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Reddy S, Simmers R, Shah A, Couser N. NPHP1-Related ciliopathies: A new case and major review of the ophthalmic manifestations of 147 reported cases. Clin Case Rep 2023; 11:e7818. [PMID: 37663822 PMCID: PMC10468586 DOI: 10.1002/ccr3.7818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/27/2023] [Accepted: 07/28/2023] [Indexed: 09/05/2023] Open
Abstract
Our case report and review contribute to the understanding of ocular manifestations in NPHP1 ciliopathies by reinforcing the relationship between pathogenic genetic variants and a wide array of ophthalmic abnormalities.
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Affiliation(s)
- Shivania Reddy
- Virginia Commonwealth University School of MedicineRichmondVirginiaUSA
| | - Russell Simmers
- Virginia Commonwealth University School of MedicineRichmondVirginiaUSA
| | - Arth Shah
- Virginia Commonwealth University School of MedicineRichmondVirginiaUSA
| | - Natario Couser
- Department of Human and Molecular GeneticsVirginia Commonwealth University School of MedicineRichmondVirginiaUSA
- Department of OphthalmologyVirginia Commonwealth University School of MedicineRichmondVirginiaUSA
- Department of PediatricsVirginia Commonwealth University School of Medicine, Children's Hospital of Richmond at VCURichmondVirginiaUSA
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2
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Tilemis FN, Marinakis NM, Veltra D, Svingou M, Kekou K, Mitrakos A, Tzetis M, Kosma K, Makrythanasis P, Traeger-Synodinos J, Sofocleous C. Germline CNV Detection through Whole-Exome Sequencing (WES) Data Analysis Enhances Resolution of Rare Genetic Diseases. Genes (Basel) 2023; 14:1490. [PMID: 37510394 PMCID: PMC10379589 DOI: 10.3390/genes14071490] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/14/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023] Open
Abstract
Whole-Exome Sequencing (WES) has proven valuable in the characterization of underlying genetic defects in most rare diseases (RDs). Copy Number Variants (CNVs) were initially thought to escape detection. Recent technological advances enabled CNV calling from WES data with the use of accurate and highly sensitive bioinformatic tools. Amongst 920 patients referred for WES, 454 unresolved cases were further analysed using the ExomeDepth algorithm. CNVs were called, evaluated and categorized according to ACMG/ClinGen recommendations. Causative CNVs were identified in 40 patients, increasing the diagnostic yield of WES from 50.7% (466/920) to 55% (506/920). Twenty-two CNVs were available for validation and were all confirmed; of these, five were novel. Implementation of the ExomeDepth tool promoted effective identification of phenotype-relevant and/or novel CNVs. Among the advantages of calling CNVs from WES data, characterization of complex genotypes comprising both CNVs and SNVs minimizes cost and time to final diagnosis, while allowing differentiation between true or false homozygosity, as well as compound heterozygosity of variants in AR genes. The use of a specific algorithm for calling CNVs from WES data enables ancillary detection of different types of causative genetic variants, making WES a critical first-tier diagnostic test for patients with RDs.
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Affiliation(s)
- Faidon-Nikolaos Tilemis
- Laboratory of Medical Genetics, St. Sophia's Children's Hospital, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Nikolaos M Marinakis
- Laboratory of Medical Genetics, St. Sophia's Children's Hospital, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
- Research University Institute for the Study and Prevention of Genetic and Malignant Disease of Childhood, St. Sophia's Children's Hospital, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Danai Veltra
- Laboratory of Medical Genetics, St. Sophia's Children's Hospital, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
- Research University Institute for the Study and Prevention of Genetic and Malignant Disease of Childhood, St. Sophia's Children's Hospital, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Maria Svingou
- Laboratory of Medical Genetics, St. Sophia's Children's Hospital, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Kyriaki Kekou
- Laboratory of Medical Genetics, St. Sophia's Children's Hospital, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Anastasios Mitrakos
- Laboratory of Medical Genetics, St. Sophia's Children's Hospital, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
- Research University Institute for the Study and Prevention of Genetic and Malignant Disease of Childhood, St. Sophia's Children's Hospital, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Maria Tzetis
- Laboratory of Medical Genetics, St. Sophia's Children's Hospital, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Konstantina Kosma
- Laboratory of Medical Genetics, St. Sophia's Children's Hospital, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Periklis Makrythanasis
- Laboratory of Medical Genetics, St. Sophia's Children's Hospital, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
- Department of Genetic Medicine and Development, Medical School, University of Geneva, 1211 Geneva, Switzerland
- Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
| | - Joanne Traeger-Synodinos
- Laboratory of Medical Genetics, St. Sophia's Children's Hospital, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Christalena Sofocleous
- Laboratory of Medical Genetics, St. Sophia's Children's Hospital, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
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Fei H, Wu Y, Wang Y, Zhang J. Exome sequencing and RNA analysis identify two novel CPLANE1 variants causing Joubert syndrome. Mol Genet Genomic Med 2022; 10:e1877. [PMID: 35092359 PMCID: PMC8922956 DOI: 10.1002/mgg3.1877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 12/26/2021] [Accepted: 01/06/2022] [Indexed: 11/07/2022] Open
Abstract
BACKGROUND Joubert syndrome (JS) is a genetically heterogeneous disorder; its genetic etiology involves more than 35 genes, and a limited number of studies have investigated the pathogenic mechanism of variants in patients with JS. RNA splicing analysis is critical to determine the functional significance for noncanonical splicing variants. METHODS Whole exome sequencing was performed to screen the causative gene variants in a JS family. Sanger sequencing was used to verify the variants. cDNA PCR products were analyzed and functional experiments were performed to determine the pathogenicity of the variants. RESULTS The clinical phenotypes and CPLANE1 variants in the JS patient were analyzed and proved consistent. We identified two novel heterozygous variants of CPLANE1 in the proband first, including c.4459del (frameshift variant) and c.7534-14G > A (intronic variant). We analyzed the pathogenic consequences of the 2 variants and classified the c.4459del as likely pathogenic according to the ACMG/AMP guidelines; however, the pathogenic significance of c.7534-14G > A was uncertain. Furthermore, we performed RNA splicing analysis and revealed that the noncanonical splicing variant (c.7534-14G > A) caused aberrant exon 37 skipping. It produced an aberrant transcript that was predicted to encode a C-terminal truncated protein. CONCLUSIONS The genetic variation spectrum of JS caused by CPLANE1 was updated. Two novel variants further deepened our insight into the disease's molecular mechanism and confirmed the significance of diagnostic whole-exome sequencing.
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Affiliation(s)
- Hongjun Fei
- Department of Reproductive Genetics, International Peace Maternity and Child Health Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yi Wu
- Department of Reproductive Genetics, International Peace Maternity and Child Health Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yanlin Wang
- Department of Reproductive Genetics, International Peace Maternity and Child Health Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Junyu Zhang
- Department of Reproductive Genetics, International Peace Maternity and Child Health Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Molecular genetics of renal ciliopathies. Biochem Soc Trans 2021; 49:1205-1220. [PMID: 33960378 DOI: 10.1042/bst20200791] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 04/12/2021] [Accepted: 04/14/2021] [Indexed: 12/25/2022]
Abstract
Renal ciliopathies are a heterogenous group of inherited disorders leading to an array of phenotypes that include cystic kidney disease and renal interstitial fibrosis leading to progressive chronic kidney disease and end-stage kidney disease. The renal tubules are lined with epithelial cells that possess primary cilia that project into the lumen and act as sensory and signalling organelles. Mutations in genes encoding ciliary proteins involved in the structure and function of primary cilia cause ciliopathy syndromes and affect many organ systems including the kidney. Recognised disease phenotypes associated with primary ciliopathies that have a strong renal component include autosomal dominant and recessive polycystic kidney disease and their various mimics, including atypical polycystic kidney disease and nephronophthisis. The molecular investigation of inherited renal ciliopathies often allows a precise diagnosis to be reached where renal histology and other investigations have been unhelpful and can help in determining kidney prognosis. With increasing molecular insights, it is now apparent that renal ciliopathies form a continuum of clinical phenotypes with disease entities that have been classically described as dominant or recessive at both extremes of the spectrum. Gene-dosage effects, hypomorphic alleles, modifier genes and digenic inheritance further contribute to the genetic complexity of these disorders. This review will focus on recent molecular genetic advances in the renal ciliopathy field with a focus on cystic kidney disease phenotypes and the genotypes that lead to them. We discuss recent novel insights into underlying disease mechanisms of renal ciliopathies that might be amenable to therapeutic intervention.
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Reches A, Hiersch L, Simchoni S, Barel D, Greenberg R, Ben Sira L, Malinger G, Yaron Y. Whole-exome sequencing in fetuses with central nervous system abnormalities. J Perinatol 2018; 38:1301-1308. [PMID: 30108342 DOI: 10.1038/s41372-018-0199-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 07/03/2018] [Accepted: 07/09/2018] [Indexed: 12/29/2022]
Abstract
OBJECTIVE We describe our experience with whole-exome sequencing (WES) in fetuses with central nervous system (CNS) abnormalities following a normal chromosomal microarray result. METHODS During the study period (2014-2017) 7 cases (9 fetuses) with prenatally diagnosed CNS abnormality, whose chromosomal microarray analysis was negative, were offered whole-exome sequencing analysis. RESULTS A pathogenic or a likely pathogenic variant was found in 5 cases including a previously described, likely pathogenic de novo TUBA1A variant (Case #1); a previously described homozygous VRK1 variant (Case #2); an X-linked ARX variant (Case #3); a likely pathogenic heterozygous variant in the TUBB3 gene (Case #5). Finally, in two fetuses of the same couple (Case #6), a compound heterozygous state was detected, consisting of the NPHP1 gene deletion and a sequence variant of uncertain significance. Two additional cases had normal WES results. CONCLUSION Whole-exome sequencing may improve prenatal diagnosis in fetuses with CNS abnormalities.
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Affiliation(s)
- Adi Reches
- Prenatal Genetic Diagnosis Unit, Genetic Institute, Tel Aviv Sourasky Medical Center, Tel Aviv-Yafo, Israel.,Department of Obstetrics and Gynecology, Lis Maternity Hospital, Tel Aviv Sourasky Medical Center, Tel Aviv-Yafo, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv-Yafo, Israel
| | - Liran Hiersch
- Prenatal Genetic Diagnosis Unit, Genetic Institute, Tel Aviv Sourasky Medical Center, Tel Aviv-Yafo, Israel. .,Department of Obstetrics and Gynecology, Lis Maternity Hospital, Tel Aviv Sourasky Medical Center, Tel Aviv-Yafo, Israel. .,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv-Yafo, Israel.
| | - Sharon Simchoni
- Prenatal Genetic Diagnosis Unit, Genetic Institute, Tel Aviv Sourasky Medical Center, Tel Aviv-Yafo, Israel
| | - Dalit Barel
- Prenatal Genetic Diagnosis Unit, Genetic Institute, Tel Aviv Sourasky Medical Center, Tel Aviv-Yafo, Israel
| | - Rotem Greenberg
- Prenatal Genetic Diagnosis Unit, Genetic Institute, Tel Aviv Sourasky Medical Center, Tel Aviv-Yafo, Israel
| | - Liat Ben Sira
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv-Yafo, Israel.,Radiology Department, Tel Aviv Sourasky Medical Center, Tel Aviv-Yafo, Israel
| | - Gustavo Malinger
- Department of Obstetrics and Gynecology, Lis Maternity Hospital, Tel Aviv Sourasky Medical Center, Tel Aviv-Yafo, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv-Yafo, Israel
| | - Yuval Yaron
- Prenatal Genetic Diagnosis Unit, Genetic Institute, Tel Aviv Sourasky Medical Center, Tel Aviv-Yafo, Israel.,Department of Obstetrics and Gynecology, Lis Maternity Hospital, Tel Aviv Sourasky Medical Center, Tel Aviv-Yafo, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv-Yafo, Israel
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6
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Overwater E, Marsili L, Baars MJH, Baas AF, van de Beek I, Dulfer E, van Hagen JM, Hilhorst-Hofstee Y, Kempers M, Krapels IP, Menke LA, Verhagen JMA, Yeung KK, Zwijnenburg PJG, Groenink M, van Rijn P, Weiss MM, Voorhoeve E, van Tintelen JP, Houweling AC, Maugeri A. Results of next-generation sequencing gene panel diagnostics including copy-number variation analysis in 810 patients suspected of heritable thoracic aortic disorders. Hum Mutat 2018; 39:1173-1192. [PMID: 29907982 PMCID: PMC6175145 DOI: 10.1002/humu.23565] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 05/23/2018] [Accepted: 05/30/2018] [Indexed: 01/02/2023]
Abstract
Simultaneous analysis of multiple genes using next-generation sequencing (NGS) technology has become widely available. Copy-number variations (CNVs) in disease-associated genes have emerged as a cause for several hereditary disorders. CNVs are, however, not routinely detected using NGS analysis. The aim of this study was to assess the diagnostic yield and the prevalence of CNVs using our panel of Hereditary Thoracic Aortic Disease (H-TAD)-associated genes. Eight hundred ten patients suspected of H-TAD were analyzed by targeted NGS analysis of 21 H-TAD associated genes. In addition, the eXome hidden Markov model (XHMM; an algorithm to identify CNVs in targeted NGS data) was used to detect CNVs in these genes. A pathogenic or likely pathogenic variant was found in 66 of 810 patients (8.1%). Of these 66 pathogenic or likely pathogenic variants, six (9.1%) were CNVs not detectable by routine NGS analysis. These CNVs were four intragenic (multi-)exon deletions in MYLK, TGFB2, SMAD3, and PRKG1, respectively. In addition, a large duplication including NOTCH1 and a large deletion encompassing SCARF2 were detected. As confirmed by additional analyses, both CNVs indicated larger chromosomal abnormalities, which could explain the phenotype in both patients. Given the clinical relevance of the identification of a genetic cause, CNV analysis using a method such as XHMM should be incorporated into the clinical diagnostic care for H-TAD patients.
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Affiliation(s)
- Eline Overwater
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, the Netherlands.,Department of Clinical Genetics, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Luisa Marsili
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, the Netherlands.,Medical Genetics Unit, Tor Vergata University Hospital, Rome, Italy
| | - Marieke J H Baars
- Department of Clinical Genetics, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Annette F Baas
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Irma van de Beek
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, the Netherlands.,Department of Clinical Genetics, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Eelco Dulfer
- Department of Genetics, University Medical Center Groningen, Groningen, the Netherlands
| | - Johanna M van Hagen
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, the Netherlands
| | | | - Marlies Kempers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Ingrid P Krapels
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Leonie A Menke
- Department of Pediatrics, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Judith M A Verhagen
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Kak K Yeung
- Department of Surgery, Institute for Cardiovascular Research, VU University Medical Center, Amsterdam, the Netherlands.,Department of Physiology, Institute for Cardiovascular Research, VU University Medical Center, Amsterdam, the Netherlands
| | - Petra J G Zwijnenburg
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, the Netherlands
| | - Maarten Groenink
- Department of Cardiology and Radiology, Academic Medical Center Amsterdam, University of Amsterdam, Amsterdam, the Netherlands
| | - Peter van Rijn
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, the Netherlands
| | - Marjan M Weiss
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, the Netherlands
| | - Els Voorhoeve
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, the Netherlands
| | - J Peter van Tintelen
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, the Netherlands.,Department of Clinical Genetics, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Arjan C Houweling
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, the Netherlands
| | - Alessandra Maugeri
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, the Netherlands
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Koyama S, Sato H, Kobayashi R, Kawakatsu S, Kurimura M, Wada M, Kawanami T, Kato T. Clinical and radiological diversity in genetically confirmed primary familial brain calcification. Sci Rep 2017; 7:12046. [PMID: 28935882 PMCID: PMC5608910 DOI: 10.1038/s41598-017-11595-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 08/25/2017] [Indexed: 01/03/2023] Open
Abstract
Primary familial brain calcification (PFBC) is a rare neuropsychiatric disorder with characteristic symmetrical brain calcifications. Patients with PFBC may have a variety of symptoms, although they also may be clinically asymptomatic. Parkinsonism is one of the most common movement disorders; however, the underlying mechanism remains unclear. This condition is typically transmitted in an autosomal dominant fashion. To date, mutations in SLC20A2, PDGFRB, PDGFB, and XPR1 have been reported to cause PFBC. The aim of the study was to identify the genetic cause of brain calcification in probands from three PFBC families and in 8 sporadic patients and to perform clinical and radiological assessments focusing on parkinsonism in mutation carriers. Three familial PFBC probands and their relatives and eight sporadic patients affected with brain calcifications were enrolled in this study. Whole-exome sequencing identified three novel mutations: c.269G > T, p.(Gly90Val) and c.516+1G > A in SLC20A2 in familial cases, and c.602-1G > T in PDGFB in a sporadic patient. The c.516+1G > A mutation resulted in exon 4 skipping in SLC20A2 (p.Val144Glyfs*85). Dopamine transporter single photon emission computed tomography using 123I-ioflupane and 123I-metaiodobenzylguanidine cardiac scintigraphy revealed pre-synaptic dopaminergic deficit and cardiac sympathetic nerve dysfunction in two SLC20A2-related PFBC patients with parkinsonism.
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Affiliation(s)
- Shingo Koyama
- Department of Neurology, Hematology, Metabolism, Endocrinology, and Diabetology, Yamagata University Faculty of Medicine, 2-2-2 Iida-nishi, Yamagata, 990-9585, Japan.
| | - Hidenori Sato
- Genomic Information Analysis Unit, Department of Genomic Cohort Research, Yamagata University Faculty of Medicine, 2-2-2 Iida-nishi, Yamagata, 990-9585, Japan
| | - Ryota Kobayashi
- Department of Psychiatry, Yamagata University Faculty of Medicine, 2-2-2 Iida-nishi, Yamagata, 990-9585, Japan
| | - Shinobu Kawakatsu
- Department of Neuropsychiatry, Aizu Medical Center, Fukushima Medical University, 21-2 Maeda, Tanisawa, Kawahigashi, Aizuwakamatsu, Fukushima, 969-3492, Japan
| | - Masayuki Kurimura
- Department of Neurology, Okitama Public General Hospital, 2000 Nishi-otsuka, Kawanishi-machi, Higashi-okitama-gun, Yamagata, 992-0601, Japan
| | - Manabu Wada
- Department of Neurology, Hematology, Metabolism, Endocrinology, and Diabetology, Yamagata University Faculty of Medicine, 2-2-2 Iida-nishi, Yamagata, 990-9585, Japan
| | - Toru Kawanami
- Department of Neurology, Hematology, Metabolism, Endocrinology, and Diabetology, Yamagata University Faculty of Medicine, 2-2-2 Iida-nishi, Yamagata, 990-9585, Japan
| | - Takeo Kato
- Department of Neurology, Hematology, Metabolism, Endocrinology, and Diabetology, Yamagata University Faculty of Medicine, 2-2-2 Iida-nishi, Yamagata, 990-9585, Japan
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