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Capkova P, Capkova Z, Rohon P, Adamová K, Zapletalova J. Short stature and SHOX (Short stature homeobox) variants-efficacy of screening using various strategies. PeerJ 2020; 8:e10236. [PMID: 33240610 PMCID: PMC7678493 DOI: 10.7717/peerj.10236] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 10/04/2020] [Indexed: 11/20/2022] Open
Abstract
Background SHOX mutations have previously been described as causes of Léri-Weill dyschondrosteosis (LWD), Langer mesomelic dysplasia (LMD), and idiopathic short stature. The loss of X chromosome—Turner syndrome or mosaic 45,X/46,XX or 46,XY—also leads to the heterozygous loss of SHOX in patients with short stature only or with features similar to LWD. The aim of this study was to assess the efficacy of the targeted screening for SHOX variants, which involved different methods in the laboratory analysis of short stature. We determined the significance and positive predictive value of short stature for the detection of SHOX variants. Methods Targeted screening for variants in SHOX involving MLPA, sequencing, karyotyping and FISH was performed in the short stature cohort (N = 174) and control cohort (N = 91). The significance of short stature and particular characteristics for the detection of SHOX variants was determined by Fisher’s exact test, and the probability of SHOX mutation occurrence was calculated using a forward/stepwise logistic regression model. Results In total, 27 and 15 variants influencing SHOX were detected in the short stature and control cohorts, respectively (p > 0.01). Sex chromosome aberrations and pathogenic CNV resulting in diagnosis were detected in eight (4.6%) and five (2.9%) patients of the short stature group and three (3.3%) and one (1.1%) individuals of the control group. VUS variants were discovered in 14 (8.0%) and 11 (12.1%) individuals of the short stature and control groups, respectively. MLPA demonstrated the detection rate of 13.22%, and it can be used as a frontline method for detection of aberrations involving SHOX. However, only mosaicism of monosomy X with a higher frequency of monosomic cells could be reliably discovered by this method. Karyotyping and FISH can compensate for this limitation; their detection rates in short stature group were 3.55% and 13.46% (N = 52), respectively. FISH proved to be more effective than karyotyping in the study as it could reveal cryptic mosaics in some cases where karyotyping initially failed to detect such a clone. We suggest adding FISH on different tissue than peripheral blood to verify sex-chromosome constitution, especially in cases with karyotypes: 45,X; mosaic 45,X/46,XX or 46,XY; 46,Xidic(Y) detected from blood; in children, where mosaic 45,X was detected prenatally but was not confirmed from peripheral blood. The correlation of short stature with the occurrence of SHOX mutations was insignificant and short stature demonstrates a low positive predictive value-15.5% as unique indicator for SHOX mutations. The typical skeletal signs of LWD, including Madelung deformity and disproportionate growth, positively correlate with the findings of pathogenic SHOX variants (p < 0.01) by Fisher’s exact test but not with the findings of VUS variants in SHOX which are more prevalent in the individuals with idiopathic short stature or in the individuals with normal height.
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Affiliation(s)
- Pavlina Capkova
- Department of Medical Genetics, University Hospital Olomouc, Olomouc, Czech Republic.,Department of Medical Genetics, Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc, Czech Republic
| | - Zuzana Capkova
- Department of Medical Genetics, University Hospital Olomouc, Olomouc, Czech Republic.,Department of Medical Genetics, Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc, Czech Republic
| | - Peter Rohon
- Department of Medical Genetics, Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc, Czech Republic
| | - Katerina Adamová
- Department of Medical Genetics, University Hospital Olomouc, Olomouc, Czech Republic
| | - Jirina Zapletalova
- Department of Pediatrics, Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc, Czech Republic
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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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Rare copy number variants in the genome of Chinese female children and adolescents with Turner syndrome. Biosci Rep 2019; 39:BSR20181305. [PMID: 30530863 PMCID: PMC6328875 DOI: 10.1042/bsr20181305] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 12/04/2018] [Accepted: 12/06/2018] [Indexed: 01/15/2023] Open
Abstract
Turner syndrome (TS) is a congenital disease caused by complete or partial loss of one X chromosome. Low bone mineral status is a major phenotypic characteristic of TS that can not be fully explained by X chromosome loss, suggesting other autosomal-linked mutations may also exist. Therefore, the present study aimed to detect potential genetic mutations in TS through examination of copy number variation (CNV). Seventeen patients with TS and 15 healthy volunteer girls were recruited. Array-based comparative genomic hybridization (a-CGH) was performed on whole blood genomic DNA (gDMA) from the 17 TS patients and 15 healthy volunteer girls to identify potential CNVs. The abnormal CNV of one identified gene (CARD11) was verified by quantitative PCR. All cases diagnosed had TS based on genotype examination and physical characteristics, including short stature and premature ovarian failure. Three rare CNVs, located individually at 7p22.3, 7p22.2, and Xp22.33, where six genes (TTYH3, AMZ1, GNA12, BC038729, CARD11, and SHOX (stature homeobox)) are located, were found in TS patients. Quantitative PCR confirmed the CNV of CARD11 in the genome of TS patients. Our results indicate that CARD11 gene is one of the mutated genes involved in TS disease. However, this CNV is rare and its contribution to TS phenotype requires further study.
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Savarese E, Di Felice B, Miconi F, Cabiati G, Celi F, Crescenzi F, Principi N, Esposito S. An Association of PTPN11 and SHOX Mutations in a Male Presenting With Syndromic Growth Failure. Front Endocrinol (Lausanne) 2018; 9:557. [PMID: 30294303 PMCID: PMC6158368 DOI: 10.3389/fendo.2018.00557] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Accepted: 08/31/2018] [Indexed: 01/13/2023] Open
Abstract
In children with genetic syndromes, short stature is frequently a characteristic feature that, when associated with other specific manifestations, significantly aids in clinical diagnosis. In this report, an atypical case of Noonan syndrome (NS) in a 5.5-year-old child with mesomelic short stature is described. Genetic tests revealed two different mutations in this child. As expected in an NS case, a mutation in PTPN11 gene related to the RAS/MAPK signal transduction pathway was identified. Moreover, a mutation in the SHOX gene that was able to cause disproportionate short stature was detected. A clinical picture of NS with mesomelic short stature makes the diagnosis even more difficult as haploinsufficiency and complete loss of function of SHOX gene are associated with the typical differentiation and proliferation of chondrocytes, leading to mesomelic appearance. This case exemplifies the difficulties that can be encountered in achieving proper diagnoses for children with syndromic diseases and highlights the role of genetic tests in identifying final diagnoses in these patients.
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Affiliation(s)
- Emanuela Savarese
- Pediatric Section, Università degli Studi di Perugia, Perugia, Italy
- Paediatric Clinic, Azienda Ospedaliera di Terni, Terni, Italy
| | - Benedetta Di Felice
- Pediatric Section, Università degli Studi di Perugia, Perugia, Italy
- Paediatric Clinic, Azienda Ospedaliera di Terni, Terni, Italy
| | - Francesco Miconi
- Pediatric Section, Università degli Studi di Perugia, Perugia, Italy
- Paediatric Clinic, Azienda Ospedaliera di Terni, Terni, Italy
| | | | - Federica Celi
- Paediatric Clinic, Azienda Ospedaliera di Terni, Terni, Italy
| | | | | | - Susanna Esposito
- Department of Surgical and Biomedical Sciences, Paediatric Clinic, Università degli Studi di Perugia, Perugia, Italy
- *Correspondence: Susanna Esposito
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Cancemi D, Iannuzzi A, Perucatti A, Montano L, Capozzi O, Spampanato C, Ventruto ML, Urciuoli M, Iannuzzi L, Ventruto V. Duplication of Yq- and proximal Yp-arms with deletion of almost all PAR1 (including SHOX) in a young man with non-obstructive azoospermia, short stature and skeletal defects. J Appl Genet 2017; 58:481-486. [PMID: 29019057 DOI: 10.1007/s13353-017-0412-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2017] [Revised: 09/21/2017] [Accepted: 09/25/2017] [Indexed: 11/25/2022]
Abstract
Duplications of Yq arm (and AZF) seems to be tolerated by fertile males, while mutations, deletions, duplications or haploinsufficiency of SHOX can originate a wide range of phenotypes, including short stature and skeletal abnormalities. We report a case of non-obstructive azoospermia in a young man with short stature, skeletal anomalies, normal intelligence and hormonal parameters. This male showed a very singular Y-chromosome aberration, consisting of a duplication of Yq and proximal regions of Yp, with a deletion of almost all PAR1 in Yptel, including SHOX. CBA- and RBA-banding and FISH-mapping with telomeric, centromeric, AZF and SHOX probes were used. These results were confirmed by array CGH, which revealed the following karyotype constitution: arr [hg19] Xp22.33 or Yp11.32p11.31 (310,932-2,646,815 or 260,932-2,596,815) ×1, Yp11.2q12 (8,641,183-59,335,913) ×2. We conclude that the haploinsufficience of SHOX may be the cause of short stature and skeletal defects in the patient, while the non-obstructive azoospermia could be related to the lack of X-Y pairing during meiosis originated by the anomalous configuration of this chromosome abnormality and large deletion which occurred in Yp-PAR1.
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Affiliation(s)
- Dino Cancemi
- Ricerche e Diagnosi Genetiche Cancemi, Corso Vittorio Emanuele, Naples, Italy
| | - Alessandra Iannuzzi
- Institute of Animal Production Systems in Mediterranean Environments (ISPAAM), Laboratory of Cytogenetics, National Research Council (CNR) of Italy, Via Argine, 1085, 80147, Naples, Italy
| | - Angela Perucatti
- Institute of Animal Production Systems in Mediterranean Environments (ISPAAM), Laboratory of Cytogenetics, National Research Council (CNR) of Italy, Via Argine, 1085, 80147, Naples, Italy
| | - Luigi Montano
- Andrology Unit, Local Health Authority (ASL) Salerno, EcoFoodFertility Project Coordination Unit, Oliveto Citra, SA, Italy
| | - Oronzo Capozzi
- Department of Biology, Study University of Bari "Aldo Moro", Bari, Italy
| | | | | | | | - Leopoldo Iannuzzi
- Institute of Animal Production Systems in Mediterranean Environments (ISPAAM), Laboratory of Cytogenetics, National Research Council (CNR) of Italy, Via Argine, 1085, 80147, Naples, Italy.
| | - Valerio Ventruto
- Institute of Genetics and Biophysics Buzzati-Traverso (IGB), National Research Council (CNR) of Italy, Naples, Italy
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David A, Kun IZ, Nyírő G, Szántó Z, Patócs A. Heterozygous Deletion in Exons 4-5 of SHOX Gene in a Patient Diagnosed as Idiopathic Short Stature. ACTA MEDICA MARISIENSIS 2017. [DOI: 10.1515/amma-2017-0028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Abstract
Introduction: Isolated Short Stature Homeobox (SHOX) gene haploinsufficiency can be found in 2-15% of individuals diagnosed with idiopathic short stature determining different skeletal phenotypes.
Case presentation: We present the history of an 11-year-old female patient diagnosed with idiopathic short stature. Clinically, she was moderately disproportionate, with cubitus valgus and palatum ogivale. Her breast development was in Tanner stage 1 at the time of diagnosis. The endocrine diagnostic tests did not reveal any abnormalities except a slightly elevated thyroid stimulating hormone. We have also assessed the bone radiological findings. Multiplex Ligation-dependent Probe Amplification technique used for the identification of SHOX gene haploinsufficiency showed a heterozygous deletion spanning exons 4-5 of SHOX gene.
Conclusions: This case is determined by deletions in exons 4-5 of SHOX gene and indicates the necessity of screening for SHOX deletions in patients diagnosed with idiopathic short stature, especially in children having increased sitting height-to-height ratio or decreased extremities-to-trunk ratio.
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Affiliation(s)
- Anna David
- University of Medicine and Pharmacy , Tirgu Mures , Romania
| | | | - Gábor Nyírő
- Department of Laboratory Medicine , Semmelweis University , Budapest , Hungary
| | | | - Attila Patócs
- Department of Laboratory Medicine , Semmelweis University , Budapest , Hungary
- MTA-SE Molecular Medicine Research Group , Budapest , Hungary
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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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