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Lee WW, Lee CG, Ki CS. KCNJ3 is a novel candidate gene for autosomal dominant pure hereditary spastic paraplegia identified using whole genome sequencing. Am J Med Genet B Neuropsychiatr Genet 2024:e32984. [PMID: 38597354 DOI: 10.1002/ajmg.b.32984] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 03/05/2024] [Accepted: 04/02/2024] [Indexed: 04/11/2024]
Abstract
Hereditary spastic paraplegia (HSP) is a group of familial diseases characterized by progressive corticospinal tract degeneration. Clinically, patients present with lower-limb spasticity and weakness. To date, more than 80 genetic HSP types have been identified. Despite advances in molecular genetics, novel HSP gene discoveries are ongoing, with a low genetic diagnostic yield. In this study, we aimed to determine pathogenic variants in a family with HSP, which was not diagnosed through conventional genetic testing. We clinically characterized a large family and conducted whole genome sequencing (WGS) analysis of four affected and three unaffected individuals in the family to identify the genetic cause of HSP. This family had autosomal dominant pure (uncomplicated) late childhood-onset HSP. The patients' symptoms accelerated between the ages of 20 and 30. Brain magnetic resonance images typically showed white matter changes, a thin corpus callosum, and cerebellar atrophy. We identified a heterozygous missense variant, KCNJ3 c.1297T>G (p.Leu433Val), through WGS and family genetic analysis, confirmed by Sanger sequencing. We suggest that the identification of KCNJ3 c.1297T>G (p.Leu433Val) constitutes the discovery of a potential novel gene responsible for HSP in this family. This is the first study to report the possible role of a KCNJ3 variant in HSP pathogenesis. Our findings further expand the phenotypic and genotypic spectrum of HSP.
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Affiliation(s)
- Woong-Woo Lee
- Department of Neurology, Nowon Eulji Medical Center, Eulji University School of Medicine, Seoul, Republic of Korea
| | - Cha Gon Lee
- Department of Pediatrics, Nowon Eulji Medical Center, Eulji University School of Medicine, Seoul, Republic of Korea
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Sung W, Noh MY, Nahm M, Kim YS, Ki CS, Kim YE, Kim HJ, Kim SH. Progranulin haploinsufficiency mediates cytoplasmic TDP-43 aggregation with lysosomal abnormalities in human microglia. J Neuroinflammation 2024; 21:47. [PMID: 38347588 PMCID: PMC10863104 DOI: 10.1186/s12974-024-03039-1] [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: 12/21/2023] [Accepted: 02/07/2024] [Indexed: 02/15/2024] Open
Abstract
BACKGROUND Progranulin (PGRN) haploinsufficiency due to progranulin gene (GRN) variants can cause frontotemporal dementia (FTD) with aberrant TAR DNA-binding protein 43 (TDP-43) accumulation. Despite microglial burden with TDP-43-related pathophysiology, direct microglial TDP-43 pathology has not been clarified yet, only emphasized in neuronal pathology. Thus, the objective of this study was to investigate TDP-43 pathology in microglia of patients with PGRN haploinsufficiency. METHODS To design a human microglial cell model with PGRN haploinsufficiency, monocyte-derived microglia (iMGs) were generated from FTD-GRN patients carrying pathogenic or likely pathogenic variants (p.M1? and p.W147*) and three healthy controls. RESULTS iMGs from FTD-GRN patients with PGRN deficiency exhibited severe neuroinflammation phenotype and failure to maintain their homeostatic molecular signatures, along with impaired phagocytosis. In FTD-GRN patients-derived iMGs, significant cytoplasmic TDP-43 aggregation and accumulation of lipid droplets with profound lysosomal abnormalities were observed. These pathomechanisms were mediated by complement C1q activation and upregulation of pro-inflammatory cytokines. CONCLUSIONS Our study provides considerable cellular and molecular evidence that loss-of-function variants of GRN in human microglia can cause microglial dysfunction with abnormal TDP-43 aggregation induced by inflammatory milieu as well as the impaired lysosome. Elucidating the role of microglial TDP-43 pathology in intensifying neuroinflammation in individuals with FTD due to PGRN deficiency and examining consequential effects on microglial dysfunction might yield novel insights into the mechanisms underlying FTD and neurodegenerative disorders.
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Affiliation(s)
- Wonjae Sung
- Department of Neurology, College of Medicine, Hanyang University, 222, Wangsimni-Ro, Seongdong-Gu, Seoul, 04763, Republic of Korea
| | - Min-Young Noh
- Department of Neurology, College of Medicine, Hanyang University, 222, Wangsimni-Ro, Seongdong-Gu, Seoul, 04763, Republic of Korea
| | - Minyeop Nahm
- Dementia Research Group, Korea Brain Research Institute, Daegu, Republic of Korea
| | - Yong Sung Kim
- Department of Neurology, College of Medicine, Hanyang University, 222, Wangsimni-Ro, Seongdong-Gu, Seoul, 04763, Republic of Korea
| | | | - Young-Eun Kim
- Department of Laboratory Medicine, College of Medicine, Hanyang University, Seoul, Republic of Korea
| | - Hee-Jin Kim
- Department of Neurology, College of Medicine, Hanyang University, 222, Wangsimni-Ro, Seongdong-Gu, Seoul, 04763, Republic of Korea
| | - Seung Hyun Kim
- Department of Neurology, College of Medicine, Hanyang University, 222, Wangsimni-Ro, Seongdong-Gu, Seoul, 04763, Republic of Korea.
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Lee CG, Kim HJ, Seol CA, Ki CS. Novel In-Frame Deletion CNOT3 Variant in a Family With Intellectual Developmental Disorder With Speech Delay and Dysmorphic Facies. Neurol Genet 2024; 10:e200116. [PMID: 38179413 PMCID: PMC10766080 DOI: 10.1212/nxg.0000000000200116] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 10/17/2023] [Indexed: 01/06/2024]
Abstract
Objectives Intellectual developmental disorder with speech delay, autism, and dysmorphic facies (IDDSADF) is caused by heterozygous CNOT3 (MIM# 604910) variants on chromosome 19q13. This study aimed to identify and describe the clinical features of a Korean family with maternally inherited speech delay and intellectual and developmental disability to elucidate the underlying genetic mechanism. Methods We conducted whole-exome sequencing and confirmatory Sanger sequencing on the proband, the mother, and unaffected grandparents with wild-type genotypes. Results The phenotypes of the mother and 2 daughters presented muscular hypotonia, global developmental delay, speech delay, intellectual disability, macrocephaly, facial dysmorphic features, and focal corpus callosum hypoplasia. Whole-exome sequencing identified a novel in-frame deletion, c.2017_2019del (p.Phe673del) in CNOT3, located in the C-terminal negative on the TATA-less-box domain. Discussion This report presents a new possible mechanism underlying IDDSADF caused by CNOT3 variants-an in-frame deletion. The findings enhance our understanding of early-life neurodevelopment and the genotype-phenotype relationships of IDDSADF caused by CNOT3 variants. In addition, this report could assist in early diagnosis and facilitate genetic counseling.
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Affiliation(s)
- Cha Gon Lee
- From the Department of Pediatrics (C.G.L.); Department of Rehabilitation Medicine (H.J.K.), Nowon Eulji Medical Center, Eulji University School of Medicine, Seoul; and GC Genome (C.A.S., C.-S.K.), Yongin, Republic of Korea
| | - Hyun Jung Kim
- From the Department of Pediatrics (C.G.L.); Department of Rehabilitation Medicine (H.J.K.), Nowon Eulji Medical Center, Eulji University School of Medicine, Seoul; and GC Genome (C.A.S., C.-S.K.), Yongin, Republic of Korea
| | - Chang Ahn Seol
- From the Department of Pediatrics (C.G.L.); Department of Rehabilitation Medicine (H.J.K.), Nowon Eulji Medical Center, Eulji University School of Medicine, Seoul; and GC Genome (C.A.S., C.-S.K.), Yongin, Republic of Korea
| | - Chang-Seok Ki
- From the Department of Pediatrics (C.G.L.); Department of Rehabilitation Medicine (H.J.K.), Nowon Eulji Medical Center, Eulji University School of Medicine, Seoul; and GC Genome (C.A.S., C.-S.K.), Yongin, Republic of Korea
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Park JE, Lee T, Ha K, Cho EH, Ki CS. Carrier frequency and incidence of alpha-mannosidosis: population database-based study-focus on the East Asian and Korean population. Front Genet 2023; 14:1297543. [PMID: 38107468 PMCID: PMC10725197 DOI: 10.3389/fgene.2023.1297543] [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: 09/20/2023] [Accepted: 11/23/2023] [Indexed: 12/19/2023] Open
Abstract
Background: Alpha-mannosidosis caused by mutations in the MAN2B1 gene is a rare genetic disorder characterized by physical abnormalities and intellectual disabilities. The objective of this study was to analyze the carrier frequency and estimated incidence of alpha-mannosidosis in East Asian populations, as limited data exists on its incidence in this group. Methods: In this study, a total of 125,748 exomes from the gnomAD database was analyzed. Additionally, 5,305 data from the KOVA and 1,722 data from the KRGDB, both representing Korean populations, were included. Results: The global carrier frequency of alpha-mannosidosis in gnomAD was 0.23%; the highest carrier frequency was observed in the Finnish at 0.49%, and East Asians had the second highest carrier frequency at 0.30%. Globally, the approximate incidence of alpha-mannosidosis was calculated at 1 in 784,535, l in 166,801 Europeans (Finnish), and l in 431,689 East Asians. By integrating the data from the 8,936 Koreans in gnomAD Korean, KOVA and KRGDB, the carrier frequency of alpha-mannosidosis in the Korean population was 0.04% and estimated incidence was 1 in 19,963,024. Conclusion: This study is the first to investigate the carrier frequencies of alpha-mannosidosis in East Asians and Koreans, including specific subpopulations, utilizing gnomAD and the Korean genomic database. The variant spectrum of MAN2B1 genes in East Asians showed significant differences compared to other ethnic groups. Our data provide valuable reference information for future investigations into alpha-mannosidosis, aiding in understanding the genetic diversity and specific variants associated with the condition in East Asian populations.
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Affiliation(s)
- Jong Eun Park
- Department of Laboratory Medicine, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri, Republic of Korea
| | | | | | - Eun Hye Cho
- Department of Laboratory Medicine, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
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Heo J, Lee S, Park J, Yang H, Park H, Ki CS, Oh YL, Kim HI, Kim SW, Chung JH, Kim K, Kim TH. Age-associated mortality is partially mediated by TERT promoter mutation status in differentiated thyroid carcinoma. PLoS One 2023; 18:e0294145. [PMID: 37948420 PMCID: PMC10637683 DOI: 10.1371/journal.pone.0294145] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 10/26/2023] [Indexed: 11/12/2023] Open
Abstract
BACKGROUND Age at diagnosis (AAD) and telomerase reverse transcriptase (TERT) promoter mutations are prognostic factors in differentiated thyroid carcinoma (DTC), and the prevalence of the mutations increases with AAD. Considering this correlation, we investigated whether an interaction between AAD and the mutations is present and whether the mutation mediates the effect of AAD on the mortality rate in DTC. METHODS The study included 393 patients with DTC who were followed-up after thyroidectomy at a single medical center in Korea from 1994 to 2004. Multivariable Cox regression was used to investigate the interaction of AAD and TERT promoter mutation. Mediation analysis was conducted using a regression-based causal mediation model. RESULTS The age-associated mortality rate increased progressively in all DTC patients and wild-type TERT group (WT-TERT) with a linear trend (p < 0.001) contrary to mutant TERT group (M-TERT) (p = 0.301). Kaplan-Meier curves declined progressively with increasing AAD in the entire group, but the change was without significance in M-TERT. The effect of AAD on mortality was not significant (adjusted HR: 1.07, 95% CI 0.38-3.05) in M-TERT. An interaction between AAD and TERT promoter mutation (p = 0.005) was found in a multivariable Cox regression. TERT promoter mutations mediated the effect of AAD on the mortality rate by 36% in DTC in a mediation analysis. CONCLUSIONS Considering the mediation of TERT promoter mutation on the effect of AAD on mortality, inclusion of TERT promoter mutation in a stage classification to achieve further individualized prediction in DTC is necessary.
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Affiliation(s)
- Jung Heo
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Myongji Hospital, Hanyang University College of Medicine, Goyang-si, Gyeonggi-do, Korea
| | - Sungjoo Lee
- Department of Digital Health, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul, Korea
| | - Jun Park
- Division of Endocrinology, Department of Medicine, Sahmyook Medical Center, Seoul, Korea
| | - Heera Yang
- Division of Endocrinology and Metabolism, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Hyunju Park
- Department of Internal Medicine, CHA Bundang Medical Center, CHA University, Seongnam-si, Gyeonggi-do, Korea
| | | | - Young Lyun Oh
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Hye In Kim
- Division of Endocrinology and Metabolism, Department of Medicine, Samsung Changwon Hospital, Sungkyunkwan University School of Medicine, Changwon-si, Gyeongsangnam-do, Korea
| | - Sun Wook Kim
- Division of Endocrinology and Metabolism, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jae Hoon Chung
- Division of Endocrinology and Metabolism, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Kyunga Kim
- Department of Digital Health, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul, Korea
- Biomedical Statistics Center, Research Institute for Future Medicine, Samsung Medical Center, Seoul, Korea
- Department of Data Convergence and Future Medicine, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Tae Hyuk Kim
- Division of Endocrinology and Metabolism, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
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Park JE, Lee T, Ha K, Cho EH, Ki CS. Carrier frequency and incidence of aromatic L-amino acid decarboxylase deficiency: a gnomAD-based study. Pediatr Res 2023; 94:1764-1770. [PMID: 37286773 DOI: 10.1038/s41390-023-02685-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [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] [Received: 04/04/2023] [Revised: 05/14/2023] [Accepted: 05/21/2023] [Indexed: 06/09/2023]
Abstract
BACKGROUND Aromatic L-amino acid decarboxylase (AADC) deficiency is an autosomal recessive neurotransmitter metabolism disorder and is clinically characterized by infancy hypotonia, ophthalmic crisis, and developmental delay. With the emergence of gene therapy for AADC deficiency, accurate prediction of AADC deficiency is required. This study aimed to analyze the carrier frequency and expected incidence of AADC deficiency using exome data from the Genome Aggregation Database (gnomAD). METHODS We analyzed 125,748 exomes from gnomAD, including 9197 East Asian exomes, for the DDC gene. All identified variants were classified according to the 2015 American College of Medical Genetics and Genomics and the Association for Molecular Pathology guidelines. RESULTS The worldwide carrier frequency of AADC deficiency was 0.17%; the highest frequency was observed in East Asians at 0.78%, and the lowest was in Latinos at 0.07%. The estimated incidence of AADC deficiency was 1 in 1,374,129 worldwide and 1 in 65,266 in East Asians. CONCLUSION The results demonstrated that East Asians have a higher carrier frequency of AADC deficiency than other ethnic groups. The variant spectrum of DDC genes in East Asian populations differed greatly from those of other ethnic groups. Our data will serve as a reference for further investigation of AADC deficiency. IMPACT This study analyzed exome data from the Genome Aggregation Database (gnomAD) to estimate the carrier frequency and expected incidence of aromatic L-amino acid decarboxylase (AADC) deficiency. The article provides updated carrier frequency and incidence estimates for AADC deficiency, particularly in East Asian populations, and emphasizes the significant differences in the variant spectrum of DDC genes in this population compared to other ethnic groups. The study provides important information for accurate prediction and early diagnosis of AADC deficiency, particularly in high-risk populations, and may aid in the development of more effective targeted screening programs and gene therapies for this disorder.
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Affiliation(s)
- Jong Eun Park
- Department of Laboratory Medicine, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri, Republic of Korea.
| | | | | | - Eun Hye Cho
- Department of Laboratory Medicine, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
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Sung W, Kim JA, Kim YS, Park J, Oh KW, Sung JJ, Ki CS, Kim YE, Kim SH. An analysis of variants in TARDBP in the Korean population with amyotrophic lateral sclerosis: comparison with previous data. Sci Rep 2023; 13:18805. [PMID: 37914747 PMCID: PMC10620191 DOI: 10.1038/s41598-023-45593-3] [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: 07/22/2023] [Accepted: 10/21/2023] [Indexed: 11/03/2023] Open
Abstract
The TARDBP gene variant is a known major cause of amyotrophic lateral sclerosis (ALS), with limited reports of Korean patients with ALS harboring the variants in TARDBP. This large cohort study introduces four ALS patients who share the p.M337V variant of the TARDBP, allowing for an investigation of clinical characteristics and prognosis by analyzing previously reported cases with the same variant. From November 2014 to August 2022, participants were recruited from two tertiary hospitals in Seoul, Korea. Clinical characteristics of patients diagnosed with ALS carrying the variant in TARDBP were evaluated. Previous articles demonstrating subjects' characteristics were reviewed. Four patients were identified with the pathogenic missense variant (c.1009A>G; p.M337V) in the TARDBP. The mean age of onset was 55 years old, and none of the patients showed severe cognitive impairment. Sixty-three patients carrying the p.M337V variant in TARDBP from this study and previous reports delineated young age of onset (51.6 years), high frequency of bulbar onset patients (61.9%), and low comorbidity of frontotemporal dementia. This study reveals the presence of pathogenic variant of TARDBP in Korea and emphasizes the importance of genetic screening of the TARDBP gene, in diagnosing ALS and evaluating prognosis among familial and simplex ALS patients in Korea.
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Affiliation(s)
- Wonjae Sung
- Department of Neurology, College of Medicine, Hanyang University, Wangsimni-ro 222, Seongdong-gu, Seoul, 04763, Republic of Korea
| | - Jin-Ah Kim
- Department of Translational Medicine, College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - Yong Sung Kim
- Department of Neurology, College of Medicine, Hanyang University, Wangsimni-ro 222, Seongdong-gu, Seoul, 04763, Republic of Korea
| | - Jinseok Park
- Department of Neurology, College of Medicine, Hanyang University, Wangsimni-ro 222, Seongdong-gu, Seoul, 04763, Republic of Korea
| | - Ki-Wook Oh
- Department of Neurology, College of Medicine, Hanyang University, Wangsimni-ro 222, Seongdong-gu, Seoul, 04763, Republic of Korea
| | - Jung-Joon Sung
- Department of Translational Medicine, College of Medicine, Seoul National University, Seoul, Republic of Korea
| | | | - Young-Eun Kim
- Department of Laboratory Medicine, College of Medicine, Hanyang University, Wangsimni-ro 222, Seongdong-gu, Seoul, 04763, Republic of Korea.
| | - Seung Hyun Kim
- Department of Neurology, College of Medicine, Hanyang University, Wangsimni-ro 222, Seongdong-gu, Seoul, 04763, Republic of Korea.
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Noh MY, Kwon MS, Oh KW, Nahm M, Park J, Kim YE, Ki CS, Jin HK, Bae JS, Kim SH. Role of NCKAP1 in the Defective Phagocytic Function of Microglia-Like Cells Derived from Rapidly Progressing Sporadic ALS. Mol Neurobiol 2023; 60:4761-4777. [PMID: 37154887 PMCID: PMC10293423 DOI: 10.1007/s12035-023-03339-2] [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: 10/21/2022] [Accepted: 04/04/2023] [Indexed: 05/10/2023]
Abstract
Microglia plays a key role in determining the progression of amyotrophic lateral sclerosis (ALS), yet their precise role in ALS has not been identified in humans. This study aimed to identify a key factor related to the functional characteristics of microglia in rapidly progressing sporadic ALS patients using the induced microglia model, although it is not identical to brain resident microglia. After confirming that microglia-like cells (iMGs) induced by human monocytes could recapitulate the main signatures of brain microglia, step-by-step comparative studies were conducted to delineate functional differences using iMGs from patients with slowly progressive ALS [ALS(S), n = 14] versus rapidly progressive ALS [ALS(R), n = 15]. Despite an absence of significant differences in the expression of microglial homeostatic genes, ALS(R)-iMGs preferentially showed defective phagocytosis and an exaggerated pro-inflammatory response to LPS stimuli compared to ALS(S)-iMGs. Transcriptome analysis revealed that the perturbed phagocytosis seen in ALS(R)-iMGs was closely associated with decreased NCKAP1 (NCK-associated protein 1)-mediated abnormal actin polymerization. NCKAP1 overexpression was sufficient to rescue impaired phagocytosis in ALS(R)-iMGs. Post-hoc analysis indicated that decreased NCKAP1 expression in iMGs was correlated with the progression of ALS. Our data suggest that microglial NCKAP1 may be an alternative therapeutic target in rapidly progressive sporadic ALS.
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Affiliation(s)
- Min-Young Noh
- Department of Neurology, College of Medicine, Hanyang University, Wangsimniro 222-1, Seoul, 04763 Republic of Korea
| | - Min-Soo Kwon
- Department of Pharmacology, Research Institute of Basic Medical Science, School of Medicine, CHA University, CHA Bio Complex, 335 Pangyo, Gyeonggi-Do 13488 Republic of Korea
| | - Ki-Wook Oh
- Department of Neurology, College of Medicine, Hanyang University, Wangsimniro 222-1, Seoul, 04763 Republic of Korea
| | - Minyeop Nahm
- Dementia Research Group, Korea Brain Research Institute, Daegu, Republic of Korea
| | - Jinseok Park
- Department of Neurology, College of Medicine, Hanyang University, Wangsimniro 222-1, Seoul, 04763 Republic of Korea
| | - Young-Eun Kim
- Department of Laboratory Medicine, College of Medicine, Hanyang University, Wangsimniro 222-1, Seoul, 04763 Republic of Korea
| | - Chang-Seok Ki
- GC Genome Corporation, Yongin, 16924 Republic of Korea
| | - Hee Kyung Jin
- KNU Alzheimer’s Disease Research Institute, Kyungpook National University, Daegu, 41566 Republic of Korea
- Department of Laboratory Animal Medicine, College of Veterinary Medicine, Kyungpook National University, Daegu, 41566 Republic of Korea
| | - Jae-sung Bae
- KNU Alzheimer’s Disease Research Institute, Kyungpook National University, Daegu, 41566 Republic of Korea
- Department of Physiology, Cell and Matrix Research Institute, School of Medicine, Kyungpook National University, Daegu, 41944 Republic of Korea
- Department of Biomedical Science, BK21 Plus KNU Biomedical Convergence Program, Kyungpook National University, Wangsimniro 222-1, Daegu, 41944 Republic of Korea
| | - Seung Hyun Kim
- Department of Neurology, College of Medicine, Hanyang University, Wangsimniro 222-1, Seoul, 04763 Republic of Korea
- Cell Therapy Center, Hanyang University Hospital, Wangsimniro 222-1, Seoul, 04763 Republic of Korea
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Park JE, Chang SA, Jang SY, Lee KS, Kim DK, Ki CS. Differential Diagnosis of Pulmonary Veno-Occlusive Disease and/or Pulmonary Capillary Hemangiomatosis after Identification of Two Novel EIF2AK4 Variants by Whole-Exome Sequencing. Mol Syndromol 2023; 14:254-257. [PMID: 37323202 PMCID: PMC10267509 DOI: 10.1159/000527524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 10/11/2022] [Indexed: 12/03/2023] Open
Abstract
Background Pulmonary veno-occlusive disease (PVOD) and/or pulmonary capillary hemangiomatosis (PCH) are rare causes of pulmonary hypertension. Pulmonary arterial hypertension (PAH) and PVOD/PCH are clinically similar, but there is a risk of drug-induced pulmonary edema when PCH patients receive the PAH therapy. Therefore, early diagnosis of PVOD/PCH is important. Objectives We report the first case in Korea of PVOD/PCH in a patient carrying compound heterozygous pathogenic variants in the EIF2AK4 gene. Case Description and Method A 19-year-old man who was previously diagnosed with idiopathic PAH suffered from dyspnea on exertion for 2 months. He had a reduced lung diffusion capacity for carbon monoxide (25% predicted). Chest computed tomography images showed diffusely scattered ground-glass opacity nodules in both lungs with an enlarged main pulmonary artery. For the molecular diagnosis of PVOD/PCH, whole-exome sequencing was performed for the proband. Results Exome sequencing identified two novel EIF2AK4 variants, c.2137_2138dup (p.Ser714Leufs*78) and c.3358-1G>A. These two variants were classified as pathogenic variants according to the 2015 American College of Medical Genetics and Genomics guidelines. Conclusions We identified two novel pathogenic variants (c.2137_2138dup and c.3358-1G>A) in the EIF2AK4 gene. Identification of possible pathogenic gene variants by whole-exome sequencing or panel sequencing is recommended as a guide to adequate treatment of patients with pulmonary hypertension.
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Affiliation(s)
- Jong Eun Park
- Department of Laboratory Medicine, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri, Republic of Korea
| | - Sung-A Chang
- Division of Cardiology, Department of Medicine, Heart Vascular Stroke Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Shin Yi Jang
- Division of Cardiology, Department of Medicine, Heart Vascular Stroke Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Kyung Soo Lee
- Department of Radiology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Duk-Kyung Kim
- Division of Cardiology, Department of Medicine, Heart Vascular Stroke Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
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Park H, Heo J, Ki CS, Shin JH, Oh YL, Son YI, Kim JS, Kim SW, Chung JH, Kim TY, Kim TH, Kim JH. Selection Criteria for Completion Thyroidectomy in Follicular Thyroid Carcinoma Using Primary Tumor Size and TERT Promoter Mutational Status. Ann Surg Oncol 2023; 30:2916-2925. [PMID: 36637642 PMCID: PMC9838536 DOI: 10.1245/s10434-022-13089-5] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 11/21/2022] [Indexed: 01/14/2023]
Abstract
BACKGROUND A stepwise surgical approach with hemithyroidectomy and completion thyroidectomy was used to achieve definite characterization of follicular thyroid carcinoma (FTC). Choosing appropriate candidates for completion thyroidectomy has been controversial. OBJECTIVE The aim of this study was to clarify the selection criteria for completion thyroidectomy using telomerase reverse transcriptase (TERT) promoter mutation. METHODS A total of 87 FTC patients who had information about TERT promoter mutation from August 1995 to November 2020 were investigated. The cumulative risk of initial distant metastasis, disease recurrence, and cancer-specific death according to primary tumor size in each of the World Health Organization (WHO) 2017 classifications were calculated. RESULTS Of the 87 patients, 8 (9.2%) had initial distant metastasis and 15 (17.2%) had persistent disease or developed structural recurrence. The threshold diameter for initial distant metastasis, disease recurrence, and cancer-specific death was 2 cm in minimally invasive FTC (MI-FTC) with mutant TERT (M-TERT) and in encapsulated angioinvasive FTC (EA-FTC) with M-TERT, while that in MI-FTC with wild-type TERT (WT-TERT) and EA-FTC with WT-TERT was 4 cm. The cumulative risk of initial distant metastasis, disease recurrence, and cancer-specific death according to primary tumor size in each WHO 2017 classification was significantly different only in patients with WT-TERT (p = 0.001, p = 0.019, and p = 0.005, respectively). CONCLUSIONS The data suggest 2 cm as a critical threshold diameter for performance of completion thyroidectomy in MI-FTC with M-TERT and EA-FTC with M-TERT. TERT promoter mutational status can help select candidates for completion thyroidectomy.
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Affiliation(s)
- Hyunju Park
- Division of Endocrinology and Metabolism, Department of Medicine, Thyroid Center, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jung Heo
- Division of Endocrinology and Metabolism, Department of Medicine, Thyroid Center, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | | | - Jung Hee Shin
- Department of Radiology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Young Lyun Oh
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Young Ik Son
- Department of Otorhinolaryngology-Head and Neck Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jee Soo Kim
- Division of Breast and Endocrine Surgery, Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Sun Wook Kim
- Division of Endocrinology and Metabolism, Department of Medicine, Thyroid Center, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jae Hoon Chung
- Division of Endocrinology and Metabolism, Department of Medicine, Thyroid Center, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Tae Yong Kim
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Tae Hyuk Kim
- Division of Endocrinology and Metabolism, Department of Medicine, Thyroid Center, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.
| | - Jung-Han Kim
- Division of Breast and Endocrine Surgery, Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.
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Park H, Heo J, Ki CS, Shin JH, Oh YL, Son YI, Kim JS, Kim SW, Chung JH, Kim TY, Kim TH, Kim JH. ASO Visual Abstract: Selection Criteria for Completion Thyroidectomy in Follicular Thyroid Carcinoma Using Primary Tumor Size and TERT Promoter Mutational Status. Ann Surg Oncol 2023; 30:2926-2927. [PMID: 36715856 DOI: 10.1245/s10434-023-13146-7] [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] [Indexed: 01/31/2023]
Affiliation(s)
- Hyunju Park
- Division of Endocrinology and Metabolism, Department of Medicine, Thyroid Center, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jung Heo
- Division of Endocrinology and Metabolism, Department of Medicine, Thyroid Center, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | | | - Jung Hee Shin
- Department of Radiology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Young Lyun Oh
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Young Ik Son
- Department of Otorhinolaryngology-Head and Neck Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jee Soo Kim
- Division of Breast and Endocrine Surgery, Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Sun Wook Kim
- Division of Endocrinology and Metabolism, Department of Medicine, Thyroid Center, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jae Hoon Chung
- Division of Endocrinology and Metabolism, Department of Medicine, Thyroid Center, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Tae Yong Kim
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Tae Hyuk Kim
- Division of Endocrinology and Metabolism, Department of Medicine, Thyroid Center, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.
| | - Jung-Han Kim
- Division of Breast and Endocrine Surgery, Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.
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Bae M, Kim G, Lee TR, Ahn JM, Park H, Park SR, Song KB, Jun E, Oh D, Lee JW, Park YS, Song KW, Byeon JS, Kim BH, Sohn JH, Kim MH, Kim GM, Chie EK, Kang HC, Kong SY, Woo SM, Lee JE, Ryu JM, Lee J, Kim D, Ki CS, Cho EH, Choi JK. Integrative modeling of tumor genomes and epigenomes for enhanced cancer diagnosis by cell-free DNA. Nat Commun 2023; 14:2017. [PMID: 37037826 PMCID: PMC10085982 DOI: 10.1038/s41467-023-37768-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 03/22/2023] [Indexed: 04/12/2023] Open
Abstract
Multi-cancer early detection remains a key challenge in cell-free DNA (cfDNA)-based liquid biopsy. Here, we perform cfDNA whole-genome sequencing to generate two test datasets covering 2125 patient samples of 9 cancer types and 1241 normal control samples, and also a reference dataset for background variant filtering based on 20,529 low-depth healthy samples. An external cfDNA dataset consisting of 208 cancer and 214 normal control samples is used for additional evaluation. Accuracy for cancer detection and tissue-of-origin localization is achieved using our algorithm, which incorporates cancer type-specific profiles of mutation distribution and chromatin organization in tumor tissues as model references. Our integrative model detects early-stage cancers, including those of pancreatic origin, with high sensitivity that is comparable to that of late-stage detection. Model interpretation reveals the contribution of cancer type-specific genomic and epigenomic features. Our methodologies may lay the groundwork for accurate cfDNA-based cancer diagnosis, especially at early stages.
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Affiliation(s)
- Mingyun Bae
- Department of Bio and Brain Engineering, KAIST, Daejeon, Republic of Korea
| | - Gyuhee Kim
- Department of Bio and Brain Engineering, KAIST, Daejeon, Republic of Korea
| | - Tae-Rim Lee
- Genome Research Center, GC Genome, Yongin, Republic of Korea
| | - Jin Mo Ahn
- Genome Research Center, GC Genome, Yongin, Republic of Korea
| | - Hyunwook Park
- Department of Bio and Brain Engineering, KAIST, Daejeon, Republic of Korea
| | - Sook Ryun Park
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Ki Byung Song
- Division of Hepato-Biliary and Pancreatic Surgery, Department of Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Eunsung Jun
- Division of Hepato-Biliary and Pancreatic Surgery, Department of Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Dongryul Oh
- Department of Radiation Oncology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Jeong-Won Lee
- Department of Obstetrics and Gynecology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Young Sik Park
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Ki-Won Song
- Division of Hepatopancreatobiliary Surgery and Liver Transplantation, Department of Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Jeong-Sik Byeon
- Department of Gastroenterology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Bo Hyun Kim
- Center for Liver and Pancreatobiliary Cancer, National Cancer Center, Goyang, Republic of Korea
| | - Joo Hyuk Sohn
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Republic of Korea
- AIMA, Inc., Avison Biomedical Research Center, Seoul, Republic of Korea
| | - Min Hwan Kim
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Gun Min Kim
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Eui Kyu Chie
- Department of Radiation Oncology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Hyun-Cheol Kang
- Department of Radiation Oncology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sun-Young Kong
- Department of Laboratory Medicine, National Cancer Center, Goyang, Republic of Korea
| | - Sang Myung Woo
- Center for Liver and Pancreatobiliary Cancer, National Cancer Center, Goyang, Republic of Korea
| | - Jeong Eon Lee
- Department of Surgery, Samsung Medical Center, Seoul, Republic of Korea
| | - Jai Min Ryu
- Department of Surgery, Samsung Medical Center, Seoul, Republic of Korea
| | - Junnam Lee
- Genome Research Center, GC Genome, Yongin, Republic of Korea
| | - Dasom Kim
- Genome Research Center, GC Genome, Yongin, Republic of Korea
| | - Chang-Seok Ki
- Genome Research Center, GC Genome, Yongin, Republic of Korea
| | - Eun-Hae Cho
- Genome Research Center, GC Genome, Yongin, Republic of Korea.
| | - Jung Kyoon Choi
- Department of Bio and Brain Engineering, KAIST, Daejeon, Republic of Korea.
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Park J, Kim M, Park SR, Song KB, Jun E, Oh D, Lee JW, Park YS, Song KW, Byeon JS, Kim BH, Ki CS, Cho E. Abstract 6697: Deep learning algorithm for cancer detection using multimodal characteristics of whole methylome sequencing of cf-DNA. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-6697] [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: 04/07/2023]
Abstract
Abstract
Background Various cell-free DNA (cfDNA) features including methylation and genomic profiles have been investigated for their potential use in early cancer detection. We developed deep learning models based the data generated by the enzymatic conversion based whole methylome sequencing of cfDNA.
Methods Cell-free whole genome Enzymatic Methyl sequencing(cfWEMseq) data were generated from 198 cancer patients (stage I: 11%, II: 17%, III: 22%, IV: 20%, unknown: 31%) and 69 healthy controls. The cancer types were consisted of breast (n=31), liver (n=24), esophageal (n=38), pancreatic (n=30), colon (n=34), ovarian (n=18), and lung (n=23). Sequence data was produced on average of 200 million reads using Novaseq 6000 (Illumina). For model training and evaluation, data partitioning was stratified by cancer type, and 5-fold cross validation was used. Coverage and methylation beta values were calculated by binning at fixed size of 100K, 1M, and 5M base and variable size from Topologically Associated Domains (TAD). Genome Coverage (GC), Genome Methylation Beta values (GMB), and Mutation Signature (MS) features were trained using a one-dimensional convolutional neural network (1D-CNN). The performance of the model was evaluated by measuring the average value of the results measured in each test set of 5 fold.
Results We tested the cancer detection performance of various feature combinations using all data from cfWEMseq (n=267). Regardless of the bin size, the GMB single model achieved higher performance than the GC single model. The best-performing model is the ensemble model of GMB (100k bin) and MS. The cancer detection performance of this ensemble model reached an accuracy 96% (CI: 93.6% to 98.1%), AUC 0.99 (CI: 0.97 to 1.0) and sensitivity 98.0% (CI: 92.4% to 99.5%) with a specificity of 90%.
Conclusions These results provide an opportunity for higher accuracies by integrating methylation information and genomic data using cfWEMseq. This research was supported through the National Research Foundation (NRF) funded by the Ministry of Science and ICT (2020M2D9A3094213).
Citation Format: Juntae Park, Minjung Kim, Sook Ryun Park, Ki-Byung Song, Eunsung Jun, Dongryul Oh, Jeong-Won Lee, Young Sik Park, Ki-Won Song, Jeong-Sik Byeon, Bo Hyun Kim, Chang-Seok Ki, Eunhae Cho. Deep learning algorithm for cancer detection using multimodal characteristics of whole methylome sequencing of cf-DNA. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6697.
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Affiliation(s)
| | | | | | | | - Eunsung Jun
- 2Asan Medical Center, Seoul, Republic of Korea
| | - Dongryul Oh
- 3Samsung Medical Center, Seoul, Republic of Korea
| | | | - Young Sik Park
- 4Seoul National University Hospital, Seoul, Republic of Korea
| | - Ki-Won Song
- 5Song, Asan Medical Center, Republic of Korea
| | | | - Bo Hyun Kim
- 6National Cancer Center, Goyang, Republic of Korea
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Kim YG, Lee NY, Ham JY, Lee T, Ki CS, Song KE. The Diagnostic Yield and Difficulties of Utilizing Soft-clipped Read Clusters Encountered in Clinical Exome Sequencing. Clin Lab 2023; 69. [PMID: 37057930 DOI: 10.7754/clin.lab.2022.220731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/15/2023]
Abstract
BACKGROUND Despite the wide use of next generation sequencing, there are still many difficulties in detecting structural variants. A split read is one of the clues of structural variants and is represented as a soft-clipped read in the raw sequencing data. Considering that most of the breakpoints of structural variants reside in non-coding regions, split read information has not been routinely used in exome sequencing or targeted panel sequencing. Recently, SCRAMble, a software capable of detecting mobile element insertion (MEI) and deletion based on soft-clipped read clusters (SCRCs), was shown to provide an additional diagnostic yield of 0.03 - 0.25%. SCRAMble is the only software that can be used for exome sequencing or targeted panel sequencing to detect structural variants based on SCRC information. The aim of present study was to establish a working procedure of utilizing SCRC information using SCRAMble in clinical exome sequencing and to assess its diagnostic yield. METHODS Raw sequencing data of clinical exome sequencing were retrospectively analyzed using SCRAMble to search MEIs and deletions. SCRAMble software was installed according to the manufacturer's instructions and default parameters except for one, mei-score, which was adjusted for sensitivity, were used. RefSeq gene annotation was performed for both MEI and deletion calls using ANNOVAR. Blacklist-based filtering was used to reduce candidate MEI/deletion calls. Clinical relevance was manually evaluated for the remaining variant calls. RESULTS One diagnostic MEI, which is a founder variant in East Asia, was detected in two cases (2/266, 0.75%). In addition, two diagnostic deletions, which had been previously detected in depth-of-coverage (DOC)-based copy number variant (CNV) callers, were detected (2/266, 0.75%). Base-level breakpoints that could not be derived by the DOC-based callers were identified for these two deletions using SCRAMble. Most SCRCs were repetitive among cases and blacklist-based filtering reduced candidate MEI/deletion calls by 49.5 - 94.5%, leaving a considerable number of variant calls to be manually validated. CONCLUSIONS SCRC screening in exome or targeted panel sequencing may provide additional diagnostic yield either by pathogenic MEI detection or reassurance of deletions identified by DOC-based CNV callers. Development of an efficient filtering algorithm is warranted.
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Lee J, Lee SM, Ahn JM, Lee TR, Kim W, Cho EH, Ki CS. Development and performance evaluation of an artificial intelligence algorithm using cell-free DNA fragment distance for non-invasive prenatal testing (aiD-NIPT). Front Genet 2022; 13:999587. [DOI: 10.3389/fgene.2022.999587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 11/09/2022] [Indexed: 11/30/2022] Open
Abstract
With advances in next-generation sequencing technology, non-invasive prenatal testing (NIPT) has been widely implemented to detect fetal aneuploidies, including trisomy 21, 18, and 13 (T21, T18, and T13). Most NIPT methods use cell-free DNA (cfDNA) fragment count (FC) in maternal blood. In this study, we developed a novel NIPT method using cfDNA fragment distance (FD) and convolutional neural network-based artificial intelligence algorithm (aiD-NIPT). Four types of aiD-NIPT algorithm (mean, median, interquartile range, and its ensemble) were developed using 2,215 samples. In an analysis of 17,678 clinical samples, all algorithms showed >99.40% accuracy for T21/T18/T13, and the ensemble algorithm showed the best performance (sensitivity: 99.07%, positive predictive value (PPV): 88.43%); the FC-based conventional Z-score and normalized chromosomal value showed 98.15% sensitivity, with 40.77% and 36.81% PPV, respectively. In conclusion, FD-based aiD-NIPT was successfully developed, and it showed better performance than FC-based NIPT methods.
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Sung W, Nahm M, Lim SM, Noh MY, Lee S, Hwang SM, Kim YH, Park J, Oh KW, Ki CS, Kim YE, Kim SH. Clinical and genetic characteristics of amyotrophic lateral sclerosis patients with ANXA11 variants. Brain Commun 2022; 4:fcac299. [PMID: 36458208 PMCID: PMC9707645 DOI: 10.1093/braincomms/fcac299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 08/26/2022] [Accepted: 11/16/2022] [Indexed: 08/12/2023] Open
Abstract
Increasing genetic evidence supports the hypothesis that variants in the annexin A11 gene (ANXA11 ) contribute to amyotrophic lateral sclerosis pathogenesis. Therefore, we studied the clinical aspects of sporadic amyotrophic lateral sclerosis patients carrying ANXA11 variants. We also implemented functional experiments to verify the pathogenicity of the hotspot variants associated with amyotrophic lateral sclerosis-frontotemporal dementia. Korean patients diagnosed with amyotrophic lateral sclerosis (n = 882) underwent genetic evaluations through next-generation sequencing, which identified 16 ANXA11 variants in 26 patients. We analysed their clinical features, such as the age of onset, progression rate, initial symptoms and cognitive status. To evaluate the functional significance of the ANXA11 variants in amyotrophic lateral sclerosis-frontotemporal dementia pathology, we additionally utilized patient fibroblasts carrying frontotemporal dementia-linked ANXA11 variants (p.P36R and p.D40G ) to perform a series of in vitro studies, including calcium imaging, stress granule dynamics and protein translation. The frequency of the pathogenic or likely pathogenic variants of ANXA11 was 0.3% and the frequency of variants classified as variants of unknown significance was 2.6%. The patients with variants in the low-complexity domain presented unique clinical features, including late-onset, a high prevalence of amyotrophic lateral sclerosis-frontotemporal dementia, a fast initial progression rate and a high tendency for bulbar-onset compared with patients carrying variants in the C-terminal repeated annexin homology domains. In addition, functional studies using amyotrophic lateral sclerosis-frontotemporal dementia patient fibroblasts revealed that the ANXA11 variants p.P36R and p.D40G impaired intracellular calcium homeostasis, stress granule disassembly and protein translation. This study suggests that the clinical manifestations of amyotrophic lateral sclerosis and amyotrophic lateral sclerosis-frontotemporal dementia spectrum patients with ANXA11 variants could be distinctively characterized depending upon the location of the variant.
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Affiliation(s)
- Wonjae Sung
- Department of Neurology, College of Medicine, Hanyang University, Seoul, Republic of Korea
| | - Minyeop Nahm
- Dementia Research Group, Korea Brain Research Institute, Daegu, Republic of Korea
| | - Su Min Lim
- Department of Neurology, College of Medicine, Hanyang University, Seoul, Republic of Korea
| | - Min-Young Noh
- Department of Neurology, College of Medicine, Hanyang University, Seoul, Republic of Korea
| | - Sanggon Lee
- Department of Neurology, College of Medicine, Hanyang University, Seoul, Republic of Korea
| | - Sung-Min Hwang
- Gachon Pain Center and Department of Physiology, College of Medicine, Gachon University, Incheon, Republic of Korea
| | - Yong Ho Kim
- Gachon Pain Center and Department of Physiology, College of Medicine, Gachon University, Incheon, Republic of Korea
| | - Jinseok Park
- Department of Neurology, College of Medicine, Hanyang University, Seoul, Republic of Korea
| | - Ki-Wook Oh
- Department of Neurology, College of Medicine, Hanyang University, Seoul, Republic of Korea
| | | | - Young-Eun Kim
- Department of Laboratory Medicine, College of Medicine, Hanyang University, Seoul, Republic of Korea
| | - Seung Hyun Kim
- Department of Neurology, College of Medicine, Hanyang University, Seoul, Republic of Korea
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Cho EH, Park JE, Lee T, Ha K, Ki CS. Carrier frequency and incidence estimation of RPE65-associated inherited retinal diseases in East Asian population by population database-based analysis. Orphanet J Rare Dis 2022; 17:409. [PMID: 36352427 PMCID: PMC9644481 DOI: 10.1186/s13023-022-02566-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 10/07/2022] [Accepted: 10/30/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Inherited retinal diseases (IRDs) are clinically and genetically heterogenous disorders leading to visual impairment and blindness. Because gene therapy for RPE65-associated IRDs was recently approved, it is necessary to predict the carrier frequency and prevalence for RPE65-associated IRDs. This study aimed to analyze the carrier frequency and expected incidence of RPE65-associated IRDs in East Asians and Koreans using exome data from the Genome Aggregation Database (gnomAD) and the Korean Reference Genome Database (KRGDB). METHODS We analyzed 9,197 exomes for East Asian populations from gnomAD comprising 1,909 Korean and 1,722 Korean genomes from KRGDB. All identified RPE65 variants were classified according to the 2015 American College of Medical Genetics and Genomics and the Association for Molecular Pathology guidelines. RESULTS The total carrier frequencies of East Asians and Koreans from both gnomAD and KRGDB were 0.10% (11/10,919) and 0.06% (2/3,631), respectively. The estimated incidence of RPE65-associated IRDs was 1/3,941,308 in East Asians and 1/13,184,161 in Koreans. CONCLUSION This study identified carrier frequencies of RPE65-associated IRDs in East Asians and Koreans using gnomAD and KRGDB. We confirmed that the carrier frequency of RPE65-associated IRDs patients was low in Koreans among all East Asian populations, and the incidence was also predicted to be lower than in other East Asian populations. The variant spectrum of RPE65 gene in East Asian and Korean populations differed greatly from those of other ethnic groups.
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Affiliation(s)
- Eun Hye Cho
- grid.264381.a0000 0001 2181 989XDepartment of Laboratory Medicine, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Jong Eun Park
- grid.412145.70000 0004 0647 3212Department of Laboratory Medicine, Hanyang University Guri Hospital, Hanyang University College of Medicine, Hanyang University Guri Hospital, 153, Gyeongchun-ro, 11923 Guri-si, Gyeonggi-do Republic of Korea
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Park H, Heo J, Ki CS, Shin JH, Oh YL, Son YI, Kim JS, Kim SW, Chung JH, Kim TY, Kim TH, Kim JH. LBODP092 Proposal Of Indication For Completion Thyroidectomy In Follicular Thyroid Carcinoma Using TERT Promoter Mutational Status. J Endocr Soc 2022. [PMCID: PMC9625808 DOI: 10.1210/jendso/bvac150.1522] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Background Stepwise surgical approach with hemithyroidectomy and completion thyroidectomy was used to solve the dilemma of definite characterization of follicular thyroid carcinoma (FTC). However, which patients will be candidates for completion thyroidectomy has been controversial. The aim of this study is to clarify the selection criteria for completion thyroidectomy using TERT promoter mutation. Methods A total of 87 FTC patients who had information about TERT promoter mutation from August 1995 to November 2020 were investigated. The cumulative risk of initial distant metastasis, disease recurrence, and cancer-specific death according to primary tumor size in each of the WHO 2017 classifications were calculated. Results Of the 87 patients, 8 patients (9.2%) had initial distant metastasis, and 15 patients (17.2%) had persistent disease or developed structural recurrence. Threshold diameter for initial distant metastasis, disease recurrence, and cancer-specific death was 2cm in minimally invasive FTC (MI-FTC) with mutant TERT (M-TERT) and in encapsulated angioinvasive FTC (EA-FTC) with M-TERT, while in MI-FTC with wild-type TERT (WT-TERT) and EA-FTC with WT-TERT it was 4cm. Cumulative risk of initial distant metastasis, disease recurrence, and cancer-specific death according to primary tumor size in each WHO 2017 classification were significantly different only in patients with WT-TERT (P = 0. 001, P = 0. 019, and P = 0. 005, respectively). Conclusions The data suggested that 2 cm may be a critical threshold diameter for deciding completion thyroidectomy in MI-FTC with M-TERT and EA-FTC with M-TERT. TERT promoter mutational status can be a game changer for selecting candidates for completion thyroidectomy. Presentation: No date and time listed
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Affiliation(s)
- Hyunju Park
- Samsung Medical Center, Seoul, Republic of Korea,Asan Medical Center, Seoul, Republic of Korea
| | - Jung Heo
- Samsung Medical Center, Seoul, Republic of Korea,Asan Medical Center, Seoul, Republic of Korea
| | - Chang-Seok Ki
- Samsung Medical Center, Seoul, Republic of Korea,Asan Medical Center, Seoul, Republic of Korea
| | - Jung Hee Shin
- Samsung Medical Center, Seoul, Republic of Korea,Asan Medical Center, Seoul, Republic of Korea
| | - Young Lyun Oh
- Samsung Medical Center, Seoul, Republic of Korea,Asan Medical Center, Seoul, Republic of Korea
| | - Young I Son
- Samsung Medical Center, Seoul, Republic of Korea,Asan Medical Center, Seoul, Republic of Korea
| | - Jee Soo Kim
- Samsung Medical Center, Seoul, Republic of Korea,Asan Medical Center, Seoul, Republic of Korea
| | - Sun Wook Kim
- Samsung Medical Center, Seoul, Republic of Korea,Asan Medical Center, Seoul, Republic of Korea
| | - Jae Hoon Chung
- Samsung Medical Center, Seoul, Republic of Korea,Asan Medical Center, Seoul, Republic of Korea
| | - Tae Young Kim
- Samsung Medical Center, Seoul, Republic of Korea,Asan Medical Center, Seoul, Republic of Korea
| | - Tae Hyuk Kim
- Samsung Medical Center, Seoul, Republic of Korea,Asan Medical Center, Seoul, Republic of Korea
| | - Jung-Han Kim
- Samsung Medical Center, Seoul, Republic of Korea,Asan Medical Center, Seoul, Republic of Korea
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19
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Kim EJ, Na DL, Kim HJ, Park KW, Lee JH, Roh JH, Kwon JC, Yoon SJ, Jung NY, Jeong JH, Jang JW, Kim HJ, Park KH, Choi SH, Kim S, Park YH, Kim BC, Youn YC, Ki CS, Kim SH, Seo SW, Kim YE. Genetic Screening in Korean Patients with Frontotemporal Dementia Syndrome. J Alzheimers Dis Rep 2022; 6:651-662. [DOI: 10.3233/adr-220030] [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] [Received: 05/05/2022] [Accepted: 09/04/2022] [Indexed: 11/15/2022] Open
Abstract
Background: Frontotemporal dementia (FTD) syndrome is a genetically heterogeneous group of diseases. However, pathogenic variants in the chromosome 9 open reading frame 72 (C9orf72), microtubule-associated protein tau (MAPT), and progranulin (GRN) genes are mainly associated with genetic FTD in Caucasian populations. Objective: To understand the genetic background of Korean patients with FTD syndrome. Methods: We searched for pathogenic variants of 52 genes related to FTD, amyotrophic lateral sclerosis, familial Alzheimer’s disease, and other dementias, and hexanucleotide repeats of the C9orf72 gene in 72 Korean patients with FTD using whole exome sequencing and the repeat-primed polymerase chain reaction, respectively. Results: One likely pathogenic variant, p.G706R of MAPT, in a patient with behavioral variant FTD (bvFTD) and 13 variants of uncertain significance (VUSs) in nine patients with FTD were identified. Of these VUSs, M232R of the PRNP gene, whose role in pathogenicity is controversial, was also found in two patients with bvFTD. Conclusions: These results indicate that known pathogenic variants of the three main FTD genes (MAPT, GRN, and C9orf72) in Western countries are rare in Korean FTD patients.
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Affiliation(s)
- Eun-Joo Kim
- Department of Neurology, Pusan National University Hospital, Pusan National University School of Medicine and Medical Research Institute, Busan, Korea
| | - Duk L. Na
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Hee-Jin Kim
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Kyung Won Park
- Department of Neurology, Dong-A Medical Center, Dong-A University College of Medicine, Busan, Korea
| | - Jae-Hong Lee
- Department of Neurology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Jee Hoon Roh
- Department of Biomedical Sciences and Department of Physiology, Korea University College of Medicine, Seoul, Republic of Korea
| | - Jay C. Kwon
- Department of Neurology, Changwon Fatima Hospital, Changwon, Korea
| | - Soo Jin Yoon
- Department of Neurology, Eulji University Hospital, Daejeon
| | - Na-Yeon Jung
- Department of Neurology, Pusan National University Yangsan Hospital, Research Institute for Convergence of Biomedical Science and Technology, Busan, Korea
| | - Jee H. Jeong
- Department of Neurology, Ewha Womans University Hospital, Seoul
| | - Jae-Won Jang
- Department of Neurology, Kangwon National University Hospital, Chuncheon
| | - Hee-Jin Kim
- Department of Neurology, Hanyang University College of Medicine, Seoul, Korea
| | - Kee Hyung Park
- Department of Neurology, Gachon University Gil Hospital, Incheon, Korea
| | - Seong Hye Choi
- Department of Neurology, Inha University School of Medicine, Incheon, Korea
| | - SangYun Kim
- Department of Neurology, Seoul National University College of Medicine and Clinical Neuroscience Center, Seoul National University Bundang Hospital, Gyeonggi-do, Korea
| | - Young Ho Park
- Department of Neurology, Seoul National University College of Medicine and Clinical Neuroscience Center, Seoul National University Bundang Hospital, Gyeonggi-do, Korea
| | - Byeong C. Kim
- Department of Neurology, Chonnam National University Medical School, Gwangju, Korea
| | - Young Chul Youn
- Department of Neurology, Chung-Ang University Hospital, Chung-Ang University College of Medicine, Seoul, Korea
| | | | - Seung-Hyun Kim
- Department of Neurology, Hanyang University College of Medicine, Seoul, Korea
| | - Sang Won Seo
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
- Department of Neurology, Gachon University Gil Hospital, Incheon, Korea
| | - Young-Eun Kim
- Department of Laboratory Medicine, Hanyang University College of Medicine, Seoul, Korea
- Department of Neurology, Gachon University Gil Hospital, Incheon, Korea
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20
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Lee TR, Ahn JM, Sohn JH, Park SR, Kim MH, Kim GM, Song KB, Jun E, Oh D, Lee JW, Noh JJ, Park YS, Kong SY, Woo SM, Kim BH, Chie EK, Kang HC, Choi YJ, Song KW, Byeon JS, Lee J, Kim D, Ki CS, Cho E. Abstract 6371: Deep learning algorithm for multi-cancer detection and classification using cf-WGS. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-6371] [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: 11/16/2022]
Abstract
Abstract
Purpose: Several cell-free DNA (cf-DNA) features, such as genome-wide coverage, fragment size, and fragment end motif frequency, have shown their potentials for cancer detection. In this study, we developed two independent models, GC (gross chromatin), and FEMS (fragment end motif frequency and size). Each model uses images generated from genome-wide normalized sequencing coverage and cf-DNA fragment end motif frequencies according to the different cf-DNA size profiles. Then we integrated them into a single ensemble model to improve cancer detection and multi-cancer type classification accuracy.
Methods: Low depth cf-WGS data was generated from 1,396 patients (stage I: 14.9%, stage II: 35.6%, stage III: 24.9%, stage IV: 24.2%, unknown: 0.4%) with breast (n=702), liver (n=213), esophageal (n=155), ovarian (n=151), pancreatic (n=85), lung (n=53), head and neck (n=16), biliary tract (n=15), and colon cancer (n=6) and 417 healthy individuals. Samples were randomly split into training, validation, and test set stratifying cancer type and stages. Cancer types with a small number of samples (<20) were excluded for multi-cancer type classification. Each model was trained using a convolutional neural network, then integrated into a single ensemble model by averaging the predicted probabilities calculated from each model.
Results: For cancer detection, the ensemble model achieved sensitivities of 85.2% [95% confidence interval (CI): 71.8% to 94.5%], 74.9% (CI: 68.0% to 88.0%), 73.2% (CI: 66.7% to 85.9%) at a specificity of 95%, 98% and 99% and the AUC value of 0.97(CI: 0.95-0.99) in the test dataset. By the cancer stages, sensitivity was 62.8% (CI: 48.8% to 83.7%) in stage I, 66.3% (CI: 57.7% to 82.7%) in stage II, 85.9% (CI: 77.5% to 94.4%) in stage III, and 76.1% (CI: 63.4% to 87.3%) in stage IV at 99% specificity. For multi-cancer classification, the overall accuracy of 85.1% (CI: 80.4% to 89.3%) was achieved including 6 cancer types.
Conclusions: Highly sensitive and accurate deep learning model for cancer detection and multi-cancer classification was generated by combining different types of cf-DNA features. This result provides the opportunity for general population multi-cancer screening using various cf-DNA features.
Citation Format: Tae-Rim Lee, Jin Mo Ahn, Joo Hyuk Sohn, Sook Ryun Park, Min Hwan Kim, Gun Min Kim, Ki-Byung Song, Eunsung Jun, Dongryul Oh, Jeong-Won Lee, Joseph J Noh, Young Sik Park, Sun-Young Kong, Sang Myung Woo, Bo Hyun Kim, Eui Kyu Chie, Hyun-Cheol Kang, Youn Jin Choi, Ki-Won Song, Jeong-Sik Byeon, Junnam Lee, Dasom Kim, Chang-Seok Ki, Eunhae Cho. Deep learning algorithm for multi-cancer detection and classification using cf-WGS [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6371.
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Affiliation(s)
| | | | - Joo Hyuk Sohn
- 2Yonsei University College of Medicine, Seoul, Republic of Korea
| | | | - Min Hwan Kim
- 2Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Gun Min Kim
- 2Yonsei University College of Medicine, Seoul, Republic of Korea
| | | | - Eunsung Jun
- 3Asan Medical Center, Seoul, Republic of Korea
| | - Dongryul Oh
- 4Samsung Medical Center, Seoul, Republic of Korea
| | | | - Joseph J Noh
- 4Samsung Medical Center, Seoul, Republic of Korea
| | - Young Sik Park
- 5Seoul National University Hospital, Seoul, Republic of Korea
| | | | | | - Bo Hyun Kim
- 6National Cancer Center, Goyang, Republic of Korea
| | - Eui Kyu Chie
- 7Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Hyun-Cheol Kang
- 7Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Youn Jin Choi
- 8Seoul St. Mary’s Hospital, Seoul, Republic of Korea
| | - Ki-Won Song
- 3Asan Medical Center, Seoul, Republic of Korea
| | | | | | - Dasom Kim
- 1GC Genome, Yongin, Republic of Korea
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21
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Kim S, Seo JD, Yun YM, Kim H, Kim TE, Lee T, Lee TR, Lee JH, Cho EH, Ki CS. Pharmacokinetics and Genetic Factors of Atorvastatin in Healthy Korean Subjects. Front Genet 2022; 13:836970. [PMID: 35664336 PMCID: PMC9160745 DOI: 10.3389/fgene.2022.836970] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 04/13/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Statins are the most popular agents for the primary and secondary prevention of cardiovascular disease; however, the pharmacokinetic parameters and associated genetic factors in the Korean population have not been fully elucidated. This study explored the pharmacokinetic properties of atorvastatin and the association between genetic variations and atorvastatin pharmacokinetics in healthy Korean subjects. Methods: Atorvastatin (80 mg) was administered to 35 healthy Korean volunteers. Plasma levels of atorvastatin and its metabolites were measured sequentially using liquid chromatography-tandem mass spectrometry from 0 to 24 h after atorvastatin administration. Customized next-generation sequencing analysis was performed covering all coding exons of 15 genes, as well as 46 single-nucleotide variants in 29 genes related to statin pharmacokinetics. Results: The mean area under the concentration-time (AUC) and Cmax (maximum peak concentration) were 269.0 ng/ml∙h and 84.3 ng/ml, respectively, which were approximately two times higher than those reported in Caucasians. Genetic analysis revealed that eight genetic variants in ABCB1, ABCG2, APOA5, CETP, and CYP7A1 contributed to the AUC of atorvastatin. The atorvastatin AUC0–24 h prediction model was developed based on age and eight genetic variants using multivariate linear regression (adjusted R2 = 0.878, p < 0.0001). Conclusion: This study shows that the pharmacokinetic properties of atorvastatin in Koreans are different from those in Caucasians and that atorvastatin AUC0–24 h could be predicted based on age and eight genetic variants of ABCB1, ABCG2, APOA5, CETP, and CYP7A1.
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Affiliation(s)
- Serim Kim
- Department of Laboratory Medicine, Shinwon Medical Foundation, Gwangmyeong-si, South Korea
| | - Jong Do Seo
- Department of Laboratory Medicine, Konkuk University Medical Center, Seoul, South Korea
| | - Yeo-Min Yun
- Department of Laboratory Medicine, Konkuk University Medical Center, Seoul, South Korea
- Department of Laboratory Medicine, Konkuk University School of Medicine, Seoul, South Korea
- *Correspondence: Yeo-Min Yun,
| | - Hanah Kim
- Department of Laboratory Medicine, Konkuk University Medical Center, Seoul, South Korea
- Department of Laboratory Medicine, Konkuk University School of Medicine, Seoul, South Korea
| | - Tae-Eun Kim
- Department of Clinical Pharmacology, Konkuk University Medical Center, Seoul, South Korea
| | | | | | - Jun Hyung Lee
- Department of Laboratory Medicine, GC Labs, Yongin-si, South Korea
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22
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Song A, Im M, Kim MS, Noh ES, Kim C, Jang J, Lee SM, Ki CS, Cho SY, Jin DK. First Korean female child with Coffin-Lowry syndrome: a novel variant in RPS6KA3 diagnosed by exome sequencing and a literature review. Ann Pediatr Endocrinol Metab 2022; 28:67-72. [PMID: 35038833 PMCID: PMC10073030 DOI: 10.6065/apem.2142134.067] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 08/06/2021] [Indexed: 11/20/2022] Open
Abstract
Coffin-Lowry Syndrome (CLS, OMIM # 303600) is a rare X-linked disorder caused by mutations in RPS6KA3. CLS is characterized by facial dysmorphism, digit abnormalities, developmental delays, growth retardation, and progressive skeletal changes in male patients. Females with CLS are variably affected, making their diagnosis more difficult. Here, we described the clinical and molecular findings in a Korean female child with CLS and reviewed the literature on female CLS. A five-year-old girl presented with short stature and developmental delays. She had a coarse facial appearance characterized by a prominent forehead, hypertelorism, thick lips, and hypodontia. She also had puffy tapering fingers and pectus excavatum. We performed exome sequencing and identified a novel heterozygous likely pathogenic variant, c.326_338delinsCTCGAGAC (p.Val109Alafs*10), in RPS6KA3 (NM_004586.2). This is the first Korean female genetically diagnosed with CLS. In contrast to delayed bone age in previous studies, our patient showed advanced bone age and central precocious puberty. CLS should be considered as a differential diagnosis of short stature, tapering fingers, and developmental delay. We suggest that molecular techniques can be a useful tool for the diagnosis of rare disorders like CLS, as this condition is not simple and the associated spectrum of phenotypes may vary.
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Affiliation(s)
- Ari Song
- Department of Pediatrics, Incheon Sejong Hospital, Incheon, Korea
| | - Minji Im
- Department of Pediatrics, Sungae Hospital, Seoul, Korea
| | - Min-Sun Kim
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Eu Seon Noh
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Chiwoo Kim
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jahyun Jang
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Sae-Mi Lee
- Green Cross Genome, Yongin, Korea.,Department of Laboratory Medicine, Kangwon National University School of Medicine, Chuncheon, Korea
| | | | - Sung Yoon Cho
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Dong-Kyu Jin
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
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23
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Park JE, Lee T, Ha K, Cho EH, Ki CS. Carrier frequency and incidence estimation of familial hemophagocytic lymphohistiocytosis in East Asian populations by genome aggregation database (gnomAD) based analysis. Front Pediatr 2022; 10:975665. [PMID: 36440336 PMCID: PMC9692074 DOI: 10.3389/fped.2022.975665] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 10/24/2022] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES Hemophagocytic lymphohistiocytosis (HLH) is a clinical syndrome characterized by a life-threatening condition caused by severe hypercytokinemia. The hereditary forms of HLH, also called familial HLH (fHLH), have 4 different genes (PRF1, UNC13D, STX11, and STXBP2) and have been identified as being causative for fHLH. This study aimed to analyze the carrier frequency and expected incidence of fHLH in East Asians and Koreans using exome data from the Genome Aggregation Database (gnomAD). METHODS We analyzed 9,197 exomes for East Asian populations from gnomAD with 1,909 Korean for four fHLH genes. All identified variants were classified according to 2015 American College of Medical Genetics and Genomics and the Association for Molecular Pathology guideline. RESULTS 19 pathogenic variant/likely pathogenic variants (PV/LPVs) were identified in 30 East Asian individuals (0.33%). Among them, 7 PV/LPVs were identified in 17 Korean individuals (0.63%). The estimated incidence of fHLH was 1 in 1,105,652 for East Asians and l in 235,128 for Koreans. CONCLUSIONS This study is the first to identify carrier frequencies in East Asian and Korean populations for fHLH using gnomAD. It was confirmed that the carrier frequency of fHLH patients was high in Koreans among East Asians and the incidence was also predicted to be higher than that of other East Asians. The variant spectrum of fHLH genes in East Asian and Korean populations differed greatly from those of other ethnic groups.
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Affiliation(s)
- Jong Eun Park
- Department of Laboratory Medicine, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri, South Korea
| | | | | | - Eun Hye Cho
- Department of Laboratory Medicine, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, South Korea
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24
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Park H, Shin HC, Yang H, Heo J, Ki CS, Kim HS, Kim JH, Hahn SY, Chung YJ, Kim SW, Chung JH, Oh YL, Kim TH. Molecular classification of follicular thyroid carcinoma based on TERT promoter mutations. Mod Pathol 2022; 35:186-192. [PMID: 34497362 PMCID: PMC8786663 DOI: 10.1038/s41379-021-00907-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [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: 05/24/2021] [Revised: 08/13/2021] [Accepted: 08/16/2021] [Indexed: 12/23/2022]
Abstract
Follicular thyroid carcinoma (FTC) has different clinicopathological characteristics than papillary thyroid carcinoma. However, there are no independent systems to predict cancer-specific survival (CSS) in FTC. Telomerase reverse transcriptase (TERT) promoter mutations are associated with tumor aggressiveness. Thus, it could be a potential prognostic marker. The aim of this study was to refine the CSS risk prediction using TERT promoter mutations in combination with the fourth edition of World Health Organization (WHO 2017) morphological classification. We investigated 77 FTC patients between August 1995 and November 2020. Cox regression was used to calculate hazard ratios to derive alternative groups. Disease-free survival (DFS) and CSS predictability were compared using Proportion of variation explained (PVE) and C-index. CSS was significantly different in encapsulated angioinvasive (EA)-FTC patients stratified by TERT promoter mutations [wild-type (WT-TERT) vs. mutant (M-TERT); P < 0.001] but not in minimally invasive (MI)-FTC and widely invasive (WI)-FTC patients (P = 0.691 and 0.176, respectively). We defined alternative groups as follows: Group 1 (MI-FTC with WT-TERT and M-TERT; EA-FTC with WT-TERT), Group 2 (WI-FTC with WT-TERT), and Group 3 (EA-FTC with M-TERT; WI-FTC with M-TERT). Both PVE (22.44 vs. 9.63, respectively) and C-index (0.831 vs. 0.731, respectively) for CSS were higher in the alternative groups than in the WHO 2017 groups. Likewise, both PVE (27.1 vs. 14.9, respectively) and C-index (0.846 vs. 0.794, respectively) for DFS were also higher in the alternative groups than in the WHO 2017 groups. Alternative group harmonizing of the WHO 2017 classification and TERT promoter mutations is effective in predicting CSS in FTC patients, thereby improving DFS predictability.
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Affiliation(s)
- Hyunju Park
- grid.264381.a0000 0001 2181 989XDepartment of Medicine, Thyroid Center, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Hyeong Chan Shin
- grid.412091.f0000 0001 0669 3109Department of Pathology, Keimyung University School of Medicine, Daegu, Korea
| | - Heera Yang
- grid.264381.a0000 0001 2181 989XDepartment of Medicine, Thyroid Center, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jung Heo
- grid.264381.a0000 0001 2181 989XDepartment of Medicine, Thyroid Center, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Chang-Seok Ki
- grid.452575.40000 0004 4657 6187Green Cross Genome, Yongin, Korea
| | - Hye Seung Kim
- grid.264381.a0000 0001 2181 989XStatistics and Data Center, Research Institute for Future Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jung-Han Kim
- grid.264381.a0000 0001 2181 989XDivision of Breast and Endocrine Surgery, Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Soo Yeon Hahn
- grid.264381.a0000 0001 2181 989XDepartment of Radiology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Yun Jae Chung
- grid.254224.70000 0001 0789 9563Department of Internal Medicine, Chung-Ang University Hospital, Chung-Ang University College of Medicine, Seoul, Korea
| | - Sun Wook Kim
- grid.264381.a0000 0001 2181 989XDepartment of Medicine, Thyroid Center, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jae Hoon Chung
- grid.264381.a0000 0001 2181 989XDepartment of Medicine, Thyroid Center, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Young Lyun Oh
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.
| | - Tae Hyuk Kim
- Department of Medicine, Thyroid Center, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.
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25
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Lee CG, Ki CS. A Novel De Novo Heterozygous ARID1A Missense Variant Cluster in cis c.[5954C>G;6314C>T;6334C>T;6843G>C] causes a Coffin-Siris Syndrome. Ann Lab Med 2021; 41:350-353. [PMID: 33303725 PMCID: PMC7748090 DOI: 10.3343/alm.2021.41.3.350] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 07/09/2020] [Accepted: 11/13/2020] [Indexed: 11/19/2022] Open
Affiliation(s)
- Cha Gon Lee
- Department of Pediatrics, Nowon Eulji Medical Center, Eulji University, Seoul, Korea
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26
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Namgoong H, Ki CS, Hyun H, Yoo IH, Cho WK, Lee JH, Oh JH. Metaphyseal Dysplasia Without Hypotrichosis Caused by RNA Component of Mitochondrial RNA-Processing Endoribonuclease ( RMRP) Gene Variants: The First Case in Korea. Ann Lab Med 2021; 41:346-349. [PMID: 33303724 PMCID: PMC7748101 DOI: 10.3343/alm.2021.41.3.346] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 08/24/2020] [Accepted: 11/11/2020] [Indexed: 11/19/2022] Open
Affiliation(s)
- Ho Namgoong
- Department of Pediatrics, College of Medicine, St. Vincent's Hospital, The Catholic University of Korea, Seoul, Korea
| | | | - Hyesun Hyun
- Department of Pediatrics, College of Medicine, St. Vincent's Hospital, The Catholic University of Korea, Seoul, Korea
| | - Il Han Yoo
- Department of Pediatrics, College of Medicine, St. Vincent's Hospital, The Catholic University of Korea, Seoul, Korea
| | - Won Kyoung Cho
- Department of Pediatrics, College of Medicine, St. Vincent's Hospital, The Catholic University of Korea, Seoul, Korea
| | - Jung Hyun Lee
- Department of Pediatrics, College of Medicine, St. Vincent's Hospital, The Catholic University of Korea, Seoul, Korea
| | - Jin-Hee Oh
- Department of Pediatrics, College of Medicine, St. Vincent's Hospital, The Catholic University of Korea, Seoul, Korea
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27
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Kim ES, Song JS, Ki CS, Choe YH, Kang B. Development of Crohn's Disease in a Child With SLC26A3-related Congenital Chloride Diarrhea: Report of the First Case in East Asia and a Novel Missense Variant. Ann Lab Med 2021; 41:255-257. [PMID: 33063691 PMCID: PMC7591294 DOI: 10.3343/alm.2021.41.2.255] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 05/11/2020] [Accepted: 09/11/2020] [Indexed: 11/19/2022] Open
Affiliation(s)
- Eun Sil Kim
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Ju Sun Song
- GC Genome, Yongin, Korea.,Department of Laboratory Medicine, Green Cross Laboratories, Yongin, Korea
| | | | - Yon Ho Choe
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Ben Kang
- Department of Pediatrics, School of Medicine, Kyungpook National University, Daegu, Korea
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28
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Nahm M, Lim SM, Kim YE, Park J, Noh MY, Lee S, Roh JE, Hwang SM, Park CK, Kim YH, Lim G, Lee J, Oh KW, Ki CS, Kim SH. ANXA11 mutations in ALS cause dysregulation of calcium homeostasis and stress granule dynamics. Sci Transl Med 2021; 12:12/566/eaax3993. [PMID: 33087501 DOI: 10.1126/scitranslmed.aax3993] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 12/15/2019] [Accepted: 07/04/2020] [Indexed: 12/14/2022]
Abstract
Dysregulation of calcium ion homeostasis and abnormal protein aggregation have been proposed as major pathogenic hallmarks underpinning selective degeneration of motor neurons in amyotrophic lateral sclerosis (ALS). Recently, mutations in annexin A11 (ANXA11), a gene encoding a Ca2+-dependent phospholipid-binding protein, have been identified in familial and sporadic ALS. However, the physiological and pathophysiological roles of ANXA11 remain unknown. Here, we report functions of ANXA11 related to intracellular Ca2+ homeostasis and stress granule dynamics. We analyzed the exome sequences of 500 Korean patients with sALS and identified nine ANXA11 variants in 13 patients. The amino-terminal variants p.G38R and p.D40G within the low-complexity domain of ANXA11 enhanced aggregation propensity, whereas the carboxyl-terminal ANX domain variants p.H390P and p.R456H altered Ca2+ responses. Furthermore, all four variants in ANXA11 underwent abnormal phase separation to form droplets with aggregates and led to the alteration of the biophysical properties of ANXA11. These functional defects caused by ALS-linked variants induced alterations in both intracellular Ca2+ homeostasis and stress granule disassembly. We also revealed that p.G228Lfs*29 reduced ANXA11 expression and impaired Ca2+ homeostasis, as caused by missense variants. Ca2+-dependent interaction and coaggregation between ANXA11 and ALS-causative RNA-binding proteins, FUS and hnRNPA1, were observed in motor neuron cells and brain from a patient with ALS-FUS. The expression of ALS-linked ANXA11 variants in motor neuron cells caused cytoplasmic sequestration of endogenous FUS and triggered neuronal apoptosis. Together, our findings suggest that disease-associated ANXA11 mutations can contribute to ALS pathogenesis through toxic gain-of-function mechanisms involving abnormal protein aggregation.
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Affiliation(s)
- Minyeop Nahm
- Department of Neurology, College of Medicine, Hanyang University, Seoul 04763, Korea.,Biomedical Research Institute, Hanyang University, Seoul 04763, Korea
| | - Su Min Lim
- Department of Neurology, College of Medicine, Hanyang University, Seoul 04763, Korea.,Biomedical Research Institute, Hanyang University, Seoul 04763, Korea
| | - Young-Eun Kim
- Department of Laboratory Medicine, College of Medicine, Hanyang University, Seoul 04763, Korea
| | - Jinseok Park
- Department of Neurology, College of Medicine, Hanyang University, Seoul 04763, Korea
| | - Min-Young Noh
- Department of Neurology, College of Medicine, Hanyang University, Seoul 04763, Korea.,Biomedical Research Institute, Hanyang University, Seoul 04763, Korea
| | - Sanggon Lee
- Department of Neurology, College of Medicine, Hanyang University, Seoul 04763, Korea
| | - Ju Eun Roh
- Gachon Pain Center and Department of Physiology, College of Medicine, Gachon University, Incheon 21999, Korea
| | - Sung-Min Hwang
- Gachon Pain Center and Department of Physiology, College of Medicine, Gachon University, Incheon 21999, Korea
| | - Chul-Kyu Park
- Gachon Pain Center and Department of Physiology, College of Medicine, Gachon University, Incheon 21999, Korea
| | - Yong Ho Kim
- Gachon Pain Center and Department of Physiology, College of Medicine, Gachon University, Incheon 21999, Korea
| | - GyuTae Lim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea.,Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon 34113, Korea
| | - Jinhyuk Lee
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea.,Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon 34113, Korea
| | - Ki-Wook Oh
- Department of Neurology, College of Medicine, Hanyang University, Seoul 04763, Korea
| | | | - Seung Hyun Kim
- Department of Neurology, College of Medicine, Hanyang University, Seoul 04763, Korea. .,Biomedical Research Institute, Hanyang University, Seoul 04763, Korea
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Affiliation(s)
- Young Jin Kim
- Department of Laboratory Medicine, Kyung Hee University Hospital, Kyung Hee University School of Medicine, Seoul, Korea
| | - Heungsup Sung
- Department of Laboratory Medicine, University of Ulsan, College of Medicine and Asan Medical Center, Seoul, Korea
| | | | - Mina Hur
- Department of Laboratory Medicine, Konkuk University School of Medicine, Seoul, Korea
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Park J, Lee S, Park J, Park H, Ki CS, Oh YL, Shin JH, Kim JS, Kim SW, Chung JH, Kim K, Kim TH. Proposal of a New Prognostic Model for Differentiated Thyroid Cancer with TERT Promoter Mutations. Cancers (Basel) 2021; 13:cancers13122943. [PMID: 34208345 PMCID: PMC8231155 DOI: 10.3390/cancers13122943] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 05/06/2021] [Revised: 06/09/2021] [Accepted: 06/09/2021] [Indexed: 11/16/2022] Open
Abstract
The role of telomerase reverse transcriptase (TERT) promoter mutations as an independent poor prognostic factor in differentiated thyroid cancer (DTC) patients is well known, but there is no prognostic system that combines the TERT promoter mutation status with tumor-node-metastasis (TNM) stage to predict cancer-specific survival (CSS). A total of 393 patients with pathologically confirmed DTC after thyroidectomy were enrolled. After incorporating wild-type TERT and mutant TERT with stages I, II, and III/IV of the AJCC TNM system 8th edition (TNM-8), we generated six combinations and calculated 10-year and 15-year CSS and adjusted hazard ratios (HRs) for cancer-related death using Cox regression. Then, a new mortality prediction model termed TNM-8T was derived based on the CSS and HR of each combination in the four groups. Of the 393 patients, there were 27 (6.9%) thyroid cancer-related deaths during a median follow-up of 14 years. Patients with a more advanced stage had a lower survival rate (10-year CSS for TNM-8T stage 1, 2, 3, and 4: 98.7%, 93.5%, 77.3%, and 63.0%, respectively; p < 0.001). TNM-8T showed a better spread of CSS (p < 0.001) than TNM-8 (p = 0.002) in the adjusted survival curves. The C-index for mortality risk predictability was 0.880 (95% CI, 0.665-0.957) in TNM-8T and 0.827 (95% CI, 0.622-0.930) in TNM-8 (p < 0.001). TNM-8T, a new prognostic system that incorporates the TERT mutational status into TNM-8, showed superior predictability to TNM-8 in the long-term survival of DTC patients.
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Affiliation(s)
- Jun Park
- Thyroid Center, Samsung Medical Center, Division of Endocrinology and Metabolism, Department of Medicine, Sungkyunkwan University School of Medicine, Seoul 06351, Korea; (J.P.); (J.P.); (H.P.); (S.-W.K.); (J.-H.C.)
- Division of Endocrinology, Department of Medicine, Sahmyook Medical Center, Seoul 02500, Korea
| | - Sungjoo Lee
- Department of Digital Health, Samsung Advanced Institute for Health Sciences & Technology, Sungkyunkwan University School of Medicine, Seoul 06351, Korea;
| | - Jiyun Park
- Thyroid Center, Samsung Medical Center, Division of Endocrinology and Metabolism, Department of Medicine, Sungkyunkwan University School of Medicine, Seoul 06351, Korea; (J.P.); (J.P.); (H.P.); (S.-W.K.); (J.-H.C.)
| | - Hyunju Park
- Thyroid Center, Samsung Medical Center, Division of Endocrinology and Metabolism, Department of Medicine, Sungkyunkwan University School of Medicine, Seoul 06351, Korea; (J.P.); (J.P.); (H.P.); (S.-W.K.); (J.-H.C.)
| | | | - Young-Lyun Oh
- Samsung Medical Center, Department of Pathology, Sungkyunkwan University School of Medicine, Seoul 06351, Korea;
| | - Jung-Hee Shin
- Samsung Medical Center, Department of Radiology, Sungkyunkwan University School of Medicine, Seoul 06351, Korea;
| | - Jee-Soo Kim
- Samsung Medical Center, Department of Surgery, Sungkyunkwan University School of Medicine, Seoul 06351, Korea;
| | - Sun-Wook Kim
- Thyroid Center, Samsung Medical Center, Division of Endocrinology and Metabolism, Department of Medicine, Sungkyunkwan University School of Medicine, Seoul 06351, Korea; (J.P.); (J.P.); (H.P.); (S.-W.K.); (J.-H.C.)
| | - Jae-Hoon Chung
- Thyroid Center, Samsung Medical Center, Division of Endocrinology and Metabolism, Department of Medicine, Sungkyunkwan University School of Medicine, Seoul 06351, Korea; (J.P.); (J.P.); (H.P.); (S.-W.K.); (J.-H.C.)
| | - Kyunga Kim
- Department of Digital Health, Samsung Advanced Institute for Health Sciences & Technology, Sungkyunkwan University School of Medicine, Seoul 06351, Korea;
- Statistics and Data Center, Samsung Medical Center, Research Institute for Future Medicine, Seoul 06355, Korea
- Correspondence: (K.K.); (T.-H.K.); Tel.: +82-2-3410-6049 (T.-H.K.)
| | - Tae-Hyuk Kim
- Thyroid Center, Samsung Medical Center, Division of Endocrinology and Metabolism, Department of Medicine, Sungkyunkwan University School of Medicine, Seoul 06351, Korea; (J.P.); (J.P.); (H.P.); (S.-W.K.); (J.-H.C.)
- Correspondence: (K.K.); (T.-H.K.); Tel.: +82-2-3410-6049 (T.-H.K.)
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Yang EJ, Shim YJ, Kim HS, Lim YT, Im HJ, Koh KN, Kim H, Suh JK, Park ES, Lee NH, Choi YB, Hah JO, Lee JM, Han JW, Lee JH, Lee YH, Jung HL, Ha JS, Ki CS. Genetic Confirmation and Identification of Novel Variants for Glanzmann Thrombasthenia and Other Inherited Platelet Function Disorders: A Study by the Korean Pediatric Hematology Oncology Group (KPHOG). Genes (Basel) 2021; 12:genes12050693. [PMID: 34066320 PMCID: PMC8148153 DOI: 10.3390/genes12050693] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 04/21/2021] [Accepted: 05/02/2021] [Indexed: 11/30/2022] Open
Abstract
The diagnosis of inherited platelet function disorders (IPFDs) is challenging owing to the unavailability of essential testing methods, including light transmission aggregometry and flow cytometry, in several medical centers in Korea. This study, conducted by the Korean Pediatric Hematology Oncology Group from March 2017 to December 2020, aimed to identify the causative genetic variants of IPFDs in Korean patients using next-generation sequencing (NGS). Targeted exome sequencing, followed by whole-genome sequencing, was performed for diagnosing IPFDs. Of the 11 unrelated patients with suspected IPFDs enrolled in this study, 10 patients and 2 of their family members were diagnosed with Glanzmann thrombasthenia (GT). The variant c.1913+5G>T of ITGB3 was the most common, followed by c.2333A>C (p.Gln778Pro) of ITGB2B. Known variants of GT, including c.917A>C (p.His306Pro) of ITGB3 and c.2975del (p.Glu992Glyfs*), c.257T>C (p.Leu86Pro), and c.1750C>T (p.Arg584*) of ITGA2B, were identified. Four novel variants of GT, c.1451G>T (p.Gly484Val) and c.1595G>T (p.Cys532Phe) of ITGB3 and c.1184G>T (p.Gly395Val) and c.2390del (p.Gly797Valfs*29) of ITGA2B, were revealed. The remaining patient was diagnosed with platelet type bleeding disorder 18 and harbored two novel RASGRP2 variants, c.1479dup (p.Arg494Alafs*54) and c.813+1G>A. We demonstrated the successful application of NGS for the accurate and differential diagnosis of heterogeneous IPFDs.
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Affiliation(s)
- Eu Jeen Yang
- Department of Pediatrics, Pusan National University School of Medicine, Pusan National University Children’s Hospital, Yangsan 50612, Korea; (E.J.Y.); (Y.T.L.)
| | - Ye Jee Shim
- Department of Pediatrics, Keimyung University School of Medicine, Keimyung University Dongsan Hospital, Daegu 42601, Korea
- Correspondence: ; Tel.: +82-53-258-7824
| | - Heung Sik Kim
- Department of Pediatrics, Keimyung University School of Medicine, Keimyung University Daegu Dongsan Hospital, Daegu 41931, Korea;
| | - Young Tak Lim
- Department of Pediatrics, Pusan National University School of Medicine, Pusan National University Children’s Hospital, Yangsan 50612, Korea; (E.J.Y.); (Y.T.L.)
| | - Ho Joon Im
- Department of Pediatrics, University of Ulsan College of Medicine, Asan Medical Center Children’s Hospital, Seoul 05505, Korea; (H.J.I.); (K.-N.K.); (H.K.)
| | - Kyung-Nam Koh
- Department of Pediatrics, University of Ulsan College of Medicine, Asan Medical Center Children’s Hospital, Seoul 05505, Korea; (H.J.I.); (K.-N.K.); (H.K.)
| | - Hyery Kim
- Department of Pediatrics, University of Ulsan College of Medicine, Asan Medical Center Children’s Hospital, Seoul 05505, Korea; (H.J.I.); (K.-N.K.); (H.K.)
| | - Jin Kyung Suh
- Department of Pediatrics, Korea Cancer Center Hospital, Seoul 01812, Korea;
| | - Eun Sil Park
- Department of Pediatrics, Gyeongsang National University College of Medicine, Gyeongsang National University Hospital, Jinju 52727, Korea;
| | - Na Hee Lee
- Department of Pediatrics, Cha Bundang Medical Center, Cha University, Seongnam 13496, Korea;
| | - Young Bae Choi
- Department of Pediatrics, Ajou University School of Medicine, Ajou University Hospital, Suwon 16499, Korea;
| | - Jeong Ok Hah
- Department of Pediatrics, Daegu Fatima Hospital, Daegu 41199, Korea;
| | - Jae Min Lee
- Department of Pediatrics, Yeungnam University College of Medicine, Daegu 42415, Korea;
| | - Jung Woo Han
- Department of Pediatrics, Yonsei University College of Medicine, Yonsei University Health System, Seoul 03722, Korea;
| | - Jae Hee Lee
- Department of Pediatrics, Chungbuk National University School of Medicine, Chungbuk National University Hospital, Cheongju 28644, Korea;
| | - Young-Ho Lee
- Department of Pediatrics, Hanyang University Seoul Hospital, Seoul 04763, Korea;
| | - Hye Lim Jung
- Deparment of Pediatrics, Sungkyunkwan University School of Medicine, Kangbuk Samsung Hospital, Seoul 03181, Korea;
| | - Jung-Sook Ha
- Department of Laboratory Medicine, Keimyung University School of Medicine, Keimyung University Dongsan Hospital, Daegu 42601, Korea;
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Kang B, Hwang SK, Choi S, Kim ES, Lee SY, Ki CS, Cho EH, Lee JH, Choe BH. Case report of juvenile polyposis/hereditary hemorrhagic telangiectasia syndrome: first report in Korea with a novel mutation in the SMAD4 gene. Transl Pediatr 2021; 10:1369-1376. [PMID: 34189096 PMCID: PMC8193005 DOI: 10.21037/tp-21-12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Juvenile polyposis/hereditary hemorrhagic telangiectasia (JPS/HHT) syndrome is a rare, autosomal dominant disorder caused by mutations in the SMAD4 gene, presenting with features of both juvenile polyposis syndrome (JPS) and HHT. Reports and studies of JPS/HHT syndrome are mostly from Western countries, while there are scarce reports from East Asian countries. We report a case of a Korean boy who had been previously diagnosed with JPS at 7 years and had first visited to our center at 15 years of age. Genetic studies of the patient and parents revealed a novel variant in the SMAD4 gene, SMAD4 c.1146_1163del; p.His382_Val387del (NM_005359.5), which had developed de novo. Numerous pedunculated and sessile polyps were observed throughout the gastrointestinal (GI) tract. Mucocutaneous telangiectases were observed on the lips, tongue, and jejunum, and arteriovenous malformations (AVMs) were observed in both lungs. This is the first case report of JPS/HHT syndrome in Korea, with a novel deletion variant in the SMAD4 gene. Patients with JPS should undergo genetic evaluation of associated genes including SMAD4, and those with genetically confirmed SMAD4 variants should undergo further evaluation for coexisting asymptomatic AVMs in order to prevent life-threatening complications of thrombotic emboli and pulmonary hemorrhage.
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Affiliation(s)
- Ben Kang
- Department of Pediatrics, School of Medicine, Kyungpook National University, Daegu, South Korea
| | - Su-Kyeong Hwang
- Department of Pediatrics, School of Medicine, Kyungpook National University, Daegu, South Korea
| | - Sujin Choi
- Department of Pediatrics, School of Medicine, Kyungpook National University, Daegu, South Korea
| | - Eun Soo Kim
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, South Korea
| | - Sang Yub Lee
- Department of Radiology, School of Medicine, Kyungpook National University, Daegu, South Korea
| | | | | | - Ji-Hyuk Lee
- Department of Pediatrics, Chungbuk National University College of Medicine, Cheongju, South Korea
| | - Byung-Ho Choe
- Department of Pediatrics, School of Medicine, Kyungpook National University, Daegu, South Korea
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Park JE, Lee T, Ha K, Ki CS. Carrier frequency and incidence estimation of Smith-Lemli-Opitz syndrome in East Asian populations by Genome Aggregation Database (gnomAD) based analysis. Orphanet J Rare Dis 2021; 16:166. [PMID: 33836803 PMCID: PMC8033735 DOI: 10.1186/s13023-021-01789-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 03/25/2021] [Indexed: 11/26/2022] Open
Abstract
Background Smith–Lemli–Opitz syndrome (SLOS) is an autosomal, recessively inherited congenital malformation syndrome characterized by multiple congenital anomalies such as microcephaly with mental defects, distinctive facial features, genital abnormalities, and 2–3 syndactyly of the toes. SLOS is caused by defective 7-dehydrocholesterol reductase, which is encoded by the DHCR7 gene. This study aimed to analyze the carrier frequency and expected incidence of SLOS in East Asians and Koreans using exome data from the Genome Aggregation Database (gnomAD) through the 2015 American College of Medical Genetics and Genomics and the Association for Molecular Pathology guideline (2015 ACMG-AMP guideline). Methods We analyzed 9197 exomes for East Asian populations from gnomAD, comprising 1909 Korean, 76 Japanese, and 7212 other East Asian populations. All identified variants were classified according to the 2015 ACMG-AMP guideline. Results According to the 2015 ACMG-AMP guideline, 15 pathogenic variant/likely pathogenic variant (PV/LPV) cases were identified in 33 East Asian individuals (33/9191 = 0.4%). Among them, four PVs/LPVs were identified in 19 Korean individuals (19/1909 = 1.0%). The predicted incidence, based upon the carrier rates of PV/LPV of DHCR7 alleles, is 1 in 310,688 in East Asians and l in 40,380 in Koreans. Conclusions This study is the first to identify carrier frequencies in East Asians and Koreans using gnomAD. It was confirmed that East Asians (0.4%) had a lower carrier frequency than did other ethnicities (1–3%) and Koreans (1.0%) had similar or lower carrier frequencies than other ethnicities. The variant spectrums of DHCR7 in East Asian and Korean populations differed greatly from those of other ethnic groups.
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Affiliation(s)
- Jong Eun Park
- Department of Laboratory Medicine, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri, Republic of Korea
| | - Taeheon Lee
- Green Cross Genome, 107, Ihyeon-ro 30beon-gil, Giheung-gu, Yongin-si, Gyeonggi-do, 16924, Republic of Korea
| | - Kyeongsu Ha
- Green Cross Genome, 107, Ihyeon-ro 30beon-gil, Giheung-gu, Yongin-si, Gyeonggi-do, 16924, Republic of Korea
| | - Chang-Seok Ki
- Green Cross Genome, 107, Ihyeon-ro 30beon-gil, Giheung-gu, Yongin-si, Gyeonggi-do, 16924, Republic of Korea.
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Yoon CW, Kim YE, Kim HJ, Ki CS, Lee H, Rha JH, Na DL, Seo SW. Comparison of Longitudinal Changes of Cerebral Small Vessel Disease Markers and Cognitive Function Between Subcortical Vascular Mild Cognitive Impairment With and Without NOTCH3 Variant: A 5-Year Follow-Up Study. Front Neurol 2021; 12:586366. [PMID: 33716917 PMCID: PMC7947323 DOI: 10.3389/fneur.2021.586366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 02/05/2021] [Indexed: 11/13/2022] Open
Abstract
No study yet has compared the longitudinal course and prognosis between subcortical vascular cognitive impairment patients with and without genetic component. In this study, we compared the longitudinal changes in cerebral small vessel disease markers and cognitive function between subcortical vascular mild cognitive impairment (svMCI) patients with and without NOTCH3 variant [NOTCH3(+) svMCI vs. NOTCH3(-) svMCI]. We prospectively recruited patients with svMCI and screened for NOTCH3 variants by sequence analysis for mutational hotspots in the NOTCH3 gene. Patients were annually followed-up for 5 years through clinical interviews, neuropsychological tests, and brain magnetic resonance imaging. Among 63 svMCI patients, 9 (14.3%) had either known mutations or possible pathogenic variants. The linear mixed effect models showed that the NOTCH3(+) svMCI group had much greater increases in the lacune and cerebral microbleed counts than the NOTCH3(-) svMCI group. However, there were no significant differences between the two groups regarding dementia conversion rate and neuropsychological score changes over 5 years.
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Affiliation(s)
- Cindy W. Yoon
- Department of Neurology, Inha University School of Medicine, Incheon, South Korea
| | - Young-Eun Kim
- Department of Laboratory Medicine, Hanyang University College of Medicine, Seoul, South Korea
| | - Hee Jin Kim
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Chang-Seok Ki
- Genome Research Center, Green Cross Genome, Yong-in, South Korea
| | - Hyejoo Lee
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Joung-Ho Rha
- Department of Neurology, Inha University School of Medicine, Incheon, South Korea
| | - Duk L. Na
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Sang Won Seo
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
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Park J, Lee S, Kim K, Park H, Ki CS, Oh YL, Shin JH, Kim JS, Kim SW, Chung JH, Kim TH. TERT Promoter Mutations and the 8th Edition TNM Classification in Predicting the Survival of Thyroid Cancer Patients. Cancers (Basel) 2021; 13:cancers13040648. [PMID: 33562809 PMCID: PMC7915040 DOI: 10.3390/cancers13040648] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [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: 01/18/2021] [Revised: 02/02/2021] [Accepted: 02/02/2021] [Indexed: 12/11/2022] Open
Abstract
Simple Summary In a cohort study involving 393 patients with differentiated thyroid cancer, TERT promoter mutations were found to act as an independent poor prognostic factor based on the American Joint Committee on Cancer (AJCC) tumor-node-metastasis 8th edition (TNM-8) in differentiated thyroid carcinoma (DTC) patients, regardless of the histological types or stage at diagnosis. Since the current AJCC TNM-8 is insufficient to distinguish the risk of mortality in patients with differentiated thyroid cancer, a proposal for a new survival prediction model that includes the TERT promoter mutational state is required. Abstract Our research group has previously shown that the presence of TERT promoter mutations is an independent prognostic factor, by applying the TERT mutation status to the variables of the AJCC 7th edition. This study aimed to determine if TERT mutations could be independent predictors of thyroid cancer-specific mortality based on the AJCC TNM 8th edition, with long-term follow-up. This was a retrospective study of 393 patients with pathologically confirmed differentiated thyroid carcinoma (DTC) after thyroidectomy at a tertiary Korean hospital from 1994 to 2004. The thyroid cancer-specific mortality rate was 6.9% (5.2% for papillary and 15.2% for follicular cancers). TERT promoter mutations were identified in 10.9% (43/393) of DTC cases (9.8% of papillary and 16.7% of follicular cancer) and were associated with older age (p < 0.001), the presence of extrathyroidal invasion (p < 0.001), distant metastasis (p = 0.001), and advanced stage at diagnosis (p < 0.001). The 10-year survival rate in mutant TERT was 67.4% for DTC patients (vs. 98% for wild-type; adjusted hazard ratio (HR) of 9.93, (95% CI: 3.67–26.90)) and 75% for patients with papillary cancer (vs. 99%; 18.55 (4.83–71.18)). In addition, TERT promoter mutations were related to poor prognosis regardless of histologic type (p < 0.001 for both papillary and follicular cancer) or initial stage (p < 0.001, p = 0.004, and p = 0.086 for stages I, II, and III and IV, respectively). TERT promoter mutations comprise an independent poor prognostic factor after adjusting for the clinicopathological risk factors of the AJCC TNM 8th edition, histologic type, and each stage at diagnosis, which could increase prognostic predictability for patients with DTC.
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Affiliation(s)
- Jun Park
- Division of Endocrinology & Metabolism, Department of Medicine, Thyroid Center, Samsung Medical Center, School of Medicine, Sungkyunkwan University, Seoul 06351, Korea; (J.P.); (H.P.); (S.W.K.); (J.H.C.)
| | - Sungjoo Lee
- Department of Digital Health, Samsung Advanced Institute for Health Sciences & Technology, School of Medicine, Sungkyunkwan University, Seoul 06351, Korea; (S.L.); (K.K.)
| | - Kyunga Kim
- Department of Digital Health, Samsung Advanced Institute for Health Sciences & Technology, School of Medicine, Sungkyunkwan University, Seoul 06351, Korea; (S.L.); (K.K.)
- Statistics and Data Center, Research Institute for Future Medicine, Samsung Medical Center, Seoul 06355, Korea
| | - Hyunju Park
- Division of Endocrinology & Metabolism, Department of Medicine, Thyroid Center, Samsung Medical Center, School of Medicine, Sungkyunkwan University, Seoul 06351, Korea; (J.P.); (H.P.); (S.W.K.); (J.H.C.)
| | | | - Young Lyun Oh
- Department of Pathology, Samsung Medical Center, School of Medicine, Sungkyunkwan University, Seoul 06351, Korea;
| | - Jung Hee Shin
- Department of Radiology, Samsung Medical Center, School of Medicine, Sungkyunkwan University, Seoul 06351, Korea;
| | - Jee Soo Kim
- Department of Surgery, Samsung Medical Center, School of Medicine, Sungkyunkwan University, Seoul 06351, Korea;
| | - Sun Wook Kim
- Division of Endocrinology & Metabolism, Department of Medicine, Thyroid Center, Samsung Medical Center, School of Medicine, Sungkyunkwan University, Seoul 06351, Korea; (J.P.); (H.P.); (S.W.K.); (J.H.C.)
| | - Jae Hoon Chung
- Division of Endocrinology & Metabolism, Department of Medicine, Thyroid Center, Samsung Medical Center, School of Medicine, Sungkyunkwan University, Seoul 06351, Korea; (J.P.); (H.P.); (S.W.K.); (J.H.C.)
| | - Tae Hyuk Kim
- Division of Endocrinology & Metabolism, Department of Medicine, Thyroid Center, Samsung Medical Center, School of Medicine, Sungkyunkwan University, Seoul 06351, Korea; (J.P.); (H.P.); (S.W.K.); (J.H.C.)
- Correspondence: ; Tel.: +82-2-3410-6049
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Lee J, Park JE, Lee C, Kim AR, Kim BJ, Park WY, Ki CS, Lee J. Genomic Analysis of Korean Patient With Microcephaly. Front Genet 2021; 11:543528. [PMID: 33584783 PMCID: PMC7876370 DOI: 10.3389/fgene.2020.543528] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 03/17/2020] [Accepted: 12/30/2020] [Indexed: 12/17/2022] Open
Abstract
Microcephaly is a prevalent phenotype in patients with neurodevelopmental problems, often with genetic causes. We comprehensively investigated the clinical phenotypes and genetic background of microcephaly in 40 Korean patients. We analyzed their clinical phenotypes and radiologic images and conducted whole exome sequencing (WES) and analysis of copy number variation (CNV). Infantile hypotonia and developmental delay were present in all patients. Thirty-four patients (85%) showed primary microcephaly. The diagnostic yield from the WES and CNV analyses was 47.5%. With WES, we detected pathogenic or likely pathogenic variants that were previously associated with microcephaly in 12 patients (30%); nine of these were de novo variants with autosomal dominant inheritance. Two unrelated patients had mutations in the KMT2A gene. In 10 other patients, we found mutations in the GNB1, GNAO1, TCF4, ASXL1, SMC1A, VPS13B, ACTG1, EP300, and KMT2D genes. Seven patients (17.5%) were diagnosed with pathogenic CNVs. Korean patients with microcephaly show a genetic spectrum that is different from that of patients with microcephaly of other ethnicities. WES along with CNV analysis represents an effective approach for diagnosis of the underlying causes of microcephaly.
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Affiliation(s)
- Jiwon Lee
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Jong Eun Park
- Department of Laboratory Medicine and Genetics, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri, South Korea
| | - Chung Lee
- Samsung Genome Institute, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Ah Reum Kim
- Samsung Genome Institute, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Byung Joon Kim
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Woong-Yang Park
- Samsung Genome Institute, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | | | - Jeehun Lee
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
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Abstract
Next-generation sequencing (NGS) technologies have changed the process of genetic diagnosis from a gene-by-gene approach to syndrome-based diagnostic gene panel sequencing (DPS), diagnostic exome sequencing (DES), and diagnostic genome sequencing (DGS). A priori information on the causative genes that might underlie a genetic condition is a prerequisite for genetic diagnosis before conducting clinical NGS tests. Theoretically, DPS, DES, and DGS do not require any information on specific candidate genes. Therefore, clinical NGS tests sometimes detect disease-related pathogenic variants in genes underlying different conditions from the initial diagnosis. These clinical NGS tests are expensive, but they can be a cost-effective approach for the rapid diagnosis of rare disorders with genetic heterogeneity, such as the glycogen storage disease, familial intrahepatic cholestasis, lysosomal storage disease, and primary immunodeficiency. In addition, DES or DGS may find novel genes that that were previously not linked to human diseases.
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Lee CG, Seol CA, Ki CS. The first familial case of inherited intellectual developmental disorder with dysmorphic facies and behavioral abnormalities (IDDFBA) with a novel FBXO11 variant. Am J Med Genet A 2020; 182:2788-2792. [PMID: 32902151 DOI: 10.1002/ajmg.a.61828] [Citation(s) in RCA: 4] [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] [Received: 06/23/2020] [Revised: 07/25/2020] [Accepted: 07/27/2020] [Indexed: 11/11/2022]
Abstract
Intellectual developmental disorder with dysmorphic facies and behavioral abnormalities (IDDFBA) caused by germline de novo variants in FBXO11 was recently recognized as a novel intellectual disability (ID) syndrome through reverse phenotyping after whole-exome sequencing (WES). Fewer than 50 disease-causing de novo FBXO11 variants in IDDFBA are reported thus far. Here, we present the first report of a family showing autosomal dominantly inherited IDDFBA, harboring a novel heterozygous variant in FBXO11 (c.2401_2405dup;p. Gly803Leufs*6) identified by WES. In this family, the mother and two daughters showed mild ID and mild facial dysmorphism. This finding is expected to increase our understanding of the genotype-phenotype of IDDFBA and to facilitate genetic counseling for the disorder caused by FBXO11.
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Affiliation(s)
- Cha Gon Lee
- Department of Pediatrics, Nowon Eulji Medical Center, Eulji University, Seoul, Republic of Korea
| | - Chang Ahn Seol
- GC Genome, Yongin, Gyeonggi-do, Republic of Korea.,GC Labs, Yongin, Gyeonggi-do, Republic of Korea
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Affiliation(s)
- Young Jin Kim
- Department of Laboratory Medicine, Kyung Hee University Hospital, Kyung Hee University School of Medicine, Seoul,
Korea
| | - Heungsup Sung
- Department of Laboratory Medicine, University of Ulsan, College of Medicine and Asan Medical Center, Seoul,
Korea
| | | | - Mina Hur
- Department of Laboratory Medicine, Konkuk University School of Medicine, Seoul,
Korea
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40
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Lee JH, Song DY, Jun SH, Song SH, Shin CH, Ki CS, Lee K, Song J. High prevalence of increased sitosterol levels in hypercholesterolemic children suggest underestimation of sitosterolemia incidence. PLoS One 2020; 15:e0238079. [PMID: 32845916 PMCID: PMC7449458 DOI: 10.1371/journal.pone.0238079] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 08/10/2020] [Indexed: 01/26/2023] Open
Abstract
Background Sitosterolemia is an inherited lipid disorder which presents with elevated serum sitosterol and can result in an increased risk of premature cardiovascular disease. However, sitosterol cannot be accurately measured by routine diagnostic assays, meaning that sitosterolemia diagnosis can often be difficult, especially with many clinical features overlapping with familial hypercholesterolemia. With such complications resulting in increasing reports of misdiagnosis, the prevalence of sitosterolemia is predicted to be much higher than previously reported. Methods Gas chromatography-mass spectrometry was utilized to measure sitosterol levels of normocholesterolemic and hypercholesterolemic children. Subsequently, an epidemiologically determined cutoff level of sitosterol was calculated and applied to estimate the prevalence of children with increased sitosterol and identify potential sitosterolemia patients. Massively parallel sequencing was used to confirm the diagnosis in suspected patients. Results Samples from 109 normocholesterolemic and 220 hypercholesterolemic were tested for phytosterols. Sitosterol and campesterol levels were significantly increased in hypercholesterolemic children (mean 22.0±45.9 μmol/L for sitosterol and 26.0±32.8 μmol/L for campesterol) compared to normocholesterolemic children (mean 12.1±4.9 μmol/L for sistosterol and 14.8±6.7 μmol/L for campesterol). Via application of a cutoff of 35.9 μmol/L, the prevalence rates for increased and overtly increased sitosterol in hypercholesterolemic children were 6.4% and 1.4% respectively. Furthermore, 3 suspected sitosterolemia patients were identified, with 2 patients receiving molecular confirmation for sitosterolemia diagnosis. Conclusions Our findings reaffirm that the prevalence of sitosterolemia is probably much higher than previously reported, which also indicates the significant risk of misdiagnosis of sitosterolemia with familial hypercholesterolemia. Special lipid testing including sitosterol, especially in children with uncontrolled hypercholesterolemia, is recommended in children in order to identify potential sitosterolemia patients that would otherwise be neglected.
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Affiliation(s)
- Joon Hee Lee
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Korea
- Department of Laboratory Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Da Young Song
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Korea
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea
| | - Sun-Hee Jun
- Department of Laboratory Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Sang Hoon Song
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Korea
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea
| | - Choong Ho Shin
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul, Korea
| | | | - Kyunghoon Lee
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Korea
- Department of Laboratory Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
- * E-mail: (KL); (JS)
| | - Junghan Song
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Korea
- Department of Laboratory Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
- * E-mail: (KL); (JS)
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Cho YY, Park SY, Shin JH, Oh YL, Choe JH, Kim JH, Kim JS, Yim HS, Kim YL, Ki CS, Kim TH, Chung JH, Kim SW. Highly Sensitive and Specific Molecular Test for Mutations in the Diagnosis of Thyroid Nodules: A Prospective Study of BRAF-Prevalent Population. Int J Mol Sci 2020; 21:ijms21165629. [PMID: 32781560 PMCID: PMC7460614 DOI: 10.3390/ijms21165629] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 07/31/2020] [Accepted: 08/04/2020] [Indexed: 12/26/2022] Open
Abstract
Molecular testing offers more objective information in the diagnosis and personalized decision making for thyroid nodules. In Korea, as the BRAF V600E mutation is detected in 70–80% of thyroid cancer specimens, its testing in fine-needle aspiration (FNA) cytology specimens alone has been used for the differential diagnosis of thyroid nodules until now. Thus, we aimed to develop a mutation panel to detect not only BRAF V600E, but also other common genetic alterations in thyroid cancer and to evaluate the diagnostic accuracy of the mutation panel for thyroid nodules in Korea. For this prospective study, FNA specimens of 430 nodules were obtained from patients who underwent thyroid surgery for thyroid nodules. A molecular test was devised using real-time PCR to detect common genetic alterations in thyroid cancer, including BRAF, N-, H-, and K-RAS mutations and rearrangements of RET/PTC and PAX8/PPARr. Positive results for the mutation panel were confirmed by sequencing. Among the 430 FNA specimens, genetic alterations were detected in 293 cases (68%). BRAF V600E (240 of 347 cases, 69%) was the most prevalent mutation in thyroid cancer. The RAS mutation was most prevalently detected for indeterminate cytology. Among the 293 mutation-positive cases, 287 (98%) were diagnosed as cancer. The combination of molecular testing and cytology improved sensitivity from 72% (cytology alone) to 89% (combination), with a specificity of 93%. We verified the excellent diagnostic performance of the mutation panel applicable for clinical practice in Korea. A plan has been devised to validate its performance using independent FNA specimens.
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Affiliation(s)
- Yoon Young Cho
- Division of Endocrinology and Metabolism, Department of Medicine, Soonchunhyang University Bucheon Hospital, Bucheon 14584, Korea;
| | - So Young Park
- Division of Endocrinology and Metabolism, Department of Medicine, Korea University Ansan Hospital, Ansan 15355, Korea;
| | - Jung Hee Shin
- Department of Radiology and Center for Imaging Science, Samsung Medical Center, Sungkyunkwan University School of Medicine, Gangnam-gu, Seoul 06351, Korea;
| | - Young Lyun Oh
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Gangnam-gu, Seoul 06351, Korea;
| | - Jun-Ho Choe
- Division of Breast and Endocrine Surgery, Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Gangnam-gu, Seoul 06351, Korea; (J.-H.C.); (J.-H.K.); (J.S.K.)
| | - Jung-Han Kim
- Division of Breast and Endocrine Surgery, Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Gangnam-gu, Seoul 06351, Korea; (J.-H.C.); (J.-H.K.); (J.S.K.)
| | - Jee Soo Kim
- Division of Breast and Endocrine Surgery, Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Gangnam-gu, Seoul 06351, Korea; (J.-H.C.); (J.-H.K.); (J.S.K.)
| | - Hyun Sook Yim
- BioSewoom Inc., Sungdong-gu, Seoul 04783, Korea; (H.S.Y.); (Y.-L.K.)
| | - Yoo-Li Kim
- BioSewoom Inc., Sungdong-gu, Seoul 04783, Korea; (H.S.Y.); (Y.-L.K.)
| | | | - Tae Hyuk Kim
- Division of Endocrinology and Metabolism, Department of Medicine, Thyroid Center, Samsung Medical Center, Sungkyunkwan University School of Medicine, Gangnam-gu, Seoul 06351, Korea; (T.H.K.); (J.H.C.)
| | - Jae Hoon Chung
- Division of Endocrinology and Metabolism, Department of Medicine, Thyroid Center, Samsung Medical Center, Sungkyunkwan University School of Medicine, Gangnam-gu, Seoul 06351, Korea; (T.H.K.); (J.H.C.)
| | - Sun Wook Kim
- Division of Endocrinology and Metabolism, Department of Medicine, Thyroid Center, Samsung Medical Center, Sungkyunkwan University School of Medicine, Gangnam-gu, Seoul 06351, Korea; (T.H.K.); (J.H.C.)
- Correspondence: ; Tel.: +82-2-3410-1653; Fax: +82-2-3410-3849
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Kim E, Ki CS, Park S, Lee KY. De Novo SCN8A Pathogenic Variant (c.5630A>G; p.Asn1877Ser) Presenting with a Relatively Mild Phenotype. Ann Child Neurol 2020. [DOI: 10.26815/acn.2020.00024] [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: 11/11/2022] Open
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Lee J, Lee C, Ki CS, Lee J. Determining the best candidates for next-generation sequencing-based gene panel for evaluation of early-onset epilepsy. Mol Genet Genomic Med 2020; 8:e1376. [PMID: 32613771 PMCID: PMC7507365 DOI: 10.1002/mgg3.1376] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 05/01/2020] [Accepted: 06/01/2020] [Indexed: 12/21/2022] Open
Abstract
Background Genetic testing is an emerging diagnostic approach in early‐onset epilepsy. Identification of the heterogeneous genetic causes of epilepsy may mitigate unnecessary evaluations and allow more accurate diagnosis and therapy. We aimed to uncover genetic causes of early‐onset epilepsy using next‐generation sequencing (NGS) to elucidate the diagnostic candidates and evaluate the diagnostic yield of targeted gene panel testing. Methods We evaluated 116 patients with early‐onset epilepsy developed before 2 years old and normal brain imaging using a NGS‐based targeted gene panel. Variants were classified according to their pathogenicity, and the diagnostic yield of the targeted genes and associated clinical factors were determined. Results We detected 40 disease‐causing variants with diagnostic yield of 34.5% (19 pathogenic, 21 likely pathogenic). Twelve variants were novel. The most commonly detected genes were SCN1A, associated with Dravet syndrome, and PRRT2, associated with benign familial infantile epilepsy. Other variants were identified in ARX, SCN2A, KCNQ2, PCDH19, STXBP1, DEPDC5, and SCN8A. The age of seizure onset and family history were associated with disease‐causing variants. Conclusion Next‐generation sequencing‐based targeted testing is an effective diagnostic test, with 30%–40% comparable diagnostic yield. Patients with earlier seizure onset and family history of epilepsy were the best candidates for testing. For pediatric patients with early‐onset epilepsy, genetic diagnosis is important for accurate prognosis and treatment.
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Affiliation(s)
- Jiwon Lee
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Chung Lee
- Samsung Genome Institute, Samsung Medical Center, Seoul, Korea
| | | | - Jeehun Lee
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
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Kim HY, Park JE, Lee SC, Jeon ES, On YK, Kim SM, Choe YH, Ki CS, Kim JW, Kim KH. Genotype-Related Clinical Characteristics and Myocardial Fibrosis and their Association with Prognosis in Hypertrophic Cardiomyopathy. J Clin Med 2020; 9:jcm9061671. [PMID: 32492895 PMCID: PMC7356272 DOI: 10.3390/jcm9061671] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 05/25/2020] [Accepted: 05/27/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The spectrum of genetic variants and their clinical significance of Hypertrophic cardiomyopathy (HCM) have been poorly studied in Asian patients. The objectives of this study were to assess the spectrum of genetic variants and genotype-phenotype relationships within a Korean HCM population. METHODS Eighty-nine consecutive unrelated HCM patients were included. All patients underwent genotypic analysis for 23 HCM-associated genes. Clinical parameters including echocardiographic and cardiac magnetic resonance (CMR) parameters were evaluated. A composite of major adverse cardiac and cerebrovascular events was assessed. RESULTS Genetic variants were detected in 55 of 89 subjects. Pathogenic variants or likely pathogenic variants were identified in 27 of HCM patients in MYBPC3, TNNI3, MYH7, and MYL7. Variants of uncertain significance were identified in 28 patients. There were significant differences in the presence of non-sustained ventricular tachycardia (p = 0.030) and myocardial fibrosis on CMR (p = 0.029) in the detected compared to the not-detected groups. Event-free survival was superior in the not-detected group (p = 0.006). CONCLUSION Genetic variants in patients with HCM are relatively common and are associated with adverse clinical events and myocardial fibrosis on CMR. Genotypic analysis may add important information to clinical variables in the assessment of long-term risk for HCM patients.
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Affiliation(s)
- Hyung Yoon Kim
- Department of Cardiovascular Medicine, Chonnam National University Medical School/Hospital, Gwangju 61469, Korea; (H.Y.K.); (K.H.K.)
| | - Jong Eun Park
- Department of Laboratory Medicine, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri 11923, Korea;
| | - Sang-Chol Lee
- Department of Internal Medicine, Cardiovascular Imaging Center, Heart, Vascular & Stroke Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea; (E.-S.J.); (Y.K.O.)
- Correspondence: ; Tel.: +82-2-3410-3419
| | - Eun-Seok Jeon
- Department of Internal Medicine, Cardiovascular Imaging Center, Heart, Vascular & Stroke Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea; (E.-S.J.); (Y.K.O.)
| | - Young Keun On
- Department of Internal Medicine, Cardiovascular Imaging Center, Heart, Vascular & Stroke Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea; (E.-S.J.); (Y.K.O.)
| | - Sung Mok Kim
- Department of Radiology, Cardiovascular Imaging Center, Heart, Vascular & Stroke Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea; (S.M.K.); (Y.H.C.)
| | - Yeon Hyeon Choe
- Department of Radiology, Cardiovascular Imaging Center, Heart, Vascular & Stroke Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea; (S.M.K.); (Y.H.C.)
| | | | - Jong-Won Kim
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea;
| | - Kye Hun Kim
- Department of Cardiovascular Medicine, Chonnam National University Medical School/Hospital, Gwangju 61469, Korea; (H.Y.K.); (K.H.K.)
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Park S, Jeon BR, Lee YK, Ki CS, Jang MA. The First Korean Case of De Novo Proximal 4p Deletion Syndrome in a Child With Developmental Delay. Ann Lab Med 2020; 40:435-437. [PMID: 32311861 PMCID: PMC7169634 DOI: 10.3343/alm.2020.40.5.435] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 12/23/2019] [Accepted: 03/13/2020] [Indexed: 11/19/2022] Open
Affiliation(s)
- Soyoung Park
- Department of Pediatrics, Soonchunhyang University Bucheon Hospital, Soonchunhyang University College of Medicine, Bucheon, Korea
| | - Byung Ryul Jeon
- Department of Laboratory Medicine and Genetics, Soonchunhyang University Bucheon Hospital, Soonchunhyang University College of Medicine, Bucheon, Korea
| | - You Kyoung Lee
- Department of Laboratory Medicine and Genetics, Soonchunhyang University Bucheon Hospital, Soonchunhyang University College of Medicine, Bucheon, Korea
| | | | - Mi-Ae Jang
- Department of Laboratory Medicine and Genetics, Soonchunhyang University Bucheon Hospital, Soonchunhyang University College of Medicine, Bucheon, Korea
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Cho EH, Huh HJ, Jeong I, Lee NY, Koh WJ, Park HC, Ki CS. A nonsense variant in NME5 causes human primary ciliary dyskinesia with radial spoke defects. Clin Genet 2020; 98:64-68. [PMID: 32185794 DOI: 10.1111/cge.13742] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [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: 12/19/2019] [Revised: 02/15/2020] [Accepted: 03/14/2020] [Indexed: 01/07/2023]
Abstract
Primary ciliary dyskinesia (PCD) is a genetically heterogeneous disorder characterized by defects in the function or structure of motitle cilia. In most cases, causative variants result in axonemal dynein arm anomalies, however, PCD due to radial spoke (RS) and central pair (CP) of microtubules has been rarely reported. To identify the molecular basis of PCD characterized by RS/CP defects, we performed whole exome sequencing in PCD patients with RS/CP defects. We identified a homozygous nonsense variant (c.572G>A; p.Trp191*) in NME5, which encodes a protein component of the RS neck, in one PCD patient with situs solitus. Morpholino knockdown of nme5 in zebrafish embryos resulted in motile cilia defects with phenotypes compatible with ciliopathy. This is the first study to show NME5 as a PCD-causative gene in humans. Our findings indicate that NME5 screening should be considered for PCD patients with RS/CP defects.
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Affiliation(s)
- Eun Hye Cho
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Hee Jae Huh
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Inyoung Jeong
- Department of Biomedical Sciences, College of Medicine, Korea University, Ansan, South Korea
| | - Nam Yong Lee
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Won-Jung Koh
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Hae-Chul Park
- Department of Biomedical Sciences, College of Medicine, Korea University, Ansan, South Korea
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Ki CS. From Genetic Testing to Treatment and Prevention of BRCA-Related Breast Cancer. Ann Lab Med 2020; 40:99-100. [PMID: 31650725 PMCID: PMC6822006 DOI: 10.3343/alm.2020.40.2.99] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Kim YE, Cho H, Kim HJ, Na DL, Seo SW, Ki CS. PSEN1 variants in Korean patients with clinically suspicious early-onset familial Alzheimer's disease. Sci Rep 2020; 10:3480. [PMID: 32103039 PMCID: PMC7044324 DOI: 10.1038/s41598-020-59829-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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: 09/10/2019] [Accepted: 01/24/2020] [Indexed: 11/09/2022] Open
Abstract
Pathogenic variants in the PSEN1 gene are known to be the most common cause of early-onset Alzheimer’s disease but there are few data on the frequency and spectrum of PSEN1 variants in Korea. In this study, we investigated PSEN1 variants in a consecutive series of clinically suspicious early-onset familial AD (EOFAD) Korean patients and their clinical characteristics and imaging findings. From January 2007 to December 2013, EOFAD patients with very early onset AD (<50 yr), early onset AD (<60 yr) with two or more relatives with AD, and early onset AD (<60 yr) with one or more first-degree relatives with very early onset AD (<50 yr) were enrolled in this study. Sequence analysis of the PSEN1 gene was performed by Sanger sequencing. Neuroimaging data and conventional brain MRIs and FDG-PET and/or [11C] PiB-PET scans were analyzed in patients with PSEN1 variants. Among the 28 patients with EOFAD, six (21.4%, 6/28) patients had pathogenic or likely pathogenic variants in the PSEN1 gene. Two pathogenic variants were p.Glu120Lys and p.Ser170Phe and four likely pathogenic variants were p.Thr119Ile, p.Tyr159Cys, p.Leu282Pro, and p.Ala285Ser. Two patients had variants of unknown significance, p.Tyr389His and p.Tyr389Ser. EOFAD patients with PSEN1 variants showed early AD onset, frequent visuospatial dysfunction, movement disorders, and rapid disease progression. Brain MRIs revealed diffuse cortical atrophy, including parietal lobe atrophy, and/or hippocampal atrophy. FDG-PET scans also revealed significant hypometabolism in the bilateral temporo-parietal regions. Our findings provide insight to better understand the genetic background of Korean EOFAD patients.
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Affiliation(s)
- Young-Eun Kim
- Department of Laboratory Medicine, Hanyang University College of Medicine, Seoul, Korea
| | - Hanna Cho
- Department of Neurology, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Hee Jin Kim
- Department of Neurology, Hanyang University College of Medicine, Seoul, Korea
| | - Duk L Na
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Sang Won Seo
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.
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Choi EH, Lee H, Chung JW, Seo WK, Kim GM, Ki CS, Kim YC, Bang OY. Ring Finger Protein 213 Variant and Plaque Characteristics, Vascular Remodeling, and Hemodynamics in Patients With Intracranial Atherosclerotic Stroke: A High-Resolution Magnetic Resonance Imaging and Hemodynamic Study. J Am Heart Assoc 2019; 8:e011996. [PMID: 31590595 PMCID: PMC6818025 DOI: 10.1161/jaha.119.011996] [Citation(s) in RCA: 20] [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] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Background Intracranial atherosclerotic stroke is prevalent in Asians. We hypothesized that patients with the ring finger protein 213 (RNF213) variant, a susceptibility locus for moyamoya disease in Asians, have different neuroimaging characteristics in terms of the vessel wall and hemodynamics. Methods and Results We analyzed consecutive patients with ischemic events in middle cerebral artery distribution and relevant plaques of the distal internal carotid artery or proximal middle cerebral artery on high‐resolution magnetic resonance imaging. Patients with carotid/cardiac sources of embolism or moyamoya disease were excluded. High‐resolution magnetic resonance imaging features (eg, outer vessel diameters and plaque characteristics) and fractional flow (as measured by adjusted signal intensity ratio on time‐of‐flight magnetic resonance angiography) were compared between RNF213 p.Arg4810Lys variant carriers and noncarriers. Among 144 patients included, 44 (29.9%) had the RNF213 variant. Clinical characteristics, including age, sex, body mass index, and vascular risk factors, were not significantly different between RNF213 variant carriers and noncarriers. However, the outer vessel diameter was smaller in RNF213 variant carriers than in noncarriers (P<0.0001 for middle cerebral artery of relevant stenosis [2.05‐mm analysis of RNF213 gene for moyamoya disease in the Chinese HAN population 2.75 mm]; P<0.0001 for contralateral side [2.42 versus 3.00 mm] and P<0.001 for basilar artery [3.19 versus 3.53 mm]). Other high‐resolution magnetic resonance imaging features, including plaque morphology and eccentricity, were not significantly different. Fractional flow was diminished in patients with smaller‐diameter intracranial arteries with a similar degree of stenosis. Conclusions The RNF213 variant may be associated with vasculogenesis, but not with atherogenesis. Patients with this variant had small intracranial arteries predisposing hemodynamic compromise in the presence of intracranial atherosclerosis. In addition to antiatherosclerotic strategies, further studies are warranted to develop novel therapeutic strategies against RNF213 vasculopathy in Asians. See Editorial Liu and Gutierrez
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Affiliation(s)
- Eun-Hyeok Choi
- Department of Neurology Samsung Medical Center Sungkyunkwan University School of Medicine Seoul Korea
| | - Hanul Lee
- Department of Neurology Samsung Medical Center Sungkyunkwan University School of Medicine Seoul Korea
| | - Jong-Won Chung
- Department of Neurology Samsung Medical Center Sungkyunkwan University School of Medicine Seoul Korea.,Translational and Stem Cell Research Laboratory on Stroke Samsung Medical Center Seoul Korea
| | - Woo-Keun Seo
- Department of Neurology Samsung Medical Center Sungkyunkwan University School of Medicine Seoul Korea
| | - Gyeong-Moon Kim
- Department of Neurology Samsung Medical Center Sungkyunkwan University School of Medicine Seoul Korea
| | - Chang-Seok Ki
- Department of Laboratory Medicine and Genetics Green Cross Genome Youngin Korea
| | - Yoon-Chul Kim
- Clinical Research Institute Samsung Medical Center Seoul Korea
| | - Oh Young Bang
- Department of Neurology Samsung Medical Center Sungkyunkwan University School of Medicine Seoul Korea.,Translational and Stem Cell Research Laboratory on Stroke Samsung Medical Center Seoul Korea
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Jhun BW, Kim SY, Moon SM, Jeon K, Kwon OJ, Huh HJ, Ki CS, Lee NY, Shin SJ, Daley CL, Koh WJ. Development of Macrolide Resistance and Reinfection in Refractory Mycobacterium avium Complex Lung Disease. Am J Respir Crit Care Med 2019; 198:1322-1330. [PMID: 29877739 DOI: 10.1164/rccm.201802-0321oc] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [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: 02/04/2023] Open
Abstract
RATIONALE Patients with refractory Mycobacterium avium complex lung disease (MAC-LD) undergo long-term macrolide therapy, but macrolide resistance develops infrequently. OBJECTIVES The aim of this study was to determine whether reinfection was a factor in the low incidence of macrolide resistance in patients with refractory MAC-LD. METHODS Among 481 patients with treatment-naive MAC-LD who started antibiotic treatment between January 2002 and December 2013, we identified 72 patients with refractory disease, characterized by persistently positive sputum cultures despite ≥12 months of treatment. Molecular analyses of the 23S ribosomal RNA gene responsible for macrolide resistance and serial mycobacterial genotyping were performed using stored MAC isolates. MEASUREMENTS AND MAIN RESULTS The median duration of treatment was 32 months (interquartile range, 24-41 mo) in 72 patients. After treatment for a median of 33 months (interquartile range, 21-44 mo), macrolide resistance developed in 16 (22%) patients. Molecular analysis of isolates from 15 patients revealed that 80% (12 of 15) had a point mutation at position 2,058 or 2,059 of the 23S ribosomal RNA gene. Of the 49 patients who had stored pre- and post-treatment isolates, mycobacterial genotyping revealed that reinfection by new MAC strains occurred in 36 (73%) patients. New MAC strains were found in 24 (49%) patients, and mixed infections with original and new strains occurred in 12 (24%) patients. Only 13 (27%) patients had persistent infections with their original MAC strains. CONCLUSIONS Refractory MAC-LD is commonly caused by reinfection with new strains rather than persistence of the original strain, which may explain the infrequent development of macrolide resistance in refractory MAC-LD. Clinical trial registered with www.clinicaltrials.gov (NCT00970801).
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Affiliation(s)
- Byung Woo Jhun
- 1 Division of Pulmonary and Critical Care Medicine, Department of Medicine, and
| | - Su-Young Kim
- 1 Division of Pulmonary and Critical Care Medicine, Department of Medicine, and
| | - Seong Mi Moon
- 1 Division of Pulmonary and Critical Care Medicine, Department of Medicine, and
| | - Kyeongman Jeon
- 1 Division of Pulmonary and Critical Care Medicine, Department of Medicine, and
| | - O Jung Kwon
- 1 Division of Pulmonary and Critical Care Medicine, Department of Medicine, and
| | - Hee Jae Huh
- 2 Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Chang-Seok Ki
- 2 Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Nam Yong Lee
- 2 Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Sung Jae Shin
- 3 Department of Microbiology, Institute for Immunology and Immunological Diseases, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, South Korea; and
| | - Charles L Daley
- 4 Division of Mycobacterial and Respiratory Infections, Department of Medicine, National Jewish Health, Denver, Colorado
| | - Won-Jung Koh
- 1 Division of Pulmonary and Critical Care Medicine, Department of Medicine, and
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