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Kim JH, Choi JH. Applications of genomic research in pediatric endocrine diseases. Clin Exp Pediatr 2023; 66:520-530. [PMID: 37321569 PMCID: PMC10694553 DOI: 10.3345/cep.2022.00948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 01/06/2023] [Accepted: 01/09/2023] [Indexed: 06/17/2023] Open
Abstract
Recent advances in molecular genetics have advanced our understanding of the molecular mechanisms involved in pediatric endocrine disorders and now play a major role in mainstream medical practice. The spectrum of endocrine genetic disorders has 2 extremes: Mendelian and polygenic. Mendelian or monogenic diseases are caused by rare variants of a single gene, each of which exerts a strong effect on disease risk. Polygenic diseases or common traits are caused by the combined effects of multiple genetic variants in conjunction with environmental and lifestyle factors. Testing for a single gene is preferable if the disease is phenotypically and/or geneically homogeneous. Next-generation sequencing (NGS) can be applied to phenotypically and genetically heterogeneous conditions. Genome-wide association studies (GWASs) have examined genetic variants across the entire genome in a large number of individuals who have been matched for population ancestry and assessed for a disease or trait of interest. Common endocrine diseases or traits, such as type 2 diabetes mellitus, obesity, height, and pubertal timing, result from the combined effects of multiple variants in various genes that are frequently found in the general population, each of which contributes a small individual effect. Isolated founder mutations can result from a true founder effect or an extreme reduction in population size. Studies of founder mutations offer powerful advantages for efficiently localizing the genes that underlie Mendelian disorders. The Korean population has settled in the Korean peninsula for thousands of years, and several recurrent mutations have been identified as founder mutations. The application of molecular technology has increased our understanding of endocrine diseases, which have impacted on the practice of pediatric endocrinology related to diagnosis and genetic counseling. This review focuses on the application of genomic research to pediatric endocrine diseases using GWASs and NGS technology for diagnosis and treatment.
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Affiliation(s)
- Ja Hye Kim
- Department of Pediatrics, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Jin-Ho Choi
- Department of Pediatrics, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
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Fagundes GFC, Freitas-Castro F, Santana LS, Afonso ACF, Petenuci J, Funari MFA, Guimaraes AG, Ledesma FL, Pereira MAA, Victor CR, Ferrari MSM, Coelho FMA, Srougi V, Tanno FY, Chambo JL, Latronico AC, Mendonca BB, Fragoso MCBV, Hoff AO, Almeida MQ. Evidence for a Founder Effect of SDHB Exon 1 Deletion in Brazilian Patients With Paraganglioma. J Clin Endocrinol Metab 2023; 108:2105-2114. [PMID: 36652439 DOI: 10.1210/clinem/dgad028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 01/10/2023] [Accepted: 01/13/2023] [Indexed: 01/19/2023]
Abstract
CONTEXT Limited information is available concerning the genetic spectrum of pheochromocytoma and paraganglioma (PPGL) patients in South America. Germline SDHB large deletions are very rare worldwide, but most of the individuals harboring the SDHB exon 1 deletion originated from the Iberian Peninsula. OBJECTIVE Our aim was to investigate the spectrum of SDHB genetic defects in a large cohort of Brazilian patients with PPGLs. METHODS Genetic investigation of 155 index PPGL patients was performed by Sanger DNA sequencing, multiplex ligation-dependent probe amplification, and/or target next-generation sequencing panel. Common ancestrality was investigated by microsatellite genotyping with haplotype reconstruction, and analysis of deletion breakpoint. RESULTS Among 155 index patients, heterozygous germline SDHB pathogenic or likely pathogenic variants were identified in 22 cases (14.2%). The heterozygous SDHB exon 1 complete deletion was the most frequent genetic defect in SDHB, identified in 8 out of 22 (36%) of patients. Haplotype analysis of 5 SDHB flanking microsatellite markers demonstrated a significant difference in haplotype frequencies in a case-control permutation test (P = 0.03). More precisely, 3 closer/informative microsatellites were shared by 6 out of 8 apparently unrelated cases (75%) (SDHB-GATA29A05-D1S2826-D1S2644 | SDHB-186-130-213), which was observed in only 1 chromosome (1/42) without SDHB exon 1 deletion (X2 = 29.43; P < 0.001). Moreover, all cases with SDHB exon 1 deletion had the same gene breakpoint pattern of a 15 678 bp deletion previously described in the Iberian Peninsula, indicating a common origin. CONCLUSION The germline heterozygous SDHB exon 1 deletion was the most frequent genetic defect in the Brazilian PPGL cohort. Our findings demonstrated a founder effect for the SDHB exon 1 deletion in Brazilian patients with paragangliomas.
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Affiliation(s)
- Gustavo F C Fagundes
- Unidade de Adrenal, Laboratório de Endocrinologia Molecular e Celular LIM/25, Divisão de Endocrinologia e Metabologia, Hospital das Clínicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-000, Brasil
| | - Felipe Freitas-Castro
- Unidade de Adrenal, Laboratório de Endocrinologia Molecular e Celular LIM/25, Divisão de Endocrinologia e Metabologia, Hospital das Clínicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-000, Brasil
| | - Lucas S Santana
- Unidade de Adrenal, Laboratório de Endocrinologia Molecular e Celular LIM/25, Divisão de Endocrinologia e Metabologia, Hospital das Clínicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-000, Brasil
| | - Ana Caroline F Afonso
- Unidade de Adrenal, Laboratório de Endocrinologia Molecular e Celular LIM/25, Divisão de Endocrinologia e Metabologia, Hospital das Clínicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-000, Brasil
| | - Janaina Petenuci
- Unidade de Adrenal, Laboratório de Endocrinologia Molecular e Celular LIM/25, Divisão de Endocrinologia e Metabologia, Hospital das Clínicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-000, Brasil
| | - Mariana F A Funari
- Unidade de Adrenal, Laboratório de Endocrinologia Molecular e Celular LIM/25, Divisão de Endocrinologia e Metabologia, Hospital das Clínicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-000, Brasil
| | - Augusto G Guimaraes
- Unidade de Adrenal, Laboratório de Endocrinologia Molecular e Celular LIM/25, Divisão de Endocrinologia e Metabologia, Hospital das Clínicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-000, Brasil
| | - Felipe L Ledesma
- Departamento de Patologia, Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-000, Brasil
| | - Maria Adelaide A Pereira
- Unidade de Adrenal, Laboratório de Endocrinologia Molecular e Celular LIM/25, Divisão de Endocrinologia e Metabologia, Hospital das Clínicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-000, Brasil
| | - Carolina R Victor
- Divisão de Oncologia Clínica, Instituto do Câncer do Estado de São Paulo (ICESP), Faculdade de Medicina da Universidade de São Paulo, São Paulo 01246-000, Brasil
- Centro de Oncologia Clínica, Rede D'Or, São Paulo 04543-000, Brasil
| | - Marcela S M Ferrari
- Divisão de Oncologia Clínica, Instituto do Câncer do Estado de São Paulo (ICESP), Faculdade de Medicina da Universidade de São Paulo, São Paulo 01246-000, Brasil
- Centro de Oncologia Clínica, Rede D'Or, São Paulo 04543-000, Brasil
| | - Fernando M A Coelho
- Instituto de Radiologia InRad, Hospital das Clínicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-000, Brasil
| | - Victor Srougi
- Divisão de Urologia, Hospital das Clínicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-000, Brasil
| | - Fabio Y Tanno
- Divisão de Urologia, Hospital das Clínicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-000, Brasil
| | - Jose L Chambo
- Divisão de Urologia, Hospital das Clínicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-000, Brasil
| | - Ana Claudia Latronico
- Unidade de Adrenal & Desenvolvimento, Laboratório de Hormônios e Genética Molecular LIM/42, Divisão de Endocrinologia e Metabologia, Hospital das Clínicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-000, Brasil
| | - Berenice B Mendonca
- Unidade de Adrenal & Desenvolvimento, Laboratório de Hormônios e Genética Molecular LIM/42, Divisão de Endocrinologia e Metabologia, Hospital das Clínicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-000, Brasil
| | - Maria Candida B V Fragoso
- Unidade de Adrenal & Desenvolvimento, Laboratório de Hormônios e Genética Molecular LIM/42, Divisão de Endocrinologia e Metabologia, Hospital das Clínicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-000, Brasil
- Divisão de Oncologia Endócrina, Instituto do Câncer do Estado de São Paulo (ICESP), Faculdade de Medicina da Universidade de São Paulo, São Paulo 01246-000, Brasil
| | - Ana O Hoff
- Centro de Oncologia Clínica, Rede D'Or, São Paulo 04543-000, Brasil
- Divisão de Oncologia Endócrina, Instituto do Câncer do Estado de São Paulo (ICESP), Faculdade de Medicina da Universidade de São Paulo, São Paulo 01246-000, Brasil
| | - Madson Q Almeida
- Unidade de Adrenal, Laboratório de Endocrinologia Molecular e Celular LIM/25, Divisão de Endocrinologia e Metabologia, Hospital das Clínicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-000, Brasil
- Divisão de Oncologia Endócrina, Instituto do Câncer do Estado de São Paulo (ICESP), Faculdade de Medicina da Universidade de São Paulo, São Paulo 01246-000, Brasil
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