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Rattanapornsompong K, Chetruengchai W, Srichomthong C, Theerapanon T, Porntaveetus T, Shotelersuk V. Unraveling the molecular diagnosis of metaphyseal enchondromatosis with D-2-hydroxyglutaric aciduria: A 22-year quest. Am J Med Genet A 2024; 194:e63557. [PMID: 38305044 DOI: 10.1002/ajmg.a.63557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 01/16/2024] [Accepted: 01/20/2024] [Indexed: 02/03/2024]
Affiliation(s)
- Khanti Rattanapornsompong
- Center of Excellence in Genomics and Precision Dentistry, Geriatric Dentistry and Special Patients Care Program, Department of Physiology, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand
| | - Wanna Chetruengchai
- 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, 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, Bangkok, Thailand
| | - Thanakorn Theerapanon
- Center of Excellence in Genomics and Precision Dentistry, Geriatric Dentistry and Special Patients Care Program, Department of Physiology, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand
| | - Thantrira Porntaveetus
- Center of Excellence in Genomics and Precision Dentistry, Geriatric Dentistry and Special Patients Care Program, Department of Physiology, Faculty of Dentistry, Chulalongkorn University, 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, Bangkok, Thailand
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Buthasane W, Shotelersuk V, Chetruengchai W, Srichomthong C, Assawapitaksakul A, Tangphatsornruang S, Pootakham W, Sonthirod C, Tongsima S, Wangkumhang P, Wilantho A, Thongphakdee A, Sanannu S, Poksawat C, Nipanunt T, Kasorndorkbua C, Koepfli KP, Pukazhenthi BS, Suriyaphol P, Wongsurawat T, Jenjaroenpun P, Suriyaphol G. Comprehensive genome assembly reveals genetic diversity and carcass consumption insights in critically endangered Asian king vultures. Sci Rep 2024; 14:9455. [PMID: 38658744 PMCID: PMC11043450 DOI: 10.1038/s41598-024-59990-9] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 04/17/2024] [Indexed: 04/26/2024] Open
Abstract
The Asian king vulture (AKV), a vital forest scavenger, is facing globally critical endangerment. This study aimed to construct a reference genome to unveil the mechanisms underlying its scavenger abilities and to assess the genetic relatedness of the captive population in Thailand. A reference genome of a female AKV was assembled from sequencing reads obtained from both PacBio long-read and MGI short-read sequencing platforms. Comparative genomics with New World vultures (NWVs) and other birds in the Family Accipitridae revealed unique gene families in AKV associated with retroviral genome integration and feather keratin, contrasting with NWVs' genes related to olfactory reception. Expanded gene families in AKV were linked to inflammatory response, iron regulation and spermatogenesis. Positively selected genes included those associated with anti-apoptosis, immune response and muscle cell development, shedding light on adaptations for carcass consumption and high-altitude soaring. Using restriction site-associated DNA sequencing (RADseq)-based genome-wide single nucleotide polymorphisms (SNPs), genetic relatedness and inbreeding status of five captive AKVs were determined, revealing high genomic inbreeding in two females. In conclusion, the AKV reference genome was established, providing insights into its unique characteristics. Additionally, the potential of RADseq-based genome-wide SNPs for selecting AKV breeders was demonstrated.
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Affiliation(s)
- Wannapol Buthasane
- Biochemistry Unit, Department of Physiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Vorasuk Shotelersuk
- Center of Excellence for Medical Genomics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Henri Dunant Road, Pathumwan, Bangkok, 10330, Thailand
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, 10330, Thailand
| | - Wanna Chetruengchai
- Center of Excellence for Medical Genomics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Henri Dunant Road, Pathumwan, Bangkok, 10330, Thailand
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, 10330, Thailand
| | - Chalurmpon Srichomthong
- Center of Excellence for Medical Genomics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Henri Dunant Road, Pathumwan, Bangkok, 10330, Thailand
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, 10330, Thailand
| | - Adjima Assawapitaksakul
- Center of Excellence for Medical Genomics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Henri Dunant Road, Pathumwan, Bangkok, 10330, Thailand
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, 10330, Thailand
| | - Sithichoke Tangphatsornruang
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, 12120, Thailand
| | - Wirulda Pootakham
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, 12120, Thailand
| | - Chutima Sonthirod
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, 12120, Thailand
| | - Sissades Tongsima
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, 12120, Thailand
| | - Pongsakorn Wangkumhang
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, 12120, Thailand
| | - Alisa Wilantho
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, 12120, Thailand
| | - Ampika Thongphakdee
- Animal Conservation and Research Institute, The Zoological Park Organization of Thailand under the Royal Patronage of H.M. The King, Bangkok, 10300, Thailand
| | - Saowaphang Sanannu
- Animal Conservation and Research Institute, The Zoological Park Organization of Thailand under the Royal Patronage of H.M. The King, Bangkok, 10300, Thailand
| | - Chaianan Poksawat
- Animal Conservation and Research Institute, The Zoological Park Organization of Thailand under the Royal Patronage of H.M. The King, Bangkok, 10300, Thailand
| | - Tarasak Nipanunt
- Huai Kha Khaeng Wildlife Breeding Center, Department of National Parks, Wildlife and Plant Conservation, Uthai Thani, 61160, Thailand
| | - Chaiyan Kasorndorkbua
- Laboratory of Raptor Research and Conservation Medicine, Department of Pathology, Faculty of Veterinary Medicine, Kasetsart University, Bangkok, 10900, Thailand
| | - Klaus-Peter Koepfli
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA, 22630, USA
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, VA, 22630, USA
| | - Budhan S Pukazhenthi
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, VA, 22630, USA
| | - Prapat Suriyaphol
- Division of Medical Bioinformatics, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Thidathip Wongsurawat
- Division of Medical Bioinformatics, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Piroon Jenjaroenpun
- Division of Medical Bioinformatics, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Gunnaporn Suriyaphol
- Biochemistry Unit, Department of Physiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand.
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Yeetong P, Dembélé ME, Pongpanich M, Cissé L, Srichomthong C, Maiga AB, Dembélé K, Assawapitaksakul A, Bamba S, Yalcouyé A, Diarra S, Mefoung SE, Rakwongkhachon S, Traoré O, Tongkobpetch S, Fischbeck KH, Gahl WA, Guinto CO, Shotelersuk V, Landouré G. Pentanucleotide Repeat Insertions in RAI1 Cause Benign Adult Familial Myoclonic Epilepsy Type 8. Mov Disord 2024; 39:164-172. [PMID: 37994247 PMCID: PMC10872918 DOI: 10.1002/mds.29654] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 10/04/2023] [Accepted: 10/24/2023] [Indexed: 11/24/2023] Open
Abstract
BACKGROUND Benign adult familial myoclonic epilepsy (BAFME) is an autosomal dominant disorder characterized by cortical tremors and seizures. Six types of BAFME, all caused by pentanucleotide repeat expansions in different genes, have been reported. However, several other BAFME cases remain with no molecular diagnosis. OBJECTIVES We aim to characterize clinical features and identify the mutation causing BAFME in a large Malian family with 10 affected members. METHODS Long-read whole genome sequencing, repeat-primed polymerase chain reaction and RNA studies were performed. RESULTS We identified TTTTA repeat expansions and TTTCA repeat insertions in intron 4 of the RAI1 gene that co-segregated with disease status in this family. TTTCA repeats were absent in 200 Malian controls. In the affected individuals, we found a read with only nine TTTCA repeat units and somatic instability. The RAI1 repeat expansions cause the only BAFME type in which the disease-causing repeats are in a gene associated with a monogenic disorder in the haploinsufficiency state (ie, Smith-Magenis syndrome [SMS]). Nevertheless, none of the Malian patients exhibited symptoms related to SMS. Moreover, leukocyte RNA levels of RAI1 in six Malian BAFME patients were no different from controls. CONCLUSIONS These findings establish a new type of BAFME, BAFME8, in an African family and suggest that haploinsufficiency is unlikely to be the main pathomechanism of BAFME. © 2023 International Parkinson and Movement Disorder Society. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.
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Affiliation(s)
- Patra Yeetong
- Division of Human Genetics, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | | | - Monnat Pongpanich
- Department of Mathematics and Computer Science, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
- Omics Sciences and Bioinformatics Center, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Lassana Cissé
- Service de Neurologie, Centre Hospitalier Universitaire du Point G, Bamako, Mali
| | - Chalurmpon Srichomthong
- Center of Excellence for Medical Genomics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok 10330, Thailand
| | | | | | - Adjima Assawapitaksakul
- Center of Excellence for Medical Genomics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok 10330, Thailand
| | - Salia Bamba
- Faculté de Médecine et d’Odontostomatologie, USTTB, Bamako, Mali
| | | | - Salimata Diarra
- Faculté de Médecine et d’Odontostomatologie, USTTB, Bamako, Mali
- Yale University, Pediatric Genomics Discovery Program, Department of Pediatrics, New Haven, CT, United States
- Neurogenetics Branch, NINDS, NIH, Bethesda, MD, United States
| | | | - Supphakorn Rakwongkhachon
- Center of Excellence for Medical Genomics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok 10330, Thailand
| | - Oumou Traoré
- Faculté de Médecine et d’Odontostomatologie, USTTB, Bamako, Mali
| | - Siraprapa Tongkobpetch
- Center of Excellence for Medical Genomics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok 10330, Thailand
| | | | - William A Gahl
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Cheick O Guinto
- Faculté de Médecine et d’Odontostomatologie, USTTB, Bamako, Mali
- Service de Neurologie, Centre Hospitalier Universitaire du Point G, Bamako, Mali
| | - Vorasuk Shotelersuk
- Center of Excellence for Medical Genomics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok 10330, Thailand
| | - Guida Landouré
- Faculté de Médecine et d’Odontostomatologie, USTTB, Bamako, Mali
- Service de Neurologie, Centre Hospitalier Universitaire du Point G, Bamako, Mali
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Suttichet TB, Chamnanphon M, Pongpanich M, Chokyakorn S, Kupatawintu P, Srichomthong C, Chetruengchai W, Chuntakaruk H, Rungrotmongkol T, Chariyavilaskul P, Shotelersuk V, Praditpornsilpa K. HLA-B*46:01:01:01 and HLA-DRB1*09:01:02:01 are associated with anti-rHuEPO-induced pure red cell aplasia. Sci Rep 2023; 13:22759. [PMID: 38123661 PMCID: PMC10733298 DOI: 10.1038/s41598-023-50211-3] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 12/16/2023] [Indexed: 12/23/2023] Open
Abstract
Treatment of anemia in patients with chronic kidney disease (CKD) with recombinant human erythropoietin (rHuEPO) can be disrupted by a severe complication, anti-rHuEPO-induced pure red cell aplasia (PRCA). Specific HLA genotypes may have played a role in the high incidence of PRCA in Thai patients (1.7/1,000 patient years vs. 0.03/10,000 patient years in Caucasians). We conducted a case-control study in 157 CKD patients with anti-rHuEPO-induced PRCA and 56 controls. The HLA typing was determined by sequencing using a highly accurate multiplex single-molecule, real-time, long-read sequencing platform. Four analytical models were deployed: Model 1 (additive: accounts for the number of alleles), Model 2 (dominant: accounts for only the presence or absence of alleles), Model 3 (adjusted additive with rHuEPO types) and Model 4 (adjusted dominant with rHuEPO types). HLA-B*46:01:01:01 and DRB1*09:01:02:01 were found to be independent risk markers for anti-rHuEPO-induced PRCA in all models [OR (95%CI), p-values for B*46:01:01:01: 4.58 (1.55-13.51), 0.006; 4.63 (1.56-13.75), 0.006; 5.72 (1.67-19.67), 0.006; and 5.81 (1.68-20.09), 0.005; for DRB1*09:01:02:01: 3.99 (1.28-12.49), 0.017, 4.50 (1.32-15.40), 0.016, 3.42 (1.09-10.74), 0.035, and 3.75 (1.08-13.07), 0.038, in Models 1-4, respectively. HLA-B*46:01:01:01 and DRB1*09:01:02:01 are susceptible alleles for anti-rHuEPO-induced PRCA. These findings support the role of HLA genotyping in helping to monitor patients receiving rHuEPO treatment.
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Affiliation(s)
- Thitima Benjachat Suttichet
- Center of Excellence in Clinical Pharmacokinetics and Pharmacogenomics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Monpat Chamnanphon
- Center of Excellence in Clinical Pharmacokinetics and Pharmacogenomics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Monnat Pongpanich
- Department of Mathematics and Computer Science, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Faculty of Science, Omics Sciences and Bioinformatics Center, Chulalongkorn University, Bangkok, Thailand
| | - Sarun Chokyakorn
- Department of Pharmacology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | | | - Chalurmpon Srichomthong
- Department of Pediatrics, Faculty of Medicine, Center of Excellence for Medical Genomics, Chulalongkorn University, Bangkok, Thailand
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, Thailand
| | - Wanna Chetruengchai
- Department of Pediatrics, Faculty of Medicine, Center of Excellence for Medical Genomics, Chulalongkorn University, Bangkok, Thailand
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, Thailand
| | - Hathaichanok Chuntakaruk
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, Thailand
- Department of Biochemistry, Faculty of Science, Center of Excellence in Structural and Computational Biology, Chulalongkorn University, Bangkok, Thailand
| | - Thanyada Rungrotmongkol
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, Thailand
- Department of Biochemistry, Faculty of Science, Center of Excellence in Structural and Computational Biology, Chulalongkorn University, Bangkok, Thailand
| | - Pajaree Chariyavilaskul
- Center of Excellence in Clinical Pharmacokinetics and Pharmacogenomics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.
- Department of Pharmacology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.
| | - Vorasuk Shotelersuk
- Department of Pediatrics, Faculty of Medicine, Center of Excellence for Medical Genomics, Chulalongkorn University, Bangkok, Thailand
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, Thailand
| | - Kearkiat Praditpornsilpa
- Division of Nephrology, Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
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5
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Pumpitakkul V, Chetruengchai W, Srichomthong C, Phokaew C, Pootakham W, Sonthirod C, Nawae W, Tongsima S, Wangkumhang P, Wilantho A, Utara Y, Thongpakdee A, Sanannu S, Maikaew U, Khuntawee S, Changpetch W, Phromwat P, Raschasin K, Sarnkhaeveerakul P, Supapannachart P, Buthasane W, Pukazhenthi BS, Koepfli KP, Suriyaphol P, Tangphatsornruang S, Suriyaphol G, Shotelersuk V. Comparative genomics and genome-wide SNPs of endangered Eld's deer provide breeder selection for inbreeding avoidance. Sci Rep 2023; 13:19806. [PMID: 37957263 PMCID: PMC10643696 DOI: 10.1038/s41598-023-47014-x] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 11/08/2023] [Indexed: 11/15/2023] Open
Abstract
Eld's deer, a conserved wildlife species of Thailand, is facing inbreeding depression, particularly in the captive Siamese Eld's deer (SED) subspecies. In this study, we constructed genomes of a male SED and a male Burmese Eld's deer (BED), and used genome-wide single nucleotide polymorphisms to evaluate the genetic purity and the inbreeding status of 35 SED and 49 BED with limited pedigree information. The results show that these subspecies diverged approximately 1.26 million years ago. All SED were found to be purebred. A low proportion of admixed SED genetic material was observed in some BED individuals. Six potential breeders from male SED with no genetic relation to any female SED and three purebred male BED with no relation to more than 10 purebred female BED were identified. This study provides valuable insights about Eld's deer populations and appropriate breeder selection in efforts to repopulate this endangered species while avoiding inbreeding.
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Affiliation(s)
- Vichayanee Pumpitakkul
- Biochemistry Unit, Department of Physiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Wanna Chetruengchai
- Center of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, 10330, Thailand
| | - Chalurmpon Srichomthong
- Center of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, 10330, Thailand
| | - Chureerat Phokaew
- Center of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, 10330, Thailand
| | - Wirulda Pootakham
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, 12120, Thailand
| | - Chutima Sonthirod
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, 12120, Thailand
| | - Wanapinun Nawae
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, 12120, Thailand
| | - Sissades Tongsima
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, 12120, Thailand
| | - Pongsakorn Wangkumhang
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, 12120, Thailand
| | - Alisa Wilantho
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, 12120, Thailand
| | - Yongchai Utara
- Zoological Park Organization of Thailand, Animal Conservation and Research Institute, Bangkok, 10800, Thailand
| | - Ampika Thongpakdee
- Zoological Park Organization of Thailand, Animal Conservation and Research Institute, Bangkok, 10800, Thailand
| | - Saowaphang Sanannu
- Zoological Park Organization of Thailand, Animal Conservation and Research Institute, Bangkok, 10800, Thailand
| | - Umaporn Maikaew
- Khao Kheow Open Zoo, Zoological Park Organization of Thailand, Chonburi, 20110, Thailand
| | - Suphattharaphonnaphan Khuntawee
- Ubon Ratchathani Zoo, Zoological Park Organization of Thailand, Ubon Ratchathani District, Ubon Ratchathani, 34000, Thailand
| | - Wirongrong Changpetch
- Nakhon Ratchasima Zoo, Zoological Park Organization of Thailand, Nakhon Ratchasima, 30000, Thailand
| | - Phairot Phromwat
- Huai Kha Khaeng Wildlife Breeding Center, Department of National Parks, Wildlife and Plant Conservation, Uthai Thani, 61160, Thailand
| | - Kacharin Raschasin
- Chulabhorn Wildlife Breeding Center, Department of National Parks, Wildlife and Plant Conservation, Sisaket, 33140, Thailand
| | - Phunyaphat Sarnkhaeveerakul
- Banglamung Wildlife Breeding Center, Department of National Parks, Wildlife and Plant Conservation, Chonburi, 20150, Thailand
| | - Pannawat Supapannachart
- Biochemistry Unit, Department of Physiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Wannapol Buthasane
- Biochemistry Unit, Department of Physiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Budhan S Pukazhenthi
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, VA, 22630, USA
| | - Klaus-Peter Koepfli
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, VA, 22630, USA
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA, 22630, USA
| | - Prapat Suriyaphol
- Office for Research and Development, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Sithichoke Tangphatsornruang
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, 12120, Thailand.
| | - Gunnaporn Suriyaphol
- Biochemistry Unit, Department of Physiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand.
| | - Vorasuk Shotelersuk
- Center of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, 10330, Thailand
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6
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Yeetong P, Kulsirichawaroj P, Kumutpongpanich T, Srichomthong C, Od-Ek P, Rakwongkhachon S, Thamcharoenvipas T, Sanmaneechai O, Pongpanich M, Shotelersuk V. Long-read Nanopore sequencing identified D4Z4 contractions in patients with facioscapulohumeral muscular dystrophy. Neuromuscul Disord 2023; 33:551-556. [PMID: 37320968 DOI: 10.1016/j.nmd.2023.05.004] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 05/10/2023] [Accepted: 05/12/2023] [Indexed: 06/17/2023]
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is a genetic muscle disorder caused by abnormal expression of the DUX4 protein, commonly resulting from a contraction of D4Z4 repeat units with the presence of a polyadenylation (polyA) signal. More than 10 units of the D4Z4 repeat, with a length of 3.3 kb per unit, are typically required to silence DUX4 expression. Consequently, molecular diagnosis of FSHD is challenging. We used Oxford Nanopore technology to perform whole-genome sequencing of seven unrelated patients with FSHD, their six unaffected parents, and 10 unaffected controls. All seven patients were successfully identified to harbor one to five D4Z4 repeat units and the polyA signal, whereas none of the 16 unaffected individuals met the molecular diagnostic criteria. Our newly developed method provides a straightforward and powerful molecular diagnostic tool for FSHD.
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Affiliation(s)
- Patra Yeetong
- Division of Human Genetics, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Pimchanok Kulsirichawaroj
- Department of Pediatrics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Theerawat Kumutpongpanich
- Department of Medicine, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Chalurmpon Srichomthong
- Center of Excellence for Medical Genomics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand; Excellence Center for Medical Genetics, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok 10330, Thailand
| | - Phichittra Od-Ek
- Center of Excellence for Medical Genomics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand; Excellence Center for Medical Genetics, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok 10330, Thailand
| | - Supphakorn Rakwongkhachon
- Center of Excellence for Medical Genomics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand; Excellence Center for Medical Genetics, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok 10330, Thailand
| | - Titaporn Thamcharoenvipas
- Division of Neurology, Department of Pediatrics, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand
| | - Oranee Sanmaneechai
- Department of Pediatrics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand.
| | - Monnat Pongpanich
- Department of Mathematics and Computer Science, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; Omics Sciences and Bioinformatics Center, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Vorasuk Shotelersuk
- Center of Excellence for Medical Genomics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand; Excellence Center for Medical Genetics, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok 10330, Thailand
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7
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Isaranuwatchai S, Chanakul A, Ittiwut C, Ittiwut R, Srichomthong C, Shotelersuk V, Suphapeetiporn K, Praditpornsilpa K. Pathogenic variant detection rate by whole exome sequencing in Thai patients with biopsy-proven focal segmental glomerulosclerosis. Sci Rep 2023; 13:805. [PMID: 36646731 PMCID: PMC9842604 DOI: 10.1038/s41598-022-26291-y] [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: 07/22/2022] [Accepted: 12/13/2022] [Indexed: 01/17/2023] Open
Abstract
The spectra of underlying genetic variants for various clinical entities including focal segmental glomerulosclerosis (FSGS) vary among different populations. Here we described the clinical and genetic characteristics of biopsy-proven FSGS patients in Thailand. Patients with FSGS pathology, without secondary causes, were included in our study. Clinical laboratory and pathological data were collected. Whole-exome sequencing (WES) was subsequently performed. 53 unrelated FSGS patients were recruited. 35 patients were adults (66.0%), and 51 patients were sporadic cases (96.2%). Clinical diagnosis before kidney biopsy was steroid-resistant nephrotic syndrome (SRNS) in 58.5%, and proteinuric chronic kidney disease in 32.1%. Using WES, disease-associated pathogenic/likely pathogenic (P/LP) variants could be identified in six patients including the two familial cases, making the P/LP detection rate of 11.3% (6/53). Of these six patients, two patients harbored novel variants with one in the COL4A4 gene and one in the MAFB gene. Four other patients carried previously reported variants in the CLCN5, LMX1B, and COL4A4 genes. Four of these patients (4/6) received immunosuppressive medications as a treatment for primary FSGS before genetic diagnosis. All four did not respond to the medications, emphasizing the importance of genetic testing to avoid unnecessary treatment. Notably, the mutation detection rates in adult and pediatric patients were almost identical, at 11.4% and 11.1%, respectively. In conclusion, the overall P/LP variant detection rate by WES in biopsy-proven FSGS patients was 11.3%. The most identified variants were in COL4A4. In addition, three novel variants associated with FSGS were detected.
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Affiliation(s)
- Suramath Isaranuwatchai
- Division of Nephrology, Department of Internal Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.,Division of Nephrology, Department of Internal Medicine, Chulabhorn Hospital, Chulabhorn Royal Academy, Bangkok, Thailand
| | - Ankanee Chanakul
- Division of Nephrology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Chupong Ittiwut
- Division of Medical Genetics and Metabolism, Department of Pediatrics, Center of Excellence for Medical Genomics, Medical Genomics Cluster, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand.,Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, Thailand
| | - Rungnapa Ittiwut
- Division of Medical Genetics and Metabolism, Department of Pediatrics, Center of Excellence for Medical Genomics, Medical Genomics Cluster, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand.,Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, Thailand
| | - Chalurmpon Srichomthong
- Division of Medical Genetics and Metabolism, Department of Pediatrics, Center of Excellence for Medical Genomics, Medical Genomics Cluster, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand.,Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, Thailand
| | - Vorasuk Shotelersuk
- Division of Medical Genetics and Metabolism, Department of Pediatrics, Center of Excellence for Medical Genomics, Medical Genomics Cluster, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand.,Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, Thailand
| | - Kanya Suphapeetiporn
- Division of Medical Genetics and Metabolism, Department of Pediatrics, Center of Excellence for Medical Genomics, Medical Genomics Cluster, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand. .,Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, Thailand.
| | - Kearkiat Praditpornsilpa
- Division of Nephrology, Department of Internal Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
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8
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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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9
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Kuptanon C, Thamkunanon V, Srichomthong C, Theerapanon T, Suphapeetiporn K, Porntaveetus T, Shotelersuk V. Novel BMP1, CRTAP, and SERPINF1 variants causing autosomal recessive osteogenesis imperfecta. Clin Genet 2022; 102:242-243. [PMID: 35703132 DOI: 10.1111/cge.14172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 05/28/2022] [Accepted: 05/30/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Chulaluck Kuptanon
- Department of Pediatrics, Queen Sirikit National Institute of Child Health, Bangkok, Thailand.,Department of Pediatrics, College of Medicine, Rangsit University, Bangkok, Thailand
| | - Verasak Thamkunanon
- Department of Orthopedics, Queen Sirikit National Institute of Child Health, 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
| | - Thanakorn Theerapanon
- Center of Excellence in Genomics and Precision Dentistry, Department of Physiology, Faculty of Dentistry, 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
| | - Thantrira Porntaveetus
- Center of Excellence in Genomics and Precision Dentistry, Department of Physiology, Faculty of Dentistry, Chulalongkorn University, 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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10
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Chetruengchai W, Singchat W, Srichomthong C, Assawapitaksakul A, Srikulnath K, Ahmad SF, Phokaew C, Shotelersuk V. Genome of Varanus salvator macromaculatus (Asian Water Monitor) Reveals Adaptations in the Blood Coagulation and Innate Immune System. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.850817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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11
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Shotelersuk V, Wichadakul D, Ngamphiw C, Srichomthong C, Phokaew C, Wilantho A, Pakchuen S, Nakhonsri V, Shaw PJ, Wasitthankasem R, Piriyapongsa J, Wangkumhang P, Assawapitaksakul A, Chetruengchai W, Lapphra K, Khuninthong A, Makarawate P, Suphapeetiporn K, Mahasirimongkol S, Satproedprai N, Porntaveetus T, Pisitkun P, Praphanphoj V, Kantaputra P, Tassaneeyakul W, Tongsima S. The Thai reference exome (T-REx) variant database. Clin Genet 2021; 100:703-712. [PMID: 34496037 DOI: 10.1111/cge.14060] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [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: 05/10/2021] [Revised: 08/31/2021] [Accepted: 09/02/2021] [Indexed: 01/19/2023]
Abstract
To maximize the potential of genomics in medicine, it is essential to establish databases of genomic variants for ethno-geographic groups that can be used for filtering and prioritizing candidate pathogenic variants. Populations with non-European ancestry are poorly represented among current genomic variant databases. Here, we report the first high-density survey of genomic variants for the Thai population, the Thai Reference Exome (T-REx) variant database. T-REx comprises exome sequencing data of 1092 unrelated Thai individuals. The targeted exome regions common among four capture platforms cover 30.04 Mbp on autosomes and chromosome X. 345 681 short variants (18.27% of which are novel) and 34 907 copy number variations were found. Principal component analysis on 38 469 single nucleotide variants present worldwide showed that the Thai population is most genetically similar to East and Southeast Asian populations. Moreover, unsupervised clustering revealed six Thai subpopulations consistent with the evidence of gene flow from neighboring populations. The prevalence of common pathogenic variants in T-REx was investigated in detail, which revealed subpopulation-specific patterns, in particular variants associated with erythrocyte disorders such as the HbE variant in HBB and the Viangchan variant in G6PD. T-REx serves as a pivotal addition to the current databases for genomic medicine.
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Affiliation(s)
- 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
| | - Duangdao Wichadakul
- Department of Computer Engineering, Faculty of Engineering, Chulalongkorn University, Bangkok, Thailand
| | - Chumpol Ngamphiw
- National Biobank of Thailand, National Science and Technology Development Agency, Pathum Thani, 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
| | - Chureerat Phokaew
- 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
| | - Alisa Wilantho
- National Biobank of Thailand, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Sujiraporn Pakchuen
- National Biobank of Thailand, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Vorthunju Nakhonsri
- National Biobank of Thailand, National Science and Technology Development Agency, Pathum Thani, Thailand.,Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Philip James Shaw
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Rujipat Wasitthankasem
- National Biobank of Thailand, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Jittima Piriyapongsa
- National Biobank of Thailand, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Pongsakorn Wangkumhang
- National Biobank of Thailand, National Science and Technology Development Agency, Pathum Thani, 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
| | - Wanna Chetruengchai
- 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
| | - Keswadee Lapphra
- Department of Pediatrics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Athiphat Khuninthong
- National Biobank of Thailand, National Science and Technology Development Agency, Pathum Thani, Thailand
| | | | - Kanya Suphapeetiporn
- 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
| | - Surakameth Mahasirimongkol
- Genomic Medicine Center, Division of Genomic Medicine and Innovation Support, Department of Medical Sciences, Ministry of Public Health, Nonthaburi, Thailand
| | - Nusara Satproedprai
- Genomic Medicine Center, Division of Genomic Medicine and Innovation Support, Department of Medical Sciences, Ministry of Public Health, Nonthaburi, Thailand
| | - Thantrira Porntaveetus
- Genomics and Precision Dentistry Research Unit, Department of Physiology, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand
| | - Prapaporn Pisitkun
- Division of Allergy, Immunology, and Rheumatology, Department of Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Verayuth Praphanphoj
- Center for Medical Genetics Research, Rajanukul Institute, Department of Mental Health, Ministry of Public Health Bangkok, Bangkok, Thailand
| | - Piranit Kantaputra
- Division of Pediatric Dentistry, Department of Orthodontics and Pediatric Dentistry, Faculty of Dentistry, Chiang Mai University, Chiang Mai, Thailand
| | | | - Sissades Tongsima
- National Biobank of Thailand, National Science and Technology Development Agency, Pathum Thani, Thailand
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12
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Urkasemsin G, Pongpanich M, Sariya L, Kongcharoen A, Buddhirongawatr R, Rungarunlert S, Ferreira JN, Chetruengchai W, Phokaew C, Srichomthong C, Shotelersuk V. Whole genome sequencing identifies a homozygous nonsense mutation in the JPH2 gene in Shih Tzu dogs with progressive retinal atrophy. Anim Genet 2021; 52:714-719. [PMID: 34231238 DOI: 10.1111/age.13118] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/24/2021] [Indexed: 11/28/2022]
Abstract
Progressive retinal atrophy (PRA), common autosomal recessive disorder affecting several dog breeds including Shih Tzu, is characterized by degeneration of photoreceptors leading to blindness. To identify PRA genetic variants, three affected and 15 unaffected Shih Tzu and 20 non-Shih Tzu were recruited. Dogs underwent ophthalmologic examination and electroretinography, revealing hallmark retina pathological changes and an abnormal electroretinography in all affected dogs but not in unaffected dogs. WGS was performed. Non-synonymous homozygous variants were searched in coding regions of genes involved in retinal diseases/development; the criterion was that variants should only be present in affected dogs and should be absent in both unaffected and 46 genomes of dogs (from an available evolutionary database). Only one out of the 109 identified variants is predicted to harbor a high-impact consequence, a nonsense c.452A>C (p.L151X) in the JPH2 gene. The genotype of JPH2 variant in all 38 dogs was determined with Sanger sequencing. All three affected dogs, but none of the 35 unaffected, were homozygous for the nonsense variant. JPH2 has been previously found to be expressed in several excitable cells/tissues including retina photoreceptors. Hence, JPH2 is a candidate gene for PRA in Shih Tzu.
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Affiliation(s)
- G Urkasemsin
- Department of Preclinic and Applied Animal Science, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom, 73170, Thailand
| | - M Pongpanich
- Department of Mathematics and Computer Science, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand.,Age-related Inflammation and Degeneration Research Unit, Chulalongkorn University, Bangkok, 10330, Thailand
| | - L Sariya
- The Monitoring and Surveillance Center for Zoonotic Diseases in Wildlife and Exotic Animals, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom, 73170, Thailand
| | - A Kongcharoen
- Prasu-Arthorn Animal Hospital, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom, 73170, Thailand
| | - R Buddhirongawatr
- Department of Clinical Sciences and Public Health, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom, 73170, Thailand
| | - S Rungarunlert
- Department of Preclinic and Applied Animal Science, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom, 73170, Thailand
| | - J N Ferreira
- Exocrine Gland Biology and Regeneration Research Group, Faculty of Dentistry, Chulalongkorn University, Bangkok, 10330, Thailand
| | - W Chetruengchai
- Department of Pediatrics, Faculty of Medicine, Center of Excellence for Medical Genomics, Medical Genomics Cluster, Chulalongkorn University, Bangkok, 10330, Thailand.,Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, 10330, Thailand
| | - C Phokaew
- Department of Pediatrics, Faculty of Medicine, Center of Excellence for Medical Genomics, Medical Genomics Cluster, Chulalongkorn University, Bangkok, 10330, Thailand.,Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, 10330, Thailand
| | - C Srichomthong
- Department of Pediatrics, Faculty of Medicine, Center of Excellence for Medical Genomics, Medical Genomics Cluster, Chulalongkorn University, Bangkok, 10330, Thailand.,Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, 10330, Thailand
| | - V Shotelersuk
- Department of Pediatrics, Faculty of Medicine, Center of Excellence for Medical Genomics, Medical Genomics Cluster, Chulalongkorn University, Bangkok, 10330, Thailand.,Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, 10330, Thailand
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13
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Kamolvisit W, Phowthongkum P, Boonsimma P, Kuptanon C, Rojnueangnit K, Wattanasirichaigoon D, Chanvanichtrakool M, Phuaksaman C, Wiromrat P, Srichomthong C, Ittiwut C, Phokaew C, Ittiwut R, Assawapitaksakul A, Chetruengchai W, Buasong A, Suphapeetiporn K, Shotelersuk V. Rapid exome sequencing as the first-tier investigation for diagnosis of acutely and severely ill children and adults in Thailand. Clin Genet 2021; 100:100-105. [PMID: 33822359 DOI: 10.1111/cge.13963] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 03/28/2021] [Accepted: 03/30/2021] [Indexed: 12/21/2022]
Abstract
The use of rapid DNA sequencing technology in severely ill children in developed countries can accurately identify diagnoses and positively impact patient outcomes. This study sought to evaluate the outcome of Thai children and adults with unknown etiologies of critical illnesses with the deployment of rapid whole exome sequencing (rWES) in Thailand. We recruited 54 unrelated patients from 11 hospitals throughout Thailand. The median age was 3 months (range, 2 days-55 years) including 47 children and 7 adults with 52% males. The median time from obtaining blood samples to issuing the rWES report was 12 days (range, 5-27 days). A molecular diagnosis was established in 25 patients (46%), resulting in a change in clinical management for 24 patients (44%) resulting in improved clinical outcomes in 16 patients (30%). Four out of seven adult patients (57%) received the molecular diagnosis which led to a change in management. The 25 diagnoses comprised 23 different diseases. Of the 34 identified variants, 15 had never been previously reported. This study suggests that use of rWES as a first-tier investigation tool can provide tremendous benefits in critically ill patients with unknown etiology across age groups in Thailand.
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Affiliation(s)
- Wuttichart Kamolvisit
- 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
| | - Prasit Phowthongkum
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, Thailand.,Division of Medical Genetics and Genomics, Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Ponghatai Boonsimma
- 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
| | - Chulaluck Kuptanon
- Department of Pediatrics, College of Medicine, Rangsit University, Bangkok, Thailand.,Division of Genetics, Department of Medical Services, Queen Sirikit National Institute of Child Health, Ministry of Public Health, Bangkok, Thailand
| | - Kitiwan Rojnueangnit
- Division of Genetics, Department of Pediatrics, Faculty of Medicine, Thammasat University, Pathumthani, Thailand
| | - Duangrurdee Wattanasirichaigoon
- Division of Medical Genetics, Department of Pediatrics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | | | - Chutima Phuaksaman
- Department of Pediatrics, Faculty of Medicine, Naresuan University, Phitsanulok, Thailand
| | - Pattara Wiromrat
- Section of Endocrinology, Department of Pediatrics, Khon Kaen University, Khon Kaen, 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
| | - Chupong Ittiwut
- 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
| | - Chureerat Phokaew
- 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
| | - Rungnapa Ittiwut
- 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
| | - Wanna Chetruengchai
- 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
| | - Kanya Suphapeetiporn
- 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
| | - 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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14
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Isaranuwatchai S, Chanakul A, Ittiwut C, Srichomthong C, Shotelersuk V, Praditpornsilpa K, Suphapeetiporn K. Whole-Exome Sequencing Solved over 2-Decade Kidney Disease Enigma. Nephron Clin Pract 2021; 145:311-316. [PMID: 33725694 DOI: 10.1159/000514293] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 01/03/2021] [Indexed: 11/19/2022] Open
Abstract
Chronic kidney disease of unknown etiology (CKDu) has been a problem in renal practice as indefinite diagnosis may lead to inappropriate management. Here, we report a 54-year-old father diagnosed with CKDu at 33 years old and his 8-year-old son with steroid-resistant nephrotic syndrome. Using whole-exome sequencing, both were found to be heterozygous for c.737G>A (p.Arg246Gln) in LMX1B. The diagnosis of LMX1B-associated nephropathy has led to changes in the treatment plan with appropriate genetic counseling. The previously reported cases with this particular mutation were also reviewed. Most children with LMX1B-associated nephropathy had nonnephrotic proteinuria with normal renal function. Interestingly, our pediatric case presented with steroid-resistant nephrotic syndrome at 8 years old and progressed to ESRD requiring peritoneal dialysis at the age of 15 years. Our report emphasized the need of genetic testing in CKDu for definite diagnosis leading to precise management.
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Affiliation(s)
- Suramath Isaranuwatchai
- Division of Nephrology, Department of Internal Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Ankanee Chanakul
- Division of Nephrology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Chupong Ittiwut
- Department of Pediatrics, Center of Excellence for Medical Genomics, Medical Genomics Cluster, 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
| | - Chalurmpon Srichomthong
- Department of Pediatrics, Center of Excellence for Medical Genomics, Medical Genomics Cluster, 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
- Department of Pediatrics, Center of Excellence for Medical Genomics, Medical Genomics Cluster, 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
| | - Kearkiat Praditpornsilpa
- Division of Nephrology, Department of Internal Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand,
| | - Kanya Suphapeetiporn
- Department of Pediatrics, Center of Excellence for Medical Genomics, Medical Genomics Cluster, 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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15
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Sriwattanapong K, Rojnueangnit K, Theerapanon T, Srichomthong C, Porntaveetus T, Shotelersuk V. Compound Heterozygosity for a Novel Frameshift Variant Causing Fatal Infantile Liver Failure and Genotype-Phenotype Correlation of POLG c.3286C>T Variant. Int J Neonatal Screen 2021; 7:ijns7010009. [PMID: 33562887 PMCID: PMC7930966 DOI: 10.3390/ijns7010009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/24/2021] [Accepted: 02/02/2021] [Indexed: 11/16/2022] Open
Abstract
A variant in the POLG gene is the leading cause of a heterogeneous group of mitochondrial disorders. No definitive treatment is currently available. Prenatal and newborn screening have the potential to improve clinical outcome of patients affected with POLG-related disorders. We reported a 4-month-old infant who presented with developmental delay, fever, and diarrhea. Within two weeks after hospital admission, the patient developed hepatic failure and died. Liver necropsy demonstrated an extensive loss of hepatocytes and bile duct proliferations. Trio-whole exome sequencing identified that the patient was compound heterozygous for a novel frameshift variant c.3102delG (p.Lys1035Serfs*59) and a common variant c.3286C>T (p.Arg1096Cys) in POLG (NM_002693.3) inherited from the mother and father, respectively. The c.3102delG (p.Lys1035Serfs*59) was a null variant and classified as pathogenic according to the American College of Medical Genetics and Genomics Standards and Guidelines. Prenatal genetic screenings using rapid whole exome sequencing successfully detected the heterozygous c.3286C>T variant in the following pregnancy and the normal alleles in the other one. Both children had been healthy. We reviewed all 34 cases identified with the POLG c.3286C>T variant and found that all 15 compound heterozygous cases had two missense variants except our patient who had the truncating variant and showed the earliest disease onset, rapid deterioration, and the youngest death. All homozygous cases had disease onset before age 2 and developed seizure. Here, we report a novel POLG variant expanding the genotypic spectrum, demonstrate the successful use of exome sequencing for prenatal and neonatal screenings of POLG-related disorders, and show the genotype-phenotype correlation of the common c.3286C>T variant.
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Affiliation(s)
- Kanokwan Sriwattanapong
- Genomics and Precision Dentistry Research Unit, Department of Physiology, Faculty of Dentistry, Chulalongkorn University, Bangkok 10330, Thailand; (K.S.); (T.T.)
| | - Kitiwan Rojnueangnit
- Department of Pediatrics, Faculty of Medicine, Thammasat University, Pathumthani 12120, Thailand;
| | - Thanakorn Theerapanon
- Genomics and Precision Dentistry Research Unit, Department of Physiology, Faculty of Dentistry, Chulalongkorn University, Bangkok 10330, Thailand; (K.S.); (T.T.)
| | - Chalurmpon Srichomthong
- Center of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand; (C.S.); (V.S.)
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok 10330, Thailand
| | - Thantrira Porntaveetus
- Genomics and Precision Dentistry Research Unit, Department of Physiology, Faculty of Dentistry, Chulalongkorn University, Bangkok 10330, Thailand; (K.S.); (T.T.)
- Correspondence: ; Tel.: +66-02218-8695
| | - Vorasuk Shotelersuk
- Center of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand; (C.S.); (V.S.)
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok 10330, Thailand
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16
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Yeetong P, Chunharas C, Pongpanich M, Bennett MF, Srichomthong C, Pasutharnchat N, Suphapeetiporn K, Bahlo M, Shotelersuk V. Founder effect of the TTTCA repeat insertions in SAMD12 causing BAFME1. Eur J Hum Genet 2020; 29:343-348. [PMID: 32973343 DOI: 10.1038/s41431-020-00729-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 07/21/2020] [Accepted: 09/08/2020] [Indexed: 11/10/2022] Open
Abstract
Benign adult familial myoclonic epilepsy type 1 (BAFME1) in several Japanese and Chinese families has recently been found to be caused by pentanucleotide repeat expansions in SAMD12. We identified a Thai family with six members affected with BAFME. Microsatellite studies suggested a linkage to the BAFME1 region on chromosome 8q24. Subsequently, long-read whole-genome sequencing showed the (TTTTA)446(TTTCA)149 in intron 4 of SAMD12 in an affected member. Repeat-primed PCR and long-range PCR revealed that the pentanucleotide repeat expansions segregated with the disease status. Our Thai family is the first non-Japanese and non-Chinese family with BAFME1. SNP array showed that the aberrant repeats had the same haplotype as those previously determined in Japanese and Chinese patients suggesting a common ancestry. The variant is estimated to arise ~12,000 years ago.
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Affiliation(s)
- Patra Yeetong
- Division of Human Genetics, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Chaipat Chunharas
- Division of Neurology, Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.,Chulalongkorn Cognitive, Clinical & Computational Neuroscience, Chulalongkorn University, Bangkok, Thailand
| | - Monnat Pongpanich
- Department of Mathematics and Computer Science, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Mark F Bennett
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3052, Australia.,Epilepsy Research Centre, Department of Medicine, The University of Melbourne, Austin Health, Heidelberg, VIC, 3084, Australia
| | - Chalurmpon Srichomthong
- Center of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand.,Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, 10330, Thailand
| | - Nath Pasutharnchat
- Division of Neurology, Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Kanya Suphapeetiporn
- Center of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand.,Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, 10330, Thailand
| | - Melanie Bahlo
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3052, Australia
| | - Vorasuk Shotelersuk
- Center of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand. .,Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, 10330, Thailand.
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17
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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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18
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Boonsimma P, Michael Gasser M, Netbaramee W, Wechapinan T, Srichomthong C, Ittiwut C, Wagner M, Krenn M, Zimprich F, Abicht A, Biskup S, Roser T, Borggraefe I, Suphapeetiporn K, Shotelersuk V. Mutational and phenotypic expansion of ATP1A3-related disorders: Report of nine cases. Gene 2020; 749:144709. [PMID: 32339621 DOI: 10.1016/j.gene.2020.144709] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 09/17/2019] [Revised: 04/18/2020] [Accepted: 04/23/2020] [Indexed: 11/24/2022]
Abstract
BACKGROUND Mutations in the ATP1A3 gene are known to be the cause of three distinct neurological syndromes including alternating hemiplegia of childhood (AHC), rapid-onset dystonia parkinsonism (RDP) and cerebellar ataxia, arefexia, pes cavus, optic atrophy and sensorineural hearing impairment (CAPOS). Recent studies have suggested the broader diversity of ATP1A3-related disorders. This study aimed to investigate the clinical spectrum in patients carrying causative mutations within the ATP1A3 gene. METHOD The medical histories of nine unrelated patients with diverse phenotypes harboring variants in ATP1A3 were retrospectively analyzed after they were referred to a tertiary epilepsy center in one of the two different health care systems (Germany or Thailand). Clinical features, neurophysiological data, imaging results, genetic characteristics and treatments were reviewed. RESULTS Three patients harbor novel mutations in the ATP1A3 gene. Atypical clinical features and imaging findings were observed in two cases, one with hemiplegia-hemiconvulsion-epilepsy syndrome, and the other with neurodegeneration with brain iron accumulation. All nine patients presented with intellectual impairment. Alternating hemiplegia of childhood (AHC) was the most common phenotype (67%). Flunarizine and topiramate led to symptom reduction in 83% and 25% of AHC cases administered, respectively. CONCLUSION The present case series expands the clinical and genetic spectrum of ATP1A3-related disorders.
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Affiliation(s)
- Ponghatai Boonsimma
- Division of Medical Genetics and Metabolism, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand; Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok 10330, Thailand
| | - Marius Michael Gasser
- Division of Pediatric Neurology, Developmental Medicine and Social Pediatrics, Department of Pediatrics, Dr. von Haunersches Childrens Hospital, Ludwig Maximilians University of Munich, Germany
| | - Wiracha Netbaramee
- Division of Neurology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Thanin Wechapinan
- Division of Neurology, Department of Pediatrics, Faculty of Medicine, Queen Sirikit National Institute of Child Health, Bangkok 10400, Thailand
| | - Chalurmpon Srichomthong
- Division of Medical Genetics and Metabolism, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand; Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok 10330, Thailand
| | - Chupong Ittiwut
- Division of Medical Genetics and Metabolism, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand; Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok 10330, Thailand
| | - Matias Wagner
- Institute of Human Genetics, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany; Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany; Institute for Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Martin Krenn
- Institute of Human Genetics, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany; Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Fritz Zimprich
- Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Angela Abicht
- Medical Genetic Center Munich, Munich, Germany; Department of Neurology, Friedrich-Baur-Institute, Klinikum der Ludwig-Maximilians-Universität München, Munich, Germany
| | - Saskia Biskup
- Praxis für Humangenetik und CeGaT GmbH, Paul-Ehrlich-Str. 23, Tuebingen, Germany
| | - Timo Roser
- Division of Pediatric Neurology, Developmental Medicine and Social Pediatrics, Department of Pediatrics, Dr. von Haunersches Childrens Hospital, Ludwig Maximilians University of Munich, Germany
| | - Ingo Borggraefe
- Division of Pediatric Neurology, Developmental Medicine and Social Pediatrics, Department of Pediatrics, Dr. von Haunersches Childrens Hospital, Ludwig Maximilians University of Munich, Germany; Comprehensive Epilepsy Center, Ludwig Maxiliams University of Munich, Germany
| | - Kanya Suphapeetiporn
- Division of Medical Genetics and Metabolism, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand; Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok 10330, Thailand.
| | - Vorasuk Shotelersuk
- Division of Medical Genetics and Metabolism, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand; Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok 10330, Thailand
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19
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Nitayavardhana I, Theerapanon T, Srichomthong C, Piwluang S, Wichadakul D, Porntaveetus T, Shotelersuk V. Four novel mutations of FAM20A in amelogenesis imperfecta type IG and review of literature for its genotype and phenotype spectra. Mol Genet Genomics 2020; 295:923-931. [PMID: 32246227 DOI: 10.1007/s00438-020-01668-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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: 01/14/2020] [Accepted: 03/18/2020] [Indexed: 02/07/2023]
Abstract
Amelogenesis imperfecta type IG (AI1G) is caused by mutations in FAM20A. Genotypic and phenotypic features of AI1G are diverse and their full spectra remain to be characterized. The aim of this study was to identify and summarize variants in FAM20A in a broad population of patients with AI1G. We identified a Thai female (Pt-1) and a Saudi male (Pt-2) affected with AI1G. Both had hypoplastic enamel, gingival hyperplasia, and intrapulpal calcification. Pt-1 also had rapidly progressive embedding of unerupted teeth, early eruption of permanent teeth, and spontaneous dental infection. Uniquely, Pt-2 had all permanent teeth erupted which was uncommon in AI1G patients. Whole exome sequencing (WES) identified that Pt-1 was heterozygous for FAM20A, c.758A > G (p.Tyr253Cys), inherited from her father. The mutation on maternal allele was not detected by WES. Pt-2 possessed compound heterozygous mutations, c.1248dupG (p.Phe417Valfs*7); c.1081C > T (p.Arg361Cys) in FAM20A. Array comparative genomic hybridization (aCGH), cDNA sequencing, and whole genome sequencing successfully identified 7531 bp deletion on Pt-1's maternal allele. This was the largest FAM20A deletion ever found. A review of all 70 patients from 50 independent families with AI1G (including two families in this study) showed that the penetrance of hypoplastic enamel and gingival hyperplasia was complete. Unerupted permanent teeth were found in all 70 patients except Pt-2. Exons 1 and 11 were mutation-prone. Most mutations were frameshift. Certain variants showed founder effect. To conclude, this study reviews and expands phenotypic and genotypic spectra of AI1G. A large deletion missed by WES can be detected by WGS. Hypoplastic enamel, gingival hyperplasia, and unerupted permanent teeth prompt genetic testing of FAM20A. Screening of nephrocalcinosis, early removal of embedded teeth, and monitoring of dental infection are recommended.
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Affiliation(s)
- Issree Nitayavardhana
- Geriatric Dentistry and Special Patients Care International Program, Faculty of Dentistry, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Thanakorn Theerapanon
- Genomics and Precision Dentistry Research Unit, Department of Physiology, Faculty of Dentistry, Chulalongkorn University, Bangkok, 10330, Thailand.,Center of Excellence for Regenerative Dentistry, Faculty of Dentistry, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Chalurmpon Srichomthong
- Center of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand.,Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, 10330, Thailand
| | - Sakkayaphab Piwluang
- Department of Computer Engineering, Master of Science in Software Engineering Program, Faculty of Engineering, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Duangdao Wichadakul
- Chulalongkorn Big Data Analytics and IoT Center (CUBIC), Department of Computer Engineering, Faculty of Engineering, Chulalongkorn University, Bangkok, 10330, Thailand.,Center of Excellence in Systems Biology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand.,Research Group on Applied Computer Engineering Technology for Medicine and Healthcare, Faculty of Engineering, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Thantrira Porntaveetus
- Geriatric Dentistry and Special Patients Care International Program, Faculty of Dentistry, Chulalongkorn University, Bangkok, 10330, Thailand. .,Genomics and Precision Dentistry Research Unit, Department of Physiology, Faculty of Dentistry, Chulalongkorn University, Bangkok, 10330, Thailand.
| | - Vorasuk Shotelersuk
- Center of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand.,Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, 10330, Thailand
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20
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Hemwong N, Phokaew C, Srichomthong C, Tongkobpetch S, Srilanchakon K, Supornsilchai V, Suphapeetiporn K, Porntaveetus T, Shotelersuk V. A patient with combined pituitary hormone deficiency and osteogenesis imperfecta associated with mutations in LHX4 and COL1A2. J Adv Res 2019; 21:121-127. [PMID: 32071780 PMCID: PMC7015471 DOI: 10.1016/j.jare.2019.10.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [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: 08/14/2019] [Revised: 10/13/2019] [Accepted: 10/15/2019] [Indexed: 11/30/2022] Open
Abstract
The mutations in two different genes should be sought in the patients with complex phenotypes. The c.1531G>T in COL1A2 leading to OI and c.364C>T (p.R122W) in LHX4 to CPHD were found in a Thai boy. The incomplete penetrance and loss-of-function are the features of p.R122W mutation in LHX4. The mutation spectra of COL1A2 and LHX4 and pathomechanism of LHX4 are expanded.
Genetic disorders have been shown to co-occur in individual patient. A Thai boy with features of osteogenesis imperfecta (OI) and combined pituitary hormone deficiency (CPHD) was identified. The causative mutations were investigated by whole exome and Sanger sequencing. Pathogenicity and pathomechanism of the variants were studied by luciferase assay. The proband was found to harbor a novel de novo heterozygous missense mutation, c.1531G > T (p.G511C), in COL1A2 leading to OI and a heterozygous missense variant, c.364C > T (p.R122W), in LHX4. The LHX4 p.R122W has never been reported to cause CPHD. The variant was predicted to be deleterious and found in the highly conserved LIM2 domain of LHX4. The luciferase assays revealed that the p.R122W was unable to activate POU1F1, GH1, and TSHB promoters, validating its pathogenic effect in CPHD. Moreover, the variant did not alter the function of wild-type LHX4, indicating its hypomorphic pathomechanism. In conclusion, the novel de novo heterozygous p.G511C mutation in COL1A2 and the heterozygous pathogenic p.R122W mutation in LHX4 were demonstrated in a patient with OI and CPHD. This study proposes that the mutations in two different genes should be sought in the patients with clinical features unable to be explained by a mutation in one gene.
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Affiliation(s)
- Nalinee Hemwong
- Medical Sciences Program, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand.,Center of Excellence for Regenerative Dentistry, Faculty of Dentistry, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Chureerat Phokaew
- Center of Excellence for Medical Genomics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand.,Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, 10330, Thailand
| | - Chalurmpon Srichomthong
- Center of Excellence for Medical Genomics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand.,Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, 10330, Thailand
| | - Siraprapa Tongkobpetch
- Center of Excellence for Medical Genomics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand.,Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, 10330, Thailand
| | - Khomsak Srilanchakon
- Division of Endocrinology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Vichit Supornsilchai
- Division of Endocrinology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Kanya Suphapeetiporn
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, 10330, Thailand.,Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, 10330, Thailand
| | - Thantrira Porntaveetus
- Genomics and Precision Dentistry Research Unit, Department of Physiology, Faculty of Dentistry, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Vorasuk Shotelersuk
- Center of Excellence for Medical Genomics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand.,Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, 10330, Thailand
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21
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Suthiworachai C, Tammachote R, Srichomthong C, Ittiwut R, Suphapeetiporn K, Sahakitrungruang T, Shotelersuk V. Identification and Functional Analysis of Six DAX1 Mutations in Patients With X-Linked Adrenal Hypoplasia Congenita. J Endocr Soc 2018; 3:171-180. [PMID: 30620004 PMCID: PMC6316980 DOI: 10.1210/js.2018-00270] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 12/07/2018] [Indexed: 11/19/2022] Open
Abstract
Context DAX1 (NR0B1) mutations cause X-linked adrenal hypoplasia congenita (AHC) and hypogonadotropic hypogonadism (HH) in affected male patients. Affected individuals typically present with early-onset adrenal insufficiency and develop HH during puberty. Rare cases can present with late-onset adrenal insufficiency or other unusual phenotypes. Objectives We sought to identify and functionally characterize DAX1 mutations in seven Thai male subjects in six families with X-linked AHC. Patients and Methods Six patients had classic phenotypes with early-onset adrenal failure. One patient presented with late-onset Addison disease at 17 years. In the early-onset group, one patient had GnRH-independent sexual precocity at 3 years of age, and another patient had growth hormone deficiency. The DAX1 gene was sequenced from all patients, and the transcriptional activities of the identified mutations were assessed in vitro using luciferase assays. Results DAX1 mutations were identified in all patients, including three novel mutations [c.363delG (p.Gly122Valfs*142), c.1062delC (p.Ala355Profs*17), and c.1156C>T (p.Leu386Phe)] and three known mutations [c.1148_1149delGG (p.Gly383Aspfs*5), c.501_502insG (p.Ala170Argfs*15), and c.805_807delGTC (p.Val269del)]. Functional studies showed that the DAX1 mutants had lower levels of repressor activity on the StAR gene promoter compared with the wild-type DAX-1 protein. Conclusions This study describes unusual phenotypes and three novel mutations, extending the phenotypic and mutational spectra of DAX1 mutations.
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Affiliation(s)
- Chanisara Suthiworachai
- Biological Sciences Program, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Rachaneekorn Tammachote
- Biological Sciences Program, Faculty of Science, Chulalongkorn University, Bangkok, Thailand.,Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Chalurmpon Srichomthong
- Center of Excellence for Medical Genetics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.,Excellence Center for Medical Genetics, Thai Red Cross Society, King Chulalongkorn Memorial Hospital, Bangkok, Thailand
| | - Rungnapa Ittiwut
- Center of Excellence for Medical Genetics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.,Excellence Center for Medical Genetics, Thai Red Cross Society, King Chulalongkorn Memorial Hospital, Bangkok, Thailand
| | - Kanya Suphapeetiporn
- Center of Excellence for Medical Genetics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.,Excellence Center for Medical Genetics, Thai Red Cross Society, King Chulalongkorn Memorial Hospital, Bangkok, Thailand
| | - Taninee Sahakitrungruang
- Division of Pediatric Endocrinology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Vorasuk Shotelersuk
- Center of Excellence for Medical Genetics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.,Excellence Center for Medical Genetics, Thai Red Cross Society, King Chulalongkorn Memorial Hospital, Bangkok, Thailand
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22
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Porntaveetus T, Theerapanon T, Srichomthong C, Shotelersuk V. Cole-Carpenter syndrome in a patient from Thailand. Am J Med Genet A 2018; 176:1706-1710. [DOI: 10.1002/ajmg.a.40358] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 05/22/2018] [Indexed: 11/10/2022]
Affiliation(s)
- Thantrira Porntaveetus
- Genomics and Precision Dentistry Research Unit; Department of Physiology, Faculty of Dentistry, Chulalongkorn University; Bangkok Thailand
| | - Thanakorn Theerapanon
- Excellence Center in Regenerative Dentistry, Faculty of Dentistry; 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 Medical Genetics; 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 Medical Genetics; King Chulalongkorn Memorial Hospital, the Thai Red Cross Society; Bangkok Thailand
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23
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Kuptanon C, Srichomthong C, Sangsin A, Kovitvanitcha D, Suphapeetiporn K, Shotelersuk V. The most 5' truncating homozygous mutation of WNT1 in siblings with osteogenesis imperfecta with a variable degree of brain anomalies: a case report. BMC Med Genet 2018; 19:117. [PMID: 30012084 PMCID: PMC6048891 DOI: 10.1186/s12881-018-0639-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [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: 01/25/2018] [Accepted: 07/03/2018] [Indexed: 01/22/2023]
Abstract
Background WNT1 mutations cause bone fragility as well as brain anomalies. There are some reported cases of WNT1 mutations with normal cognition. Genotype and phenotype correlation of WNT1 mutations has not been established. Case presentation Here we present two female siblings with osteogenesis imperfecta (OI) born to a consanguineous couple. Both sustained severe bone deformities. However, only the younger had severe brain anomalies resulting in an early death from pneumonia, while the older had normal intellectual development. Next generation sequencing showed a homozygous mutation, c.6delG, p.Leu3Serfs*36 in WNT1. To our knowledge, it is the most 5′ truncating mutation to date. Conclusion This report emphasizes the intrafamilial variability of brain anomalies found in this OI type and suggests that WNT1 may not be necessary for normal human cognitive development.
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Affiliation(s)
- Chulaluck Kuptanon
- Department of Pediatrics, Queen Sirikit National Institute of Child Health, Bangkok, 10400, Thailand
| | - Chalurmpon Srichomthong
- Center of Excellence for Medical Genomics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand.,Excellence Center for Medical Genetics, the Thai Red Cross Society, King Chulalongkorn Memorial Hospital, Bangkok, 10330, Thailand
| | - Apiruk Sangsin
- Center of Excellence for Medical Genomics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand.,Excellence Center for Medical Genetics, the Thai Red Cross Society, King Chulalongkorn Memorial Hospital, Bangkok, 10330, Thailand.,Department of Orthopaedics, Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Dool Kovitvanitcha
- Department of Orthopedics, Queen Sirikit National Institute of Child Health, Bangkok, 10400, Thailand
| | - Kanya Suphapeetiporn
- Center of Excellence for Medical Genomics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand. .,Excellence Center for Medical Genetics, the Thai Red Cross Society, King Chulalongkorn Memorial Hospital, Bangkok, 10330, Thailand. .,Division of Medical Genetics and Metabolism, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Sor Kor Building 11th floor, Bangkok, 10330, Thailand.
| | - Vorasuk Shotelersuk
- Center of Excellence for Medical Genomics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand.,Excellence Center for Medical Genetics, the Thai Red Cross Society, King Chulalongkorn Memorial Hospital, Bangkok, 10330, Thailand
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24
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Porntaveetus T, Osathanon T, Nowwarote N, Pavasant P, Srichomthong C, Suphapeetiporn K, Shotelersuk V. Dental properties, ultrastructure, and pulp cells associated with a novel DSPP
mutation. Oral Dis 2018; 24:619-627. [DOI: 10.1111/odi.12801] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 10/28/2017] [Accepted: 10/30/2017] [Indexed: 12/12/2022]
Affiliation(s)
- T Porntaveetus
- Craniofacial Genetics and Stem Cells Research Group; Faculty of Dentistry; Chulalongkorn University; Bangkok Thailand
- Department of Physiology; Faculty of Dentistry; Chulalongkorn University; Bangkok Thailand
| | - T Osathanon
- Department of Physiology; Faculty of Dentistry; Chulalongkorn University; Bangkok Thailand
- Mineralized Tissue Research Unit and Department of Anatomy; Faculty of Dentistry; Chulalongkorn University; Bangkok Thailand
| | - N Nowwarote
- Mineralized Tissue Research Unit and Department of Anatomy; Faculty of Dentistry; Chulalongkorn University; Bangkok Thailand
| | - P Pavasant
- Mineralized Tissue Research Unit and Department of Anatomy; Faculty of Dentistry; Chulalongkorn University; Bangkok Thailand
| | - C Srichomthong
- Center of Excellence for Medical Genetics; Department of Pediatrics; Faculty of Medicine; Chulalongkorn University; Bangkok Thailand
- Excellence Center for Medical Genetics; King Chulalongkorn Memorial Hospital; the Thai Red Cross Society; Bangkok Thailand
| | - K Suphapeetiporn
- Center of Excellence for Medical Genetics; Department of Pediatrics; Faculty of Medicine; Chulalongkorn University; Bangkok Thailand
- Excellence Center for Medical Genetics; King Chulalongkorn Memorial Hospital; the Thai Red Cross Society; Bangkok Thailand
| | - V Shotelersuk
- Center of Excellence for Medical Genetics; Department of Pediatrics; Faculty of Medicine; Chulalongkorn University; Bangkok Thailand
- Excellence Center for Medical Genetics; King Chulalongkorn Memorial Hospital; the Thai Red Cross Society; Bangkok Thailand
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25
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Porntaveetus T, Abid MF, Theerapanon T, Srichomthong C, Ohazama A, Kawasaki K, Kawasaki M, Suphapeetiporn K, Sharpe PT, Shotelersuk V. Expanding the Oro-Dental and Mutational Spectra of Kabuki Syndrome and Expression of KMT2D and KDM6A in Human Tooth Germs. Int J Biol Sci 2018; 14:381-389. [PMID: 29725259 PMCID: PMC5930470 DOI: 10.7150/ijbs.23517] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [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: 10/27/2017] [Accepted: 02/26/2018] [Indexed: 12/12/2022] Open
Abstract
Kabuki syndrome is a rare genetic disorder characterized by distinct dysmorphic facial features, intellectual disability, and multiple developmental abnormalities. Despite more than 350 documented cases, the oro-dental spectrum associated with kabuki syndrome and expression of KMT2D (histone-lysine N-methyltransferase 2D) or KDM6A (lysine-specific demethylase 6A) genes in tooth development have not been well defined. Here, we report seven unrelated Thai patients with Kabuki syndrome having congenital absence of teeth, malocclusion, high-arched palate, micrognathia, and deviated tooth shape and size. Exome sequencing successfully identified that six patients were heterozygous for mutations in KMT2D, and one in KDM6A. Six were novel mutations, of which five were in KMT2D and one in KDM6A. They were truncating mutations including four frameshift deletions and two nonsense mutations. The predicted non-functional KMT2D and KDM6A proteins are expected to cause disease by haploinsufficiency. Our study expands oro-dental, medical, and mutational spectra associated with Kabuki syndrome. We also demonstrate for the first time that KMT2D and KDM6A are expressed in the dental epithelium of human tooth germs.
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Affiliation(s)
- Thantrira Porntaveetus
- Craniofacial Genetics and Stem Cells Research Group, Department of Physiology, Faculty of Dentistry, Chulalongkorn University, Bangkok 10330, Thailand
| | - Mushriq F Abid
- Centre for Craniofacial and Regenerative Biology, Dental Institute, King's College London, London, SE1 9RT, UK
| | - Thanakorn Theerapanon
- Excellence Center in Regenerative Dentistry, Faculty of Dentistry, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Chalurmpon Srichomthong
- Center of Excellence for Medical Genetics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand.,Excellence Center for Medical Genetics, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok 10330, Thailand
| | - Atsushi Ohazama
- Division of Oral Anatomy, Niigata University, Niigata 951-8514, Japan
| | | | - Maiko Kawasaki
- Division of Oral Anatomy, Niigata University, Niigata 951-8514, Japan
| | - Kanya Suphapeetiporn
- Center of Excellence for Medical Genetics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand.,Excellence Center for Medical Genetics, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok 10330, Thailand
| | - Paul T Sharpe
- Centre for Craniofacial and Regenerative Biology, Dental Institute, King's College London, London, SE1 9RT, UK
| | - Vorasuk Shotelersuk
- Center of Excellence for Medical Genetics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand.,Excellence Center for Medical Genetics, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok 10330, Thailand
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26
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Chaiyasap P, Ittiwut C, Srichomthong C, Sangsin A, Suphapeetiporn K, Shotelersuk V. Massive parallel sequencing as a new diagnostic approach for phenylketonuria and tetrahydrobiopterin-deficiency in Thailand. BMC Med Genet 2017; 18:102. [PMID: 28915855 PMCID: PMC5602921 DOI: 10.1186/s12881-017-0464-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Accepted: 09/08/2017] [Indexed: 01/04/2023]
Abstract
BACKGROUND Hyperphenylalaninemia (HPA) can be classified into phenylketonuria (PKU) which is caused by mutations in the phenylalanine hydroxylase (PAH) gene, and BH4 deficiency caused by alterations in genes involved in tetrahydrobiopterin (BH4) biosynthesis pathway. Dietary restriction of phenylalanine is considered to be the main treatment of PKU to prevent irreversible intellectual disability. However, the same dietary intervention in BH4 deficiency patients is not as effective, as BH4 is also a cofactor in many neurotransmitter syntheses. METHOD We utilized next generation sequencing (NGS) technique to investigate four unrelated Thai patients with hyperphenylalaninemia. RESULT We successfully identified all eight mutant alleles in PKU or BH4-deficiency associated genes including three novel mutations, one in PAH and two in PTS, thus giving a definite diagnosis to these patients. Appropriate management can then be provided. CONCLUSION This study identified three novel mutations in either the PAH or PTS gene and supported the use of NGS as an alternative molecular genetic approach for definite diagnosis of hyperphenylalaninemia, thus leading to proper management of these patients in Thailand.
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Affiliation(s)
- Pongsathorn Chaiyasap
- Center of Excellence for Medical Genetics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Chupong Ittiwut
- Center of Excellence for Medical Genetics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
- Excellence Center for Medical Genetics, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, 10330, Thailand
| | - Chalurmpon Srichomthong
- Center of Excellence for Medical Genetics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
- Excellence Center for Medical Genetics, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, 10330, Thailand
| | - Apiruk Sangsin
- Department of Orthopedics, Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Kanya Suphapeetiporn
- Center of Excellence for Medical Genetics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand.
- Excellence Center for Medical Genetics, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, 10330, Thailand.
- Division of Medical Genetics and Metabolism, Department of Pediatrics, Sor Kor Building 11th floor, King Chulalongkorn Memorial Hospital, Bangkok, 10330, Thailand.
| | - Vorasuk Shotelersuk
- Center of Excellence for Medical Genetics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
- Excellence Center for Medical Genetics, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, 10330, Thailand
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27
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Porntaveetus T, Srichomthong C, Suphapeetiporn K, Shotelersuk V. Monoallelic FGFR3
and Biallelic ALPL
mutations in a Thai girl with hypochondroplasia and hypophosphatasia. Am J Med Genet A 2017; 173:2747-2752. [DOI: 10.1002/ajmg.a.38370] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 06/16/2017] [Accepted: 06/25/2017] [Indexed: 01/22/2023]
Affiliation(s)
- Thantrira Porntaveetus
- Craniofacial Genetics and Stem Cells Research Group, Faculty of Dentistry, Department of Physiology; Chulalongkorn University; Bangkok Thailand
| | - Chalurmpon Srichomthong
- Center of Excellence for Medical Genetics, Faculty of Medicine, Department of Pediatrics; Chulalongkorn University; Bangkok Thailand
- Excellence Center for Medical Genetics, King Chulalongkorn Memorial Hospital; The Thai Red Cross Society; Bangkok Thailand
| | - Kanya Suphapeetiporn
- Center of Excellence for Medical Genetics, Faculty of Medicine, Department of Pediatrics; Chulalongkorn University; Bangkok Thailand
- Excellence Center for Medical Genetics, King Chulalongkorn Memorial Hospital; The Thai Red Cross Society; Bangkok Thailand
| | - Vorasuk Shotelersuk
- Center of Excellence for Medical Genetics, Faculty of Medicine, Department of Pediatrics; Chulalongkorn University; Bangkok Thailand
- Excellence Center for Medical Genetics, King Chulalongkorn Memorial Hospital; The Thai Red Cross Society; Bangkok Thailand
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28
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Porntaveetus T, Srichomthong C, Ohazama A, Suphapeetiporn K, Shotelersuk V. A novel GJA1 mutation in oculodentodigital dysplasia with extensive loss of enamel. Oral Dis 2017; 23:795-800. [PMID: 28258662 DOI: 10.1111/odi.12663] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [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: 01/03/2017] [Revised: 02/11/2017] [Accepted: 02/23/2017] [Indexed: 01/18/2023]
Abstract
OBJECTIVE To characterize clinical features and identify genetic causes of a patient with oculodentodigital dysplasia (ODDD). SUBJECTS AND METHODS Clinical, dental, radiological features were obtained. DNA was collected from an affected Thai family. Whole-exome sequencing was employed to identify the disease-causing mutation causing ODDD. The presence of the identified variant was confirmed by Sanger sequencing. RESULTS The proband suffered with extensive enamel hypoplasia, polysyndactyly and clinodactyly of the 3rd-5th fingers, microphthalmia, and unique facial characteristics of ODDD. Mutation analysis revealed a novel missense mutation, c. 31C>A, p.L11I, in the GJA1 gene which encodes gap junction channel protein connexin 43. Bioinformatics and structural modeling suggested the mutation to be pathogenic. The parents did not harbor the mutation. CONCLUSIONS This study identified a novel de novo mutation in the GJA1 gene associated with severe tooth defects. These results expand the mutation spectrum and understanding of pathologic dental phenotypes related to ODDD.
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Affiliation(s)
- T Porntaveetus
- Department of Physiology, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand.,STAR on Craniofacial and Skeletal Disorders, Chulalongkorn University, Bangkok, Thailand
| | - C Srichomthong
- Department of Pediatrics, Center of Excellence for Medical Genetics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.,Excellence Center for Medical Genetics, King Chulalongkorn Memorial Hospital, Bangkok, Thailand
| | - A Ohazama
- Division of Oral Anatomy, Niigata University, Niigata, Japan
| | - K Suphapeetiporn
- Department of Pediatrics, Center of Excellence for Medical Genetics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.,Excellence Center for Medical Genetics, King Chulalongkorn Memorial Hospital, Bangkok, Thailand
| | - V Shotelersuk
- Department of Pediatrics, Center of Excellence for Medical Genetics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.,Excellence Center for Medical Genetics, King Chulalongkorn Memorial Hospital, Bangkok, Thailand
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29
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Sangsin A, Kuptanon C, Srichomthong C, Pongpanich M, Suphapeetiporn K, Shotelersuk V. Two novel compound heterozygous BMP1 mutations in a patient with osteogenesis imperfecta: a case report. BMC Med Genet 2017; 18:25. [PMID: 28257626 PMCID: PMC5336636 DOI: 10.1186/s12881-017-0384-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [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: 09/28/2016] [Accepted: 02/27/2017] [Indexed: 11/10/2022]
Abstract
Background Osteogenesis imperfecta (OI) is a collagen-related bone dysplasia leading to a susceptibility to fractures. OI can be caused by mutations in several genes including BMP1. It encodes two isoforms, bone morphogenetic protein 1 (BMP1) and mammalian tolloid (mTLD); both have proteolytic activity to remove the C-propeptide from procollagen. Case presentation We report a Thai OI patient who had his first fracture at the age of three months. Using next generation sequencing, we successfully identified two novel compound heterozygous BMP1 mutations. One mutation, c.796_797delTT (p.Phe266Argfs*25) affects both BMP1 and mTLD isoforms, while the other, c.2108-2A > G, affects only the BMP1 isoform. Preservation of the mTLD may explain the relatively less severe clinical phenotype in this patient. Intravenous bisphosphonate was given from the age of 8 months to 5 years. He was free from fractures for 9 months before discontinuation. Conclusion This case expands the mutation spectrum of BMP1, strengthens the correlation between genotype and phenotype, and supports the benefits of bisphosphonate in OI patients with BMP1 mutations.
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Affiliation(s)
- Apiruk Sangsin
- Department of Orthopaedics, Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand.,Center of Excellence for Medical Genetics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand.,Excellence Center for Medical Genetics, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, 10330, Thailand
| | - Chulaluck Kuptanon
- Department of Pediatrics, Queen Sirikit National Institute of Child Health, Bangkok, 10400, Thailand
| | - Chalurmpon Srichomthong
- Center of Excellence for Medical Genetics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand.,Excellence Center for Medical Genetics, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, 10330, Thailand
| | - Monnat Pongpanich
- Department of Mathematics and Computer Science, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand.,Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Kanya Suphapeetiporn
- Center of Excellence for Medical Genetics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand. .,Excellence Center for Medical Genetics, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, 10330, Thailand. .,Division of Medical Genetics and Metabolism, Department of Pediatrics, King Chulalongkorn Memorial Hospital, Sor Kor Building 11th floor, Bangkok, 10330, Thailand.
| | - Vorasuk Shotelersuk
- Center of Excellence for Medical Genetics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand.,Excellence Center for Medical Genetics, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, 10330, Thailand
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30
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Chaiyasap P, Srichomthong C, Tongkobpetch S, Suphapeetiporn K, Shotelersuk V. Identification of a mitochondrial 12S rRNA A1555G mutation causing aminoglycoside-induced deafness in a large Thai family. ASIAN BIOMED 2017. [DOI: 10.5372/1905-7415.0902.389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Abstract
Background
Hearing loss is among the most frequent sensory disorders. Preventable causes include medications given to genetically susceptible individuals. Several families around the world with an A1555G mitochondrial mutation who became profoundly deaf after receiving aminoglycosides have been described. However, none has been reported in Thailand.
Objectives
To identify the cause of hearing loss of a large Thai family with 11 members who reportedly turned deaf after receiving antibiotics.
Methods
We obtained blood samples from 5 members; 4 of whom had hearing loss. Mutation analyses were performed using molecular techniques including polymerase chain reaction, Sanger sequencing, and restriction fragment length polymorphism.
Results
All 4 affected members were found to harbor the same A1555G mitochondrial mutation, while the unaffected had only the wild-type A.
Conclusions
We have identified the mitochondrial mutation leading to aminoglycoside-induced hearing loss in a Thai population. Raising awareness for medical practitioners of this genetic susceptibility in Thailand is warranted. Avoidance of certain medications in these individuals would prevent this acquired permanent hearing loss.
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Affiliation(s)
- Pongsathorn Chaiyasap
- Interdepartment of Biomedical Sciences , Faculty of Graduate School , Chulalongkorn University , Bangkok 10330 , Thailand
| | - Chalurmpon Srichomthong
- Center of Excellence for Medical Genetics , Department of Pediatrics, Faculty of Medicine , Chulalongkorn University , Bangkok 10330 , Thailand
- Excellence Center for Medical Genetics , King Chulalongkorn Memorial Hospital, the Thai Red Cross , Bangkok 10330 , Thailand
| | - Siraprapa Tongkobpetch
- Center of Excellence for Medical Genetics , Department of Pediatrics, Faculty of Medicine , Chulalongkorn University , Bangkok 10330 , Thailand
- Excellence Center for Medical Genetics , King Chulalongkorn Memorial Hospital, the Thai Red Cross , Bangkok 10330 , Thailand
| | - Kanya Suphapeetiporn
- Center of Excellence for Medical Genetics , Department of Pediatrics, Faculty of Medicine , Chulalongkorn University , Bangkok 10330 , Thailand
- Excellence Center for Medical Genetics , King Chulalongkorn Memorial Hospital, the Thai Red Cross , Bangkok 10330 , Thailand
| | - Vorasuk Shotelersuk
- Center of Excellence for Medical Genetics , Department of Pediatrics, Faculty of Medicine , Chulalongkorn University , Bangkok 10330 , Thailand
- Excellence Center for Medical Genetics , King Chulalongkorn Memorial Hospital, the Thai Red Cross , Bangkok 10330 , Thailand
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Sangsin A, Srichomthong C, Pongpanich M, Suphapeetiporn K, Shotelersuk V. Short stature, platyspondyly, hip dysplasia, and retinal detachment: an atypical type II collagenopathy caused by a novel mutation in the C-propeptide region of COL2A1: a case report. BMC Med Genet 2016; 17:96. [PMID: 27955642 PMCID: PMC5153895 DOI: 10.1186/s12881-016-0357-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [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: 05/31/2016] [Accepted: 11/30/2016] [Indexed: 01/01/2023]
Abstract
Background Heterozygous mutations in COL2A1 create a spectrum of clinical entities called type II collagenopathies that range from in utero lethal to relatively mild conditions which become apparent only during adulthood. We aimed to characterize the clinical, radiological, and molecular features of a family with an atypical type II collagenopathy. Case presentation A family with three affected males in three generations was described. Prominent clinical findings included short stature with platyspondyly, flat midface and Pierre Robin sequence, severe dysplasia of the proximal femora, and severe retinopathy that could lead to blindness. By whole exome sequencing, a novel heterozygous deletion, c.4161_4165del, in COL2A1 was identified. The phenotype is atypical for those described for mutations in the C-propeptide region of COL2A1. Conclusions We have described an atypical type II collagenopathy caused by a novel out-of-frame deletion in the C-propeptide region of COL2A1. Of all the reported truncating mutations in the C-propeptide region that result in short-stature type II collagenopathies, this mutation is the farthest from the C-terminal of COL2A1.
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Affiliation(s)
- Apiruk Sangsin
- Center of Excellence for Medical Genetics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand.,Excellence Center for Medical Genetics, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, 10330, Bangkok, Thailand.,Department of Orthopedics, Faculty of Medicine, Chiang Mai University, 50200, Chiang Mai, Thailand.,Interdepartment Program of Biomedical Sciences, Faculty of Graduate School, Chulalongkorn University, 10330, Bangkok, Thailand
| | - Chalurmpon Srichomthong
- Center of Excellence for Medical Genetics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand.,Excellence Center for Medical Genetics, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, 10330, Bangkok, Thailand
| | - Monnat Pongpanich
- Department of Mathematics and Computer Science, Faculty of Science, Chulalongkorn University, 10330, Bangkok, Thailand.,Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, 10330, Bangkok, Thailand
| | - Kanya Suphapeetiporn
- Center of Excellence for Medical Genetics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand. .,Excellence Center for Medical Genetics, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, 10330, Bangkok, Thailand. .,Division of Medical Genetics and Metabolism, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Sor Kor Building 11th floor, 10330, Bangkok, Thailand.
| | - Vorasuk Shotelersuk
- Center of Excellence for Medical Genetics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand.,Excellence Center for Medical Genetics, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, 10330, Bangkok, Thailand
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Ittiwut C, Boonbuamas S, Srichomthong C, Ittiwut R, Suphapeetiporn K, Shotelersuk V. Novel Mutations, Including a Large Deletion in the ARSB Gene, Causing Mucopolysaccharidosis Type VI. Genet Test Mol Biomarkers 2016; 21:58-62. [PMID: 27797586 DOI: 10.1089/gtmb.2016.0221] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
OBJECTIVE Mucopolysaccharidosis type VI (MPS VI; Maroteaux-Lamy syndrome), a rare autosomal recessive lysosomal storage disease, is caused by mutations in the N-acetylgalactosamine-4-sulfatase (arylsulfatase B, or ARSB) gene, resulting in a deficiency of ARSB activity. This study aimed to characterize the clinical and molecular features of four unrelated Thai patients with MPS VI. Two were products of consanguineous marriages. MATERIALS AND METHODS The diagnosis was confirmed by biochemical and genetic tests. We performed mutation analysis by polymerase chain reaction-sequencing on the entire coding region of the ARSB gene. Array-based comparative genomic hybridization (aCGH) analysis combined with direct sequencing was also used to search for a deletion boundary. RESULTS The causative mutations were detected in all cases. Of four different mutations identified, three have never been previously described, which included two missense mutations (p.C155Y and p.R388T) and a deletion encompassing exons 2 and 3. Both missense mutations were absent in 110 unaffected ethnic-matched control chromosomes and an in-house database of 180 Thai exomes. The p.C155Y and p.R388T mutations were located in highly conserved residues. A CGH analysis combined with direct sequencing identified the breakpoints of a large 13,788 base pair deletion. It is the largest deletion of ARSB described to date in patients with MPS VI. CONCLUSION This study expanded the known mutational spectrum of ARSB; we identified three novel mutations; two of which are missense mutations and one that represents the largest deletion mutation identified to date in this gene.
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Affiliation(s)
- Chupong Ittiwut
- 1 Department of Pediatrics, Faculty of Medicine, Center of Excellence for Medical Genetics, Chulalongkorn University , Bangkok, Thailand .,2 Excellence Center for Medical Genetics, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society , Bangkok, Thailand
| | - Sukanya Boonbuamas
- 3 Department of Pediatrics, Faculty of Medicine, Chulalongkorn University , Bangkok, Thailand
| | - Chalurmpon Srichomthong
- 1 Department of Pediatrics, Faculty of Medicine, Center of Excellence for Medical Genetics, Chulalongkorn University , Bangkok, Thailand .,2 Excellence Center for Medical Genetics, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society , Bangkok, Thailand
| | - Rungnapa Ittiwut
- 1 Department of Pediatrics, Faculty of Medicine, Center of Excellence for Medical Genetics, Chulalongkorn University , Bangkok, Thailand .,2 Excellence Center for Medical Genetics, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society , Bangkok, Thailand
| | - Kanya Suphapeetiporn
- 1 Department of Pediatrics, Faculty of Medicine, Center of Excellence for Medical Genetics, Chulalongkorn University , Bangkok, Thailand .,2 Excellence Center for Medical Genetics, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society , Bangkok, Thailand
| | - Vorasuk Shotelersuk
- 1 Department of Pediatrics, Faculty of Medicine, Center of Excellence for Medical Genetics, Chulalongkorn University , Bangkok, Thailand .,2 Excellence Center for Medical Genetics, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society , Bangkok, Thailand
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Lindert U, Cabral WA, Ausavarat S, Tongkobpetch S, Ludin K, Barnes AM, Yeetong P, Weis M, Krabichler B, Srichomthong C, Makareeva EN, Janecke AR, Leikin S, Röthlisberger B, Rohrbach M, Kennerknecht I, Eyre DR, Suphapeetiporn K, Giunta C, Marini JC, Shotelersuk V. MBTPS2 mutations cause defective regulated intramembrane proteolysis in X-linked osteogenesis imperfecta. Nat Commun 2016; 7:11920. [PMID: 27380894 PMCID: PMC4935805 DOI: 10.1038/ncomms11920] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [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: 12/01/2015] [Accepted: 05/12/2016] [Indexed: 11/09/2022] Open
Abstract
Osteogenesis imperfecta (OI) is a collagen-related bone dysplasia. We identified an X-linked recessive form of OI caused by defects in MBTPS2, which encodes site-2 metalloprotease (S2P). MBTPS2 missense mutations in two independent kindreds with moderate/severe OI cause substitutions at highly conserved S2P residues. Mutant S2P has normal stability, but impaired functioning in regulated intramembrane proteolysis (RIP) of OASIS, ATF6 and SREBP transcription factors, consistent with decreased proband secretion of type I collagen. Further, hydroxylation of the collagen lysine residue (K87) critical for crosslinking is reduced in proband bone tissue, consistent with decreased lysyl hydroxylase 1 in proband osteoblasts. Reduced collagen crosslinks presumptively undermine bone strength. Also, proband osteoblasts have broadly defective differentiation. These mutations provide evidence that RIP plays a fundamental role in normal bone development. Osteogenesis imperfecta (OI) is genetically linked to autosomal dominant or autosomal recessive mutations. Here, Marini et al. describe two families with X-chromosome-linked OI with mutations in MBTPS2 that alter regulated intramembrane proteolysis and subsequent defects in collagen crosslinking and osteoblast function.
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Affiliation(s)
- Uschi Lindert
- Division of Metabolism, Connective Tissue Unit and Children's Research Center, University Children's Hospital Zurich, Zurich 8032, Switzerland
| | - Wayne A Cabral
- Section on Heritable Disorders of Bone and Extracellular Matrix, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Surasawadee Ausavarat
- Center of Excellence for Medical Genetics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand.,Excellence Center for Medical Genetics, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok 10330, Thailand
| | - Siraprapa Tongkobpetch
- Center of Excellence for Medical Genetics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand.,Excellence Center for Medical Genetics, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok 10330, Thailand
| | - Katja Ludin
- Center for Laboratory Medicine, Department of Medical Genetics, Kantonsspital Aarau, Aarau 5001, Switzerland
| | - Aileen M Barnes
- Section on Heritable Disorders of Bone and Extracellular Matrix, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Patra Yeetong
- Center of Excellence for Medical Genetics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand.,Excellence Center for Medical Genetics, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok 10330, Thailand
| | - Maryann Weis
- Department of Orthopedics and Sports Medicine, University of Washington, Seattle, Washington 98195, USA
| | - Birgit Krabichler
- Division of Human Genetics, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Chalurmpon Srichomthong
- Center of Excellence for Medical Genetics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand.,Excellence Center for Medical Genetics, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok 10330, Thailand
| | - Elena N Makareeva
- Section on Physical Biochemistry, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Andreas R Janecke
- Division of Human Genetics, Medical University of Innsbruck, Innsbruck 6020, Austria.,Department of Pediatrics I, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Sergey Leikin
- Section on Physical Biochemistry, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Benno Röthlisberger
- Center for Laboratory Medicine, Department of Medical Genetics, Kantonsspital Aarau, Aarau 5001, Switzerland
| | - Marianne Rohrbach
- Division of Metabolism, Connective Tissue Unit and Children's Research Center, University Children's Hospital Zurich, Zurich 8032, Switzerland
| | - Ingo Kennerknecht
- Institute of Human Genetics, Westfälische Wilhelms University, Münster 48149, Germany
| | - David R Eyre
- Department of Orthopedics and Sports Medicine, University of Washington, Seattle, Washington 98195, USA
| | - Kanya Suphapeetiporn
- Center of Excellence for Medical Genetics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand.,Excellence Center for Medical Genetics, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok 10330, Thailand
| | - Cecilia Giunta
- Division of Metabolism, Connective Tissue Unit and Children's Research Center, University Children's Hospital Zurich, Zurich 8032, Switzerland
| | - Joan C Marini
- Section on Heritable Disorders of Bone and Extracellular Matrix, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Vorasuk Shotelersuk
- Center of Excellence for Medical Genetics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand.,Excellence Center for Medical Genetics, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok 10330, Thailand
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Suratannon N, Yeetong P, Srichomthong C, Amarinthnukrowh P, Chatchatee P, Sosothikul D, van Hagen PM, van der Burg M, Wentink M, Driessen GJ, Suphapeetiporn K, Shotelersuk V. Adaptive immune defects in a patient with leukocyte adhesion deficiency type III with a novel mutation in FERMT3. Pediatr Allergy Immunol 2016; 27:214-7. [PMID: 26359933 DOI: 10.1111/pai.12485] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Narissara Suratannon
- Division of Allergy and Immunology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.,Department of Immunology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Patra Yeetong
- Center of Excellence for Medical Genetics, Chulalongkorn University, Bangkok, Thailand.,Excellence Center for Medical Genetics, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, Thailand.,Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Chalurmpon Srichomthong
- Center of Excellence for Medical Genetics, Chulalongkorn University, Bangkok, Thailand.,Excellence Center for Medical Genetics, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, Thailand
| | - Pramuk Amarinthnukrowh
- Center of Excellence for Medical Genetics, Chulalongkorn University, Bangkok, Thailand.,Excellence Center for Medical Genetics, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, Thailand
| | - Pantipa Chatchatee
- Division of Allergy and Immunology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Darintr Sosothikul
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - P Martin van Hagen
- Department of Immunology, Erasmus Medical Center, Rotterdam, the Netherlands.,Department of Internal Medicine, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Mirjam van der Burg
- Department of Immunology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Marjolein Wentink
- Department of Immunology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Gertjan J Driessen
- Department of Immunology, Erasmus Medical Center, Rotterdam, the Netherlands.,Department of Pediatric Infectious Disease and Immunology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Kanya Suphapeetiporn
- Center of Excellence for Medical Genetics, Chulalongkorn University, Bangkok, Thailand. .,Excellence Center for Medical Genetics, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, Thailand. .,Division of Medical Genetics and Metabolism, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.
| | - Vorasuk Shotelersuk
- Center of Excellence for Medical Genetics, Chulalongkorn University, Bangkok, Thailand.,Excellence Center for Medical Genetics, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, Thailand
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35
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Sangsin A, Srichomthong C, Pongpanich M, Suphapeetiporn K, Shotelersuk V. Whole-exome sequencing reveals a novel COL2A1 mutation in a patient with spondyloepiphyseal dysplasia congenita. Genet Mol Res 2016; 15:15017624. [DOI: 10.4238/gmr.15017624] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Panmontha W, Rerknimitr P, Yeetong P, Srichomthong C, Suphapeetiporn K, Shotelersuk V. A Frameshift Mutation in PEN-2 Causes Familial Comedones Syndrome. Dermatology 2015; 231:77-81. [DOI: 10.1159/000382122] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 04/05/2015] [Indexed: 11/19/2022] Open
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Rattanasopha S, Tongkobpetch S, Srichomthong C, Kitidumrongsook P, Suphapeetiporn K, Shotelersuk V. Absent expression of the osteoblast-specific maternally imprinted genes,DLX5andDLX6,causes split hand/split foot malformation type I. J Med Genet 2014; 51:817-23. [DOI: 10.1136/jmedgenet-2014-102576] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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Sahakitrungruang T, Srichomthong C, Pornkunwilai S, Amornfa J, Shuangshoti S, Kulawonganunchai S, Suphapeetiporn K, Shotelersuk V. Germline and somatic DICER1 mutations in a pituitary blastoma causing infantile-onset Cushing's disease. J Clin Endocrinol Metab 2014; 99:E1487-92. [PMID: 24823459 DOI: 10.1210/jc.2014-1016] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
CONTEXT Pituitary blastoma causing Cushing's syndrome in infancy is very rare, and its molecular pathomechanism is not well understood. OBJECTIVE Our objective was to identify genetic changes of a pituitary blastoma causing infantile-onset Cushing's syndrome in a Thai girl without a family history of cancers. METHODS Genomic DNA from both leukocytes and tumor tissues was used for whole-exome sequencing (WES) and Sanger sequencing of DICER1. The cDNA reverse-transcribed from RNA extracted from both leukocytes and tumor tissues was used for Sanger sequencing, quantitative real-time PCR (qRT-PCR), and pyrosequencing of DICER1. RESULTS WES of leukocytes identified a novel heterozygous c.3046delA (p.S1016VfsX1065) mutation in the DICER1 gene. WES of the tumor tissues detected the same frameshift germline mutation and another novel somatic missense c.5438A→T (p.E1813V) mutation. Both mutations were validated by Sanger sequencing. Quantitative real-time PCR revealed that the DICER1 mRNA levels of the tumor tissues were 54% compared with those of her leukocytes. Pyrosequencing showed that the deletion allele constituted 12% and 0% of the DICER1 cDNA of the proband's leukocytes and tumor tissues, respectively. CONCLUSION Our study extends the phenotypic and mutational spectrum of DICER1 mutations to include infantile-onset Cushing's disease and 2 novel mutations. Loss of function of both DICER1 alleles appears to be crucial to initiate tumor development.
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Affiliation(s)
- Taninee Sahakitrungruang
- Division of Pediatric Endocrinology (T.S., S.P.), Center of Excellence for Medical Genetics, Department of Pediatrics (C.S., S.K., K.S., V.S.), Division of Neurosurgery, Departments of Surgery (J.A.) and Pathology (S.S.), Faculty of Medicine, Chulalongkorn University; and Excellence Center for Medical Genetics (C.S., S.K., K.S., V.S.), King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok 10330, Thailand
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Norbnop P, Srichomthong C, Suphapeetiporn K, Shotelersuk V. ZRS 406A>G mutation in patients with tibial hypoplasia, polydactyly and triphalangeal first fingers. J Hum Genet 2014; 59:467-70. [PMID: 24965254 DOI: 10.1038/jhg.2014.50] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 06/03/2014] [Accepted: 06/03/2014] [Indexed: 11/09/2022]
Abstract
Werner mesomelic syndrome (WMS), an autosomal dominant disorder characterized by hypoplastic tibiae, triphalangeal thumbs and polydactyly, is caused by a specific point mutation at the position 404 in zone of polarizing activity regulatory sequence (ZRS). Here we identified two additional families with WMS. All three patients in three generations of Family 1 were found to harbor the same heterozygous 406A>G mutation in ZRS. The fourth patient from Family 2 was a sporadic case with the known 404 point mutation. The novel 406A>G mutation expands mutational spectrum in ZRS causing WMS, provides evidence for a functionally important nucleotide position 406 of ZRS in humans and has implications for genetic counseling.
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Affiliation(s)
- Phatchara Norbnop
- 1] Doctor of Philosophy Program in Medical Sciences, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand [2] Center of Excellence for Medical Genetics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Chalurmpon Srichomthong
- 1] Center of Excellence for Medical Genetics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand [2] Excellence Center for Medical Genetics, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, Thailand
| | - Kanya Suphapeetiporn
- 1] Center of Excellence for Medical Genetics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand [2] Excellence Center for Medical Genetics, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, Thailand
| | - Vorasuk Shotelersuk
- 1] Center of Excellence for Medical Genetics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand [2] Excellence Center for Medical Genetics, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, Thailand
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Chaiyasap P, Kulawonganunchai S, Srichomthong C, Tongsima S, Suphapeetiporn K, Shotelersuk V. Whole genome and exome sequencing of monozygotic twins with trisomy 21, discordant for a congenital heart defect and epilepsy. PLoS One 2014; 9:e100191. [PMID: 24950249 PMCID: PMC4064986 DOI: 10.1371/journal.pone.0100191] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2013] [Accepted: 05/23/2014] [Indexed: 12/31/2022] Open
Abstract
Congenital heart defects (CHD) occur in 40% of patients with trisomy 21, while the other 60% have a structurally normal heart. This suggests that the increased dosage of genes on chromosome 21 is a risk factor for abnormal heart development. Interaction of genes on chromosome 21 or their gene products with certain alleles of genes on other chromosomes could contribute to CHD. Here, we identified a pair of monozygotic twins with trisomy 21 but discordant for a ventricular septal defect and epilepsy. Twin-zygosity was confirmed by microsatellite genotyping. We hypothesized that some genetic differences from post-twinning mutations caused the discordant phenotypes. Thus, next generation sequencing (NGS) technologies were applied to sequence both whole genome and exome of their leukocytes. The post-analyses of the sequencing data revealed 21 putative discordant exonic variants between the twins from either genome or exome data. However, of the 15 variants chosen for validation with conventional Sanger sequencing, these candidate variants showed no differences in both twins. The fact that no discordant DNA variants were found suggests that sequence differences of DNA from leukocytes of monozygotic twins might be extremely rare. It also emphasizes the limitation of the current NGS technology in identifying causative genes for discordant phenotypes in monozygotic twins.
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Affiliation(s)
- Pongsathorn Chaiyasap
- Interdepartment of Biomedical Sciences, Faculty of Graduate School, Chulalongkorn University, Bangkok, Thailand
| | - Supasak Kulawonganunchai
- Interdepartment of Biomedical Sciences, Faculty of Graduate School, Chulalongkorn University, Bangkok, Thailand
- Genome Institute, National Center for Genetic Engineering and Biotechnology, Khlong Nueng, Khlong Luang, Pathum Thani, Thailand
| | - Chalurmpon Srichomthong
- Center of Excellence for Medical Genetics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Excellence Center for Medical Genetics, King Chulalongkorn Memorial Hospital, Thai Red Cross, Bangkok, Thailand
| | - Sissades Tongsima
- Genome Institute, National Center for Genetic Engineering and Biotechnology, Khlong Nueng, Khlong Luang, Pathum Thani, Thailand
| | - Kanya Suphapeetiporn
- Center of Excellence for Medical Genetics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Excellence Center for Medical Genetics, King Chulalongkorn Memorial Hospital, Thai Red Cross, Bangkok, Thailand
- * E-mail:
| | - Vorasuk Shotelersuk
- Center of Excellence for Medical Genetics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Excellence Center for Medical Genetics, King Chulalongkorn Memorial Hospital, Thai Red Cross, Bangkok, Thailand
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Leoyklang P, Suphapeetiporn K, Srichomthong C, Tongkobpetch S, Fietze S, Dorward H, Cullinane AR, Gahl WA, Huizing M, Shotelersuk V. Disorders with similar clinical phenotypes reveal underlying genetic interaction: SATB2 acts as an activator of the UPF3B gene. Hum Genet 2013; 132:1383-93. [PMID: 23925499 DOI: 10.1007/s00439-013-1345-9] [Citation(s) in RCA: 22] [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] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Accepted: 07/24/2013] [Indexed: 01/01/2023]
Abstract
Two syndromic cognitive impairment disorders have very similar craniofacial dysmorphisms. One is caused by mutations of SATB2, a transcription regulator and the other by heterozygous mutations leading to premature stop codons in UPF3B, encoding a member of the nonsense-mediated mRNA decay complex. Here we demonstrate that the products of these two causative genes function in the same pathway. We show that the SATB2 nonsense mutation in our patient leads to a truncated protein that localizes to the nucleus, forms a dimer with wild-type SATB2 and interferes with its normal activity. This suggests that the SATB2 nonsense mutation has a dominant negative effect. The patient's leukocytes had significantly decreased UPF3B mRNA compared to controls. This effect was replicated both in vitro, where siRNA knockdown of SATB2 in HEK293 cells resulted in decreased UPF3B expression, and in vivo, where embryonic tissue of Satb2 knockout mice showed significantly decreased Upf3b expression. Furthermore, chromatin immunoprecipitation demonstrates that SATB2 binds to the UPF3B promoter, and a luciferase reporter assay confirmed that SATB2 expression significantly activates gene transcription using the UPF3B promoter. These findings indicate that SATB2 activates UPF3B expression through binding to its promoter. This study emphasizes the value of recognizing disorders with similar clinical phenotypes to explore underlying mechanisms of genetic interaction.
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Affiliation(s)
- Petcharat Leoyklang
- Biomedical Science Program, Faculty of Graduate School, Chulalongkorn University, Bangkok, Thailand
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Tammachote R, Tongkobpetch S, Srichomthong C, Phipatthanananti K, Pungkanon S, Wattanasirichaigoon D, Suphapeetiporn K, Shotelersuk V. A common and two novel GBA mutations in Thai patients with Gaucher disease. J Hum Genet 2013; 58:594-9. [PMID: 23719189 DOI: 10.1038/jhg.2013.60] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2013] [Revised: 04/27/2013] [Accepted: 05/01/2013] [Indexed: 11/09/2022]
Abstract
Gaucher disease (GD) is an autosomal recessive disorder caused by mutations in the glucocerebrosidase (GBA) gene, leading to a deficiency of lysosomal β-glucosidase and accumulation of glycosphingolipids in macrophages. We studied five Thai families with GD (four with GD type 1 and one with GD type 2). Using long-template PCR, PCR using specific primers for the functional gene, direct sequencing of all coding regions of GBA and restriction enzyme digestions, all 10 mutant alleles were successfully identified. The common c.1448T>C (p.L483P or L444P) mutation was identified in 60% of mutant alleles. Of the two patients homozygous for the p.L483P (L444P) mutation, one died from hepatic failure at age 16 years and the other died from sepsis at age 12 years. This p.L483P (L444P) mutation was found in four different haplotypes, suggesting that it was a recurrent mutation, not caused by a founder effect. Two novel mutations, a missense (c.1204T>C, p.Y402H), and a termination codon mutation (c.1609T>C, p.X537A) were found. Studies to determine the molecular pathomechanism of the p.X537A mutation, the first of its kind in this gene, showed that it decreased the amount of protein being expressed and the enzymatic activity, while it was still correctly localized.
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Affiliation(s)
- Rachaneekorn Tammachote
- 1] Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok, Thailand [2] Department of Pediatrics, Center of Excellence for Medical Genetics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
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Tammachote R, Kingsuwannapong N, Tongkobpetch S, Srichomthong C, Yeetong P, Kingwatanakul P, Monico CG, Suphapeetiporn K, Shotelersuk V. Primary hyperoxaluria type 1 and brachydactyly mental retardation syndrome caused by a novel mutation in AGXT and a terminal deletion of chromosome 2. Am J Med Genet A 2012; 158A:2124-30. [PMID: 22821680 DOI: 10.1002/ajmg.a.35495] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Accepted: 05/07/2012] [Indexed: 12/12/2022]
Abstract
Primary hyperoxaluria type 1 (PH1) is an autosomal recessive disorder caused by mutations in the alanine:glyoxylate aminotransferase (AGXT) gene, located on chromosome 2q37. Mutant AGXT leads to excess production and excretion of oxalate, resulting in accumulation of calcium oxalate in the kidney, and progressive loss of renal function. Brachydactyly mental retardation syndrome (BDMR) is an autosomal dominant disorder, caused by haploinsufficiency of histone deacetylase 4 (HDAC4), also on chromosome 2q37. It is characterized by skeletal abnormalities and developmental delay. Here, we report on a girl who had phenotypes of both PH1 and BDMR. PCR-sequencing of the coding regions of AGXT showed a novel missense mutation, c.32C>G (p.Pro11Arg) inherited from her mother. Functional analyses demonstrated that it reduced the enzymatic activity to 31% of the wild-type and redirected some percentage of the enzyme away from the peroxisome. Microsatellite and array-CGH analyses indicated that the proband had a paternal de novo telomeric deletion of chromosome 2q, which included HDAC4. To our knowledge, this is the first report of PH1 and BDMR, with a novel AGXT mutation and a de novo telomeric deletion of chromosome 2q.
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Affiliation(s)
- Rachaneekorn Tammachote
- Faculty of Science, Human Genetics Research, Department of Botany, Chulalongkorn University, Bangkok, Thailand
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Prommajan K, Ausavarat S, Srichomthong C, Puangsricharern V, Suphapeetiporn K, Shotelersuk V. A novel p.E276K IDUA mutation decreasing α-L-iduronidase activity causes mucopolysaccharidosis type I. Mol Vis 2011; 17:456-60. [PMID: 21364962 PMCID: PMC3042362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2010] [Accepted: 02/05/2011] [Indexed: 11/01/2022] Open
Abstract
PURPOSE To characterize the pathogenic mutations causing mucopolysaccharidosis type I (MPS I) in two Thai patients: one with Hurler syndrome (MPS IH), the most severe form, and the other with Scheie syndrome (MPS IS), the mildest. Both presented with distinctive phenotype including corneal clouding. METHODS The entire coding regions of the α-L-iduronidase (IDUA) gene were amplified by PCR and sequenced. Functional characterization of the mutant IDUA was determined by transient transfection of the construct into COS-7 cells. RESULTS Mutation analyses revealed that the MPS IH patient was homozygous for a previously reported mutation, c.252insC, while the MPS IS patient was found to harbor a novel c.826G>A (p.E276K) mutation. The novel p.E276K mutation was not detected in 100 unaffected ethnic-matched control chromosomes. In addition, the glutamic acid residue at codon 276 was located at a well conserved residue. Transient transfection of the p.E276K construct revealed a significant reduction of IDUA activity compared to that of the wild-type IDUA suggesting it as a disease-causing mutation. CONCLUSIONS This study reports a novel mutation, expanding the mutational spectrum for MPS I.
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Affiliation(s)
- Korrakot Prommajan
- Center of Excellence for Medical Genetics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand,Molecular Genetics Diagnostic Center, King Chulalongkorn Memorial Hospital, Thai Red Cross, Bangkok, Thailand
| | - Surasawadee Ausavarat
- Center of Excellence for Medical Genetics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand,Molecular Genetics Diagnostic Center, King Chulalongkorn Memorial Hospital, Thai Red Cross, Bangkok, Thailand
| | - Chalurmpon Srichomthong
- Center of Excellence for Medical Genetics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand,Molecular Genetics Diagnostic Center, King Chulalongkorn Memorial Hospital, Thai Red Cross, Bangkok, Thailand
| | - Vilavun Puangsricharern
- Department of Ophthalmology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Kanya Suphapeetiporn
- Center of Excellence for Medical Genetics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand,Molecular Genetics Diagnostic Center, King Chulalongkorn Memorial Hospital, Thai Red Cross, Bangkok, Thailand
| | - Vorasuk Shotelersuk
- Center of Excellence for Medical Genetics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand,Molecular Genetics Diagnostic Center, King Chulalongkorn Memorial Hospital, Thai Red Cross, Bangkok, Thailand
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Srichomthong C, Siriwan P, Shotelersuk V. Significant association between IRF6 820G->A and non-syndromic cleft lip with or without cleft palate in the Thai population. J Med Genet 2006; 42:e46. [PMID: 15994871 PMCID: PMC1736106 DOI: 10.1136/jmg.2005.032235] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
BACKGROUND Previous data have shown an association between DNA sequence variants in the IRF6 gene and an increased risk of non-syndromic cleft lip with or without cleft palate (CL/P) in some populations. OBJECTIVE To investigate Thai CL/P patients and relative for a 820G-->A polymorphism. SUBJECTS 192 CL/P Thai patients, 177 of their mothers, 73 of their fathers, and 278 controls. RESULTS There were significant differences in the frequency distributions of both genotypes (p = 0.02) and alleles (p = 0.04) among probands as compared with the control group. The odds ratio calculated for the patients having the GG genotype compared with the other two genotypes (GA and AA) was 1.67 (95% confidence interval, 1.13 to 2.47). This pattern is consistent with a recessive effect of the G allele. No association between any of the parents' genotypes and CL/P was found. The IRF6 820G-->A was responsible for 16.7% of the genetic contribution to CL/P. CONCLUSIONS The findings confirm that IRF6 820G-->A is associated with CL/P.
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Affiliation(s)
- C Srichomthong
- Division of Medical Genetics and Metabolism, Department of Paediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
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Phupong V, Srichomthong C, Shotelersuk V. Prenatal exclusion of Crouzon syndrome by mutation analysis of FGFR2. Southeast Asian J Trop Med Public Health 2004; 35:977-9. [PMID: 15916101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Crouzon Syndrome is an autosomal dominant syndromic craniosynostosis characterized by premature closure of cranial sutures, exophthalmos, and midface hypoplasia. It is caused by multiple mutations in the fibroblast growth factor receptor 2 (FGFR2). We describe prenatal genetic testing of FGFR2 in a fetus of a mother whose previous child had Crouzon Syndrome due to an apparently de novo mutation, S351C. Sequence electropherograms of the exon 10 of FGFR2 encompassing the codon 351 revealed only the normal sequence, thus predicting a very high likelihood of an unaffected fetus. The study was confirmed by the birth of a normal neonate. We report the use of molecular genetic testing to exclude Crouzon Syndrome due to FGFR2 mutation prenatally. Prenatal diagnostic testing for a known mutation is a reasonable option for couples at risk for having a child with Crouzon Syndrome due to germline mosaicism. Molecular testing is more accurate and reliable than ultrasonography and provides families with reassurance.
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Affiliation(s)
- Vorapong Phupong
- Department of Obstetrics and Gynecology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.
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Chatchatee P, Srichomthong C, Chewatavorn A, Shotelersuk V. A novel termination codon mutation of the WAS gene in a Thai family with Wiskott-Aldrich syndrome. Int J Mol Med 2003. [DOI: 10.3892/ijmm.12.6.939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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Chatchatee P, Srichomthong C, Chewatavorn A, Shotelersuk V. A novel termination codon mutation of the WAS gene in a Thai family with Wiskott-Aldrich syndrome. Int J Mol Med 2003; 12:939-41. [PMID: 14612970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/27/2023] Open
Abstract
Wiskott-Aldrich syndrome (WAS) is an X-linked recessive disorder characterized by microthrombocytopenia, eczema, immunodeficiency, and susceptibility to lymphoid malignancy. Loss-of-function mutations in WAS gene have been identified to cause disorders with platelet defects including WAS and X-linked thrombocytopenia. Mutations anticipated to yield truncated or no protein have been associated with the more severe presentations of WAS. Activating mutations in WAS gene result in an entirely different phenotype, an X-linked severe congenital neutropenia. We describe a Thai family with classic WAS. The proband, a one-year-old boy presented with recurrent mucous bloody diarrhea, recurrent otitis media, chronic eczema, thrombocytopenia, and small platelet sizes. The patient's older brother who also had persistent thrombocytopenia died at the age of seven months from severe pneumonia. Immunoblot analysis demonstrated that the proband's cells lacked WAS protein expression. Mutation analysis of the proband and his mother for the entire coding region of WAS identified a novel type of mutation, a termination codon mutation, X503R. The change is expected to result in an elongated mRNA that would code for a WASP of 581 amino acid residues instead of the normal 502 residues. Because of the absence of WASP expression, we speculate that the termination codon mutation causes reduced mRNA stability. Our findings supported that WAS mutations resulted in no protein are associated with a severe phenotype of WAS.
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Affiliation(s)
- Pantipa Chatchatee
- Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
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Shotelersuk V, Srichomthong C, Yoshiura KI, Niikawa N. A novel mutation, 1234del(C), of the IRF6 in a Thai family with Van der Woude syndrome. Int J Mol Med 2003. [DOI: 10.3892/ijmm.11.4.505] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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