1
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Miranda V, Sabeh P, Seiltgens C, Molidperee S, Janelle C, Lemyre E, Campeau PM. Mild phenotypes in patients with different deletions in the 3' enhancer region of SHOX. Eur J Hum Genet 2024:10.1038/s41431-024-01646-3. [PMID: 38914686 DOI: 10.1038/s41431-024-01646-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 04/06/2024] [Accepted: 06/08/2024] [Indexed: 06/26/2024] Open
Abstract
Haploinsufficiency of the short stature homeobox-containing (SHOX) gene leads to a phenotypic spectrum ranging from Leri-Weill dyschondrosteosis (LWD) to SHOX-deficient short stature. SHOX nullizygosity leads to Langer mesomelic dysplasia. Pathogenic variants can include whole or partial gene deletions or duplications, point mutations within the coding sequence, and deletions of upstream and downstream regulatory elements. Here we report two families: a non-consanguineous family with a deletion downstream of SHOX, in which the homozygous proband presented with isolated Madelung deformity, without LWD or short stature, as well as a 9-year-old girl with Madelung deformities, mesomelia, a dominant family history of Madelung deformity and a heterozygous deletion of the CNE9 region in the 3' downstream region of SHOX. These case reports provide additional information on the effects of 3' downstream deletions of SHOX, by demonstrating the limited phenotype associated with the recurrent 47.5 kb deletion in a homozygous state and the CNE9 deletion in a heterozygous state.
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Affiliation(s)
- Valancy Miranda
- Shriners Hospital for Children, Montreal, QC, Canada
- Sainte Justine University Health Centre, Montreal, QC, Canada
| | - Pascale Sabeh
- Sainte Justine University Health Centre, Montreal, QC, Canada
| | | | | | - Chantal Janelle
- Shriners Hospital for Children, Montreal, QC, Canada
- Sainte Justine University Health Centre, Montreal, QC, Canada
| | | | - Philippe M Campeau
- Shriners Hospital for Children, Montreal, QC, Canada.
- Sainte Justine University Health Centre, Montreal, QC, Canada.
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2
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Bunyan DJ, Hobbs JI, Duncan-Flavell PJ, Howarth RJ, Beal S, Baralle D, Thomas NS. SHOX Whole Gene Duplications Are Overrepresented in SHOX Haploinsufficiency Phenotype Cohorts. Cytogenet Genome Res 2023; 162:587-598. [PMID: 36927524 DOI: 10.1159/000530171] [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: 12/19/2022] [Accepted: 03/13/2023] [Indexed: 03/18/2023] Open
Abstract
Transcription of SHOX is dependent upon the interaction of the gene with a complex array of flanking regulatory elements. Duplications that contain flanking regulatory elements but not the SHOX gene have been reported in individuals with SHOX haploinsufficiency syndromes, suggesting that alterations to the physical organisation or genomic architecture may affect SHOX transcription. Individuals with tall stature and an additional X or Y chromosome have an extra copy of both the SHOX gene and the entire SHOX regulatory region, so all three copies of SHOX can be expressed fully. However, for a duplication of the SHOX gene that does not include all of the flanking regulatory elements, the potential effect on SHOX expression is difficult to predict. We present nine unpublished individuals with a SHOX whole gene duplication in whom the duplication contains variable amounts of the SHOX regulatory region, and we review 29 similar cases from the literature where phenotypic data were clearly stated. While tall stature was present in a proportion of these cases, we present evidence that SHOX whole gene duplications can also result in a phenotype more typically associated with SHOX haploinsufficiency and are significantly overrepresented in Leri-Weill dyschondrosteosis and idiopathic short stature probands compared to population controls. Although similar-looking duplications do not always produce a consistent phenotype, there may be potential genotype-phenotype correlations regarding the duplication size, regulatory element content, and the breakpoint proximity to the SHOX gene. Although ClinGen does not currently consider SHOX whole gene duplications to be clinically significant, the ClinGen triplosensitivity score does not take into account the context of the duplication, and more is now known about SHOX duplications and the role of flanking elements in SHOX regulation. The evidence presented here suggests that these duplications should not be discounted without considering the extent of the duplication and the patient phenotype, and should be included in diagnostic laboratory reports as variants of uncertain significance. Given the uncertain pathogenicity of these duplications, any reports should encourage the exclusion of all other causes of short stature where possible.
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Affiliation(s)
- David J Bunyan
- Wessex Genomics Laboratory Service, Salisbury District Hospital, Salisbury, UK
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - James I Hobbs
- Wessex Genomics Laboratory Service, Salisbury District Hospital, Salisbury, UK
| | | | - Rachel J Howarth
- Wessex Genomics Laboratory Service, Salisbury District Hospital, Salisbury, UK
| | - Sarah Beal
- Wessex Genomics Laboratory Service, Salisbury District Hospital, Salisbury, UK
| | - Diana Baralle
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
- Wessex Clinical Genetics Service, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Nicholas Simon Thomas
- Wessex Genomics Laboratory Service, Salisbury District Hospital, Salisbury, UK
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
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3
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Perchard R, Murray PG, Clayton PE. Approach to the Patient With Short Stature: Genetic Testing. J Clin Endocrinol Metab 2023; 108:1007-1017. [PMID: 36355576 DOI: 10.1210/clinem/dgac637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 10/24/2022] [Indexed: 11/12/2022]
Abstract
The first step in the evaluation of the short child is to decide whether growth parameters in the context of the history are abnormal or a variant of normal. If growth is considered abnormal, system and hormonal tests are likely to be required, followed by more directed testing, such as skeletal survey and/or genetic screening with karyotype or microarray. In a small percentage of short children in whom a diagnosis has not been reached, this will need to be followed by detailed genetic analysis; currently, exome sequencing using targeted panels relevant to the phenotype is the commonly used test. Clinical scenarios are presented that illustrate how such genetic testing can be used to establish a molecular diagnosis, and how that diagnosis contributes to the management of the short child. New genetic causes for short stature are being recognized on a frequent basis, while the clinical spectrum for known genes is being extended. We recommend that an international repository for short stature conditions is established for new findings to aid dissemination of knowledge, but also to help in the definition of the clinical spectrum both for new and established conditions.
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Affiliation(s)
- Reena Perchard
- Department of Developmental Biology and Medicine, University of Manchester, Manchester M13 9PL, UK
- Department of Paediatric Endocrinology, Royal Manchester Children's Hospital, Manchester M13 9WL, UK
- Manchester Academic Health Science Centre, Manchester M13 9PL, UK
| | - Philip George Murray
- Department of Developmental Biology and Medicine, University of Manchester, Manchester M13 9PL, UK
- Department of Paediatric Endocrinology, Royal Manchester Children's Hospital, Manchester M13 9WL, UK
- Manchester Academic Health Science Centre, Manchester M13 9PL, UK
| | - Peter Ellis Clayton
- Department of Developmental Biology and Medicine, University of Manchester, Manchester M13 9PL, UK
- Department of Paediatric Endocrinology, Royal Manchester Children's Hospital, Manchester M13 9WL, UK
- Manchester Academic Health Science Centre, Manchester M13 9PL, UK
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4
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Belyaeva EO, Lebedev IN. Interloci CNV Interactions in Variability of the Phenotypes of Neurodevelopmental Disorders. RUSS J GENET+ 2022. [DOI: 10.1134/s1022795422100027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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5
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Identification of candidate enhancers controlling the transcriptome during the formation of interphalangeal joints. Sci Rep 2022; 12:12835. [PMID: 35896673 PMCID: PMC9329285 DOI: 10.1038/s41598-022-16951-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 07/19/2022] [Indexed: 11/09/2022] Open
Abstract
The formation of the synovial joint begins with the visible emergence of a stripe of densely packed mesenchymal cells located between distal ends of the developing skeletal anlagen called the interzone. Recently the transcriptome of the early synovial joint was reported. Knowledge about enhancers would complement these data and lead to a better understanding of the control of gene transcription at the onset of joint development. Using ChIP-sequencing we have mapped the H3-signatures H3K27ac and H3K4me1 to locate regulatory elements specific for the interzone and adjacent phalange, respectively. This one-stage atlas of candidate enhancers (CEs) was used to map the association between these respective joint tissue specific CEs and biological processes. Subsequently, integrative analysis of transcriptomic data and CEs identified new putative regulatory elements of genes expressed in interzone (e.g., GDF5, BMP2 and DACT2) and phalange (e.g., MATN1, HAPLN1 and SNAI1). We also linked such CEs to genes known as crucial in synovial joint hypermobility and osteoarthritis, as well as phalange malformations. These analyses show that the CE atlas can serve as resource for identifying, and as starting point for experimentally validating, putative disease-causing genomic regulatory regions in patients with synovial joint dysfunctions and/or phalange disorders, and enhancer-controlled synovial joint and phalange formation.
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Genetic Analysis Algorithm for the Study of Patients with Multiple Congenital Anomalies and Isolated Congenital Heart Disease. Genes (Basel) 2022; 13:genes13071172. [PMID: 35885957 PMCID: PMC9317700 DOI: 10.3390/genes13071172] [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: 04/29/2022] [Revised: 06/16/2022] [Accepted: 06/27/2022] [Indexed: 11/20/2022] Open
Abstract
Congenital anomalies (CA) affect 3–5% of newborns, representing the second-leading cause of infant mortality in Argentina. Multiple congenital anomalies (MCA) have a prevalence of 2.26/1000 births in newborns, while congenital heart diseases (CHD) are the most frequent CA with a prevalence of 4.06/1000 births. The aim of this study was to identify the genetic causes in Argentinian patients with MCA and isolated CHD. We recruited 366 patients (172 with MCA and 194 with isolated CHD) born between June 2015 and August 2019 at public hospitals. DNA from peripheral blood was obtained from all patients, while karyotyping was performed in patients with MCA. Samples from patients presenting conotruncal CHD or DiGeorge phenotype (n = 137) were studied using MLPA. Ninety-three samples were studied by array-CGH and 18 by targeted or exome next-generation sequencing (NGS). A total of 240 patients were successfully studied using at least one technique. Cytogenetic abnormalities were observed in 13 patients, while 18 had clinically relevant imbalances detected by array-CGH. After MLPA, 26 patients presented 22q11 deletions or duplications and one presented a TBX1 gene deletion. Following NGS analysis, 12 patients presented pathogenic or likely pathogenic genetic variants, five of them, found in KAT6B, SHH, MYH11, MYH7 and EP300 genes, are novel. Using an algorithm that combines molecular techniques with clinical and genetic assessment, we determined the genetic contribution in 27.5% of the analyzed patients.
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Fukami M, Shindo J, Ogata T, Kageyama I, Kamimaki T. SHOX far-downstream deletion in a patient with nonsyndromic short stature. Am J Med Genet A 2022; 188:2173-2177. [PMID: 35319168 DOI: 10.1002/ajmg.a.62734] [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: 01/05/2022] [Revised: 02/20/2022] [Accepted: 03/04/2022] [Indexed: 11/08/2022]
Abstract
Haploinsufficiency of SHOX represents one of the major genetic causes of nonsyndromic short stature. To date, eight DNA elements around SHOX exons have been proposed as putative enhancer regions. Although six copy-number variations (CNVs) downstream to the known enhancer regions have recently been identified in patients with short stature, the pathogenicity of these CNVs remains uncertain. Here, we identified a paternally derived SHOX far-downstream deletion in a boy. The deletion involved a ~100 kb genomic interval at a position >60 kb away from the known enhancer regions. The boy exhibited moderate short stature with nonspecific skeletal changes. The height of the father was within the normal range but lower than the mid-parental height. The deletion of the boy and the six previously reported CNVs mostly overlapped; however, all CNVs had unique breakpoints. The deletion of our case encompassed a ~30 kb genomic interval that has previously been associated with a 4C-seq peak, as well as several SHOX-regulatory SNPs/indels. These results indicate that the SHOX far-downstream region contains a novel cis-acting enhancer, whose deletion leads to nonsyndromic short stature of various degree. In addition, our data highlight genomic instability of SHOX-flanking regions that underlies diverse nonrecurrent CNVs.
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Affiliation(s)
- Maki Fukami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Junya Shindo
- Department of Pediatrics, Shizuoka City Shimizu Hospital, Shizuoka, Japan
| | - Tsutomu Ogata
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan.,Hamamatsu Medical Center, Hamamatsu, Japan
| | - Ikuko Kageyama
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Tsutomu Kamimaki
- Department of Pediatrics, Shizuoka City Shimizu Hospital, Shizuoka, Japan
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8
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Bunyan DJ, Gevers E, Hobbs JI, Duncan-Flavell PJ, Howarth RJ, Holder-Espinasse M, Klee P, Van-Heurk R, Lemmens L, Carminho-Rodrigues MT, Mohamed Z, Goturu A, Hughes CR, Ajzensztejn M, Thomas NS. Rare dosage abnormalities flanking the SHOX gene. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2021. [DOI: 10.1186/s43042-021-00209-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Transcriptional regulation of the SHOX gene is highly complex. Much of our understanding has come from the study of copy number changes of conserved non-coding sequences both upstream and downstream of the gene. Downstream deletions have been frequently reported in patients with Leri–Weill dyschondrosteosis or idiopathic short stature. In contrast, there are only four cases in the literature of upstream deletions that remove regulatory elements. Although duplications flanking the SHOX gene have also been reported, their pathogenicity is more difficult to establish. To further evaluate the role of flanking copy number variants in SHOX-related disorders, we describe nine additional patients from a large SHOX diagnostic cohort.
Results
The nine cases presented here include five with duplications (two upstream of SHOX and three downstream), one with a downstream triplication and three with upstream deletions. Two of the deletions remove a single conserved non-coding element (CNE-3) while the third does not remove any known regulatory element but is just 4 kb upstream of SHOX, and the deleted region may be important in limb bud development. We also describe six families with novel sequence gains flanking SHOX. Three families had increased dosage of a proposed regulatory element approximately 380 kb downstream of SHOX (X:970,000), including one family with the first ever reported triplication of this region. One family had two in cis downstream duplications co-segregating with LWD, and the two others had a duplication of just the upstream SHOX regulatory element CNE-5.
Conclusions
This study further extends our knowledge of the range of variants that may potentially cause SHOX-related phenotypes and may aid in determining the clinical significance of similar variants.
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9
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Fanelli A, Vannelli S, Babu D, Mellone S, Cucci A, Monzani A, Al Essa W, Secco A, Follenzi A, Bellone S, Prodam F, Giordano M. Copy number variations residing outside the SHOX enhancer region are involved in Short Stature and Léri-Weill dyschondrosteosis. Mol Genet Genomic Med 2021; 10:e1793. [PMID: 34811950 PMCID: PMC8801136 DOI: 10.1002/mgg3.1793] [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: 11/16/2020] [Revised: 07/19/2021] [Accepted: 08/16/2021] [Indexed: 11/25/2022] Open
Abstract
Background SHOX enhancer CNVs, affecting one or more of the seven recognized evolutionary conserved non‐coding elements (CNEs) represent one of the most frequent cause of SHOX‐haploinsufficiency. During the diagnostic workflow deletions/duplications have been identified downstream SHOX not including any of the these CNEs. Methods Fine tiling aCGH and breakpoint PCR were used to characterize the critical interval and to search for novel alterations in a cohort of selected patients. Results Screening of 252 controls provided evidence that duplications in this area represent likely benign variants whereas none of the deletions were detected. These findings suggested that other alterations relevant for SHOX‐haploinsufficiency might be missed by the standard diagnostic methods. To identify such undisclosed elements, the aCGH was used to reanalyze 52 unresolved cases with clinical features strongly suggestive of SHOX‐haploinsufficiency. This analysis followed by the screening of 210 patients detected two partially overlapping small deletions of ~12 and ~8 kb in four unrelated individuals, approximately 15 kb downstream SHOX, that were absent in 720 normal stature individuals. Conclusion Our results strengthen the hypothesis that alterations of yet unidentified cis‐regulatory elements residing outside those investigated through conventional methods, might explain the phenotype in ISS/LWD patients thus enlarging the spectrum of variants contributing to SHOX‐haploinsufficiency.
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Affiliation(s)
- Antonella Fanelli
- Dipartimento di Scienze della Salute, Università del Piemonte Orientale, Novara, Italy
| | - Silvia Vannelli
- Endocrinologia Pediatrica, Dipartimento di Pediatria e Specialità Pediatriche, Ospedale Regina Margherita, Citta della Salute e della Scienza, Torino, Italy
| | - Deepak Babu
- Dipartimento di Scienze della Salute, Università del Piemonte Orientale, Novara, Italy
| | - Simona Mellone
- Laboratorio di Genetica, S.C.D.U Biochimica Clinica, Azienda Ospedaliera Universitaria "Maggiore della Carità", Novara, Italy
| | - Alessia Cucci
- Dipartimento di Scienze della Salute, Università del Piemonte Orientale, Novara, Italy
| | - Alice Monzani
- Divisione di Pediatria, AOU "Maggiore della Carità", Novara, Italy
| | - Wael Al Essa
- Dipartimento di Scienze della Salute, Università del Piemonte Orientale, Novara, Italy
| | - Andrea Secco
- SC Pediatria e DEA Pediatrico, Azienda Ospedaliera SS. Antonio e Biagio e Cesare Arrigo, Alessandria, Italy
| | - Antonia Follenzi
- Dipartimento di Scienze della Salute, Università del Piemonte Orientale, Novara, Italy
| | - Simonetta Bellone
- Dipartimento di Scienze della Salute, Università del Piemonte Orientale, Novara, Italy.,Divisione di Pediatria, AOU "Maggiore della Carità", Novara, Italy
| | - Flavia Prodam
- Dipartimento di Scienze della Salute, Università del Piemonte Orientale, Novara, Italy.,Divisione di Endocrinologia, AOU "Maggiore della Carità", Novara, Italy
| | - Mara Giordano
- Dipartimento di Scienze della Salute, Università del Piemonte Orientale, Novara, Italy.,Laboratorio di Genetica, S.C.D.U Biochimica Clinica, Azienda Ospedaliera Universitaria "Maggiore della Carità", Novara, Italy
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Detection of Del/Dup Inside SHOX/PAR1 Region in Children and Young Adults with Idiopathic Short Stature. Genes (Basel) 2021; 12:genes12101546. [PMID: 34680940 PMCID: PMC8535414 DOI: 10.3390/genes12101546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/23/2021] [Accepted: 09/27/2021] [Indexed: 12/05/2022] Open
Abstract
Short stature is a common growth disorder defined as a body height two standard deviations (SD) or more below the mean for a given age, gender, and population. A large part of the cases remains unexplained and is referred to as having idiopathic short stature (ISS). One of the leading genetic causes of short stature is variants of short stature homeobox-containing gene (SHOX) and is considered to be responsible for 2–15% of ISS. We aimed to analyse the regulatory and coding region of SHOX in Slovenian children and young adults with ISS and to investigate the pathogenicity of detected variants. Our cohort included 75 children and young adults with ISS. Multiplex ligation-dependent probe amplification (MLPA) was performed in all participants for the detection of larger copy number variations (CNVs). Sanger sequencing was undertaken for the detection of point variants, small deletions, and insertions. A total of one deletion and two duplications were discovered using the MLPA technique. Only one of these four variants was identified as disease-causing and occurred in one individual, which represents 1.3% of the cohort. With Sanger sequencing, two variants were discovered, but none of them appeared to have a pathogenic effect on height. According to the results, in the Slovenian population of children and young adults with ISS, SHOX deficiency is less frequent than expected considering existing data from other populations.
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Eid OM, Eid MM, Abdelrahman AH, Abdel kader RMA, Farid M, Mahrous R, Mekkawy MK, Kamel AK, Mazen I, El-Bassyouni HT. Screening of the SHOX/PAR1 region using MLPA and miRNA expression profiling in a group of Egyptian children with non-syndromic short stature. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2020. [DOI: 10.1186/s43042-020-00090-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Short stature is defined as a body height below the third percentile, based on chronological age, or 2 standard deviations (SD) below the national height standard. The prevalence of short stature is around 2% of children worldwide. Several gene deficiencies have been associated with the etiology of short stature. The SHOX is an important candidate gene for short stature, as its haploinsufficiency underlies syndromic and non-syndromic short stature. Partial and complete duplications of SHOX have been reported in patients with short stature. Proper genetic diagnosis of these children allows for appropriate therapeutic approaches to be administered. Since copy number variation (CNV) is a possible mechanism of interhuman variability and pathogenic disease, the multiplex ligation-dependent probe amplification technique (MLPA) can be used as an initial screening technique. Cartilage tissue expresses specific microRNAs (miRNAs), which play an essential role in the regulation of chondrocyte proliferation and differentiation during growth plate development. We aimed to assess the SHOX/PAR1 region using CNV profiling for non-syndromic short stature in Egyptian children with and without growth hormone deficiency using the MLPA technique and expression profiling of miR-1, miR-15a, and miR-140 using quantitative real-time polymerase chain reaction (qRT-PCR) in a group of Egyptian children with non-syndromic short stature.
Results
Of the fifty cases included in this study, different CNVs were detected in ten children (20%), in/outside the SHOX region. Moreover, in children with short stature, the expression level of miRNA-140 was significantly different from that of healthy controls.
Conclusions
This is one of the first studies that have assessed CNVs in the SHOX/PAR1 region in a group of Egyptian children with short stature. MLPA analysis of SHOX/PAR1 identified different CNVs in children with non-syndromic short stature, suggesting that the MLPA should be used as an initial screening technique in short children, as proper genetic diagnosis of these children leads to implementation of the appropriate therapeutic approach. Alterations in the levels of miRNA-140 in children with short stature suggest that changes in the expression levels of this miRNA are associated with the pathogenesis of short stature.
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Xu XJ, Xin SJ, Mao HY, Zhang HJ, Chen LN, Li L, Bai HL, Huang HH, Shu M. SHOX CNE9/10 Knockout in U2OS Osteosarcoma Cells and Its Effects on Cell Growth and Apoptosis. Med Sci Monit 2020; 26:e921233. [PMID: 32032347 PMCID: PMC7020756 DOI: 10.12659/msm.921233] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Background Osteosarcoma is a common malignant tumor of musculoskeletal stromal cells. Osteosarcoma clinical behavior depends mostly on the histologic grade, the site of primary tumor, the response to chemotherapy, and the presence of pulmonary metastases. The aim of this study was to knockout SHOX CNE9/10 in U2OS osteosarcoma cells and to analyze the effects on cell growth and apoptosis. Material/Methods U2OS cells with CNE9 knockout and U2OS cells with CNE10 knockout were established via the CRISPR/Cas9 system. Sanger sequencing was used to detect the success of the knockdown experiment. Western blotting and quantitative polymerase chain reaction were used to detect the expression levels of short stature homeobox-containing gene (SHOX) protein and messenger RNA (mRNA) after knockdown of CNE9 and CNE10. The cell viability and apoptotic rate were detected by the Cell Counting Kit-8 method and by flow cytometry. Results The Sanger sequencing results showed that the knockdown experiment was successful. The levels of SHOX mRNA and protein were significantly reduced after knocking down CNE9 and CNE10. Knockdown of CNE9 and CNE10 significantly increased the growth and inhibited the apoptosis of U2OS osteosarcoma cells. CNE9/CNE10 knockdown U2OS cells were successfully constructed. Conclusions Knockdown of CNE9 and CNE10 promoted U2OS cell growth and inhibited apoptosis by decreasing SHOX expression. This CNE9/CNE10 knockout U2OS cell model could provide a bridge for the research on SHOX and CNEs in osteosarcoma.
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Affiliation(s)
- Xue-Jiao Xu
- Department of Endocrinology, Children's Hospital of Chongqing Medical University, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, China (mainland)
| | - Shi-Jie Xin
- Department of Endocrinology, Children's Hospital of Chongqing Medical University, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, China (mainland)
| | - Hui-Ying Mao
- Department of Endocrinology, Children's Hospital of Chongqing Medical University, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, China (mainland)
| | - Hui-Jiao Zhang
- Department of Endocrinology, Children's Hospital of Chongqing Medical University, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, China (mainland)
| | - Lan-Ni Chen
- Department of Endocrinology, Children's Hospital of Chongqing Medical University, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, China (mainland)
| | - Li Li
- Department of Endocrinology, Children's Hospital of Chongqing Medical University, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, China (mainland)
| | - Hua-Lei Bai
- Department of Endocrinology, Children's Hospital of Chongqing Medical University, Chongqing, China (mainland)
| | - Hai-Hua Huang
- Department of Endocrinology, Children's Hospital of Chongqing Medical University, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, China (mainland)
| | - Min Shu
- Department of Endocrinology, Children's Hospital of Chongqing Medical University, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, China (mainland)
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Nowosad K, Hordyjewska-Kowalczyk E, Tylzanowski P. Mutations in gene regulatory elements linked to human limb malformations. J Med Genet 2019; 57:361-370. [PMID: 31857429 DOI: 10.1136/jmedgenet-2019-106369] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 10/09/2019] [Accepted: 11/03/2019] [Indexed: 01/08/2023]
Abstract
Most of the human genome has a regulatory function in gene expression. The technological progress made in recent years permitted the revision of old and discovery of new mutations outside of the protein-coding regions that do affect human limb morphology. Steadily increasing discovery rate of such mutations suggests that until now the largely neglected part of the genome rises to its well-deserved prominence. In this review, we describe the recent technological advances permitting this unprecedented advance in identifying non-coding mutations. We especially focus on the mutations in cis-regulatory elements such as enhancers, and trans-regulatory elements such as miRNA and long non-coding RNA, linked to hereditary or inborn limb defects. We also discuss the role of chromatin organisation and enhancer-promoter interactions in the aetiology of limb malformations.
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Affiliation(s)
- Karol Nowosad
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, Lublin, Poland.,The Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Ewa Hordyjewska-Kowalczyk
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, Lublin, Poland.,The Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Przemko Tylzanowski
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, Lublin, Poland .,Department of Development and Regeneration, Skeletal Biology and Engineering Research Center, University of Leuven, Leuven, Belgium
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14
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Whitmore KM, Buzon MR. Two cases of skeletal dysplasia from New Kingdom (c. 1400-1050 BCE) Tombos, Sudan. INTERNATIONAL JOURNAL OF PALEOPATHOLOGY 2019; 26:135-144. [PMID: 31377579 DOI: 10.1016/j.ijpp.2019.07.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 07/16/2019] [Accepted: 07/21/2019] [Indexed: 06/10/2023]
Abstract
OBJECTIVE This project investigates two cases of skeletal dysplasia from archaeological excavations of the New Kingdom Period (c. 1400-1050 BCE) portion of the Tombos cemetery in Sudan. MATERIALS Fair to well-preserved skeletal remains of two individuals, one adult and one juvenile, are examined here. METHODS All available skeletal elements were analyzed macroscopically. A differential diagnosis was conducted for each individual. RESULTS The adult individual, U36.Sh2.B10, displays bilateral mesomelic dysplasia and Madelung's deformity. The juvenile individual, U36.Sh2.B5, also displays bilateral mesomelic dysplasia and characteristics associated with Madelung's deformity. CONCLUSIONS A differential diagnosis of Léri-Weill dyschondrosteosis (LWD) is suggested for the adult female individual (U36.Sh2.B10). The second case (U36.Sh2.B5) is an approximately three to five-year-old individual and is difficult to diagnose given the young age; however, LWD remains the most likely diagnosis. SIGNIFICANCE There are few cases of LWD in the paleopathological literature, and fewer still of juveniles. The cases described are useful examples in expanding research demonstrating the variability in the expression of skeletal dysplasias in juveniles and adults. LIMITATIONS Taphonomic alterations and fragmentation of the crania and portions of the postcrania limited the observation of the full suite of characteristics associated with skeletal dysplasias. U36.Sh2.B5 is difficult to diagnose given the individual's young age and the possibility that this individual had not yet developed the more observable characteristics associated with these conditions. SUGGESTIONS FOR FURTHER RESEARCH Researchers are encouraged to continue examining the range of expression of skeletal dysplasias in juveniles and adults.
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Affiliation(s)
- Katie M Whitmore
- Department of Anthropology, Purdue University, 700 W. State Street, Suite 219, West Lafayette, IN 47907, USA.
| | - Michele R Buzon
- Department of Anthropology, Purdue University, 700 W. State Street, Suite 219, West Lafayette, IN 47907, USA.
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15
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Leri-Weill Dyschondrosteosis Syndrome: Analysis via 3DCT Scan. MEDICINES 2019; 6:medicines6020060. [PMID: 31146331 PMCID: PMC6631815 DOI: 10.3390/medicines6020060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 05/23/2019] [Accepted: 05/27/2019] [Indexed: 11/17/2022]
Abstract
Background: Leri-Weill dyschondrosteosis (LWD) is a pseudoautosomal form of skeletal dysplasia, characterized by abnormal craniofacial phenotype, short stature, and mesomelia of the upper and lower limbs. Methods: We describe two female patients with LWD. Their prime clinical complaints were severe bouts of migraine and antalgic gait. Results: Interestingly, via a 3D reconstruction CT scan we encountered several major anomalies. Notable features of craniosynostosis through premature fusion of the squamosal sutures and partial closure of the coronal sutures were the reason behind the development of abnormal craniofacial contour. A 3D reconstruction CT scan showed apparent bulging of the clavarium through the partially synostosed coronal and totally synostosed squamosal sutures. Additional deformities include deficient number of ribs (10 ribs on both sides), defective ossification of the ischium and dysplasia of the iliac-ischial junction, and coxa valga have been noted. Conclusions: The constellation of observed deformities can be considered as a novel features associated with LWD.
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16
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Roumelioti FM, Louizou E, Karras S, Neroutsou R, Velissariou V, Gagos S. Unbalanced X;9 translocation in an infertile male with de novo duplication Xp22.31p22.33. J Assist Reprod Genet 2019; 36:769-775. [PMID: 30675680 DOI: 10.1007/s10815-019-01405-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 01/09/2019] [Indexed: 12/12/2022] Open
Abstract
PURPOSE Male carriers of an X-autosome translocation are generally infertile, regardless of the position of the breakpoint on the X chromosome while the pathogenicity of Xp22.3 subtelomeric duplications is under debate. To shed light into this controversy, we present a rare case, of an azoospermic male with no other significant clinical findings, in whom classical cytogenetics revealed additional unbalanced chromosomal material, at the telomere of the long arm of one homolog of chromosome 9. METHODS In peripheral blood specimens of the index case and his parents, we performed GBanding, Inverted-DAPI Banding, AgNOR staining, Telomere specific Fluorescence in Situ Hybridization (FISH), Molecular karyotyping by Multi-color FISH, whole genome SNP microarrays, sub-telomeric MLPA, and transcription analysis of the expression of KAL1 gene by RT-PCR. RESULTS Multi-color FISH revealed an unbalanced translocation involving the short arm of chromosome X. SNP microarray analysis combined to classical cytogenetics and MLPA demonstrated a de novo 8.796 Mb duplication of Xp22.31-p22.33. Compared to three control specimens, the patient presented significantly elevated expression levels of KAL1 mRNA in peripheral blood, suggesting transcriptional functionality of the duplicated segment. CONCLUSIONS The duplicated segment contains the pseudo-autosomal region PAR1 and more than 30 genes including SHOX, ARSE, STS, KAL1, and FAM9A and is not listed as polymorphic. Our data advocate that duplications of the Xp22.3 region may not be associated with a clinical consequence.
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Affiliation(s)
- Fani-Marlen Roumelioti
- Laboratory of Genetics, Center of Experimental Medicine and Translational Research, Biomedical Research Foundation of the Academy of Athens, (BRFAA), Athens, Greece
| | - Eirini Louizou
- Department of Cytogenetics and Molecular Genetics, Bioiatriki, Group of Health Sciences, Athens, Greece
| | - Spyridon Karras
- Division of Endocrinology and Metabolism, First Department of Internal Medicine, Medical School, Aristotle University of Thessaloniki, AHEPA Hospital, Thessaloniki, Greece
| | - Rozalia Neroutsou
- Department of Cytogenetics and Molecular Genetics, Bioiatriki, Group of Health Sciences, Athens, Greece
| | - Voula Velissariou
- Department of Cytogenetics and Molecular Genetics, Bioiatriki, Group of Health Sciences, Athens, Greece
| | - Sarantis Gagos
- Laboratory of Genetics, Center of Experimental Medicine and Translational Research, Biomedical Research Foundation of the Academy of Athens, (BRFAA), Athens, Greece.
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17
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Skuplik I, Benito-Sanz S, Rosin JM, Bobick BE, Heath KE, Cobb J. Identification of a limb enhancer that is removed by pathogenic deletions downstream of the SHOX gene. Sci Rep 2018; 8:14292. [PMID: 30250174 PMCID: PMC6155277 DOI: 10.1038/s41598-018-32565-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 09/11/2018] [Indexed: 01/06/2023] Open
Abstract
Haploinsufficiency of the human SHOX gene causes Léri-Weill dyschondrosteosis (LWD), characterized by shortening of the middle segments of the limbs and Madelung deformity of the wrist. As many as 35% of LWD cases are caused by deletions of non-coding sequences downstream of SHOX that presumably remove an enhancer or enhancers necessary for SHOX expression in developing limbs. We searched for these active sequences using a transgenic mouse assay and identified a 563 basepair (bp) enhancer with specific activity in the limb regions where SHOX functions. This enhancer has previously escaped notice because of its poor evolutionary conservation, although it does contain 100 bp that are conserved in non-rodent mammals. A primary cell luciferase assay confirmed the enhancer activity of the conserved core sequence and demonstrated that putative HOX binding sites are required for its activity. This enhancer is removed in most non-coding deletions that cause LWD. However, we did not identify any likely pathogenic variants of the enhancer in a screen of 124 LWD individuals for whom no causative mutation had been found, suggesting that only larger deletions in the region commonly cause LWD. We hypothesize that loss of this enhancer contributes to the pathogenicity of deletions downstream of SHOX.
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Affiliation(s)
- Isabella Skuplik
- Department of Biological Sciences, University of Calgary, 2500 University Drive N.W., Calgary, Alberta, T2N 1N4, Canada
| | - Sara Benito-Sanz
- Instituto de Genética Médica y Molecular (INGEMM), IdiPAZ and Skeletal dysplasia multidisciplinary unit (UMDE), Hospital Universitario La Paz, Universidad Autónoma de Madrid, P° Castellana 261, 28046, Madrid, Spain.,CIBERER, ISCIII, Madrid, Spain
| | - Jessica M Rosin
- Department of Biological Sciences, University of Calgary, 2500 University Drive N.W., Calgary, Alberta, T2N 1N4, Canada
| | - Brent E Bobick
- Department of Biological Sciences, University of Calgary, 2500 University Drive N.W., Calgary, Alberta, T2N 1N4, Canada
| | - Karen E Heath
- Instituto de Genética Médica y Molecular (INGEMM), IdiPAZ and Skeletal dysplasia multidisciplinary unit (UMDE), Hospital Universitario La Paz, Universidad Autónoma de Madrid, P° Castellana 261, 28046, Madrid, Spain. .,CIBERER, ISCIII, Madrid, Spain.
| | - John Cobb
- Department of Biological Sciences, University of Calgary, 2500 University Drive N.W., Calgary, Alberta, T2N 1N4, Canada.
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18
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Ramachandrappa S, Kulkarni A, Gandhi H, Ellis C, Hutt R, Roberts L, Hamid R, Papageorghiou A, Mansour S. SHOX haploinsufficiency presenting with isolated short long bones in the second and third trimester. Eur J Hum Genet 2018; 26:350-358. [PMID: 29330548 DOI: 10.1038/s41431-017-0080-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Revised: 10/16/2017] [Accepted: 10/24/2017] [Indexed: 12/20/2022] Open
Abstract
Haploinsufficiency of the transcription factor short stature homeobox (SHOX) manifests as a spectrum of clinical phenotypes, ranging from disproportionate short stature and Madelung deformity to isolated short stature. Here, we describe five infants with molecularly confirmed diagnoses of SHOX haploinsufficiency who presented in utero with short long bones during routine antenatal scanning from as early as 19 weeks gestation. Other foetal growth parameters were normal. The molecular basis of SHOX haploinsufficiency was distinct in each case. In four cases, SHOX haploinsufficiency was inherited from a previously undiagnosed parent. In our de novo case, SHOX haploinsufficiency reflected the formation of a derivative sex chromosome during paternal meiosis. Final adult height in the SHOX-deficient parents ranged from -1.9 to -1.2 SDS. All affected parents had disproportionately short limbs and two affected mothers had bilateral Madelung deformity. To our knowledge, SHOX haploinsufficiency has not previously been reported to present in utero. Our experience illustrates that SHOX deficiency should form part of the differential diagnosis of foetal short long bones and suggests a low threshold for genetic testing. This should be particularly targeted at, but not limited to, families with a history of features suggestive of SHOX deficiency. Data on the postnatal growth of our index cases is presented which demonstrates that antenatal presentation of SHOX haploinsufficiency is not indicative of severe postnatal growth restriction. Early identification of SHOX deficiency will enable accurate genetic counselling reflecting a good postnatal outcome and facilitate optimal initiation of growth hormone therapy.
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Affiliation(s)
- Shwetha Ramachandrappa
- South West Thames Regional Genetics Unit, St George's University of London, Cranmer Terrace, London, SW17 0RE, UK
| | - Abhijit Kulkarni
- South West Thames Regional Genetics Unit, St George's University of London, Cranmer Terrace, London, SW17 0RE, UK
| | - Hina Gandhi
- Department of Obstetrics and Gynaecology, Surrey and Sussex Healthcare NHS Trust, Canada Avenue, Redhill, RH1 5RH, UK
| | - Cheryl Ellis
- Department of Obstetrics and Gynaecology, Epsom and St Helier University Hospitals NHS Trust, Wrythe Lane, Carshalton, SM5 1AA, UK
| | - Renata Hutt
- Department of Obstetrics and Gynaecology, Royal Surrey County Hospital NHS Foundation Trust, Egerton Road, Guildford, GU2 7XX, UK
| | - Lesley Roberts
- Department of Obstetrics and Gynaecology, Royal Surrey County Hospital NHS Foundation Trust, Egerton Road, Guildford, GU2 7XX, UK
| | - Rosol Hamid
- Department of Obstetrics and Gynaecology, Croydon Health Services NHS Trust, London Road, Croydon, CR7 7YE, UK
| | - Aris Papageorghiou
- Fetal Medicine Unit, St George's University of London, Cranmer Terrace, London, SW17 0RE, UK
| | - Sahar Mansour
- South West Thames Regional Genetics Unit, St George's University of London, Cranmer Terrace, London, SW17 0RE, UK.
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19
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Harel T, Lupski JR. Genomic disorders 20 years on-mechanisms for clinical manifestations. Clin Genet 2017; 93:439-449. [PMID: 28950406 DOI: 10.1111/cge.13146] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 09/01/2017] [Accepted: 09/21/2017] [Indexed: 12/18/2022]
Abstract
Genomic disorders result from copy-number variants (CNVs) or submicroscopic rearrangements of the genome rather than from single nucleotide variants (SNVs). Diverse technologies, including array comparative genomic hybridization (aCGH) and single nucleotide polymorphism (SNP) microarrays, and more recently, whole genome sequencing and whole-exome sequencing, have enabled robust genome-wide unbiased detection of CNVs in affected individuals and in reportedly healthy controls. Sequencing of breakpoint junctions has allowed for elucidation of upstream mechanisms leading to genomic instability and resultant structural variation, whereas studies of the association between CNVs and specific diseases or susceptibility to morbid traits have enhanced our understanding of the downstream effects. In this review, we discuss the hallmarks of genomic disorders as they were defined during the first decade of the field, including genomic instability and the mechanism for rearrangement defined as nonallelic homologous recombination (NAHR); recurrent vs nonrecurrent rearrangements; and gene dosage sensitivity. Moreover, we highlight the exciting advances of the second decade of this field, including a deeper understanding of genomic instability and the mechanisms underlying complex rearrangements, mechanisms for constitutional and somatic chromosomal rearrangements, structural intra-species polymorphisms and susceptibility to NAHR, the role of CNVs in the context of genome-wide copy number and single nucleotide variation, and the contribution of noncoding CNVs to human disease.
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Affiliation(s)
- T Harel
- Department of Genetic and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - J R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Department of Pediatrics, Baylor College of Medicine, Houston, Texas.,Texas Children's Hospital, Houston, Texas.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
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20
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Hirschfeldova K, Solc R. Comparison of SHOX and associated elements duplications distribution between patients (Lėri-Weill dyschondrosteosis/idiopathic short stature) and population sample. Gene 2017. [PMID: 28629824 DOI: 10.1016/j.gene.2017.06.034] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The effect of heterozygous duplications of SHOX and associated elements on Lėri-Weill dyschondrosteosis (LWD) and idiopathic short stature (ISS) development is less distinct when compared to reciprocal deletions. The aim of our study was to compare frequency and distribution of duplications within SHOX and associated elements between population sample and LWD (ISS) patients. A preliminary analysis conducted on Czech population sample of 250 individuals compared to our previously reported sample of 352 ISS/LWD Czech patients indicated that rather than the difference in frequency of duplications it is the difference in their distribution. Particularly, there was an increased frequency of duplications residing to the CNE-9 enhancer in our LWD/ISS sample. To see whether the obtained data are consistent across published studies we made a literature survey to get published cases with SHOX or associated elements duplication and formed the merged LWD, the merged ISS, and the merged population samples. Relative frequency of particular region duplication in each of those merged samples were calculated. There was a significant difference in the relative frequency of CNE-9 enhancer duplications (11 vs. 3) and complete SHOX (exon1-6b) duplications (4 vs. 24) (p-value 0.0139 and p-value 0.000014, respectively) between the merged LWD sample and the merged population sample. We thus propose that partial SHOX duplications and small duplications encompassing CNE-9 enhancer could be highly penetrant alleles associated with ISS and LWD development.
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Affiliation(s)
- Katerina Hirschfeldova
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Albertov 4, 128 00 Prague, Czech Republic.
| | - Roman Solc
- Department of Anthropology and Human Genetics, Faculty of Science, Charles University in Prague, Vinicna 7, 128 43 Prague, Czech Republic.
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21
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Auger J, Baptiste A, Benabbad I, Thierry G, Costa JM, Amouyal M, Kottler ML, Leheup B, Touraine R, Schmitt S, Lebrun M, Cormier Daire V, Bonnefont JP, de Roux N, Elie C, Rosilio M. Genotype-Phenotype Relationship in Patients and Relatives with SHOX Region Anomalies in the French Population. Horm Res Paediatr 2017; 86:309-318. [PMID: 27676402 DOI: 10.1159/000448282] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 07/08/2016] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND The aim of our study was to describe a large population with anomalies involving the SHOX region, responsible for idiopathic short stature and Léri-Weill dyschondrosteosis (LWD), and to identify a possible genotype/phenotype correlation. METHODS We performed a retrospective multicenter study on French subjects with a SHOX region anomaly diagnosed by multiplex ligation-dependent probe amplification or Sanger sequencing. Phenotypes were collected in each of the 7 genetic laboratories practicing this technique for SHOX analysis. RESULTS Among 205 index cases and 100 related cases, 91.3% had LWD. For index cases, median age at evaluation was 11.7 (9.0; 15.9) years and mean height standard deviation score was -2.3 ± 1.1. A deletion of either SHOX or PAR1 or both was found in 74% of patients. Duplications and point mutations/indels affected 8 and 18% of the population, respectively. Genotype-phenotype correlation showed that deletions were more frequently associated with Madelung deformity and mesomelic shortening in girls, as well as with presence of radiologic anomalies, than duplications. CONCLUSIONS Our results highlight genotype-phenotype relationships in the French population with a SHOX defect and provide new information showing that clinical expression is milder in cases of duplication compared to deletions.
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Affiliation(s)
- Julie Auger
- Department of Pediatrics and Medical Genetics, Brabois Hospital, Vandoeuvre-lès-Nancy, France
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22
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Marchini A, Ogata T, Rappold GA. A Track Record on SHOX: From Basic Research to Complex Models and Therapy. Endocr Rev 2016; 37:417-48. [PMID: 27355317 PMCID: PMC4971310 DOI: 10.1210/er.2016-1036] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
SHOX deficiency is the most frequent genetic growth disorder associated with isolated and syndromic forms of short stature. Caused by mutations in the homeobox gene SHOX, its varied clinical manifestations include isolated short stature, Léri-Weill dyschondrosteosis, and Langer mesomelic dysplasia. In addition, SHOX deficiency contributes to the skeletal features in Turner syndrome. Causative SHOX mutations have allowed downstream pathology to be linked to defined molecular lesions. Expression levels of SHOX are tightly regulated, and almost half of the pathogenic mutations have affected enhancers. Clinical severity of SHOX deficiency varies between genders and ranges from normal stature to profound mesomelic skeletal dysplasia. Treatment options for children with SHOX deficiency are available. Two decades of research support the concept of SHOX as a transcription factor that integrates diverse aspects of bone development, growth plate biology, and apoptosis. Due to its absence in mouse, the animal models of choice have become chicken and zebrafish. These models, therefore, together with micromass cultures and primary cell lines, have been used to address SHOX function. Pathway and network analyses have identified interactors, target genes, and regulators. Here, we summarize recent data and give insight into the critical molecular and cellular functions of SHOX in the etiopathogenesis of short stature and limb development.
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Affiliation(s)
- Antonio Marchini
- Tumour Virology Division F010 (A.M.), German Cancer Research Center, 69120 Heidelberg, Germany; Department of Oncology (A.M.), Luxembourg Institute of Health 84, rue Val Fleuri L-1526, Luxembourg; Department of Pediatrics (T.O.), Hamamatsu University School of Medicine, Higashi-ku, Hamamatsu 431-3192, Japan; and Department of Human Molecular Genetics (G.A.R.), Institute of Human Genetics, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Tsutomu Ogata
- Tumour Virology Division F010 (A.M.), German Cancer Research Center, 69120 Heidelberg, Germany; Department of Oncology (A.M.), Luxembourg Institute of Health 84, rue Val Fleuri L-1526, Luxembourg; Department of Pediatrics (T.O.), Hamamatsu University School of Medicine, Higashi-ku, Hamamatsu 431-3192, Japan; and Department of Human Molecular Genetics (G.A.R.), Institute of Human Genetics, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Gudrun A Rappold
- Tumour Virology Division F010 (A.M.), German Cancer Research Center, 69120 Heidelberg, Germany; Department of Oncology (A.M.), Luxembourg Institute of Health 84, rue Val Fleuri L-1526, Luxembourg; Department of Pediatrics (T.O.), Hamamatsu University School of Medicine, Higashi-ku, Hamamatsu 431-3192, Japan; and Department of Human Molecular Genetics (G.A.R.), Institute of Human Genetics, Heidelberg University Hospital, 69120 Heidelberg, Germany
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23
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Tropeano M, Howley D, Gazzellone MJ, Wilson CE, Ahn JW, Stavropoulos DJ, Murphy CM, Eis PS, Hatchwell E, Dobson RJB, Robertson D, Holder M, Irving M, Josifova D, Nehammer A, Ryten M, Spain D, Pitts M, Bramham J, Asherson P, Curran S, Vassos E, Breen G, Flinter F, Ogilvie CM, Collier DA, Scherer SW, McAlonan GM, Murphy DG. Microduplications at the pseudoautosomal SHOX locus in autism spectrum disorders and related neurodevelopmental conditions. J Med Genet 2016; 53:536-47. [PMID: 27073233 DOI: 10.1136/jmedgenet-2015-103621] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 03/10/2016] [Indexed: 11/04/2022]
Abstract
BACKGROUND The pseudoautosomal short stature homeobox-containing (SHOX) gene encodes a homeodomain transcription factor involved in cell-cycle and growth regulation. SHOX/SHOX enhancers deletions cause short stature and skeletal abnormalities in a female-dominant fashion; duplications appear to be rare. Neurodevelopmental disorders (NDDs), such as autism spectrum disorders (ASDs), are complex disorders with high heritability and skewed sex ratio; several rare (<1% frequency) CNVs have been implicated in risk. METHODS We analysed data from a discovery series of 90 adult ASD cases, who underwent clinical genetic testing by array-comparative genomic hybridisation (CGH). Twenty-seven individuals harboured CNV abnormalities, including two unrelated females with microduplications affecting SHOX. To determine the prevalence of SHOX duplications and delineate their associated phenotypic spectrum, we subsequently examined array-CGH data from a follow-up sample of 26 574 patients, including 18 857 with NDD (3541 with ASD). RESULTS We found a significant enrichment of SHOX microduplications in the NDD cases (p=0.00036; OR 2.21) and, particularly, in those with ASD (p=9.18×10(-7); OR 3.63) compared with 12 594 population-based controls. SHOX duplications affecting the upstream or downstream enhancers were enriched only in females with NDD (p=0.0043; OR 2.69/p=0.00020; OR 7.20), but not in males (p=0.404; OR 1.38/p=0.096; OR 2.21). CONCLUSIONS Microduplications at the SHOX locus are a low penetrance risk factor for ASD/NDD, with increased risk in both sexes. However, a concomitant duplication of SHOX enhancers may be required to trigger a NDD in females. Since specific SHOX isoforms are exclusively expressed in the developing foetal brain, this may reflect the pathogenic effect of altered SHOX protein dosage on neurodevelopment.
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Affiliation(s)
- Maria Tropeano
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Arcavacata di Rende, CS, Italy
| | - Deirdre Howley
- Department of Forensic and Neurodevelopmental Sciences, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK Adult Autism Spectrum and ADHD Services, Behavioural and Developmental Psychiatry, Clinical Academic Group, King's Health Partners, London, UK Department of Clinical Genetics, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Matthew J Gazzellone
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - C Ellie Wilson
- Department of Forensic and Neurodevelopmental Sciences, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK Adult Autism Spectrum and ADHD Services, Behavioural and Developmental Psychiatry, Clinical Academic Group, King's Health Partners, London, UK Individual Differences, Language and Cognition Lab, Department of Developmental and Educational Psychology, University of Seville, Seville, Spain
| | - Joo Wook Ahn
- Department of Cytogenetics, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Dimitri J Stavropoulos
- Genome Diagnostics, Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Clodagh M Murphy
- Department of Forensic and Neurodevelopmental Sciences, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK Adult Autism Spectrum and ADHD Services, Behavioural and Developmental Psychiatry, Clinical Academic Group, King's Health Partners, London, UK
| | - Peggy S Eis
- Population Diagnostics, Inc., Melville, New York, USA
| | - Eli Hatchwell
- Population Diagnostics, Inc., Melville, New York, USA
| | - Richard J B Dobson
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Dene Robertson
- Adult Autism Spectrum and ADHD Services, Behavioural and Developmental Psychiatry, Clinical Academic Group, King's Health Partners, London, UK
| | - Muriel Holder
- Department of Clinical Genetics, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Melita Irving
- Department of Clinical Genetics, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Dragana Josifova
- Department of Clinical Genetics, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Annelise Nehammer
- Department of Clinical Genetics, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Mina Ryten
- Department of Clinical Genetics, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Debbie Spain
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK Department of Forensic and Neurodevelopmental Sciences, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Mark Pitts
- Adult Autism Spectrum and ADHD Services, Behavioural and Developmental Psychiatry, Clinical Academic Group, King's Health Partners, London, UK
| | - Jessica Bramham
- UCD School of Psychology, University College Dublin, Dublin, Ireland
| | - Philip Asherson
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Sarah Curran
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Evangelos Vassos
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Gerome Breen
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK National Institute for Health Research (NIHR) Biomedical Research Centre for Mental Health at South London and Maudsley NHS Foundation Trust and Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Frances Flinter
- Department of Clinical Genetics, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | | | - David A Collier
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK Discovery Neuroscience Research, Eli Lilly and Company Ltd, Erl Wood Manor, Windlesham, Surrey, UK
| | - Stephen W Scherer
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada Department of Molecular Genetics, McLaughlin Centre, University of Toronto, Toronto, Ontario, Canada
| | - Grainne M McAlonan
- Department of Forensic and Neurodevelopmental Sciences, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK Adult Autism Spectrum and ADHD Services, Behavioural and Developmental Psychiatry, Clinical Academic Group, King's Health Partners, London, UK National Institute for Health Research (NIHR) Biomedical Research Centre for Mental Health at South London and Maudsley NHS Foundation Trust and Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Declan G Murphy
- Department of Forensic and Neurodevelopmental Sciences, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK Adult Autism Spectrum and ADHD Services, Behavioural and Developmental Psychiatry, Clinical Academic Group, King's Health Partners, London, UK National Institute for Health Research (NIHR) Biomedical Research Centre for Mental Health at South London and Maudsley NHS Foundation Trust and Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
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24
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Shima H, Tanaka T, Kamimaki T, Dateki S, Muroya K, Horikawa R, Kanno J, Adachi M, Naiki Y, Tanaka H, Mabe H, Yagasaki H, Kure S, Matsubara Y, Tajima T, Kashimada K, Ishii T, Asakura Y, Fujiwara I, Soneda S, Nagasaki K, Hamajima T, Kanzaki S, Jinno T, Ogata T, Fukami M. Systematic molecular analyses of SHOX in Japanese patients with idiopathic short stature and Leri-Weill dyschondrosteosis. J Hum Genet 2016; 61:585-91. [PMID: 26984564 DOI: 10.1038/jhg.2016.18] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 02/09/2016] [Accepted: 02/15/2016] [Indexed: 02/07/2023]
Abstract
The etiology of idiopathic short stature (ISS) and Leri-Weill dyschondrosteosis (LWD) in European patients is known to include SHOX mutations and copy-number variations (CNVs) involving SHOX and/or the highly evolutionarily conserved non-coding DNA elements (CNEs) flanking the gene. However, the frequency and types of SHOX abnormalities in non-European patients and the clinical importance of mutations in the CNEs remains to be clarified. Here, we performed systematic molecular analyses of SHOX for 328 Japanese patients with ISS or LWD. SHOX abnormalities accounted for 3.8% of ISS and 50% of LWD cases. CNVs around SHOX were identified in 16 cases, although the ~47 kb deletion frequently reported in European patients was absent in our cases. Probably damaging mutations and benign/silent substitutions were detected in four cases, respectively. Although CNE-linked substitutions were detected in 15 cases, most of them affected poorly conserved nucleotides and were shared by unaffected individuals. These results suggest that the frequency and mutation spectrum of SHOX abnormalities are comparable between Asian and European patients, with the exception of a European-specific downstream deletion. Furthermore, this study highlights the clinical importance and genetic heterogeneity of the SHOX-flanking CNVs, and indicates a limited clinical significance of point mutations in the CNEs.
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Affiliation(s)
- Hirohito Shima
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan.,Department of Advanced Pediatric Medicine, Tohoku University School of Medicine, Tokyo, Japan
| | | | - Tsutomu Kamimaki
- Department of Pediatrics, Shizuoka City Shimizu Hospital, Shizuoka, Japan
| | - Sumito Dateki
- Department of Pediatrics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Koji Muroya
- Department of Endocrinology and Metabolism, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Reiko Horikawa
- Division of Endocrinology and Metabolism, National Center for Child Health and Development, Tokyo, Japan
| | - Junko Kanno
- Department of Pediatrics, Tohoku University School of Medicine, Sendai, Japan
| | - Masanori Adachi
- Department of Endocrinology and Metabolism, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Yasuhiro Naiki
- Division of Endocrinology and Metabolism, National Center for Child Health and Development, Tokyo, Japan
| | - Hiroyuki Tanaka
- Department of Pediatrics, Okayama Saiseikai General Hospital, Okayama, Japan
| | - Hiroyo Mabe
- Department of Child Development, Kumamoto University Hospital, Kumamoto, Japan
| | - Hideaki Yagasaki
- Department of Pediatrics, Faculty of Medicine, University of Yamanashi, Chuo, Japan
| | - Shigeo Kure
- Department of Pediatrics, Tohoku University School of Medicine, Sendai, Japan
| | - Yoichi Matsubara
- Department of Advanced Pediatric Medicine, Tohoku University School of Medicine, Tokyo, Japan.,National Research Institute for Child Health and Development, Tokyo, Japan
| | - Toshihiro Tajima
- Department of Pediatrics, Hokkaido University School of Medicine, Sapporo, Japan
| | - Kenichi Kashimada
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Tomohiro Ishii
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
| | - Yumi Asakura
- Department of Endocrinology and Metabolism, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Ikuma Fujiwara
- Environment and Genome Research Center, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Shun Soneda
- Department of Pediatrics, St Marianna University School of Medicine, Kawasaki, Japan
| | - Keisuke Nagasaki
- Division of Pediatrics, Department of Homeostatic Regulation and Development, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Takashi Hamajima
- Division of Endocrinology and Metabolism, Aichi Children's Health and Medical Center, Obu, Japan
| | - Susumu Kanzaki
- Division of Pediatrics and Perinatology, Tottori University Faculty of Medicine, Yonago, Japan
| | - Tomoko Jinno
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Tsutomu Ogata
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Maki Fukami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
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