Jung Min Ko
- Department of Pediatrics, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea.,Rare Disease Center, Seoul National University Children's Hospital, Seoul National University College of Medicine, Seoul, Korea
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Quantitative DNA Methylation Analysis and Epigenotype-Phenotype Correlations in Taiwanese Patients with Beckwith-Wiedemann Syndrome. J Pers Med 2021; 11:jpm11111066. [PMID: 34834418 PMCID: PMC8622080 DOI: 10.3390/jpm11111066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/17/2021] [Accepted: 10/21/2021] [Indexed: 11/17/2022] Open
Abstract
Background: Beckwith-Wiedemann syndrome (BWS; OMIM 130650) is a rare overgrowth syndrome with tumor predisposition resulting from the abnormal expression or function of imprinted genes of the chromosome 11p15.5 imprinting gene cluster. The aim of this study was to identify the epigenotype-phenotype correlations of these patients using quantitative DNA methylation analysis. Methods: One hundred and four subjects with clinically suspected BWS were enrolled in this study. All of the subjects had been referred for diagnostic testing which was conducted using methylation profiling of H19-associated imprinting center (IC) 1 and KCNQ1OT1-associated IC2 in high-resolution melting analysis and methylation quantification with the MassARRAY assay. Correlations between the quantitative DNA methylation status and clinical manifestations of the enrolled subjects were analyzed. Results: Among the 104 subjects, 19 had IC2 hypomethylation, 2 had IC1 hypermethylation, and 10 had paternal uniparental disomy (pUPD). The subjects with IC2 hypomethylation were characterized by significantly more macroglossia but less hemihypertrophy compared to the subjects with pUPD (p < 0.05). For 19 subjects with IC2 hypomethylation, the IC2 methylation level was significantly different (p < 0.05) between the subjects with and without features including macroglossia (IC2 methylation level: 11.1% vs. 30.0%) and prenatal or postnatal overgrowth (8.5% vs. 16.9%). The IC2 methylation level was negatively correlated with birth weight z score (p < 0.01, n = 19) and birth height z score (p < 0.05, n = 13). For 36 subjects with clinically diagnosed BWS, the IC2 methylation level was negatively correlated with the BWS score (r = −0.592, p < 0.01). The IC1 methylation level showed the tendency of positive correlation with the BWS score without statistical significance (r = 0.137, p > 0.05). Conclusions: Lower IC2 methylation and higher IC1 methylation levels were associated with greater disease severity in the subjects with clinically diagnosed BWS. Quantitative DNA methylation analysis using the MassARRAY assay could improve the detection of epigenotype-phenotype correlations, which could further promote better genetic counseling and medical care for these patients.
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Kim SY, Shin CH, Lee YA, Shin CH, Yang SW, Cho TJ, Ko JM. Clinical Application of Sequential Epigenetic Analysis for Diagnosis of Silver-Russell Syndrome. Ann Lab Med 2021; 41:401-408. [PMID: 33536359 PMCID: PMC7884196 DOI: 10.3343/alm.2021.41.4.401] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 07/13/2020] [Accepted: 11/19/2020] [Indexed: 11/19/2022] Open
Abstract
Background Silver-Russell syndrome (SRS) is a pre- or post-natal growth retardation disorder caused by (epi)genetic alterations. We evaluated the molecular basis and clinical value of sequential epigenetic analysis in pediatric patients with SRS. Methods Twenty-eight patients who met≥3 Netchine-Harbison clinical scoring system (NH-CSS) criteria for SRS were enrolled;26 (92.9%) were born small for gestational age, and 25 (89.3%) showed postnatal growth failure. Relative macrocephaly, body asymmetry, and feeding difficulty were noted in 18 (64.3%), 13 (46.4%), and 9 (32.1%) patients, respectively. Methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) on chromosome 11p15 was performed as the first diagnostic step. Subsequently, bisulfite pyrosequencing (BP) for imprinting center 1 and 2 (IC1 and IC2) at chromosome 11p15, MEST on chromosome 7q32.2, and MEG3 on chromosome 14q32.2 was performed. Results. Seventeen (60.7%) patients exhibited methylation defects, including loss of IC1 methylation (N=14; 11 detected by MS-MLPA and three detected by BP) and maternal uniparental disomy 7 (N=3). The diagnostic yield was comparable between patients who met three or four of the NH-CSS criteria (53.8% vs 50.0%). Patients with methylation defects responded better to growth hormone treatment. Conclusions NH-CSS is a powerful tool for SRS screening. However, in practice, genetic analysis should be considered even in patients with a low NH-CSS score. BP analysis detected additional methylation defects that were missed by MS-MLPA and might be considered as a first-line diagnostic tool for SRS.
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Affiliation(s)
- Soo Yeon Kim
- Pediatric Clinical Neuroscience Center, Department of Pediatrics, Seoul National University Children's Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Chang Ho Shin
- Division of Pediatric Orthopedics, Department of Orthopaedic Surgery, Seoul National University Children's Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Young Ah Lee
- Division of Endocrinology, Department Pediatrics, Seoul National University Children's Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Choong Ho Shin
- Division of Endocrinology, Department Pediatrics, Seoul National University Children's Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Sei Won Yang
- Division of Endocrinology, Department Pediatrics, Seoul National University Children's Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Tae-Joon Cho
- Division of Pediatric Orthopedics, Department of Orthopaedic Surgery, Seoul National University Children's Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Jung Min Ko
- Division of Clinical Genetics, Department of Pediatrics, Seoul National University Children's Hospital, Seoul National University College of Medicine, Seoul, Korea
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Zhang M, Sun C, Liu R, Dong C, Cheng R, Zheng Z, Wu B, Luo F, Pei Z, Lu W. Phenotypes and epigenetic errors in patients with Beckwith-Wiedemann syndrome in China. Transl Pediatr 2020; 9:653-661. [PMID: 33209728 PMCID: PMC7658761 DOI: 10.21037/tp-20-243] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Beckwith-Wiedemann syndrome (BWS) is primarily caused by epigenetic errors. This study aimed to analyze the relationship between the epigenetic errors and phenotypes of BWS and to evaluate the efficacy of diagnosing BWS using patients' clinical characteristics. METHODS Patients clinically diagnosed with BWS were subjected to methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) for (epi)genotyping. The patients' clinical characteristics were analyzed and compared using regression models. The diagnostic efficacy of previous criteria and scoring systems was compared using area under the receiving operating curve (ROC). RESULTS The most common clinical features observed in BWS patients were macroglossia (83.2%), abdominal wall defects (71.3%), and ear creases/pits (55.3%). Patients with the loss of methylation at imprinting control 2 (IC2-LOM) and gaining of methylation at imprinting control 1 (IC1-GOM) subtypes had significantly higher frequencies of ear creases/pits and facial nevus flammeus, and visceromegaly, respectively. Paternal uniparental isodisomy (pUPD) was characterized by significantly less macroglossia but more hemihypertrophy. The area under the curve (AUC) was comparably good in both recently developed scoring systems (0.87 for Ibrahim and 0.82 for Brioude.) and in the scoring system developed using the current cohort (0.88). CONCLUSIONS This study, which is the largest cohort study of BWS cases in China published to date, confirmed the diagnostic efficacy of a recently developed symptom-based BWS scoring system in a Chinese population. Significant differences exist between the phenotypes of BWS epigenetic subtypes; however, the pattern is similar between Asian and European populations.
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Affiliation(s)
- Miaoying Zhang
- Department of Endocrinology and Inherited Metabolic Diseases, Children's Hospital of Fudan University, Shanghai, China
| | - Chengjun Sun
- Department of Endocrinology and Inherited Metabolic Diseases, Children's Hospital of Fudan University, Shanghai, China
| | - Renchao Liu
- The Molecular Genetic Diagnosis Center, Pediatrics Research Institute, Children's Hospital of Fudan University, Shanghai, China
| | - Chenbin Dong
- Plastic Surgery Department, Children's Hospital of Fudan University, Shanghai, China
| | - Ruoqian Cheng
- Department of Endocrinology and Inherited Metabolic Diseases, Children's Hospital of Fudan University, Shanghai, China
| | - Zhangqian Zheng
- Department of Endocrinology and Inherited Metabolic Diseases, Children's Hospital of Fudan University, Shanghai, China
| | - Bingbing Wu
- The Molecular Genetic Diagnosis Center, Pediatrics Research Institute, Children's Hospital of Fudan University, Shanghai, China
| | - Feihong Luo
- Department of Endocrinology and Inherited Metabolic Diseases, Children's Hospital of Fudan University, Shanghai, China
| | - Zhou Pei
- Department of Endocrinology and Inherited Metabolic Diseases, Children's Hospital of Fudan University, Shanghai, China
| | - Wei Lu
- Department of Endocrinology and Inherited Metabolic Diseases, Children's Hospital of Fudan University, Shanghai, China
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Baker SW, Duffy KA, Richards-Yutz J, Deardorff MA, Kalish JM, Ganguly A. Improved molecular detection of mosaicism in Beckwith-Wiedemann Syndrome. J Med Genet 2020; 58:178-184. [PMID: 32430359 DOI: 10.1136/jmedgenet-2019-106498] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 03/19/2020] [Accepted: 04/02/2020] [Indexed: 12/17/2022]
Abstract
BACKGROUND Beckwith-Wiedemann Syndrome (BWS) is characterised by overgrowth and tumour predisposition. While multiple epigenetic and genetic mechanisms cause BWS, the majority are caused by methylation defects in imprinting control regions on chromosome 11p15.5. Disease-causing methylation defects are often mosaic within affected individuals. Phenotypic variability among individuals with chromosome 11p15.5 defects and tissue mosaicism led to the definition of the Beckwith-Wiedemann Spectrum (BWSp). Molecular diagnosis of BWSp requires use of multiple sensitive diagnostic techniques to reliably detect low-level aberrations. METHODS Multimodal BWS diagnostic testing was performed on samples from 1057 individuals. Testing included use of a sensitive qRT-PCR-based quantitation method enabling identification of low-level mosaic disease, identification of CNVs within 11p15.5 via array comparative genomic hybridisation or qRT-PCR, and Sanger sequencing of CDKN1C. RESULTS A molecular diagnosis was confirmed for 27.4% of individuals tested, of whom 43.4% had mosaic disease. The presence of a single cardinal feature was associated with a molecular diagnosis of BWSp in 20% of cases. Additionally, significant differences in the prevalence of mosaic disease among BWS molecular subtypes were identified. Finally, the diagnostic yield obtained by testing solid tissue samples from individuals with negative blood testing results shows improved molecular diagnosis. CONCLUSION This study highlights the prevalence of mosaic disease among individuals with BWSp and the increases in diagnostic yield obtained via testing both blood and solid tissue samples from affected individuals. Additionally, the results establish the presence of a molecular diagnosis in individuals with very subtle features of BWSp.
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Affiliation(s)
- Samuel W Baker
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Kelly A Duffy
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Jennifer Richards-Yutz
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Matthew A Deardorff
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Jennifer M Kalish
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA .,Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Arupa Ganguly
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
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Wang R, Xiao Y, Li D, Hu H, Li X, Ge T, Yu R, Wang Y, Zhang T. Clinical and molecular features of children with Beckwith-Wiedemann syndrome in China: a single-center retrospective cohort study. Ital J Pediatr 2020; 46:55. [PMID: 32349794 PMCID: PMC7191772 DOI: 10.1186/s13052-020-0819-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 04/16/2020] [Indexed: 01/20/2023] Open
Abstract
Background Beckwith-Wiedemann syndrome (BWS) is a genetic overgrowth disorder with variable clinical features and cancer predisposition. In this study, we aim to characterize the clinical features and molecular defects of BWS patients in China. Methods Thirty-one patients with clinical suspicion of BWS were retrospectively recruited to the study from Shanghai Children’s Hospital between January 2014 and December 2017. Clinical data, including demographics, clinical features, and molecular testing results were extracted and systematically analyzed. Results Twenty-one patients with a BWS score ≥ 4 (6, IQR 4, 7) were clinically diagnosed with BWS, and 10 children with a BWS score ≥ 2 and < 4 (2, IQR 2, 3) were clinically suspected BWS patients. The most common cardinal feature of clinically diagnosed patients was macroglossia (71.4%) followed by lateralized overgrowth (33.3%) and exomphalos (14.3%), and the major suggestive features were umbilical hernia and/or diastasis recti (65.0%) and ear creases or pits (61.9%). Among 10 clinically suspected BWS patients, macroglossia and lateralized overgrowth were observed in 3 (30%) and 2 (20%) patients, and umbilical hernia and/or diastasis recti occurred in 7 (70.0%) patients. Seven (33.3%) clinically diagnosed patients and 3 (30%) suspected patients were identified with loss of methylation at KCNQ1OT1:TSS differentially methylated region (DMR; IC2 LOM), 5 (23.8%) clinically diagnosed BWS patients were identified with gain of methylation at H19/IGF2:IG-DMR (IC1 GOM), and 1 (4.8%) clinically diagnosed BWS patients was identified with paternal uniparental isodisomy 11 (pUPD11). The phenotype-genotype correlation analysis showed no significant difference among patients with IC2 LOM, IC1 GOM, and pUPD11. Conclusions The current study presents the first cohort study of BWS patients in mainland China. The clinical and molecular features of the patients are similar to those of other reported BWS patients in the Chinese population.
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Affiliation(s)
- Ruixue Wang
- Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, 200062, China
| | - Yongmei Xiao
- Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, 200062, China
| | - Dan Li
- Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, 200062, China
| | - Hui Hu
- Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, 200062, China
| | - Xiaolu Li
- Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, 200062, China
| | - Ting Ge
- Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, 200062, China
| | - Ronghua Yu
- Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, 200062, China
| | - Yizhong Wang
- Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, 200062, China.
| | - Ting Zhang
- Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, 200062, China.
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Duffy KA, Sajorda BJ, Yu AC, Hathaway ER, Grand KL, Deardorff MA, Kalish JM. Beckwith-Wiedemann syndrome in diverse populations. Am J Med Genet A 2019; 179:525-533. [PMID: 30719840 DOI: 10.1002/ajmg.a.61053] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 12/18/2018] [Accepted: 12/21/2018] [Indexed: 11/06/2022]
Abstract
Beckwith-Wiedemann syndrome (BWS) is the most common epigenetic overgrowth disorder and presents with patients affected by a variety of clinical features. Although genotype-phenotype correlations have been demonstrated in BWS and although BWS has been reported to occur equally among racial and ethnic backgrounds, no study to date has evaluated the frequency of findings in different backgrounds. In this study, we evaluated the incidence of clinical features and molecular diagnoses among patients with BWS in Caucasian, Mixed, and non-Caucasian groups. These results suggest that clinical features and molecular diagnoses differ between race/ethnicity groups and raise the possibility of race and ethnicity effects on genotype-phenotype correlations in BWS.
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Affiliation(s)
- Kelly A Duffy
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Brian J Sajorda
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Alice C Yu
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Evan R Hathaway
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Katheryn L Grand
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Matthew A Deardorff
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Pediatrics, Perelman School of Medicine, The University of Pennsylvania, Philadelphia, Pennsylvania
| | - Jennifer M Kalish
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Pediatrics, Perelman School of Medicine, The University of Pennsylvania, Philadelphia, Pennsylvania.,Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
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10
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Lin HY, Chuang CK, Tu RY, Fang YY, Su YN, Chen CP, Chang CY, Liu HC, Chu TH, Niu DM, Lin SP. Epigenotype, genotype, and phenotype analysis of patients in Taiwan with Beckwith-Wiedemann syndrome. Mol Genet Metab 2016; 119:8-13. [PMID: 27436784 DOI: 10.1016/j.ymgme.2016.07.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Revised: 07/10/2016] [Accepted: 07/10/2016] [Indexed: 01/02/2023]
Abstract
BACKGROUND Beckwith-Wiedemann syndrome (BWS) is a congenital overgrowth disorder predisposing to tumorigenesis that results from abnormal expression or function of imprinted genes of chromosome 11p15.5. METHODS Forty-seven patients in Taiwan with clinical suspicion of BWS were referred for diagnostic testing based on methylation profiling of H19-associated imprinting center (IC) 1 and KCNQ1OT1-associated IC2 using high-resolution melting analysis, multiplex ligation-dependent probe amplification, or high-resolution quantitative methylation profiling. RESULTS Twenty-eight patients received a clinical diagnosis of BWS (the presence of 3 major features or 2 major features and at least 1 minor feature), 18 had suspected BWS (the presence of at least 1 major feature), and 1 had isolated Wilms' tumor. Nineteen patients were identified with IC2 hypomethylation (including 1 with isolated Wilms' tumor), 1 with IC1 hypermethylation, 2 with paternal uniparental disomy, and 1 with CDKN1C mutation. Several clinical features were found to be statistically different (P<0.05) between the 2 groups-clinical diagnosis of BWS (n=28) or suspected BWS (n=18)-including macroglossia, pre- or postnatal gigantism, abdominal wall defect, ear creases, facial nevus flammeus, BWS score, and the molecular diagnosis rate. Molecular lesion was detected in 81% of patients with the presence of three major features, compared with 33% and 28% of those with two or one major feature, respectively. The mean BWS score was 5.6 for 19 subjects with "IC2 hypomethylation", compared with 3.8 for 2 subjects with pUPD. The BWS score of one subject with CDKN1C mutation and one with IC1 hypermethylation was 6 and 7, respectively. CONCLUSIONS The BWS score was positively correlated with the molecular diagnosis rate (P<0.01). The BWS database of epigenotype, genotype, and phenotype is expected to promote better genetic counseling and medical care of these patients.
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Affiliation(s)
- Hsiang-Yu Lin
- Department of Medicine, Mackay Medical College, New Taipei City, Taiwan; Department of Pediatrics, Mackay Memorial Hospital, Taipei, Taiwan; Department of Medical Research, Mackay Memorial Hospital, Taipei, Taiwan; Mackay Junior College of Medicine, Nursing and Management, Taipei, Taiwan; Institute of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Chih-Kuang Chuang
- Department of Medical Research, Mackay Memorial Hospital, Taipei, Taiwan; Medical College, Fu-Jen Catholic University, Taipei, Taiwan; Institute of Biotechnology, National Taipei University of Technology, Taipei, Taiwan
| | - Ru-Yi Tu
- Department of Medical Research, Mackay Memorial Hospital, Taipei, Taiwan
| | - Yi-Ya Fang
- Department of Medical Research, Mackay Memorial Hospital, Taipei, Taiwan
| | - Yi-Ning Su
- Department of Obstetrics and Gynecology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Chih-Ping Chen
- Department of Medical Research, Mackay Memorial Hospital, Taipei, Taiwan; Department of Obstetrics and Gynecology, Mackay Memorial Hospital, Taipei, Taiwan
| | - Chia-Ying Chang
- Department of Pediatrics, Mackay Memorial Hospital, Hsinchu, Taiwan
| | - Hsi-Che Liu
- Department of Medicine, Mackay Medical College, New Taipei City, Taiwan; Department of Pediatrics, Mackay Memorial Hospital, Taipei, Taiwan
| | - Tzu-Hung Chu
- Department of Pediatrics, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Dau-Ming Niu
- Institute of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan; Department of Pediatrics, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Shuan-Pei Lin
- Department of Medicine, Mackay Medical College, New Taipei City, Taiwan; Department of Pediatrics, Mackay Memorial Hospital, Taipei, Taiwan; Department of Medical Research, Mackay Memorial Hospital, Taipei, Taiwan; Department of Infant and Child Care, National Taipei University of Nursing and Health Sciences, Taipei, Taiwan.
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11
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Russo S, Calzari L, Mussa A, Mainini E, Cassina M, Di Candia S, Clementi M, Guzzetti S, Tabano S, Miozzo M, Sirchia S, Finelli P, Prontera P, Maitz S, Sorge G, Calcagno A, Maghnie M, Divizia MT, Melis D, Manfredini E, Ferrero GB, Pecile V, Larizza L. A multi-method approach to the molecular diagnosis of overt and borderline 11p15.5 defects underlying Silver-Russell and Beckwith-Wiedemann syndromes. Clin Epigenetics 2016; 8:23. [PMID: 26933465 PMCID: PMC4772365 DOI: 10.1186/s13148-016-0183-8] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 02/08/2016] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Multiple (epi)genetic defects affecting the expression of the imprinted genes within the 11p15.5 chromosomal region underlie Silver-Russell (SRS) and Beckwith-Wiedemann (BWS) syndromes. The molecular diagnosis of these opposite growth disorders requires a multi-approach flowchart to disclose known primary and secondary (epi)genetic alterations; however, up to 20 and 30 % of clinically diagnosed BWS and SRS cases remain without molecular diagnosis. The complex structure of the 11p15 region with variable CpG methylation and low-rate mosaicism may account for missed diagnoses. Here, we demonstrate the relevance of complementary techniques for the assessment of different CpGs and the importance of testing multiple tissues to increase the SRS and BWS detection rate. RESULTS Molecular testing of 147 and 450 clinically diagnosed SRS and BWS cases provided diagnosis in 34 SRS and 185 BWS patients, with 9 SRS and 21 BWS cases remaining undiagnosed and herein referred to as "borderline." A flowchart including complementary techniques and, when applicable, the analysis of buccal swabs, allowed confirmation of the molecular diagnosis in all borderline cases. Comparison of methylation levels by methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) in borderline and control cases defined an interval of H19/IGF2:IG-DMR loss of methylation that was distinct between "easy to diagnose" and "borderline" cases, which were characterized by values ≤mean -3 standard deviations (SDs) compared to controls. Values ≥mean +1 SD at H19/IGF2: IG-DMR were assigned to borderline hypermethylated BWS cases and those ≤mean -2 SD at KCNQ1OT1: TSS-DMR to hypomethylated BWS cases; these were supported by quantitative pyrosequencing or Southern blot analysis. Six BWS cases suspected to carry mosaic paternal uniparental disomy of chromosome 11 were confirmed by SNP array, which detected mosaicism till 10 %. Regarding the clinical presentation, borderline SRS were representative of the syndromic phenotype, with exception of one patient, whereas BWS cases showed low frequency of the most common features except hemihyperplasia. CONCLUSIONS A conclusive molecular diagnosis was reached in borderline methylation cases, increasing the detection rate by 6 % for SRS and 5 % for BWS cases. The introduction of complementary techniques and additional tissue analyses into routine diagnostic work-up should facilitate the identification of cases undiagnosed because of mosaicism, a distinctive feature of epigenetic disorders.
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Affiliation(s)
- Silvia Russo
- Human Molecular Genetics Laboratory, IRCCS Istituto Auxologico Italiano, Milano, Italy
| | - Luciano Calzari
- Human Molecular Genetics Laboratory, IRCCS Istituto Auxologico Italiano, Milano, Italy
| | - Alessandro Mussa
- Department of Pediatric and Public Health Sciences, University of Turin, Torino, Italy
| | - Ester Mainini
- Human Molecular Genetics Laboratory, IRCCS Istituto Auxologico Italiano, Milano, Italy
| | - Matteo Cassina
- Clinical Genetics Unit, Department of Women's and Children's Health, University of Padua, Padova, Italy
| | - Stefania Di Candia
- Department of Pediatrics, San Raffaele Scientific Institute, Milano, Italy
| | - Maurizio Clementi
- Clinical Genetics Unit, Department of Women's and Children's Health, University of Padua, Padova, Italy
| | - Sara Guzzetti
- Human Molecular Genetics Laboratory, IRCCS Istituto Auxologico Italiano, Milano, Italy
| | - Silvia Tabano
- Division of Pathology - Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Department of Pathophysiology and Transplantation, University of Milan, Milano, Italy
| | - Monica Miozzo
- Division of Pathology - Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Department of Pathophysiology and Transplantation, University of Milan, Milano, Italy
| | - Silvia Sirchia
- Department of Health Sciences, University of Milan, Milano, Italy
| | - Palma Finelli
- Human Molecular Genetics Laboratory, IRCCS Istituto Auxologico Italiano, Milano, Italy
| | - Paolo Prontera
- Medical Genetics Unit, Department of Surgical and Biomedical Sciences, University of Perugia, Hospital "S. M. della Misericordia", Perugia, Italy
| | - Silvia Maitz
- Clinical Pediatric Genetics Unit, Pediatrics Clinics, MBBM Foundation, S. Gerardo Hospital, Monza, Italy
| | - Giovanni Sorge
- Department of Pediatrics and Medical Sciences, AO "Policlinico Vittorio Emanuele", Catania, Italy
| | - Annalisa Calcagno
- Pediatric Endocrine Unit, Department of Pediatrics, IRCCS, Children's Hospital Giannina Gaslini, Genova, Italy
| | - Mohamad Maghnie
- Pediatric Endocrine Unit, Department of Pediatrics, IRCCS, Children's Hospital Giannina Gaslini, Genova, Italy
| | - Maria Teresa Divizia
- Department of Medical Genetics, IRCCS, Children's Hospital Giannina Gaslini, Genova, Italy
| | - Daniela Melis
- Clinical Pediatric Genetics, Department of Pediatrics, University "Federico II", Napoli, Italy
| | - Emanuela Manfredini
- Medical Genetics Unit, Department of Laboratory Medicine, Niguarda Ca' Granda Hospital, Milano, Italy
| | | | - Vanna Pecile
- Institute for Maternal and Child Health, Foundation IRCCS Burlo Garofolo Institute, Trieste, Italy
| | - Lidia Larizza
- Human Molecular Genetics Laboratory, IRCCS Istituto Auxologico Italiano, Milano, Italy
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12
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Schenkel LC, Rodenhiser DI, Ainsworth PJ, Paré G, Sadikovic B. DNA methylation analysis in constitutional disorders: Clinical implications of the epigenome. Crit Rev Clin Lab Sci 2016; 53:147-65. [PMID: 26758403 DOI: 10.3109/10408363.2015.1113496] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Genomic, chromosomal, and gene-specific changes in the DNA sequence underpin both phenotypic variations in populations as well as disease associations, and the application of genomic technologies for the identification of constitutional (inherited) or somatic (acquired) alterations in DNA sequence forms a cornerstone of clinical and molecular genetics. In addition to the disruption of primary DNA sequence, the modulation of DNA function by epigenetic phenomena, in particular by DNA methylation, has long been known to play a role in the regulation of gene expression and consequent pathogenesis. However, these epigenetic factors have been identified only in a handful of pediatric conditions, including imprinting disorders. Technological advances in the past decade that have revolutionized clinical genomics are now rapidly being applied to the emerging discipline of clinical epigenomics. Here, we present an overview of epigenetic mechanisms with a focus on DNA modifications, including the molecular mechanisms of DNA methylation and subtypes of DNA modifications, and we describe the classic and emerging genomic technologies that are being applied to this study. This review focuses primarily on constitutional epigenomic conditions associated with a spectrum of developmental and intellectual disabilities. Epigenomic disorders are discussed in the context of global genomic disorders, imprinting disorders, and single gene disorders. We include a section focused on integration of genetic and epigenetic mechanisms together with their effect on clinical phenotypes. Finally, we summarize emerging epigenomic technologies and their impact on diagnostic aspects of constitutional genetic and epigenetic disorders.
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Affiliation(s)
| | - David I Rodenhiser
- b Departments of Biochemistry , Oncology and Paediatrics, Western University , London , ON , Canada .,c London Regional Cancer Program, London Health Sciences Centre , London , ON , Canada .,e Children's Health Research Institute , London , ON , Canada
| | - Peter J Ainsworth
- a Departments of Pathology and Laboratory Medicine .,b Departments of Biochemistry , Oncology and Paediatrics, Western University , London , ON , Canada .,c London Regional Cancer Program, London Health Sciences Centre , London , ON , Canada .,d Molecular Genetics Laboratory, London Health Sciences Centre , London , ON , Canada .,e Children's Health Research Institute , London , ON , Canada
| | - Guillaume Paré
- f Department of Pathology and Molecular Medicine , and.,g Department of Clinical Epidemiology and Biostatistics , McMaster University , Hamilton , ON , Canada
| | - Bekim Sadikovic
- a Departments of Pathology and Laboratory Medicine .,c London Regional Cancer Program, London Health Sciences Centre , London , ON , Canada .,d Molecular Genetics Laboratory, London Health Sciences Centre , London , ON , Canada .,e Children's Health Research Institute , London , ON , Canada
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13
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Primordial dwarfism: overview of clinical and genetic aspects. Mol Genet Genomics 2015; 291:1-15. [PMID: 26323792 DOI: 10.1007/s00438-015-1110-y] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 08/21/2015] [Indexed: 01/16/2023]
Abstract
Primordial dwarfism is a group of genetic disorders which include Seckel Syndrome, Silver-Russell Syndrome, Microcephalic Osteodysplastic Primordial Dwarfism types I/III, II and Meier-Gorlin Syndrome. This genetic disorder group is characterized by intra-uterine growth retardation and post-natal growth abnormalities which occur as a result of disorganized molecular and genomic changes in embryonic stage and, thus, it represents a unique area to study growth and developmental abnormalities. Lot of research has been carried out on different aspects; however, a consolidated review that discusses an overall spectrum of this disorder is not accessible. Recent research in this area points toward important molecular and cellular mechanisms in human body that regulate the complexity of growth process. Studies have emerged that have clearly associated with a number of abnormal chromosomal, genetic and epigenetic alterations that can predispose an embryo to develop PD-associated developmental defects. Finding and associating such fundamental changes to its subtypes will help in re-examination of alleged functions at both cellular and developmental levels and thus reveal the intrinsic mechanism that leads to a balanced growth. Although such findings have unraveled a subtle understanding of growth process, we further require active research in terms of identification of reliable biomarkers for different subtypes as an immediate requirement for clinical utilization. It is hoped that further study will advance the understanding of basic mechanisms regulating growth relevant to human health. Therefore, this review has been written with an aim to present an overview of chromosomal, molecular and epigenetic modifications reported to be associated with different subtypes of this heterogenous disorder. Further, latest findings with respect to clinical and molecular genetics research have been summarized to aid the medical fraternity in their clinical utility, for diagnosing disorders where there are overlapping physical attributes and simultaneously inform about the latest developments in PD biology.
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14
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Abstract
PURPOSE OF REVIEW To review the recent advances in the clinical and molecular characterization of primordial dwarfism, an extreme growth deficiency disorder that has its onset during embryonic development and persists throughout life. RECENT FINDINGS The last decade has witnessed an unprecedented acceleration in the discovery of genes mutated in primordial dwarfism, from one gene to more than a dozen genes. These genetic discoveries have confirmed the notion that primordial dwarfism is caused by defects in basic cellular processes, most notably centriolar biology and DNA damage response. Fortunately, the increasing number of reported clinical primordial dwarfism subtypes has been accompanied by more accurate molecular classification. SUMMARY Qualitative defects of centrioles with resulting abnormal mitosis dynamics, reduced proliferation, and increased apoptosis represent the predominant molecular pathogenic mechanism in primordial dwarfism. Impaired DNA damage response is another important mechanism, which we now know is not mutually exclusive to abnormal centrioles. Molecular characterization of primordial dwarfism is helping families by enabling more reproductive choices and may pave the way for the future development of therapeutics.
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Affiliation(s)
- Fowzan S Alkuraya
- aDepartment of Genetics, King Faisal Specialist Hospital and Research Center bDepartment of Anatomy and Cell Biology, College of Medicine, Alfasial University, Riyadh, Saudi Arabia
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15
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European guidance for the molecular diagnosis of pseudohypoparathyroidism not caused by point genetic variants at GNAS: an EQA study. Eur J Hum Genet 2014; 23:438-44. [PMID: 25005735 DOI: 10.1038/ejhg.2014.127] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Revised: 05/20/2014] [Accepted: 05/30/2014] [Indexed: 12/19/2022] Open
Abstract
Pseudohypoparathyroidism is a rare endocrine disorder that can be caused by genetic (mainly maternally inherited inactivating point mutations, although intragenic and gross deletions have rarely been reported) or epigenetic alterations at GNAS locus. Clinical and molecular characterization of this disease is not that easy because of phenotypic, biochemical and molecular overlapping features between both subtypes of the disease. The European Consortium for the study of PHP (EuroPHP) designed the present work with the intention of generating the standards of diagnostic clinical molecular (epi)genetic testing in PHP patients. With this aim, DNA samples of eight independent PHP patients carrying GNAS genetic and/or epigenetic defects (three patients with GNAS deletions, two with 20q uniparental disomy and three with a methylation defect of unknown origin) without GNAS point mutations were anonymized and sent to the five participant laboratories for their routine genetic analysis (methylation-specific (MS)-MLPA, pyrosequencing and EpiTYPER) and interpretations. All laboratories were able to detect methylation defects and, after the data analysis, the Consortium compared the results to define technical advantages and disadvantages of different techniques. To conclude, we propose as first-level investigation in PHP patients copy number and methylation analysis by MS-MLPA. Then, in patients with partial methylation defect, the result should be confirmed by single CpG bisulphite-based methods (ie pyrosequencing), whereas in case of a complete methylation defect without detectable deletion, microsatellites or SNP genotyping should be performed to exclude uniparental disomy 20.
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