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Lam CW. Ending diagnostic odyssey using clinical whole-exome sequencing (CWES). J LAB MED 2021. [DOI: 10.1515/labmed-2021-0127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract
Objectives
Most rare diseases are genetic diseases. Due to the diversity of rare diseases and the high likelihood of patients with rare diseases to be undiagnosed or misdiagnosed, it is not unusual that these patients undergo a long diagnostic odyssey before they receive a definitive diagnosis. This situation presents a clear need to set up a dedicated clinical service to end the diagnostic odyssey of patients with rare diseases.
Methods
Therefore, in 2014, we started an Undiagnosed Diseases Program in Hong Kong with the aim of ending the diagnostic odyssey of patients and families with rare diseases by clinical whole-exome sequencing (CWES), who have not received a definitive diagnosis after extensive investigation.
Results
In this program, we have shown that genetic diseases diagnosed by CWES were different from that using traditional approaches indicating that CWES is an essential tool to diagnose rare diseases and ending diagnostic odysseys. In addition, we identified several novel genes responsible for monogenic diseases. These include the TOP2B gene for autism spectrum disorder, the DTYMK gene for severe cerebral atrophy, the KIF13A gene for a new mosaic ectodermal syndrome associated with hypomelanosis of Ito, and the CDC25B gene for a new syndrome of cardiomyopathy and endocrinopathy.
Conclusions
With the incorporation of CWES in an Undiagnosed Diseases Program, we have ended diagnostic odysseys of patients with rare diseases in Hong Kong in the past 7 years. In this program, we have shown that CWES is an essential tool to end diagnostic odysseys. With the declining cost of next-generation sequencers and reagents, CWES set-ups are now affordable for clinical laboratories. Indeed, owing to the increasing availability of CWES and treatment modalities for rare diseases, precedence can be given to both common and rare medical conditions.
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Affiliation(s)
- Ching-Wan Lam
- Department of Pathology , The University of Hong Kong , Hong Kong , P.R. China
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Zhou Z, Wang K, Zhou J, Wang C, Li X, Cui L, Han L, Liu Z, Ren W, Wang X, Zhang K, Li Z, Pan D, Li C, Shi Y. Amplicon targeted resequencing for SLC2A9 and SLC22A12 identified novel mutations in hypouricemia subjects. Mol Genet Genomic Med 2019; 7:e00722. [PMID: 31131560 PMCID: PMC6625124 DOI: 10.1002/mgg3.722] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 02/19/2019] [Accepted: 04/15/2019] [Indexed: 01/05/2023] Open
Abstract
Background To identify potential causative mutations in SLC2A9 and SLC22A12 that lead to hypouricemia or hyperuricemia (HUA). Methods Targeted resequencing of whole exon regions of SLC2A9 and SLC22A12 was performed in three cohorts of 31 hypouricemia, 288 HUA and 280 normal controls. Results A total of 84 high‐quality variants were identified in these three cohorts. Eighteen variants were nonsynonymous or in splicing region, and then included in the following association analysis. For common variants, no significant effects on hypouricemia or HUA were identified. For rare variants, six single nucleotide variations (SNVs) p.T21I and p.G13D in SLC2A9, p.W50fs, p.Q382L, p.V547L and p.E458K in SLC22A12, occurred in totally six hypouricemia subjects and were absent in HUA and normal controls. Allelic and genotypic frequency distributions of the six SNVs differed significantly between the hypouricemia and normal controls even after multiple testing correction, and p.G13D in SLC2A9 and p.V547L in SLC22A12 were newly reported. All these mutations had no significant effects on HUA susceptibility, while the gene‐based analyses substantiated the significant results on hypouricemia. Conclusion Our study first presents a comprehensive mutation spectrum of hypouricemia in a large Chinese cohort.
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Affiliation(s)
- Zhaowei Zhou
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiaric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Ke Wang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiaric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Juan Zhou
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiaric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Can Wang
- Qingdao Key Laboratory of Gout, The Affiliated Hospital of Qingdao University, Qingdao, P.R. China.,Shandong Provincial Key Laboratory of Metabolic Disease, The Affiliated Hospital of Qingdao University, Qingdao, P.R. China.,Metabolic Disease Institute, Qingdao University, Qingdao, P.R. China
| | - Xinde Li
- Qingdao Key Laboratory of Gout, The Affiliated Hospital of Qingdao University, Qingdao, P.R. China.,Shandong Provincial Key Laboratory of Metabolic Disease, The Affiliated Hospital of Qingdao University, Qingdao, P.R. China.,Metabolic Disease Institute, Qingdao University, Qingdao, P.R. China
| | - Lingling Cui
- Qingdao Key Laboratory of Gout, The Affiliated Hospital of Qingdao University, Qingdao, P.R. China.,Shandong Provincial Key Laboratory of Metabolic Disease, The Affiliated Hospital of Qingdao University, Qingdao, P.R. China.,Metabolic Disease Institute, Qingdao University, Qingdao, P.R. China
| | - Lin Han
- Qingdao Key Laboratory of Gout, The Affiliated Hospital of Qingdao University, Qingdao, P.R. China.,Shandong Provincial Key Laboratory of Metabolic Disease, The Affiliated Hospital of Qingdao University, Qingdao, P.R. China.,Metabolic Disease Institute, Qingdao University, Qingdao, P.R. China
| | - Zhen Liu
- Qingdao Key Laboratory of Gout, The Affiliated Hospital of Qingdao University, Qingdao, P.R. China.,Shandong Provincial Key Laboratory of Metabolic Disease, The Affiliated Hospital of Qingdao University, Qingdao, P.R. China.,Metabolic Disease Institute, Qingdao University, Qingdao, P.R. China
| | - Wei Ren
- Qingdao Key Laboratory of Gout, The Affiliated Hospital of Qingdao University, Qingdao, P.R. China.,Shandong Provincial Key Laboratory of Metabolic Disease, The Affiliated Hospital of Qingdao University, Qingdao, P.R. China.,Metabolic Disease Institute, Qingdao University, Qingdao, P.R. China
| | - Xuefeng Wang
- Qingdao Key Laboratory of Gout, The Affiliated Hospital of Qingdao University, Qingdao, P.R. China.,Shandong Provincial Key Laboratory of Metabolic Disease, The Affiliated Hospital of Qingdao University, Qingdao, P.R. China.,Metabolic Disease Institute, Qingdao University, Qingdao, P.R. China
| | - Keke Zhang
- Qingdao Key Laboratory of Gout, The Affiliated Hospital of Qingdao University, Qingdao, P.R. China.,Shandong Provincial Key Laboratory of Metabolic Disease, The Affiliated Hospital of Qingdao University, Qingdao, P.R. China.,Metabolic Disease Institute, Qingdao University, Qingdao, P.R. China.,The Department of Endocrinology and Metabolism, The Affiliated Hospital of Qingdao University, Qingdao, P.R. China
| | - Zhiqiang Li
- Biomedical Sciences Institute, the Qingdao Branch of SJTU Bio-X Institutes, Qingdao University, Qingdao, P.R. China
| | - Dun Pan
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiaric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Changgui Li
- Qingdao Key Laboratory of Gout, The Affiliated Hospital of Qingdao University, Qingdao, P.R. China.,Shandong Provincial Key Laboratory of Metabolic Disease, The Affiliated Hospital of Qingdao University, Qingdao, P.R. China.,Metabolic Disease Institute, Qingdao University, Qingdao, P.R. China.,The Department of Endocrinology and Metabolism, The Affiliated Hospital of Qingdao University, Qingdao, P.R. China
| | - Yongyong Shi
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiaric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, P.R. China.,Qingdao Key Laboratory of Gout, The Affiliated Hospital of Qingdao University, Qingdao, P.R. China.,Shandong Provincial Key Laboratory of Metabolic Disease, The Affiliated Hospital of Qingdao University, Qingdao, P.R. China.,Biomedical Sciences Institute, the Qingdao Branch of SJTU Bio-X Institutes, Qingdao University, Qingdao, P.R. China
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Zhou Z, Ma L, Zhou J, Song Z, Zhang J, Wang K, Chen B, Pan D, Li Z, Li C, Shi Y. Renal hypouricemia caused by novel compound heterozygous mutations in the SLC22A12 gene: a case report with literature review. BMC MEDICAL GENETICS 2018; 19:142. [PMID: 30097038 PMCID: PMC6086067 DOI: 10.1186/s12881-018-0595-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 04/26/2018] [Indexed: 12/20/2022]
Abstract
Background Renal hypouricemia (RHUC) is a heterogeneous genetic disorder that is characterized by decreased serum uric acid concentration and increased fractional excretion of uric acid. Previous reports have revealed many functional mutations in two urate transporter genes, SLC22A12 and/or SLC2A9, to be the causative genetic factors of this disorder. However, there are still unresolved patients, suggesting the existence of other causal genes or new mutations. Here, we report an RHUC patient with novel compound heterozygous mutations in the SLC22A12 gene. Case presentation A 27-year-old female presenting with recurrent hypouricemia during routine checkups was referred to our hospital. After obtaining the patient’s consent, both the patient and her healthy parents were analyzed using whole-exome sequencing (WES) and Sanger sequencing to discover and validate causal mutations, respectively. The prioritization protocol of WES screened out two mutations of c.269G > A/p.R90H and c.1289_1290insGG/p.M430fsX466, which are both located in the SLC22A12 gene, in the patient. Sanger sequencing further confirmed that the patient’s heterozygous c.269G > A/p.R90H mutation, which has been reported previously, derived from her mother, and the heterozygous c.1289_1290insGG/p.M430fsX466 mutation, which was found for the first time, derived from her father. p.R90H, which is highly conserved among different species, may decrease the stability of this domain and was considered to be almost damaging in silicon analysis. p.M430fsX466 lacks the last three transmembrane domains, including the tripeptide motif (S/T)XΦ (X = any amino acid and Φ = hydrophobic residue), at the C-terminal, which interact with scaffolding protein PDZK1 and thus will possibly lead to weak functioning of urate transport through the disruption of the “transporter complex” that is formed by URAT1 and PDZK1. Conclusions We report a Chinese patient with RHUC, which was caused by compound heterozygous mutations of the SLC22A12 gene, using WES and Sanger sequencing for the first time. Mutation-induced structural instability or malfunction of the urate transporter complex may be the main mechanisms for this hereditary disorder. Electronic supplementary material The online version of this article (10.1186/s12881-018-0595-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zhaowei Zhou
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, No. 1954 Huashan Road, Shanghai, 200030, People's Republic of China
| | - Lidan Ma
- Shandong Gout Clinical Medical Center, Qingdao, 266003, People's Republic of China.,Shandong Provincial Key Laboratory of Metabolic Disease, The Affiliated Hospital of Qingdao University, No. 16 Jiangsu Road, Qingdao, 266003, People's Republic of China.,The Department of Endocrinology and Metabolism, The Affiliated Hospital of Qingdao University, Qingdao, 266003, People's Republic of China
| | - Juan Zhou
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, No. 1954 Huashan Road, Shanghai, 200030, People's Republic of China
| | - Zhijian Song
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, No. 1954 Huashan Road, Shanghai, 200030, People's Republic of China
| | - Jinmai Zhang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, No. 1954 Huashan Road, Shanghai, 200030, People's Republic of China
| | - Ke Wang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, No. 1954 Huashan Road, Shanghai, 200030, People's Republic of China
| | - Boyu Chen
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, No. 1954 Huashan Road, Shanghai, 200030, People's Republic of China
| | - Dun Pan
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, No. 1954 Huashan Road, Shanghai, 200030, People's Republic of China
| | - Zhiqiang Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, No. 1954 Huashan Road, Shanghai, 200030, People's Republic of China.,Biomedical Sciences Institute, the Qingdao Branch of SJTU Bio-X Institutes, Qingdao University, Qingdao, 266003, People's Republic of China
| | - Changgui Li
- Shandong Gout Clinical Medical Center, Qingdao, 266003, People's Republic of China. .,Shandong Provincial Key Laboratory of Metabolic Disease, The Affiliated Hospital of Qingdao University, No. 16 Jiangsu Road, Qingdao, 266003, People's Republic of China. .,The Department of Endocrinology and Metabolism, The Affiliated Hospital of Qingdao University, Qingdao, 266003, People's Republic of China. .,Metabolic Disease Institute, Qingdao University, Qingdao, 266003, People's Republic of China.
| | - Yongyong Shi
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, No. 1954 Huashan Road, Shanghai, 200030, People's Republic of China. .,Shandong Gout Clinical Medical Center, Qingdao, 266003, People's Republic of China. .,Shandong Provincial Key Laboratory of Metabolic Disease, The Affiliated Hospital of Qingdao University, No. 16 Jiangsu Road, Qingdao, 266003, People's Republic of China. .,Biomedical Sciences Institute, the Qingdao Branch of SJTU Bio-X Institutes, Qingdao University, Qingdao, 266003, People's Republic of China.
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Takagi S, Omae R, Makanga JO, Kawahara T, Inazu T. Simple and rapid detection method for the mutations in SLC22A12 that cause hypouricemia by allele-specific real-time polymerase chain reaction. Clin Chim Acta 2012; 415:330-3. [PMID: 23148994 DOI: 10.1016/j.cca.2012.10.046] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Accepted: 10/26/2012] [Indexed: 01/26/2023]
Abstract
BACKGROUND Hypouricemia is a disorder that serum urate level is less than 2.0 mg/dl, and relatively common in the Japanese population, where the main genetic cause of hypouricemia is W258X and R90H mutations in human urate trasnsporter 1(SLC22A12). Small scale screening has relied on time-consuming traditional ways like polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). Therefore, it is beneficial that we have an easy and rapid detection method for these mutations. METHODS In this report, we established a touchdown allele-specific real-time polymerase chain reaction (ASPCR) assay for detecting W258X and R90H mutations in SLC22A12, respectively. RESULTS Quantifiable discrimination was successfully achieved by ∆Ct value. Furthermore, we conducted W258X and R90H screening against 120 control genome sets, whereby frequency was 2.92% for W258X, and not detected for R90H, respectively. CONCLUSIONS The two mutations, W258X and R90H in SLC22A12 were successfully genotyped by an easy and rapid ASPCR assay.
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Affiliation(s)
- Shota Takagi
- Department of Pharmacy, College of Pharmaceutical Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
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