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Tabib A, Talebi T, Ghasemi S, Pourirahim M, Naderi N, Maleki M, Kalayinia S. A novel stop-gain pathogenic variant in FLT4 and a nonsynonymous pathogenic variant in PTPN11 associated with congenital heart defects. Eur J Med Res 2022; 27:286. [PMID: 36496429 PMCID: PMC9737984 DOI: 10.1186/s40001-022-00920-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 11/30/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Congenital heart defects (CHDs) are the most common congenital malformations, including structural malformations in the heart and great vessels. CHD complications such as low birth weight, prematurity, pregnancy termination, mortality, and morbidity depend on the type of defect. METHODS In the present research, genetic analyses via whole-exome sequencing (WES) was performed on 3 unrelated pedigrees with CHDs. The candidate variants were confirmed, segregated by PCR-based Sanger sequencing, and evaluated by bioinformatics analysis. RESULTS A novel stop-gain c.C244T:p.R82X variant in the FLT4 gene, as well as a nonsynonymous c.C1403T:p.T468M variant in the PTPN11 gene, was reported by WES. FLT4 encodes a receptor tyrosine kinase involved in lymphatic development and is known as vascular endothelial growth factor 3. CONCLUSIONS We are the first to report a novel c.C244T variant in the FLT4 gene associated with CHDs. Using WES, we also identified a nonsynonymous variant affecting protein-tyrosine phosphatase, the non-receptor type 11 (PTPN11) gene. The clinical implementation of WES can determine gene variants in diseases with high genetic and phenotypic heterogeneity like CHDs.
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Affiliation(s)
- Avisa Tabib
- grid.411746.10000 0004 4911 7066Heart Valve Diseases Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Taravat Talebi
- grid.411746.10000 0004 4911 7066Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Serwa Ghasemi
- grid.411463.50000 0001 0706 2472Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Maryam Pourirahim
- grid.411746.10000 0004 4911 7066Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Niloofar Naderi
- grid.411746.10000 0004 4911 7066Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Majid Maleki
- grid.411746.10000 0004 4911 7066Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Samira Kalayinia
- grid.411746.10000 0004 4911 7066Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
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Ahn J, Oh J, Suh J, Song K, Kwon A, Chae HW, Oh JS, Lee HI, Lee MS, Kim HS. Next-generation sequencing-based mutational analysis of idiopathic short stature and isolated growth hormone deficiency in Korean pediatric patients. Mol Cell Endocrinol 2022; 544:111489. [PMID: 34653508 DOI: 10.1016/j.mce.2021.111489] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 10/04/2021] [Accepted: 10/08/2021] [Indexed: 11/27/2022]
Abstract
We investigated the distribution of short stature-associated mutations in Korean pediatric patients with idiopathic short stature (ISS) and isolated growth hormone deficiency (IGHD) via targeted next-generation sequencing (TNGS). We employed a 96-gene TNGS panel for short stature in a total of 144 patients (5-19 years-old) previously diagnosed with ISS or IGHD and identified heterozygous pathogenic or likely pathogenic genetic variants in 14 (10%) patients. Of the mutated genes, PROKR2 (n = 3) is associated with gonadotropin-releasing hormone deficiency or hypopituitarism, while FGFR1 (n = 1) and NPR2 (n = 3) encode growth plate paracrine factors. FBN1 (n = 1), COL9A1 (n = 1), MATN3 (n = 1), and ACAN (n = 3) regulate the cartilage extracellular matrix, while PTPN11 (n = 1) controls intracellular pathways. Six patients had IGHD, and eight patients had ISS. The current findings highlight the utility of TNGS for determining the genetic etiology in these patients.
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Affiliation(s)
- Jungmin Ahn
- Department of Pediatrics, Severance Children's Hospital, College of Medicine Yonsei University, Seoul, South Korea; Department of Pediatrics, Jeju National University, College of Medicine and Graduate, School of Medicine, Jeju, South Korea
| | - Jiyoung Oh
- Division of Clinical Genetics, Department of Pediatrics, Severance Children's Hospital, College of Medicine Yonsei University, Seoul, South Korea
| | - Junghwan Suh
- Department of Pediatrics, Severance Children's Hospital, College of Medicine Yonsei University, Seoul, South Korea
| | - Kyungchul Song
- Department of Pediatrics, Severance Children's Hospital, College of Medicine Yonsei University, Seoul, South Korea
| | - Ahreum Kwon
- Department of Pediatrics, Severance Children's Hospital, College of Medicine Yonsei University, Seoul, South Korea
| | - Hyun Wook Chae
- Department of Pediatrics, Severance Children's Hospital, College of Medicine Yonsei University, Seoul, South Korea
| | - Jun Suk Oh
- Department of Pediatrics, Severance Children's Hospital, College of Medicine Yonsei University, Seoul, South Korea
| | - Hae In Lee
- Department of Pediatrics, Severance Children's Hospital, College of Medicine Yonsei University, Seoul, South Korea
| | - Myeong Seob Lee
- Department of Pediatrics, Severance Children's Hospital, College of Medicine Yonsei University, Seoul, South Korea
| | - Ho-Seong Kim
- Department of Pediatrics, Severance Children's Hospital, College of Medicine Yonsei University, Seoul, South Korea.
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Bell JM, Considine EM, McCallen LM, Chatfield KC. The Prevalence of Noonan Spectrum Disorders in Pediatric Patients with Pulmonary Valve Stenosis. J Pediatr 2021; 234:134-141.e5. [PMID: 33794220 DOI: 10.1016/j.jpeds.2021.03.050] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 03/23/2021] [Accepted: 03/25/2021] [Indexed: 12/18/2022]
Abstract
OBJECTIVE To investigate the prevalence of Noonan spectrum disorders in a pediatric population with pulmonary valve stenosis (PVS) and explore other characteristics of Noonan spectrum disorders associated with PVS. STUDY DESIGN A retrospective medical record review was completed for patients with a diagnosis of PVS seen at the Children's Hospital Colorado Cardiology clinic between 2009 and 2019. Syndromic diagnoses, genotypes, cardiac characteristics, and extracardiac characteristics associated with Noonan spectrum disorders were recorded; statistical analysis was conducted using R. RESULTS Syndromic diagnoses were made in 16% of 686 pediatric patients with PVS, with Noonan spectrum disorders accounting for 9% of the total diagnoses. Individuals with Noonan spectrum disorders were significantly more likely to have an atrial septal defect and/or hypertrophic cardiomyopathy than the non-Noonan spectrum disorder individuals. Supravalvar pulmonary stenosis was also correlated significantly with Noonan spectrum disorders. Extracardiac clinical features presenting with PVS that were significantly associated with Noonan spectrum disorders included feeding issues, failure to thrive, developmental delay, short stature, and ocular findings. The strongest predictors of a Noonan spectrum disorder diagnosis were cryptorchidism (70%), pectus abnormalities (66%), and ocular findings (48%). The presence of a second characteristic further increased this likelihood, with the highest probability occurring with cryptorchidism combined with ocular findings (92%). CONCLUSIONS The 9% prevalence of Noonan spectrum disorder in patients with PVS should alert clinicians to consider Noonan spectrum disorders when encountering a pediatric patient with PVS. The presence of PVS with 1 or more Noonan spectrum disorder-related features should prompt a genetic evaluation and genetic testing for RAS pathway defects. Noonan spectrum disorders should also be included in the differential when a patient presents with supravalvar pulmonary stenosis.
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Affiliation(s)
- Janet M Bell
- Department of Pediatrics, University of Colorado School of Medicine, Children's Hospital Colorado, Aurora, CO
| | - Ellen M Considine
- Department of Applied Mathematics, University of Colorado College of Engineering & Applied Science, Laboratory for Interdisciplinary Statistical Analysis (LISA), Boulder, CO
| | - Leslie M McCallen
- Department of Pediatrics, University of Colorado School of Medicine, Children's Hospital Colorado, Aurora, CO
| | - Kathryn C Chatfield
- Department of Pediatrics, University of Colorado School of Medicine, Children's Hospital Colorado, Aurora, CO.
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Abstract
We report a case of a Chinese neonate who was diagnosed with Noonan syndrome and had persistent, self-limited thrombocytopenia. The neonate was admitted to the Neonatology Department 20 minutes after birth because of respiratory distress. From birth until 2 months of age, platelet values fluctuated between approximately 6 and 30 × 109/L. There was no intracranial hemorrhage. However, the child had a transient hypocalcemic seizure and fever. We excluded thrombocytopenia caused by perinatal asphyxia, immune thrombocytopenia, fetomaternal alloimmune thrombocytopenia, juvenile myelomonocytic leukemia, and chromosome 13, 18, and 21 trisomy syndromes. Despite treatment with anti-infective agents and transfusion of platelets and immunoglobulin, the platelet count did not return to the normal range. Genetic testing confirmed a PTPN11 gene mutation, which led to the diagnosis of Noonan syndrome. At 3 months of age, the platelet count gradually increased without intervention and returned to the normal range by 6 months. We speculate that the thrombocytopenia in this case was closely related to Noonan syndrome.
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Affiliation(s)
- Meng Li
- Department of Pediatrics, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Jinghui Zhang
- Department of Pediatrics, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Nianzheng Sun
- Department of Pediatrics, Qilu Hospital of Shandong University, Jinan, Shandong, China
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Athota JP, Bhat M, Nampoothiri S, Gowrishankar K, Narayanachar SG, Puttamallesh V, Farooque MO, Shetty S. Molecular and clinical studies in 107 Noonan syndrome affected individuals with PTPN11 mutations. BMC Med Genet 2020; 21:50. [PMID: 32164556 PMCID: PMC7068896 DOI: 10.1186/s12881-020-0986-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 02/25/2020] [Indexed: 02/08/2023]
Abstract
Background Noonan syndrome (NS), an autosomal dominant developmental genetic disorder, is caused by germline mutations in genes associated with the RAS / mitogen-activated protein kinase (MAPK) pathway. In several studies PTPN11 is one of the genes with a significant number of pathogenic variants in NS-affected patients. Therefore, clinically diagnosed NS individuals are initially tested for pathogenic variants in PTPN11 gene to confirm the relationship before studying genotype–phenotype correlation. Methods Individuals (363) with clinically diagnosed NS from four hospitals in South India were recruited and the exons of PTPN11 gene were sequenced. Results Thirty-two previously described pathogenic variants in eight different exons in PTPN11 gene were detected in 107 patients, of whom 10 were familial cases. Exons 3, 8 and 13 had the highest number of pathogenic variants. The most commonly identified pathogenic variants in this series were in exon 8 (c.922A > G, c.923A > G), observed in 22 of the affected. Congenital cardiac anomalies were present in 84% of the mutation-positive cohort, the majority being defects in the right side of the heart. The most common facial features were downward-slanting palpebral fissures, hypertelorism and low-set posteriorly rotated ears. Other clinical features included short stature (40%), pectus excavatum (54%) and, in males, unilateral or bilateral cryptorchidism (44%). Conclusion The clinical features and mutational spectrum observed in our cohort are similar to those reported in other large studies done worldwide. This is the largest case series of NS-affected individuals with PTPN11 mutations described till date from India.
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Affiliation(s)
| | - Meenakshi Bhat
- Molecular Genetics, Centre for Human Genetics, Bengaluru, 560100, India.,Pediatric Genetics, Indira Gandhi Institute of Child Health, Bengaluru, 560029, India
| | - Sheela Nampoothiri
- Pediatric Genetics, Amrita Institute of Medical Sciences & Research Centre (AIMS), Kochi, 682041, India
| | | | | | | | | | - Swathi Shetty
- Molecular Genetics, Centre for Human Genetics, Bengaluru, 560100, India.
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Šimčíková D, Heneberg P. Refinement of evolutionary medicine predictions based on clinical evidence for the manifestations of Mendelian diseases. Sci Rep 2019; 9:18577. [PMID: 31819097 PMCID: PMC6901466 DOI: 10.1038/s41598-019-54976-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 11/21/2019] [Indexed: 12/28/2022] Open
Abstract
Prediction methods have become an integral part of biomedical and biotechnological research. However, their clinical interpretations are largely based on biochemical or molecular data, but not clinical data. Here, we focus on improving the reliability and clinical applicability of prediction algorithms. We assembled and curated two large non-overlapping large databases of clinical phenotypes. These phenotypes were caused by missense variations in 44 and 63 genes associated with Mendelian diseases. We used these databases to establish and validate the model, allowing us to improve the predictions obtained from EVmutation, SNAP2 and PoPMuSiC 2.1. The predictions of clinical effects suffered from a lack of specificity, which appears to be the common constraint of all recently used prediction methods, although predictions mediated by these methods are associated with nearly absolute sensitivity. We introduced evidence-based tailoring of the default settings of the prediction methods; this tailoring substantially improved the prediction outcomes. Additionally, the comparisons of the clinically observed and theoretical variations led to the identification of large previously unreported pools of variations that were under negative selection during molecular evolution. The evolutionary variation analysis approach described here is the first to enable the highly specific identification of likely disease-causing missense variations that have not yet been associated with any clinical phenotype.
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Affiliation(s)
- Daniela Šimčíková
- Charles University, Third Faculty of Medicine, Prague, Czech Republic
| | - Petr Heneberg
- Charles University, Third Faculty of Medicine, Prague, Czech Republic.
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