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Tantirukdham N, Sahakitrungruang T, Chaisiwamongkol R, Pongpanich M, Srichomthong C, Assawapitaksakul A, Buasong A, Tongkobpetch S, Yeetong P, Shotelersuk V. Long-read Amplicon Sequencing of the CYP21A2 in 48 Thai Patients With Steroid 21-Hydroxylase Deficiency. J Clin Endocrinol Metab 2022; 107:1939-1947. [PMID: 35363313 DOI: 10.1210/clinem/dgac187] [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] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Indexed: 11/19/2022]
Abstract
CONTEXT Congenital adrenal hyperplasia is most commonly caused by 21-hydroxylase deficiency (21-OHD), an autosomal recessive disorder resulting from biallelic pathogenic variants (PVs) in CYP21A2. With a highly homologous pseudogene and various types of single nucleotide and complex structural variants, identification of PVs in CYP21A2 has been challenging. OBJECTIVE To leverage long-read next-generation sequencing combined with locus-specific polymerase chain reaction (PCR) to detect PVs in CYP21A2 and to determine its diagnostic yield in patients with 21-OHD. METHODS Forty-eight Thai patients with 21-OHD comprising 38 sporadic cases and 5 pairs of siblings were enrolled. Two previously described locus-specific PCR methods were performed. Amplicons were subject to long-read sequencing. RESULTS Ninety-six PVs in CYP21A2 in the 48 patients were successfully identified. The combined techniques were able to detect 26 structural chimeric variants (27%; 26/96) in 22 patients with 18 having monoallelic and 4 having biallelic chimeras. The remaining PVs were pseudogene-derived mutations (63%; 60/96), entire gene deletions (2%; 2/96), missense variants (3%; 3/96), a splice-site variant (2%; 2/96), frameshift variants (2%; 2/96), and a nonsense variant (1%; 1/96). Notably, a splice-site variant, IVS7 + 1G > T, which was identified in a pair of siblings, has not previously been reported. CONCLUSIONS Our approach exploiting locus-specific PCR and long-read DNA sequencing has a 100% diagnostic yield for our cohort of 48 patients with 21-OHD.
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Affiliation(s)
- Nithiphut Tantirukdham
- Genetics Program, Division of Human Genetics, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Molecular and Genomics Research Laboratory, Chulabhorn Learning and Research Centre, Chulabhorn Royal Academy, Bangkok, Thailand
| | - Taninee Sahakitrungruang
- Division of Pediatric Endocrinology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Ratikorn Chaisiwamongkol
- Division of Pediatric Endocrinology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Monnat Pongpanich
- Department of Mathematics and Computer Science, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Omics Sciences and Bioinformatics Center, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Chalurmpon Srichomthong
- Center of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, Thailand
| | - Adjima Assawapitaksakul
- Center of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, Thailand
| | - Aayalida Buasong
- Center of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, Thailand
| | - Siraprapa Tongkobpetch
- Center of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, Thailand
| | - Patra Yeetong
- Division of Human Genetics, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Vorasuk Shotelersuk
- Center of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, Thailand
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Wiriyaukaradecha K, Nimsanor S, Tantirukdham N, Tongsom J, Bunyoo C, Soonklang K, Sritana N, Auewarakul C. Study of CALR, MPL, and c-kit Gene Mutations in Thai Patients with JAK2 V617F Negative Myeloproliferative Neoplasms. Asian Pac J Cancer Prev 2022; 23:1671-1678. [PMID: 35633552 PMCID: PMC9587876 DOI: 10.31557/apjcp.2022.23.5.1671] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Indexed: 11/25/2022] Open
Abstract
Objective: The aim of this study to determine the prevalence of CALR, MPL and c-kit gene mutations in JAK2 V617F negative-MPN patients. Methods: The retrospective study of CALR, MPL and c-kit mutations were analyzed in 113 samples collected from March 2010 to May 2017 and identified as JAK2 V617F–negative MPN Thai patients. The samples were analysis by gel electrophoresis and direct sequencing. Results: 28.3% of JAK2 V617F–negative MPN patients showed CALR gene mutations. Within the MPN patients with CALR mutation, 46.9% were classified as essential thrombocythemia (ET) and 20.9% were classified as primary myelofibrosis (PMF). Previous studies classified CALR mutations into three types using negatively charged amino acid stretches at the C-terminal domain. Type 1-like mutations were observed in 12 of 49 (24.5%) ET patients and type 2-like mutations were observed in 10 of 49 (20.4%) patients. In addition, 8 of 43 (18.6%) PMF patients showed type 1-like mutations and 1 of 43 (2.3%) showed type 2-like CALR mutation. Interestingly, platelet counts were higher in patients with CALR gene mutation than in patients without CALR gene mutation. MPL mutations (W515K and W515L) were identified in 2 of 109 (1.8%) MPN patients; the MPL mutations were only found in ET patients, which was consistent with previous studies. We did not detect exon 17 c-kit mutation in JAK2-negative MPN patients but detected intronic single nucleotide polymorphisms at c.74,978 and c.75,255 in these samples. Approximately 66% of patients did not have mutations in CALR and MPL genes, in addition to lacking JAK2 gene mutation, and these cases are classified as triple-mutations. Conclusion: Our results showed that 66% of cases were triple-negative mutation MPN because they lacked mutations in JAK2, CALR and MPL genes. The frequencies of CALR and MPL mutation in this study are similar to other CALR and MPL patient data.
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Affiliation(s)
- Kriangpol Wiriyaukaradecha
- Molecular and Genomics Research Laboratory, Centre of Learning and Research in Celebration of HRH Princess Chulabhorn's 60th Birthday Anniversary, Chulabhorn Royal Academy, Bangkok, Thailand
| | - Supanee Nimsanor
- Molecular and Genomics Research Laboratory, Centre of Learning and Research in Celebration of HRH Princess Chulabhorn's 60th Birthday Anniversary, Chulabhorn Royal Academy, Bangkok, Thailand
| | - Nithiphut Tantirukdham
- Molecular and Genomics Research Laboratory, Centre of Learning and Research in Celebration of HRH Princess Chulabhorn's 60th Birthday Anniversary, Chulabhorn Royal Academy, Bangkok, Thailand
| | - Jin Tongsom
- Molecular and Genomics Research Laboratory, Centre of Learning and Research in Celebration of HRH Princess Chulabhorn's 60th Birthday Anniversary, Chulabhorn Royal Academy, Bangkok, Thailand
| | - Chakrit Bunyoo
- Center of Laboratories and Instruments for Research, Centre of Learning and Research in Celebration of HRH Princess Chulabhorn's 60th Birthday Anniversary, Chulabhorn Royal Academy, Bangkok, Thailand
| | - Kamonwan Soonklang
- Data Management Unit, Centre of Learning and Research in Celebration of HRH Princess Chulabhorn's 60th Birthday Anniversary, Chulabhorn Royal Academy, Bangkok, Thailand
| | - Narongrit Sritana
- Molecular and Genomics Research Laboratory, Centre of Learning and Research in Celebration of HRH Princess Chulabhorn's 60th Birthday Anniversary, Chulabhorn Royal Academy, Bangkok, Thailand
| | - Chirayu Auewarakul
- Centre of Learning and Research in Celebration of HRH Princess Chulabhorn's 60th Birthday Anniversary, Chulabhorn Royal Academy, Bangkok, Thailand
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Yeetong P, Pongpanich M, Srichomthong C, Assawapitaksakul A, Shotelersuk V, Tantirukdham N, Chunharas C, Suphapeetiporn K, Shotelersuk V. TTTCA repeat insertions in an intron of YEATS2 in benign adult familial myoclonic epilepsy type 4. Brain 2020; 142:3360-3366. [PMID: 31539032 DOI: 10.1093/brain/awz267] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 06/02/2019] [Accepted: 07/04/2019] [Indexed: 11/13/2022] Open
Abstract
Epilepsy is a common neurological disorder and identification of its causes is important for a better understanding of its pathogenesis. We previously studied a Thai family with a type of epilepsy, benign adult familial myoclonic epilepsy type 4 (BAFME4), and localized its gene to chromosome 3q26.32-q28. Here, we used single-molecule real-time sequencing and found expansions of TTTTA and insertions of TTTCA repeats in intron 1 of YEATS2 in one affected member of the family. Of all the available members in the family-comprising 13 affected and eight unaffected-repeat-primed PCR and long-range PCR revealed the co-segregation of the TTTCA repeat insertions with the TTTTA repeat expansions and the disease status. For 1116 Thai control subjects, none were found to harbour the TTTCA repeats while four had the TTTTA repeat expansions. Therefore, our findings suggest that BAFME4 is caused by the insertions of the intronic TTTCA repeats in YEATS2. Interestingly, all four types of BAFMEs for which underlying genes have been found (BAFMEs 1, 4, 6 and 7) are caused by the same molecular pathology, suggesting that the insertions of non-coding TTTCA repeats are involved in their pathogenesis.
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Affiliation(s)
- Patra Yeetong
- Division of Human Genetics, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Monnat Pongpanich
- Department of Mathematics and Computer Science, Faculty of Science, Chulalongkorn University, Bangkok, Thailand.,Omics Sciences and Bioinformatics Center, Faculty of Science, Chulalongkorn University, Bangkok,, Thailand
| | - Chalurmpon Srichomthong
- Center of Excellence for Medical Genomics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.,Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, Thailand
| | - Adjima Assawapitaksakul
- Center of Excellence for Medical Genomics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.,Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, Thailand
| | - Varote Shotelersuk
- Center of Excellence for Medical Genomics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.,Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, Thailand
| | - Nithiphut Tantirukdham
- Division of Human Genetics, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Chaipat Chunharas
- Division of Neurology, Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Kanya Suphapeetiporn
- Center of Excellence for Medical Genomics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.,Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, Thailand
| | - Vorasuk Shotelersuk
- Center of Excellence for Medical Genomics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.,Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, Thailand
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