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Park HK, Lee KJ, Cheong HS, Bae HJ. Reply to "Clinical Relevance of Genetic Variants in Juvenile Stroke Patients: A Plea for a Precise Classification". Ann Neurol 2023; 94:609. [PMID: 37463060 DOI: 10.1002/ana.26739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 06/27/2023] [Indexed: 07/20/2023]
Affiliation(s)
- Hong-Kyun Park
- Department of Neurology, Inje University Ilsan Paik Hospital, Inje University College of Medicine, Goyang, South Korea
| | - Keon-Joo Lee
- Department of Neurology, Korea University Guro Hospital, Seoul, South Korea
| | - Hyun Sub Cheong
- Research Institute for Life Science, GW Vitek, Inc., Seoul, South Korea
| | - Hee-Joon Bae
- Department of Neurology, Cerebrovascular Center, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, South Korea
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Park HK, Lee KJ, Park JM, Kang K, Lee SJ, Kim JG, Cha JK, Kim DH, Han MK, Kang J, Kim BJ, Park TH, Park MS, Lee KB, Lee J, Hong KS, Cho YJ, Lee BC, Yu KH, Oh MS, Kim JT, Choi KH, Kim DE, Ryu WS, Choi JC, Kwon JH, Kim WJ, Shin DI, Sohn SI, Hong JH, Lee J, Lee K, Song J, Bae JS, Cheong HS, Debette S, Bae HJ. Prevalence of Mutations in Mendelian Stroke Genes in Early Onset Stroke Patients. Ann Neurol 2023; 93:768-782. [PMID: 36541592 DOI: 10.1002/ana.26575] [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: 03/15/2022] [Revised: 11/25/2022] [Accepted: 11/29/2022] [Indexed: 12/24/2022]
Abstract
OBJECTIVE Heritability of stroke is assumed not to be low, especially in the young stroke population. However, most genetic studies have been performed in highly selected patients with typical clinical or neuroimaging characteristics. We investigated the prevalence of 15 Mendelian stroke genes and explored the relationships between variants and the clinical and neuroimaging characteristics in a large, unselected, young stroke population. METHODS We enrolled patients aged ≤55 years with stroke or transient ischemic attack from a prospective, nationwide, multicenter stroke registry. We identified clinically relevant genetic variants (CRGVs) in 15 Mendelian stroke genes (GLA, NOTCH3, HTRA1, RNF213, ACVRL1, ENG, CBS, TREX1, ABCC6, COL4A1, FBN1, NF1, COL3A1, MT-TL1, and APP) using a customized, targeted next generation sequencing panel. RESULTS Among 1,033 patients, 131 (12.7%) had 28 CRGVs, most frequently in RNF213 (n = 59), followed by ABCC6 (n = 53) and NOTCH3 (n = 15). The frequency of CRGVs differed by ischemic stroke subtypes (p < 0.01): the highest in other determined etiology (20.1%), followed by large artery atherosclerosis (13.6%). It also differed between patients aged ≤35 years and those aged 51 to 55 years (17.1% vs 9.3%, p = 0.02). Only 27.1% and 26.7% of patients with RNF213 and NOTCH3 variants had typical neuroimaging features of the corresponding disorders, respectively. Variants of uncertain significance (VUSs) were found in 15.4% patients. INTERPRETATION CRGVs in 15 Mendelian stroke genes may not be uncommon in the young stroke population. The majority of patients with CRGVs did not have typical features of the corresponding monogenic disorders. Clinical implications of having CRGVs or VUSs should be explored. ANN NEUROL 2023;93:768-782.
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Affiliation(s)
- Hong-Kyun Park
- Department of Neurology, Inje University Ilsan Paik Hospital, Inje University College of Medicine, Goyang, South Korea
| | - Keon-Joo Lee
- Department of Neurology, Cerebrovascular Center, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, South Korea
- Department of Neurology, Korea University Guro Hospital, Seoul, South Korea
| | - Jong-Moo Park
- Department of Neurology, Uijeongbu Eulji Medical Center, Eulji University, Uijeongbu, South Korea
| | - Kyusik Kang
- Department of Neurology, Nowon Eulji Medical Center, Eulji University, Seoul, South Korea
| | - Soo Joo Lee
- Department of Neurology, Eulji University Hospital, Eulji University, Daejeon, South Korea
| | - Jae Guk Kim
- Department of Neurology, Eulji University Hospital, Eulji University, Daejeon, South Korea
| | - Jae-Kwan Cha
- Department of Neurology, Dong-A University Hospital, Busan, South Korea
| | - Dae-Hyun Kim
- Department of Neurology, Dong-A University Hospital, Busan, South Korea
| | - Moon-Ku Han
- Department of Neurology, Cerebrovascular Center, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, South Korea
| | - Jihoon Kang
- Department of Neurology, Cerebrovascular Center, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, South Korea
| | - Beom Joon Kim
- Department of Neurology, Cerebrovascular Center, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, South Korea
| | - Tai Hwan Park
- Department of Neurology, Seoul Medical Center, Seoul, South Korea
| | - Moo-Seok Park
- Department of Neurology, Seoul Hospital, Ewha Woman's University College of Medicine, Seoul, South Korea
| | - Kyung Bok Lee
- Department of Neurology, Soonchunhyang University Hospital, Seoul, South Korea
| | - Jun Lee
- Department of Neurology, Yeungnam University Hospital, Daegu, South Korea
| | - Keun-Sik Hong
- Department of Neurology, Inje University Ilsan Paik Hospital, Inje University College of Medicine, Goyang, South Korea
| | - Yong-Jin Cho
- Department of Neurology, Inje University Ilsan Paik Hospital, Inje University College of Medicine, Goyang, South Korea
| | - Byung-Chul Lee
- Department of Neurology, Hallym University Sacred Heart Hospital, Anyang, South Korea
| | - Kyung-Ho Yu
- Department of Neurology, Hallym University Sacred Heart Hospital, Anyang, South Korea
| | - Mi Sun Oh
- Department of Neurology, Hallym University Sacred Heart Hospital, Anyang, South Korea
| | - Joon-Tae Kim
- Department of Neurology, Chonnam National University Hospital, Gwangju, South Korea
| | - Kang-Ho Choi
- Department of Neurology, Chonnam National University Hospital, Gwangju, South Korea
| | - Dong-Eog Kim
- Department of Neurology, Dongguk University Ilsan Hospital, Goyang, South Korea
| | - Wi-Sun Ryu
- Department of Neurology, Dongguk University Ilsan Hospital, Goyang, South Korea
- Research Center for Artificial Intelligence, JLK Corporation, Seoul, South Korea
| | - Jay Chol Choi
- Department of Neurology, Jeju National University Hospital, Jeju National University School of Medicine, Jeju, South Korea
| | - Jee-Hyun Kwon
- Department of Neurology, Ulsan University College of Medicine, Ulsan, South Korea
| | - Wook-Joo Kim
- Department of Neurology, Ulsan University College of Medicine, Ulsan, South Korea
| | - Dong-Ick Shin
- Department of Neurology, Chungbuk University Hospital, Cheongju, South Korea
| | - Sung Il Sohn
- Department of Neurology, Keimyung University Dongsan Medical Center, Daegu, South Korea
| | - Jeong-Ho Hong
- Department of Neurology, Keimyung University Dongsan Medical Center, Daegu, South Korea
| | - Juneyoung Lee
- Department of Biostatistics, Korea University College of Medicine, Seoul, South Korea
| | - Kyunghoon Lee
- Department of Laboratory Medicine, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, South Korea
| | - Junghan Song
- Department of Laboratory Medicine, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, South Korea
| | - Joon Seol Bae
- Research Institute of Future Medicine, Samsung Medical Center, Seoul, South Korea
| | - Hyun Sub Cheong
- Research Institute for Life Science, GW Vitek, Seoul, South Korea
| | - Stéphanie Debette
- University of Bordeaux, Bordeaux Population Health Research Center, Bordeaux, France
| | - Hee-Joon Bae
- Department of Neurology, Cerebrovascular Center, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, South Korea
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Kim YJ, Go YH, Jeong HC, Kwon EJ, Kim SM, Cheong HS, Kim W, Shin HD, Lee H, Cha HJ. TPX2 prompts mitotic survival via the induction of BCL2L1 through YAP1 protein stabilization in human embryonic stem cells. Exp Mol Med 2023; 55:32-42. [PMID: 36596852 PMCID: PMC9898288 DOI: 10.1038/s12276-022-00907-9] [Citation(s) in RCA: 4] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 10/07/2022] [Accepted: 10/31/2022] [Indexed: 01/05/2023] Open
Abstract
Genetic alterations have been reported for decades in most human embryonic stem cells (hESCs). Survival advantage, a typical trait acquired during long-term in vitro culture, results from the induction of BCL2L1 upon frequent copy number variation (CNV) at locus 20q11.21 and is one of the strongest candidates associated with genetic alterations that occur via escape from mitotic stress. However, the underlying mechanisms for BCL2L1 induction remain unknown. Furthermore, abnormal mitosis and the survival advantage that frequently occur in late passage are associated with the expression of BCL2L1, which is in locus 20q11.21. In this study, we demonstrated that the expression of TPX2, a gene located in 20q11.21, led to BCL2L1 induction and consequent survival traits under mitotic stress in isogenic pairs of hESCs and human induced pluripotent stem cells (iPSCs) with normal and 20q11.21 CNVs. High Aurora A kinase activity by TPX2 stabilized the YAP1 protein to induce YAP1-dependent BCL2L1 expression. A chemical inhibitor of Aurora A kinase and knockdown of YAP/TAZ significantly abrogated the high tolerance to mitotic stress through BCL2L1 suppression. These results suggest that the collective expression of TPX2 and BCL2L1 from CNV at loci 20q11.21 and a consequent increase in YAP1 signaling promote genome instability during long-term in vitro hESC culture.
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Affiliation(s)
- Yun-Jeong Kim
- grid.31501.360000 0004 0470 5905College of Pharmacy, Seoul National University, Seoul, 08826 Republic of Korea
| | - Young-Hyun Go
- grid.263736.50000 0001 0286 5954Department of Life Sciences, Sogang University, Seoul, 04107 Republic of Korea
| | - Ho-Chang Jeong
- grid.263736.50000 0001 0286 5954Department of Life Sciences, Sogang University, Seoul, 04107 Republic of Korea
| | - Eun-Ji Kwon
- grid.31501.360000 0004 0470 5905College of Pharmacy, Seoul National University, Seoul, 08826 Republic of Korea
| | - Seong-Min Kim
- grid.31501.360000 0004 0470 5905College of Pharmacy, Seoul National University, Seoul, 08826 Republic of Korea
| | - Hyun Sub Cheong
- grid.412670.60000 0001 0729 3748Drug Information Research Institute, College of Pharmacy, Sookmyung Women’s University, Seoul, 04310 Republic of Korea
| | - Wantae Kim
- grid.254230.20000 0001 0722 6377Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon, 34134 Republic of Korea
| | - Hyoung Doo Shin
- grid.263736.50000 0001 0286 5954Department of Life Sciences, Sogang University, Seoul, 04107 Republic of Korea
| | - Haeseung Lee
- grid.262229.f0000 0001 0719 8572College of Pharmacy, Pusan National University, Busan, 46241 Korea
| | - Hyuk-Jin Cha
- College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea.
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Baek IK, Cheong HS, Namgoong S, Kim JH, Kang SG, Yoon SJ, Kim SH, Chang JH, Kim LH, Shin HD. Two independent variants of epidermal growth factor receptor associated with risk of glioma in a Korean population. Sci Rep 2022; 12:19014. [PMID: 36347915 PMCID: PMC9643523 DOI: 10.1038/s41598-022-23217-6] [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: 04/22/2022] [Accepted: 10/26/2022] [Indexed: 11/10/2022] Open
Abstract
Gliomas are the most common primary tumors in the brain and spinal cord. In previous GWASs, SNPs in epidermal growth factor receptor (EGFR) have been reported as risk loci for gliomas. However, EGFR variants associated with gliomas in the Korean population remain unstudied. This study explored the association of EGFR SNPs with the risk of glioma. We genotyped 13 EGFR exon SNPs in a case-control study that included 324 Korean patients diagnosed with glioma and 480 population-based controls. Statistical analyses of the association between EGFR SNPs and glioma risk were conducted using logistic regression. Both stepwise analysis and conditional logistic analysis were performed to identify independent associations among genotyped variants. We confirmed that two SNPs (rs2227983, rs1050171) were significantly associated with glioma (rs2227983: odds ratio = 1.42, Pcorr = 0.009; rs1050171: odds ratio = 1.68, Pcorr = 0.005). Additionally, the stepwise analysis and conditional logistic analysis indicated that both SNPs created variants with independent genetic effects. This study is the first to show evidence that functional variants of EGFR, namely, rs2227983 (K521R) and rs1050171 (Q787Q), are associated with an increased risk of glioma in the Korean population. Future work should confirm the functional association between EGFR variants and glioma.
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Affiliation(s)
- In Ki Baek
- grid.263736.50000 0001 0286 5954Department of Life Science, Sogang University, Seoul, 04107 Republic of Korea
| | - Hyun Sub Cheong
- Research Institute for Life Science, GW Vitek, Inc., Seoul, Republic of Korea
| | - Seok Namgoong
- Research Institute for Life Science, GW Vitek, Inc., Seoul, Republic of Korea
| | - Jeong-Hyun Kim
- grid.267370.70000 0004 0533 4667Department of Medicine, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Seok-Gu Kang
- grid.15444.300000 0004 0470 5454Department of Neurosurgery, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Seon-Jin Yoon
- grid.15444.300000 0004 0470 5454Department of Neurosurgery, Yonsei University College of Medicine, Seoul, Republic of Korea ,grid.15444.300000 0004 0470 5454Department of Biochemistry and Molecular Biology, College of Medicine, Yonsei University, Seoul, Republic of Korea
| | - Se Hoon Kim
- grid.15444.300000 0004 0470 5454Department of Pathology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jong Hee Chang
- grid.15444.300000 0004 0470 5454Department of Neurosurgery, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Lyoung Hyo Kim
- Research Institute for Life Science, GW Vitek, Inc., Seoul, Republic of Korea
| | - Hyoung Doo Shin
- grid.263736.50000 0001 0286 5954Department of Life Science, Sogang University, Seoul, 04107 Republic of Korea ,grid.263736.50000 0001 0286 5954Research Institute for Basic Science, Sogang University, Seoul, Republic of Korea
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Youn BJ, Cheong HS, Namgoong S, Kim LH, Baek IK, Kim JH, Yoon SJ, Kim EH, Kim SH, Chang JH, Kim SH, Shin HD. Asian-specific 3'UTR variant in CDKN2B associated with risk of pituitary adenoma. Mol Biol Rep 2022; 49:10339-10346. [PMID: 36097105 DOI: 10.1007/s11033-022-07796-1] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 06/13/2022] [Accepted: 07/13/2022] [Indexed: 12/01/2022]
Abstract
BACKGROUND Previous genomewide association studies (GWASs), single nucleotide polymorphisms (SNPs) on cyclin-dependent kinase inhibitor 2 A (CDKN2A), cyclin-dependent kinase inhibitor 2B (CDKN2B), and cyclin-dependent kinase inhibitor 2B antisense RNA1 (CDKN2B-AS1) were reported as risk loci for glioma, a subgroup of the brain tumor. To further characterize this association with the risk of brain tumors in a Korean population, we performed a fine-mapping association study of CDKN2A, CDKN2B, and CDKN2B-AS1. METHODS AND RESULTS A total of 17 SNPs were selected and genotyped in 1,439 subjects which were comprised of 959 patients (pituitary adenoma 335; glioma 324; meningioma 300) and 480 population controls (PCs). We discovered that a 3'untranslated region (3'UTR) variant, rs181031884 of CDKN2B (Asian-specific variant), had significant association with the risk of pituitary adenoma (PA) (Odds ratio = 0.58, P = 0.00003). Also, rs181031884 appeared as an independent causal variant among the significant variants in CDKN2A and CDKN2B, and showed dose-dependent effects on PA. CONCLUSIONS Although further studies are needed to verify the impact of this variant on PA susceptibility, our results may help to understand CDKN2B polymorphism and the risk of PA.
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Affiliation(s)
- Byeong Ju Youn
- Department of Life Science, Sogang University, 04107, Seoul, Republic of Korea.,Forensic DNA Division, National Forensic Service, 26460, Wonju, Republic of Korea
| | - Hyun Sub Cheong
- Department of Genetic Epidemiology, SNP Genetics Inc, Seoul, Republic of Korea
| | - Suhg Namgoong
- Department of Genetic Epidemiology, SNP Genetics Inc, Seoul, Republic of Korea
| | - Lyoung Hyo Kim
- Department of Genetic Epidemiology, SNP Genetics Inc, Seoul, Republic of Korea
| | - In Ki Baek
- Department of Life Science, Sogang University, 04107, Seoul, Republic of Korea
| | - Jeong-Hyun Kim
- Asan Institute for Life Sciences, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Seon-Jin Yoon
- Department of Neurosurgery, Yonsei University College of Medicine, Seoul, Republic of Korea.,Department of Biochemistry and Molecular Biology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Eui Hyun Kim
- Department of Neurosurgery, Yonsei University College of Medicine, Seoul, Republic of Korea.
| | - Se Hoon Kim
- Department of Pathology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jong Hee Chang
- Department of Neurosurgery, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Sun Ho Kim
- Department of Neurosurgery, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Hyoung Doo Shin
- Department of Life Science, Sogang University, 04107, Seoul, Republic of Korea. .,Department of Genetic Epidemiology, SNP Genetics Inc, Seoul, Republic of Korea. .,Research Institute for Basic Science, Sogang University, Seoul, Republic of Korea.
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Seo JY, Shin JG, Youn BJ, Namgoong S, Cheong HS, Kim LH, Kim JO, Shin HD, Kim YJ. A non-synonymous variant rs12614 of complement factor B associated with risk of chronic hepatitis B in a Korean population. BMC Med Genet 2020; 21:241. [PMID: 33334325 PMCID: PMC7745368 DOI: 10.1186/s12881-020-01177-w] [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] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 11/23/2020] [Indexed: 11/10/2022]
Abstract
Background Hepatitis B is known to cause several forms of liver diseases including chronic hepatitis B (CHB), and hepatocellular carcinoma. Previous genome-wide association study of CHB risk has demonstrated that rs12614 of complement factor B (CFB) was significantly associated with CHB risk. In this study, fine-mapping study of previously reported GWAS single nucleotide polymorphism (SNP; CFB rs12614) was performed to validate genetic effect of rs12614 on CHB susceptibility and identify possible additional causal variants around rs12614 in a Korean population. This association study was conducted in order to identify genetic effects of CFB single nucleotide polymorphisms (SNPs) and to identify additional independent CHB susceptible causal markers within a Korean population. Methods A total of 10 CFB genetic polymorphisms were selected and genotyped in 1716 study subjects comprised of 955 CHB patients and 761 population controls. Results A non-synonymous variant, rs12614 (Arg32Trp) in exon2 of CFB, had significant associations with risk of CHB (odds ratio = 0.43, P = 5.91 × 10− 10). Additional linkage disequilibrium and conditional analysis confirmed that rs12614 had independent genetic effect on CHB susceptibility with previously identified CHB markers. The genetic risk scores (GRSs) were calculated and the CHB patients had higher GRSs than the population controls. Moreover, OR was found to increase significantly with cumulative GRS. Conclusions rs12614 showed significant genetic effect on CHB risk within the Korean population. As such rs12614 may be used as a possible causal genetic variant for CHB susceptibility. Supplementary Information The online version contains supplementary material available at 10.1186/s12881-020-01177-w.
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Affiliation(s)
- Jung Yeon Seo
- Current address: Department of Core Technology, R&D Center, LG Household & Healthcare (LG H&H), Seoul, 07795, South Korea.,Department of Life Science, Sogang University, Seoul, 04107, Republic of Korea
| | - Joong-Gon Shin
- Current address: Department of Core Technology, R&D Center, LG Household & Healthcare (LG H&H), Seoul, 07795, South Korea.,Research Institute for Basic Science, Sogang University, Seoul, 04107, Republic of Korea
| | - Byeong Ju Youn
- Department of Life Science, Sogang University, Seoul, 04107, Republic of Korea
| | - Suhg Namgoong
- Department of Life Science, Sogang University, Seoul, 04107, Republic of Korea.,Department of Genetic Epidemiology, SNP Genetics Inc., Seoul, 04107, Republic of Korea
| | - Hyun Sub Cheong
- Department of Genetic Epidemiology, SNP Genetics Inc., Seoul, 04107, Republic of Korea
| | - Lyoung Hyo Kim
- Department of Genetic Epidemiology, SNP Genetics Inc., Seoul, 04107, Republic of Korea
| | - Ji On Kim
- Research Institute for Basic Science, Sogang University, Seoul, 04107, Republic of Korea
| | - Hyoung Doo Shin
- Department of Life Science, Sogang University, Seoul, 04107, Republic of Korea. .,Research Institute for Basic Science, Sogang University, Seoul, 04107, Republic of Korea. .,Department of Genetic Epidemiology, SNP Genetics Inc., Seoul, 04107, Republic of Korea.
| | - Yoon Jun Kim
- Department of Internal Medicine and Liver Research Institute, Seoul National University, 103 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea.
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Abstract
BACKGROUND Lung cancer is the leading cause of cancer-related deaths worldwide. Copy number variation (CNV) in several genetic regions correlate with cancer susceptibility. Hence, this study evaluated the association between CNV and non-small cell lung cancer (NSCLC) in the peripheral blood. METHODS Blood samples of 150 patients with NSCLC and 150 normal controls were obtained from a bioresource center (Seoul, Korea). Through an epigenome-wide analysis using the MethylationEPIC BeadChip method, we extracted CNVs by using an SVS8 software-supplied multivariate method. We compared CNV frequencies between the NSCLC and controls, and then performed stratification analyses according to smoking status. RESULTS We acquired 979 CNVs, with 582 and 967 copy-number gains and losses, respectively. We identified five nominally significant associations (ACOT1, NAA60, GSDMD, HLA-DPA1, and SLC35B3 genes). Among the current smokers, the NSCLC group had more CNV losses and gains at the GSDMD gene in chromosome 8 (P=0.02) and at the ACOT1 gene in chromosome 14 (P=0.03) than the control group. It also had more CNV losses at the NAA60 gene in chromosome 16 (P=0.03) among non-smokers. In the NSCLC group, current smokers had more CNV gains and losses at the ACOT1 gene in chromosome 14 (P=0.003) and at HLA-DPA1 gene in chromosome 6 (P=0.02), respectively, than non-smokers. CONCLUSION Five nominally significant associations were found between the NSCLC and CNVs. CNVs are associated with the mechanism of lung cancer development. However, the role of CNVs in lung cancer development needs further investigation.
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Affiliation(s)
- Yeonjeong Heo
- Department of Internal Medicine, Kangwon National University, Kangwon National University Hospital, Chuncheon, Korea
| | - Jeongwon Heo
- Department of Internal Medicine, Kangwon National University, Kangwon National University Hospital, Chuncheon, Korea
- Department of Internal Medicine and Environmental Health Center, Kangwon National University, Kangwon National University Hospital, Chuncheon, Korea
| | - Seon-Sook Han
- Department of Internal Medicine, Kangwon National University, Kangwon National University Hospital, Chuncheon, Korea
- Department of Internal Medicine and Environmental Health Center, Kangwon National University, Kangwon National University Hospital, Chuncheon, Korea
| | - Woo Jin Kim
- Department of Internal Medicine, Kangwon National University, Kangwon National University Hospital, Chuncheon, Korea
- Department of Internal Medicine and Environmental Health Center, Kangwon National University, Kangwon National University Hospital, Chuncheon, Korea
| | - Hyun Sub Cheong
- Department of Genetic Epidemiology, SNP Genetics, Inc., Sogang University, Mapo-gu, Seoul, Republic of Korea
| | - Yoonki Hong
- Department of Internal Medicine, Kangwon National University, Kangwon National University Hospital, Chuncheon, Korea
- Department of Internal Medicine and Environmental Health Center, Kangwon National University, Kangwon National University Hospital, Chuncheon, Korea
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Kim YW, Lee YH, Kim JS, Lee J, Kim YJ, Cheong HS, Kim SH, Park KH, Kim DM, Choi HJ, Jeoung JW. Genetic analysis of primary open-angle glaucoma-related risk alleles in a Korean population: the GLAU-GENDISK study. Br J Ophthalmol 2020; 105:1307-1312. [PMID: 32933932 DOI: 10.1136/bjophthalmol-2020-316089] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 02/17/2020] [Revised: 07/21/2020] [Accepted: 08/22/2020] [Indexed: 11/04/2022]
Abstract
AIM To validate six previously known primary open-angle glaucoma (POAG)-related loci in a Korean population. METHODS Representative POAG-related single-nucleotide polymorphisms (SNPs) from six loci (cyclin-dependent kinase 4 inhibitor B antisense RNA 1 (CDKN2B)-AS1, sineoculis homeobox homolog 1/sineoculis homeobox homolog 6(SIX1/SIX6), atonal BHLH transcription factor 7 (ATOH7), cell division cycle 7-transforming growth factor beta receptor 3, CAV1, transmembrane and coiled-coil domain family 1 (TMCO1) were selected and genotyped from discovery (POAG=309, heathy=5400) and replication cohorts (POAG=310, healthy=5612 and POAG=221, healthy=6244, respectively). Data were analysed using logistic regression to calculate the OR for POAG risk associated with SNP. RESULTS From the discovery cohort, rs1900004 in ATOH7 (OR=1.29, p=0.0024); rs1063192 (OR=0.69, p=0.0006), rs2157719 (OR=0.63, p=0.0007) and rs7865618 (OR=0.63, p=0.0006) in CDKN2B-AS1, and rs10483727 in SIX1/SIX6 (OR=0.68, p=7.9E-05) were nominally associated with the risk of POAG. The replication cohorts revealed nominal associations with rs2157719 (OR=0.72, p=0.0135), rs1063192 (OR=0.63, p=0.0007) and rs7865618 (OR=0.52, p=0.0004) in CDKN2B-AS1. A mega-analysis from the entire Korean population revealed significance with rs1063192 (OR=0.77, p=6.0E-05), rs2157719 (OR=0.63, p=0.0007) and rs7865618 (OR=0.58, p=1.9E-06) in CDKN2B-AS1 and with rs10483727 in SIX1/SIX6 (OR=0.79, p=9.4E-05), with the same direction of effect between the discovery association and the replication sample. CONCLUSIONS Variants near CDKN2B-AS1 and SIX1/SIX6 may require further investigation to obtain more genetic information on POAG development in a Korean population.
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Affiliation(s)
- Yong Woo Kim
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul, Korea.,Department of Ophthalmology, Seoul National University Hospital, Seoul, Korea
| | - Yun Hwan Lee
- Department of Public Health Sciences, Seoul National University, Seoul, Korea
| | - Jin-Soo Kim
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul, Korea.,Department of Ophthalmology, Chungnam National University Sejong Hospital, Sejong, Korea
| | - Jinho Lee
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul, Korea.,Department of Ophthalmology, Hallym University Chuncheon Sacred Heart Hospital, Chuncheon, Korea
| | - Yu Jeong Kim
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul, Korea
| | - Hyun Sub Cheong
- Department of Genetic Epidemiology, SNP Genetics, Inc., Seoul, Korea
| | - Seok Hwan Kim
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul, Korea.,Department of Ophthalmology, Seoul National University Boramae Medical Center, Seoul, Korea
| | - Ki Ho Park
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul, Korea.,Department of Ophthalmology, Seoul National University Hospital, Seoul, Korea
| | - Dong Myung Kim
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul, Korea
| | - Hyuk Jin Choi
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul, Korea.,Seoul National University Hospital Healthcare System Gangnam Center, Seoul, Korea
| | - Jin Wook Jeoung
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul, Korea .,Department of Ophthalmology, Seoul National University Hospital, Seoul, Korea
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9
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Kim YW, Kim YJ, Cheong HS, Shiga Y, Hashimoto K, Song YJ, Kim SH, Choi HJ, Nishiguchi KM, Kawai Y, Nagasaki M, Nakazawa T, Park KH, Kim DM, Jeoung JW. Exploring the Novel Susceptibility Gene Variants for Primary Open-Angle Glaucoma in East Asian Cohorts: The GLAU-GENDISK Study. Sci Rep 2020; 10:221. [PMID: 31937794 PMCID: PMC6959350 DOI: 10.1038/s41598-019-57066-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 12/19/2019] [Indexed: 12/19/2022] Open
Abstract
Primary open-angle glaucoma (POAG) can develop even within normal ranges of intraocular pressure, and this type of glaucoma (so-called ‘normal-tension glaucoma [NTG]’) is highly prevalent in East Asia including Korea and Japan. We conducted exome chip analysis to identify low-frequency and rare variants associated with POAG from the primary cohort (309 POAG patients and 5,400 control, all Koreans). For replication, Korean (310 POAG patients and 5,612 controls) and Japanese (565 POAG patients and 1,104 controls) cohorts were further investigated by targeted genotyping. SNP rs116121322 in LRRC27 showed nominally significant association with POAG in the discovery cohort (OR = 29.85, P = 2E–06). This SNP was validated in the Korean replication cohort but only in the NTG subgroups (OR = 9.86, P = 0.007). Japanese replication cohort did not show significant association with POAG (P .00.44). However, the meta-analysis in the entire cohort revealed significant association of rs116121322 with POAG (ORcombined = 10.28, Pcombined = 1.4E–07). The LRRC27 protein expression was confirmed from human trabecular meshwork cells. For gene-based testing, METTL20 showed a significant association in POAG (Pcombined = 0.002) and in the subgroup of NTG (Pcombined = 0.02), whereas ZNF677 were significantly associated with only in the subgroup of high-tension glaucoma (Pcombined = 1.5E–06). Our findings may provide further genetic backgrounds into the pathogenesis of POAG, especially for the patients who have lower baseline intraocular pressures.
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Affiliation(s)
- Yong Woo Kim
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul, Korea.,Department of Ophthalmology, Seoul National University Hospital, Seoul, Korea
| | - Yu Jeong Kim
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul, Korea
| | - Hyun Sub Cheong
- Department of Genetic Epidemiology, SNP Genetics, Inc., Seoul, Korea
| | - Yukihiro Shiga
- Department of Ophthalmic Imaging and Information Analytics, Tohoku University Graduate School of Medicine, Miyagi, Japan.,Department of Ophthalmology, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | - Kazuki Hashimoto
- Department of Ophthalmology, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | - Yong Ju Song
- Department of Ophthalmology, Chosun University College of Medicine, Gwangju, Korea
| | - Seok Hwan Kim
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul, Korea.,Department of Ophthalmology, Seoul National University Boramae Hospital, Seoul, Korea
| | - Hyuk Jin Choi
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul, Korea.,Healthcare System Gangnam Center, Seoul National University Hospital, Seoul, Korea
| | - Koji M Nishiguchi
- Department of Advanced Ophthalmic Medicine, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | - Yosuke Kawai
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Miyagi, Japan.,Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Masao Nagasaki
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Miyagi, Japan.,Graduate School of Information Sciences, Tohoku University, Miyagi, Japan
| | - Toru Nakazawa
- Department of Ophthalmic Imaging and Information Analytics, Tohoku University Graduate School of Medicine, Miyagi, Japan.,Department of Ophthalmology, Tohoku University Graduate School of Medicine, Miyagi, Japan.,Department of Advanced Ophthalmic Medicine, Tohoku University Graduate School of Medicine, Miyagi, Japan.,Department of Retinal Disease Control, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | - Ki Ho Park
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul, Korea.,Department of Ophthalmology, Seoul National University Hospital, Seoul, Korea
| | - Dong Myung Kim
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul, Korea
| | - Jin Wook Jeoung
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul, Korea. .,Department of Ophthalmology, Seoul National University Hospital, Seoul, Korea.
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10
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Heo J, Heo Y, Hong Y, Han SS, Cheong HS, Kim WJ. Difference of Copy number variation in the blood between patients with lung cancer and control. Lung Cancer 2019. [DOI: 10.1183/13993003.congress-2019.pa3659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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11
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Lee JU, Son JH, Shim EY, Cheong HS, Shin SW, Shin HD, Baek AR, Ryu S, Park CS, Chang HS, Park JS. Global DNA Methylation Pattern of Fibroblasts in Idiopathic Pulmonary Fibrosis. DNA Cell Biol 2019; 38:905-914. [DOI: 10.1089/dna.2018.4557] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Jong-Uk Lee
- Department of Interdisciplinary Program in Biomedical Science Major, Soonchunhyang University, Bucheon, Republic of Korea
| | - Ji-Hye Son
- Department of Interdisciplinary Program in Biomedical Science Major, Soonchunhyang University, Bucheon, Republic of Korea
| | - Eun-Young Shim
- Department of Interdisciplinary Program in Biomedical Science Major, Soonchunhyang University, Bucheon, Republic of Korea
| | - Hyun Sub Cheong
- Department of Genetic Epidemiology, SNP Genetics, Inc., Sogang University, Seoul, Republic of Korea
| | - Seung-Woo Shin
- Department of Interdisciplinary Program in Biomedical Science Major, Soonchunhyang University, Bucheon, Republic of Korea
| | - Hyoung Doo Shin
- Department of Genetic Epidemiology, SNP Genetics, Inc., Sogang University, Seoul, Republic of Korea
- Department of Life Science, Sogang University, Seoul, Republic of Korea
| | - Ae Rin Baek
- Division of Allergy and Respiratory Medicine, Department of Internal Medicine, Soonchunhyang University Bucheon Hospital, Bucheon, Republic of Korea
| | - Seongho Ryu
- Soonchunhyang Institute of Med-Bioscience (SIMS), Soonchunhyang University, Cheonan-Si, Republic of Korea
| | - Choon-Sik Park
- Department of Interdisciplinary Program in Biomedical Science Major, Soonchunhyang University, Bucheon, Republic of Korea
- Division of Allergy and Respiratory Medicine, Department of Internal Medicine, Soonchunhyang University Bucheon Hospital, Bucheon, Republic of Korea
| | - Hun Soo Chang
- Department of Interdisciplinary Program in Biomedical Science Major, Soonchunhyang University, Bucheon, Republic of Korea
| | - Jong-Sook Park
- Division of Allergy and Respiratory Medicine, Department of Internal Medicine, Soonchunhyang University Bucheon Hospital, Bucheon, Republic of Korea
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12
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Hong Y, Choi HM, Cheong HS, Shin HD, Choi CM, Kim WJ. Epigenome-Wide Association Analysis of Differentially Methylated Signals in Blood Samples of Patients with Non-Small-Cell Lung Cancer. J Clin Med 2019; 8:jcm8091307. [PMID: 31450665 PMCID: PMC6780065 DOI: 10.3390/jcm8091307] [Citation(s) in RCA: 9] [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: 07/29/2019] [Revised: 08/22/2019] [Accepted: 08/23/2019] [Indexed: 12/19/2022] Open
Abstract
Lung cancer is a common form of cancer and the leading cause of cancer-related deaths worldwide. Early diagnosis using noninvasive biomarkers may play an important role in increasing the survival rate of patients with lung cancer. Biomarkers of DNA methylation in blood samples may improve the early diagnosis of lung cancer. Here, we used peripheral blood samples obtained from 150 patients diagnosed with non-small-cell lung cancer (NSCLC) and 150 healthy controls. The latter were selected by frequency matching with the 150 patients with NSCLC, based on age, sex, and smoking status. Genome-wide methylation profiles were obtained using a MethylationEPIC BeadChip Kit, which covers the 850k bp cytosine–phosphate–guanine site. This analysis showed two significant differentially methylated changes (cg12169243 [DPH6] and cg25429010 [IMP3]) associated with NSCLC in current smokers, six changes (cg09245319, cg17183999 [USP7], cg06366994 [CPE], cg24992236 [MEG9], cg22144719, and cg22448179 [epidermal growth factor receptor]) associated with epidermal growth factor receptor mutation in patients with adenocarcinoma, and four changes (cg25021476 [RSL24D1], cg04989085 [FAM113B], cg20905681 [CKAP4], and cg26379694) associated with advanced-stage NSCLC compared with stage I NSCLC. The validation of these DNA methylation changes and further research on the related genes may help develop easily accessible biomarkers for the early diagnosis or prognosis of NSCLC.
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Affiliation(s)
- Yoonki Hong
- Department of Internal Medicine, School of Medicine, Kangwon National University, Chuncheon 200-701, Korea
| | - Hye-Mi Choi
- Division of Biomedical Convergence, College of Biomedical Science, and Institute of Bioscience & Biotechnology, Kangwon National University, Chuncheon 200-701, Korea
| | - Hyun Sub Cheong
- Department of Genetic Epidemiology, SNP Genetics, Inc., Sogang University, Seoul, 04107, Korea
| | - Hyoung Doo Shin
- Department of Genetic Epidemiology, SNP Genetics, Inc., Sogang University, Seoul, 04107, Korea
- Department of Life Science, Sogang University, Seoul 121-742, Korea
| | - Chang Min Choi
- Department of Pulmonary and Critical Care Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea.
| | - Woo Jin Kim
- Department of Internal Medicine, School of Medicine, Kangwon National University, Chuncheon 200-701, Korea.
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13
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Ock CY, Seo H, Kim DY, Min BJ, Park Y, Cheong HS, Kim HL, Song EY, Kim I, Yoon SS, Kim JH, Koh Y. Discovery of donor genotype associated with long-term survival of patients with hematopoietic stem cell transplantation in refractory acute myeloid leukemia. Leuk Lymphoma 2018; 60:1775-1781. [PMID: 30507323 DOI: 10.1080/10428194.2018.1542142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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: 01/12/2023]
Abstract
Allogeneic hematopoietic stem cell transplantation (allo-HSCT) has been the only treatment option for acute myeloid leukemia (AML) refractory to induction chemotherapy, with only 10-20% of patients achieving long-term survival. Certain donor genotypes may confer leukemia-clearing effects after allo-HSCT. We performed whole-exome sequencing of five pairs of the germ lines in AML patients who achieved long-term remission after allo-HSCT and in their donors, and found two significant variants: EGFR c.2982C > T and CDH11 c.945G > A. To validate the protective effects of these leukemia-clearing genotypes (LCGs), AML patients who received allo-HSCT in a complete-remission status were also analyzed. Twenty-two of 96 donors (22.9%) had LCGs in their genomes, and overall survival was significantly longer in patients who received allo-HSCT from donors with germ-line LCGs (hazard ratio=0.47, 95% confidence interval=0.24-0.94, p = .033). These findings indicate that donor germ-line LCGs have phenotypically leukemia-clearing effects and are biomarkers for predicting clinical outcomes in allogeneic transplantation in AML patients.
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Affiliation(s)
- Chan-Young Ock
- a Department of Internal Medicine , Seoul National University Hospital , Seoul , Korea
| | - Heewon Seo
- b Division of Biomedical Informatics Seoul National University College of Medicine , Seoul National University Biomedical Informatics (SNUBI) , Seoul , Korea
| | - Dae-Yoon Kim
- c Biomedical Research Institute , Seoul National University Hospital , Seoul , Korea
| | - Byung Joo Min
- b Division of Biomedical Informatics Seoul National University College of Medicine , Seoul National University Biomedical Informatics (SNUBI) , Seoul , Korea
| | - Yoomi Park
- b Division of Biomedical Informatics Seoul National University College of Medicine , Seoul National University Biomedical Informatics (SNUBI) , Seoul , Korea
| | - Hyun Sub Cheong
- d Department of Genetic Epidemiology , Sogang University , Seoul , Korea
| | - Hyung-Lae Kim
- e Department of Biochemistry , Ewha Medical Research Institute , Seoul , Korea
| | - Eun-Young Song
- f Department of Laboratory Medicine , Seoul National University Hospital , Seoul , Korea
| | - Inho Kim
- a Department of Internal Medicine , Seoul National University Hospital , Seoul , Korea
| | - Sung-Soo Yoon
- a Department of Internal Medicine , Seoul National University Hospital , Seoul , Korea.,c Biomedical Research Institute , Seoul National University Hospital , Seoul , Korea
| | - Ju Han Kim
- b Division of Biomedical Informatics Seoul National University College of Medicine , Seoul National University Biomedical Informatics (SNUBI) , Seoul , Korea
| | - Youngil Koh
- a Department of Internal Medicine , Seoul National University Hospital , Seoul , Korea.,c Biomedical Research Institute , Seoul National University Hospital , Seoul , Korea
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14
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Namgoong S, Cheong HS, Kim JH, Kim LH, Seo JY, Kang SG, Yoon SJ, Kim SH, Chang JH, Shin HD. Association analysis of RTEL1 variants with risk of adult gliomas in a Korean population. PLoS One 2018; 13:e0207660. [PMID: 30462709 PMCID: PMC6248978 DOI: 10.1371/journal.pone.0207660] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [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: 02/19/2018] [Accepted: 11/04/2018] [Indexed: 01/28/2023] Open
Abstract
Previous studies have identified multiple loci for inherited susceptibility to glioma development, including the regulator of telomere elongation helicase 1 (RTEL1). However, the association between RTEL1 variants and risk of glioma has not been well understood. Therefore, we sought to comprehensively examine the genetic interaction between RTEL1 variants and risk of glioma with respect to defined histological and molecular subtypes. We employed a case-control study involving 250 adult glioma patients with previous molecular alterations and 375 population–based controls within Korean populations. Statistical analyses on the association between RTEL1 single nucleotide polymorphisms (SNPs) and glioma risk were conducted using unconditional logistic regression. Additional conditional and stepwise analyses were performed on significant RTEL1 SNPs. We detected significant associations (Bonferroni P < .05) between six SNPs (rs6089953, rs3848669, rs6010620, rs3787089, rs6062302, and rs115303435) and risk of glioma in the Korean subjects. The two coding variants, rs6062302 (D664D) and rs115303435 (A1059T), were plausibly causal variants and were independent among the significantly associated RTEL1 variants. The glioma subgroup analyses showed that the causal variants (rs6062302 and rs115303435) may be associated with increased risk of glioma regardless of histological grades and molecular alterations. This study provides a deeper understanding of relationships between RTEL1 variants and risk of glioma. Further studies are required to ascertain the impact of those variants on glioma susceptibility.
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Affiliation(s)
- Suhg Namgoong
- Department of Life Science, Sogang University, Seoul, Republic of Korea
| | - Hyun Sub Cheong
- Department of Genetic Epidemiology, SNP Genetics Inc., Seoul, Republic of Korea
| | - Jeong-Hyun Kim
- Asan Institute for Life Sciences, University of Ulsan Collage of Medicine, Seoul, Republic of Korea
| | - Lyoung Hyo Kim
- Department of Genetic Epidemiology, SNP Genetics Inc., Seoul, Republic of Korea
| | - Jung Yeon Seo
- Department of Life Science, Sogang University, Seoul, Republic of Korea
| | - Seok-Gu Kang
- Department of Neurosurgery, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Seon-Jin Yoon
- Department of Neurosurgery, Yonsei University College of Medicine, Seoul, Republic of Korea
- Department of Biochemistry and Molecular Biology, College of Medicine, Yonsei University, Seoul, Republic of Korea
| | - Se Hoon Kim
- Department of Pathology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jong Hee Chang
- Department of Neurosurgery, Yonsei University College of Medicine, Seoul, Republic of Korea
- * E-mail: (HDS); (JHC)
| | - Hyoung Doo Shin
- Department of Life Science, Sogang University, Seoul, Republic of Korea
- Research Institute for Basic Science, Sogang University, Seoul, Republic of Korea
- * E-mail: (HDS); (JHC)
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15
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Namgoong S, Shin JG, Cheong HS, Kim LH, Kim JO, Seo JY, Shin HD, Kim YJ. Genetic association of complement component 2 variants with chronic hepatitis B in a Korean population. Liver Int 2018; 38:1576-1582. [PMID: 29283494 DOI: 10.1111/liv.13675] [Citation(s) in RCA: 4] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 11/30/2017] [Indexed: 12/11/2022]
Abstract
BACKGROUND & AIMS Numerous single nucleotide polymorphisms associated with an increased risk of liver diseases, chronic hepatitis B and chronic hepatitis B-related hepatocellular carcinoma have been identified. In this study, we scrutinized the genetic effects of C2 variants, which were conflicting in previous results, on the risk of chronic hepatitis B in a Korean population. METHODS We genotyped 22 common C2 genetic variants of 977 chronic hepatitis B cases including 302 chronic hepatitis B-related hepatocellular carcinoma cases and 785 population controls. Statistical analysis was performed to examine the effects of genotype on the risk of chronic hepatitis B and chronic hepatitis B-related hepatocellular carcinoma. RESULTS Logistic regression analyses showed that six C2 single nucleotide polymorphisms had significant associations with the risk of chronic hepatitis B and chronic hepatitis B-related hepatocellular carcinoma among the Korean subjects. Stepwise analysis revealed that causal markers (rs9267665 and rs10947223) were identified among the C2 variants (stepwise P = 3.32 × 10-9 and 2.04 × 10-5 respectively). In further conditional analysis with previous chronic hepatitis B-associated loci, these two single nucleotide polymorphisms were independently associated with the risk of chronic hepatitis B. In addition, we investigated the ability of genetic risk scores combining 12 multi-chronic hepatitis B loci to predict the risk of chronic hepatitis B. Individuals with higher genetic risk scores showed increased risk for chronic hepatitis B. CONCLUSIONS Our results suggested that the C2 gene might be a susceptibility locus for chronic hepatitis B in Korean populations. The cumulative genetic effects may contribute to future etiological explanations for chronic hepatitis B.
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Affiliation(s)
- Suhg Namgoong
- Department of Life Science, Sogang University, Seoul, Korea
| | - Joong-Gon Shin
- Research Institute for Basic Science, Sogang University, Seoul, Korea
| | - Hyun Sub Cheong
- Department of Genetic Epidemiology, SNP Genetics Inc., Seoul, Korea
| | - Lyoung Hyo Kim
- Department of Genetic Epidemiology, SNP Genetics Inc., Seoul, Korea
| | - Ji On Kim
- Department of Genetic Epidemiology, SNP Genetics Inc., Seoul, Korea
| | - Jung Yeon Seo
- Department of Life Science, Sogang University, Seoul, Korea
| | - Hyoung Doo Shin
- Department of Life Science, Sogang University, Seoul, Korea.,Research Institute for Basic Science, Sogang University, Seoul, Korea
| | - Yoon Jun Kim
- Department of Internal Medicine and Liver Research Institute, Seoul National University, Seoul, Korea
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16
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Kim S, Cheong HS, Shin HD, Lee SS, Roh HJ, Jeon DY, Cho CY. Genetic diversity and divergence among Korean cattle breeds assessed using a BovineHD single-nucleotide polymorphism chip. Asian-Australas J Anim Sci 2018; 31:1691-1699. [PMID: 30056676 PMCID: PMC6212751 DOI: 10.5713/ajas.17.0419] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 06/22/2018] [Indexed: 01/07/2023]
Abstract
Objective In Korea, there are three main cattle breeds, which are distinguished by coat color: Brown Hanwoo (BH), Brindle Hanwoo (BRH), and Jeju Black (JB). In this study, we sought to compare the genetic diversity and divergence among there Korean cattle breeds using a BovineHD chip genotyping array. Methods Sample data were collected from 168 cattle in three populations of BH (48 cattle), BRH (96 cattle), and JB (24 cattle). The single-nucleotide polymorphism (SNP) genotyping was performed using the Illumina BovineHD SNP 777K Bead chip. Results Heterozygosity, used as a measure of within-breed genetic diversity, was higher in BH (0.293) and BRH (0.296) than in JB (0.266). Linkage disequilibrium decay was more rapid in BH and BRH than in JB, reaching an average r2 value of 0.2 before 26 kb in BH and BRH, whereas the corresponding value was reached before 32 kb in JB. Intra-population, inter-population, and Fst analyses were used to identify candidate signatures of positive selection in the genome of a domestic Korean cattle population and 48, 11, and 11 loci were detected in the genomic region of the BRH breed, respectively. A Neighbor-Joining phylogenetic tree showed two main groups: a group comprising BH and BRH on one side and a group containing JB on the other. The runs of homozygosity analysis between Korean breeds indicated that the BRH and JB breeds have high inbreeding within breeds compared with BH. An analysis of differentiation based on a high-density SNP chip showed differences between Korean cattle breeds and the closeness of breeds corresponding to the geographic regions where they are evolving. Conclusion Our results indicate that although the Korean cattle breeds have common features, they also show reliable breed diversity.
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Affiliation(s)
- Seungchang Kim
- Animal Genetic Resources Center, National Institute of Animal Science, RDA, Namwon 55717, Korea
| | - Hyun Sub Cheong
- Department of Genetic Epidemiology, SNP Genetics, Inc., Seoul 04107, Korea
| | - Hyoung Doo Shin
- Department of Genetic Epidemiology, SNP Genetics, Inc., Seoul 04107, Korea.,Department of Life Science, Sogang University, Seoul 04107, Korea
| | - Sung-Soo Lee
- Animal Genetic Resources Center, National Institute of Animal Science, RDA, Namwon 55717, Korea
| | - Hee-Jong Roh
- Animal Genetic Resources Center, National Institute of Animal Science, RDA, Namwon 55717, Korea
| | - Da-Yeon Jeon
- Animal Genetic Resources Center, National Institute of Animal Science, RDA, Namwon 55717, Korea
| | - Chang-Yeon Cho
- Animal Genetic Resources Center, National Institute of Animal Science, RDA, Namwon 55717, Korea
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17
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Lee JS, Cheong HS, Shin HD. Prediction of cholesterol ratios within a Korean population. R Soc Open Sci 2018; 5:171204. [PMID: 29410832 PMCID: PMC5792909 DOI: 10.1098/rsos.171204] [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] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 11/29/2017] [Indexed: 06/08/2023]
Abstract
Cholesterol ratios (total cholesterol (TC)/high-density lipoprotein cholesterol (HDL-c) and triglyceride (TG)/HDL-c) have been suggested as better indicators to predict various clinical features such as insulin resistance and heart disease. Therefore, we aimed to build a single nucleotide polymorphism (SNP) set to predict constitutional lipid metabolism. The genotype data of 7795 samples were obtained from the Korea Association Resource. Among the total of 7795 samples, 7016 subjects were used to perform 10-fold cross-validation. We selected the SNPs that showed significance constantly throughout all 10 cross-validation sets; another 779 samples were used as the final validation set. After performing the 10-fold cross-validation, the six SNPs (rs4420638 (APOC1), rs12421652 (BUD13), rs17411126 (LPL), rs6589566 (ZPR1), rs16940212 (LOC101928635) and rs10852765 (ABCA8)) were finally selected for predicting cholesterol ratios. The weighted genetic risk scores (wGRS) were calculated based on the regression slopes of the six selected SNPs. Our results showed upward trends of wGRS for both the TC/HDL-c and TG/HDL-c ratios within the 10-fold cross-validation. Similarly, the wGRS of the six SNPs also showed upward trends in analyses using the SNP selection set and final validation set. The selected six SNPs can be used to explain both the TC/HDL-c and TG/HDL-c ratios. Our results may be useful for the prospective predictions of cholesterol-related diseases.
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Affiliation(s)
- Jin Sol Lee
- Department of Life Science, Sogang University, Baekbumro 35, Mapo-gu, Seoul 04107, Republic of Korea
- Research Institute for Basic Science, Sogang University, Mapo-gu, Seoul, 121-742, Republic of Korea
| | - Hyun Sub Cheong
- Department of Genetic Epidemiology, SNP Genetics, Inc., Taihard building 1007, Sogang University, Baekbumro 35, Mapo-gu, Seoul, Republic of Korea
| | - Hyoung Doo Shin
- Department of Life Science, Sogang University, Baekbumro 35, Mapo-gu, Seoul 04107, Republic of Korea
- Research Institute for Basic Science, Sogang University, Mapo-gu, Seoul, 121-742, Republic of Korea
- Department of Genetic Epidemiology, SNP Genetics, Inc., Taihard building 1007, Sogang University, Baekbumro 35, Mapo-gu, Seoul, Republic of Korea
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18
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Shin JG, Cheong HS, Kim JY, Lee JH, Yu SJ, Yoon JH, Cheong JY, Cho SW, Park NH, Namgoong S, Kim LH, Kim YJ, Shin HD. Identification of additional EHMT2 variant associated with the risk of chronic hepatitis B by GWAS follow-up study. Genes Immun 2017; 20:1-9. [PMID: 29238036 DOI: 10.1038/s41435-017-0004-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 07/12/2017] [Accepted: 07/13/2017] [Indexed: 02/07/2023]
Abstract
Chronic hepatitis B (CHB) is a precursor to liver cirrhosis and hepatocellular carcinoma, caused by a Hepatitis B viral infection. Genome-wide association studies (GWASs) have been conducted to find genes associated with CHB risk. In previous GWAS, EHMT2 was identified as one of the susceptibility genes for CHB. To further characterize this association and discover possible causal variants, we conducted an additional association study. A total of 11 EHMT2 single-nucleotide polymorphisms (SNP) were selected and genotyped in 3902 subjects (1046 CHB patients and 2856 controls). An additional eight imputed SNPs were also included in further analysis. As a result, rs35875104 showed a strong association with the CHB, along with the previously reported genetic marker for CHB risk, rs652888 (odds ratio (OR) = 0.53, P = 2.20 × 10-8 at rs35875104 and OR = 1.58, P = 9.90 × 10-12 at rs652888). In addition, linkage disequilibrium and conditional analysis identified one SNP (rs35875104) as a novel genetic marker for CHB susceptibility. The GRSs (genetic risk scores) were calculated to visualize the combined genetic effects of all known CHB-associated loci, including EHMT2 rs35875104, which was additionally identified in this study. The findings from the present study may be useful for further understanding of the genetic etiology of CHB.
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Affiliation(s)
- Joong-Gon Shin
- Department of Life Science, Sogang University, 1 Shinsu-dong, Mapo-gu, Seoul, 121-742, Republic of Korea.,Research Institute for Basic Science, Sogang University, Seoul, 121-742, Republic of Korea
| | - Hyun Sub Cheong
- Department of Genetic Epidemiology, SNP Genetics, Sogang University, Inc., Taihard building 1007, 1 Shinsu-dong, Mapo-gu, Seoul, 121-742, Republic of Korea
| | - Jason Yongha Kim
- Department of Life Science, Sogang University, 1 Shinsu-dong, Mapo-gu, Seoul, 121-742, Republic of Korea
| | - Jeong-Hoon Lee
- Department of Internal Medicine and Liver Research Institute, Seoul National University, 28 Yungun-dong, Chongro-Gu, Seoul, 110-744, Republic of Korea
| | - Su Jong Yu
- Department of Internal Medicine and Liver Research Institute, Seoul National University, 28 Yungun-dong, Chongro-Gu, Seoul, 110-744, Republic of Korea
| | - Jung-Hwan Yoon
- Department of Internal Medicine and Liver Research Institute, Seoul National University, 28 Yungun-dong, Chongro-Gu, Seoul, 110-744, Republic of Korea
| | - Jae Youn Cheong
- Department of Internal Medicine, Seoul National University Boramae Medical Center, 20 Boramae-ro 5-gil, Dongjak-gu, Seoul, 156-707, Republic of Korea
| | - Sung Won Cho
- Department of Gastroenterology, Ajou University School of Medicine, San-5 Wonchon-dong, Youngtong-gu, Suwon, 442-721, Republic of Korea
| | - Neung Hwa Park
- Department of Internal Medicine, Ulsan University Hospital, 877 Bangeojin Sunhwan-doro, Dong-gu, Ulsan, 682-714, Republic of Korea
| | - Suhg Namgoong
- Department of Life Science, Sogang University, 1 Shinsu-dong, Mapo-gu, Seoul, 121-742, Republic of Korea.,Department of Genetic Epidemiology, SNP Genetics, Sogang University, Inc., Taihard building 1007, 1 Shinsu-dong, Mapo-gu, Seoul, 121-742, Republic of Korea
| | - Lyoung Hyo Kim
- Department of Genetic Epidemiology, SNP Genetics, Sogang University, Inc., Taihard building 1007, 1 Shinsu-dong, Mapo-gu, Seoul, 121-742, Republic of Korea
| | - Yoon Jun Kim
- Department of Internal Medicine and Liver Research Institute, Seoul National University, 28 Yungun-dong, Chongro-Gu, Seoul, 110-744, Republic of Korea.
| | - Hyoung Doo Shin
- Department of Life Science, Sogang University, 1 Shinsu-dong, Mapo-gu, Seoul, 121-742, Republic of Korea. .,Research Institute for Basic Science, Sogang University, Seoul, 121-742, Republic of Korea. .,Department of Genetic Epidemiology, SNP Genetics, Sogang University, Inc., Taihard building 1007, 1 Shinsu-dong, Mapo-gu, Seoul, 121-742, Republic of Korea.
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Tang CSM, Gui H, Kapoor A, Kim JH, Luzón-Toro B, Pelet A, Burzynski G, Lantieri F, So MT, Berrios C, Shin HD, Fernández RM, Le TL, Verheij JBGM, Matera I, Cherny SS, Nandakumar P, Cheong HS, Antiñolo G, Amiel J, Seo JM, Kim DY, Oh JT, Lyonnet S, Borrego S, Ceccherini I, Hofstra RMW, Chakravarti A, Kim HY, Sham PC, Tam PKH, Garcia-Barceló MM. Trans-ethnic meta-analysis of genome-wide association studies for Hirschsprung disease. Hum Mol Genet 2017; 25:5265-5275. [PMID: 27702942 DOI: 10.1093/hmg/ddw333] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 09/28/2016] [Indexed: 02/04/2023] Open
Abstract
Hirschsprung disease (HSCR) is the most common cause of neonatal intestinal obstruction. It is characterized by the absence of ganglia in the nerve plexuses of the lower gastrointestinal tract. So far, three common disease-susceptibility variants at the RET, SEMA3 and NRG1 loci have been detected through genome-wide association studies (GWAS) in Europeans and Asians to understand its genetic etiologies. Here we present a trans-ethnic meta-analysis of 507 HSCR cases and 1191 controls, combining all published GWAS results on HSCR to fine-map these loci and narrow down the putatively causal variants to 99% credible sets. We also demonstrate that the effects of RET and NRG1 are universal across European and Asian ancestries. In contrast, we detected a European-specific association of a low-frequency variant, rs80227144, in SEMA3 [odds ratio (OR) = 5.2, P = 4.7 × 10-10]. Conditional analyses on the lead SNPs revealed a secondary association signal, corresponding to an Asian-specific, low-frequency missense variant encoding RET p.Asp489Asn (rs9282834, conditional OR = 20.3, conditional P = 4.1 × 10-14). When in trans with the RET intron 1 enhancer risk allele, rs9282834 increases the risk of HSCR from 1.1 to 26.7. Overall, our study provides further insights into the genetic architecture of HSCR and has profound implications for future study designs.
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Affiliation(s)
- Clara Sze-Man Tang
- Department of Surgery.,Centre for Genomic Sciences.,Dr Li Dak-Sum Research Centre, The University of Hong Kong - Karolinska Institutet Collaboration in Regenerative Medicine, Hong Kong SAR, China
| | | | - Ashish Kapoor
- Center for Complex Disease Genomics, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jeong-Hyun Kim
- Research Institute for Basic Science, Sogang University, Seoul 121-742, Republic of Korea
| | - Berta Luzón-Toro
- Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), Seville, Spain
| | - Anna Pelet
- Laboratory of Embryology and Genetics of Congenital Malformations, Institut National de la Santé et de la Recherche Médicale (INSERM) U1163, Institut Imagine, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France
| | - Grzegorz Burzynski
- Department of Clinical Genetic, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | | | - Courtney Berrios
- Center for Complex Disease Genomics, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Hyoung Doo Shin
- Research Institute for Basic Science, Sogang University, Seoul 121-742, Republic of Korea.,Department of Life Science, Sogang University, Seoul 121-742, Republic of Korea
| | - Raquel M Fernández
- Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), Seville, Spain
| | - Thuy-Linh Le
- Laboratory of Embryology and Genetics of Congenital Malformations, Institut National de la Santé et de la Recherche Médicale (INSERM) U1163, Institut Imagine, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France
| | - Joke B G M Verheij
- Department of Clinical Genetic, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Ivana Matera
- UOC Genetica Medica, Istituto Giannina Gaslini, 16148 Genova, Italy
| | - Stacey S Cherny
- Centre for Genomic Sciences.,Department of Psychiatry.,State Key Laboratory of Brain and Cognitive Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Priyanka Nandakumar
- Center for Complex Disease Genomics, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Hyun Sub Cheong
- Department of Genetic Epidemiology, SNP Genetics, Inc., Seoul 121-742, Republic of Korea
| | - Guillermo Antiñolo
- Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), Seville, Spain
| | - Jeanne Amiel
- Laboratory of Embryology and Genetics of Congenital Malformations, Institut National de la Santé et de la Recherche Médicale (INSERM) U1163, Institut Imagine, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France
| | - Jeong-Meen Seo
- Division of Pediatric Surgery, Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 135-710, Republic of Korea
| | - Dae-Yeon Kim
- Department of Pediatric Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul 138-736, Republic of Korea
| | - Jung-Tak Oh
- Department of Pediatric Surgery, Severance Children's Hospital, Yonsei University College of Medicine, Seoul 120-752, Republic of Korea
| | - Stanislas Lyonnet
- Laboratory of Embryology and Genetics of Congenital Malformations, Institut National de la Santé et de la Recherche Médicale (INSERM) U1163, Institut Imagine, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France
| | - Salud Borrego
- Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), Seville, Spain
| | | | - Robert M W Hofstra
- Department of Clinical Genetic, Erasmus Medical Center, Rotterdam, The Netherlands.,Stem Cells and Regenerative Medicine, Birth Defects Research Centre UCL Institute of Child Health, London, UK
| | - Aravinda Chakravarti
- Center for Complex Disease Genomics, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Hyun-Young Kim
- Department of Pediatric Surgery, Seoul National University Children's Hospital, Seoul 110-744, Republic of Korea
| | - Pak Chung Sham
- Centre for Genomic Sciences.,Department of Psychiatry.,State Key Laboratory of Brain and Cognitive Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Paul K H Tam
- Department of Surgery.,Dr Li Dak-Sum Research Centre, The University of Hong Kong - Karolinska Institutet Collaboration in Regenerative Medicine, Hong Kong SAR, China
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20
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Sio CA, Jung K, Kim JH, Cheong HS, Shin E, Jang H, Yoon M, Jang H, Shin HD. Sotos syndrome associated with Hirschsprung's disease: a new case and exome-sequencing analysis. Pediatr Res 2017; 82:87-92. [PMID: 28399120 DOI: 10.1038/pr.2017.106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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] [Received: 12/16/2016] [Accepted: 04/02/2017] [Indexed: 11/09/2022]
Abstract
BackgroundSotos syndrome (SoS) is an overgrowth disorder with various congenital anomalies and is usually accompanied by other clinical problems. However, anorectal malformations have not been documented as part of the SoS entity. Our objective is to report on a case of SoS associated with Hirschsprung's disease (HSCR) and subsequent genetic analysis.MethodsA 2-year-old boy with SoS experienced constipation since infancy and ultimately showed an aganglionic segment in the histopathologic examination, which was followed by exome-sequencing analysis.ResultsIn the genetic test for SoS diagnosis, two novel mutations of NDS1, c.2465C>A (p.Ser822Tyr) and c.4347T>A (p.Cys1449*), were observed and verified by resequencing in the patient and his parents. In further whole-exome-sequencing analysis using the patient's blood DNA, which was followed by a comparison analysis with the results of our previously reported genome-wide association study (GWAS) of HSCR, three genes (ZNF827, FGD2, and KCNJ12) with significance for HSCR from our previous GWAS were overlapped among the genes showing variants in the exome sequencing.ConclusionThis is the first reported patient with SoS and HSCR. Further studies are required to determine whether there is a genetic relationship between SoS and HSCR.
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Affiliation(s)
- Cherry Ann Sio
- Department of Surgery, Seoul National University Bundang Hospital, Seongnam, Gyeonggi, Republic of Korea
| | - Kyuwhan Jung
- Department of Surgery, Jeju National University Hospital, Jeju, Republic of Korea
| | - Jeong-Hyun Kim
- Research Institute for Basic Science, Sogang University, Seoul, Republic of Korea
| | - Hyun Sub Cheong
- Department of Genetic Epidemiology, SNP Genetics, Seoul, Republic of Korea
| | - Eun Shin
- Department of Pathology, Seoul National University Bundang Hospital, Seongnam, Gyeonggi, Republic of Korea
| | - Hyejin Jang
- Department of Surgery, Seoul National University Bundang Hospital, Seongnam, Gyeonggi, Republic of Korea
| | - Miok Yoon
- Department of Surgery, Seoul National University Bundang Hospital, Seongnam, Gyeonggi, Republic of Korea
| | - Huijeong Jang
- Department of Surgery, Seoul National University Bundang Hospital, Seongnam, Gyeonggi, Republic of Korea
| | - Hyoung Doo Shin
- Research Institute for Basic Science, Sogang University, Seoul, Republic of Korea.,Department of Life Science, Sogang University, Seoul, Republic of Korea
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21
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Abstract
BACKGROUND Body Mass Index (BMI) is widely regarded as an important clinical trait for obesity and other diseases such as Type 2 diabetes, coronary heart disease, and osteoarthritis. METHODS This study uses 6,011 samples of genotype data from ethnic Korean subjects. The data was retrieved from the Korea Association Resource. To identify the BMI-related markers within the Korean population, we collected genome-wide association study (GWAS) markers using a GWAS catalog and also obtained other markers from nearby regions. Of the total 6,011 samples, 5,410 subjects were used as part of a single nucleotide polymorphism (SNP) selection set in order to identify the overlapping BMI-associated SNPs within a 10-fold cross validation. RESULTS We selected nine SNPs (rs12566985 (FPGT-TNNI3K), rs6545809 (ADCY3), rs2943634 (located near LOC646736), rs734597 (located near TFAP2B), rs11030104 (BDNF), rs7988412 (GTF3A), rs2241423 (MAP2K5), rs7202116 (FTO), and rs6567160 (located near LOC105372152) to assist in BMI prediction. The calculated weighted genetic risk scores based on the selected 9 SNPs within the SNP selection set were applied to the final validation set consisting of 601 samples. Our results showed upward trends in the BMI values (P < 0.0001) within the 10-fold cross validation process for R2 > 0.22. These trends were also observed within the validation set for all subjects, as well as within the validation sets divided by gender (P < 0.0001, R2 > 0.46). DISCUSSION The set of nine SNPs identified in this study may be useful for prospective predictions of BMI.
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Affiliation(s)
- Jin Sol Lee
- Research Institute for Basic Science, Sogang University, Seoul, Republic of Korea.,Department of Life Science, Sogang University, Seoul, South Korea
| | - Hyun Sub Cheong
- Department of Genetic Epidemiology, SNP Genetics, Inc., Seoul, Republic of Korea
| | - Hyoung-Doo Shin
- Research Institute for Basic Science, Sogang University, Seoul, Republic of Korea.,Department of Life Science, Sogang University, Seoul, South Korea.,Department of Genetic Epidemiology, SNP Genetics, Inc., Seoul, Republic of Korea
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22
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Kim JH, Jung SM, Shin JG, Cheong HS, Seo JM, Kim DY, Oh JT, Kim HY, Jung K, Shin HD. Potential association between ITPKC genetic variations and Hirschsprung disease. Mol Biol Rep 2017; 44:307-313. [PMID: 28664405 DOI: 10.1007/s11033-017-4111-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 06/24/2017] [Indexed: 02/03/2023]
Abstract
Hirschsprung disease (HSCR) is a congenital and complex disorder characterized by intestinal obstruction due to the absence of enteric neurons along variable lengths of the hindgut. Our recent genome-wide association study (GWAS) has revealed regional associations with HSCR at several loci of inositol-trisphosphate 3-kinase C (ITPKC). For fine mapping, we additionally selected and genotyped a total of 12 single nucleotide polymorphisms (SNPs) of ITPKC in 187 HSCR patients and 283 unaffected controls, and performed a further combined imputation analysis based on genotype data from this second stage of fine mapping and our previous GWAS stage, totaling 902 subjects (187 HSCR cases and 715 controls). As a result, several SNPs (minimum P = 0.004) and a haplotype (P = 0.02) were found to be significantly associated with HSCR. In further in silico analyses to ascertain the potential functions of the significant variants, the change from the common allele to the rare allele of the highly conserved nonsynonymous rs76785336 showed a difference in mRNA folding structure. In the case of intronic SNPs, rs2607420 with a high consensus value was predicted to be a new splice site. Although this study has limitations (such as lack of functional evaluations, small number of cases, and further need of replication in other cohorts), our findings suggest that genetic variants of ITPKC may have a potential association with HSCR susceptibility and/or developmental diseases related to enteric nervous system development.
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Affiliation(s)
- Jeong-Hyun Kim
- Research Institute for Basic Science, Sogang University, Seoul, 04107, Republic of Korea
| | - Soo-Min Jung
- Department of Surgery, Konkuk University Medical Center, Seoul, 05030, Republic of Korea
| | - Joong-Gon Shin
- Department of Life Science, Sogang University, Seoul, 04107, Republic of Korea
| | - Hyun Sub Cheong
- Department of Genetic Epidemiology, SNP Genetics, Inc., Seoul, 04107, Republic of Korea
| | - Jeong-Meen Seo
- Division of Pediatric Surgery, Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06351, Republic of Korea
| | - Dae-Yeon Kim
- Department of Pediatric Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, Republic of Korea
| | - Jung-Tak Oh
- Department of Pediatric Surgery, Severance Children's Hospital, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Hyun-Young Kim
- Department of Pediatric Surgery, Seoul National University Children's Hospital, Seoul, 03080, Republic of Korea
| | - Kyuwhan Jung
- Department of Surgery, Jeju National University Hospital, Jeju, 63241, Republic of Korea
| | - Hyoung Doo Shin
- Research Institute for Basic Science, Sogang University, Seoul, 04107, Republic of Korea. .,Department of Life Science, Sogang University, Seoul, 04107, Republic of Korea.
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23
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Jung K, Koh I, Kim JH, Cheong HS, Park T, Nam SH, Jung SM, Sio CA, Kim SY, Jung E, Lee B, Kim HR, Shin E, Jung SE, Choi CW, Kim BI, Jung E, Shin HD. RNA-Seq for Gene Expression Profiling of Human Necrotizing Enterocolitis: a Pilot Study. J Korean Med Sci 2017; 32:817-824. [PMID: 28378556 PMCID: PMC5383615 DOI: 10.3346/jkms.2017.32.5.817] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 01/27/2017] [Indexed: 12/11/2022] Open
Abstract
Necrotizing enterocolitis (NEC) characterized by inflammatory intestinal necrosis is a major cause of mortality and morbidity in newborns. Deep RNA sequencing (RNA-Seq) has recently emerged as a powerful technology enabling better quantification of gene expression than microarrays with a lower background signal. A total of 10 transcriptomes from 5 pairs of NEC lesions and adjacent normal tissues obtained from preterm infants with NEC were analyzed. As a result, a total of 65 genes (57 down-regulated and 8 up-regulated) revealed significantly different expression levels in the NEC lesion compared to the adjacent normal region, based on a significance at fold change ≥ 1.5 and P ≤ 0.05. The most significant gene, DPF3 (P < 0.001), has recently been reported to have differential expressions in colon segments. Our gene ontology analysis between NEC lesion and adjacent normal tissues showed that down-regulated genes were included in nervous system development with the most significance (P = 9.3 × 10⁻⁷; P(corr) = 0.0003). In further pathway analysis using Pathway Express based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, genes involved in thyroid cancer and axon guidance were predicted to be associated with different expression (P(corr) = 0.008 and 0.020, respectively). Although further replications using a larger sample size and functional evaluations are needed, our results suggest that altered gene expression and the genes' involved functional pathways and categories may provide insight into NEC development and aid in future research.
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Affiliation(s)
- Kyuwhan Jung
- Department of Surgery, Jeju National University Hospital, Jeju, Korea
| | - Insong Koh
- Department of Physiology, College of Medicine, Hanyang University, Seoul, Korea
| | - Jeong Hyun Kim
- Research Institute for Basic Science, Sogang University, Seoul, Korea
| | - Hyun Sub Cheong
- Department of Genetic Epidemiology, SNP Genetics, Inc., Seoul, Korea
| | - Taejin Park
- Department of Surgery, Gyeongsang National University Hospital, Jinju, Korea
| | - So Hyun Nam
- Department of Surgery, Donga University Hospital, Busan, Korea
| | - Soo Min Jung
- Department of Surgery, Konkuk University Medical Center, Konkuk University School of Medicine, Seoul, Korea
| | - Cherry Ann Sio
- Department of Surgery, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Su Yeong Kim
- Department of Surgery, Donga University Hospital, Busan, Korea
| | - Euiseok Jung
- Department of Neonatology, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Byoungkook Lee
- Department of Neonatology, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Hye Rim Kim
- Department of Neonatology, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Eun Shin
- Department of Pathology, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Sung Eun Jung
- Department of Pediatric Surgery, Seoul National University Children's Hospital, Seoul, Korea
| | - Chang Won Choi
- Department of Neonatology, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Beyong Il Kim
- Department of Neonatology, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Eunyoung Jung
- Department of Surgery, Gyemyoung University Dongsan Hospital, Daegu, Korea
| | - Hyoung Doo Shin
- Research Institute for Basic Science, Sogang University, Seoul, Korea
- Department of Life Science, Sogang University, Seoul, Korea.
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Na HS, Lee JS, Cheong HS, Shin HJ, Kang TS, Park HJ, Shin HD, Chung MW. Expression efficiency of NAT2 haplotypes in a Korean population. Genes Genet Syst 2017; 91:277-281. [PMID: 27853051 DOI: 10.1266/ggs.15-00081] [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: 11/23/2022] Open
Abstract
Since NAT2 single-nucleotide polymorphisms (SNPs) are responsible for the efficacy of arylamines and hydrazine drugs, defining the effects of these SNPs in various ethnicities is an important factor in the development of personalized medicine. In the present study, we examined the expression efficiency of NAT2 using promoter haplotypes identified in a Korean population. To construct NAT2 promoter haplotypes, seven NAT2 promoter SNPs (rs4646241, rs4646242, rs4646243, rs4646267, rs4345600, rs4271002 and rs4646246) were genotyped in a total of 192 Korean subjects. A luciferase assay was performed using the three commonest haplotypes to evaluate enzyme expression level of NAT2 promoter haplotypes. The most common haplotype (TACGAGG) showed the lowest enzyme expression level (0.72 ± 0.06 relative light units (RLU)/[β-galactosidase]). The second (CGTAAGA) and third (TATAACA) commonest haplotypes showed intermediate and the highest enzyme expression level (0.99 ± 0.05 and 1.45 ± 0.11 RLU/[β-galactosidase]), respectively. Haplotype comparison among populations showed that Asian populations had a high proportion of the haplotype for lowest enzyme expression. Haplotype frequencies of Caucasian and African ethnicities were markedly different from those of Korean ethnicity. Results from the present study should contribute to the expansion of our current understanding of the pharmacogenetics field.
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Affiliation(s)
- Han Sung Na
- Clinical Research Division, Toxicological Evaluation and Research Department, National Institute of Food and Drug Safety Evaluation, Osong Health Technology Administration Complex
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25
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Shin JG, Cheong HS, Lee K, Ju BG, Lee JH, Yu SJ, Yoon JH, Cheong JY, Cho SW, Park NH, Namgoong S, Kim LH, Kim YJ, Shin HD. Identification of novel OCT4 genetic variant associated with the risk of chronic hepatitis B in a Korean population. Liver Int 2017; 37:354-361. [PMID: 27596359 DOI: 10.1111/liv.13245] [Citation(s) in RCA: 5] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 08/28/2016] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Hepatitis B viral infection is a serious risk factor for chronic hepatitis B (CHB), cirrhosis and hepatocellular carcinoma. Recently, several genome-wide association studies (GWASs) have been conducted to identify important genetic variant associated with the risk of CHB. In our previous GWAS, TCF19 was identified as one of the susceptibility genes for CHB risk (P=4.2×10-9 at rs1419881). In order to discover possible additional causal variants around TCF19, we performed an association study by genotyping single nucleotide polymorphisms (SNPs) in OCT4, a nearby gene to TCF19. METHODS Nineteen OCT4 genetic variants were selected and genotyped in 3902 subjects (1046 CHB patients and 2856 population controls). RESULTS Logistic regression analysis revealed that OCT4 rs1265163 showed the most significant association signal for the risk of CHB (OR=1.46, P=4.78×10-12 ). Linkage disequilibrium and conditional analysis confirmed rs1265163 in OCT4 as a novel genetic marker for CHB susceptibility. The genetic risk scores (GRSs) were calculated to visualize the combined genetic effects of all known CHB-associated loci, including OCT4 rs1265163, which had been identified in this study. Individuals with higher cumulative GRSs showed significantly increased ORs. The luciferase activity of rs885952, a tagging SNP of rs1265163, showed that OCT4 promoter activity was significantly different between the wild-type and SNP mutant form (P<.05). CONCLUSIONS This follow-up study to our previous GWAS identified a possible causal genetic variant associated with the risk of CHB, and findings from this study may prove useful in the understanding of genetic susceptibility to CHB.
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Affiliation(s)
- Joong-Gon Shin
- Department of Life Science, Sogang University, Seoul, Korea.,Research Institute for Basic Science, Sogang University, Seoul, Korea
| | - Hyun Sub Cheong
- Department of Genetic Epidemiology, SNP Genetics Inc., Sogang University, Seoul, Korea
| | - Kwanghyun Lee
- Department of Life Science, Sogang University, Seoul, Korea
| | - Bong-Gun Ju
- Department of Life Science, Sogang University, Seoul, Korea.,Research Institute for Basic Science, Sogang University, Seoul, Korea
| | - Jeong-Hoon Lee
- Department of Internal Medicine and Liver Research Institute, Seoul National University, Seoul, Korea
| | - Su Jong Yu
- Department of Internal Medicine and Liver Research Institute, Seoul National University, Seoul, Korea
| | - Jung-Hwan Yoon
- Department of Internal Medicine and Liver Research Institute, Seoul National University, Seoul, Korea
| | - Jae Youn Cheong
- Department of Internal Medicine, Seoul National University Boramae Medical Center, Seoul, Korea
| | - Sung Won Cho
- Department of Gastroenterology, Ajou University School of Medicine, Suwon, Korea
| | - Neung Hwa Park
- Department of Internal Medicine, Ulsan University Hospital, Ulsan, Korea
| | - Suhg Namgoong
- Department of Life Science, Sogang University, Seoul, Korea.,Department of Genetic Epidemiology, SNP Genetics Inc., Sogang University, Seoul, Korea
| | - Lyoung Hyo Kim
- Department of Life Science, Sogang University, Seoul, Korea.,Department of Genetic Epidemiology, SNP Genetics Inc., Sogang University, Seoul, Korea
| | - Yoon Jun Kim
- Department of Internal Medicine and Liver Research Institute, Seoul National University, Seoul, Korea
| | - Hyoung Doo Shin
- Department of Life Science, Sogang University, Seoul, Korea.,Research Institute for Basic Science, Sogang University, Seoul, Korea.,Department of Genetic Epidemiology, SNP Genetics Inc., Sogang University, Seoul, Korea
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Lee JU, Cheong HS, Shim EY, Bae DJ, Chang HS, Uh ST, Kim YH, Park JS, Lee B, Shin HD, Park CS. Gene profile of fibroblasts identify relation of CCL8 with idiopathic pulmonary fibrosis. Respir Res 2017; 18:3. [PMID: 28057004 PMCID: PMC5216573 DOI: 10.1186/s12931-016-0493-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 12/13/2016] [Indexed: 01/15/2023] Open
Abstract
Background Idiopathic pulmonary fibrosis (IPF) is characterized by the complex interaction of cells involved in chronic inflammation and fibrosis. Global gene expression of a homogenous cell population will identify novel candidate genes. Methods Gene expression of fibroblasts derived from lung tissues (8 IPF and 4 controls) was profiled, and ontology and functional pathway were analyzed in the genes exhibiting >2 absolute fold changes with p-values < 0.05. CCL8 mRNA and protein levels were quantified using real-time PCR and ELISA. CCL8 localization was evaluated by immunofluorescence staining. Results One hundred seventy eight genes differentially expressed and 15 genes exhibited >10-fold change. Among them, 13 were novel in relation with IPF. CCL8 expression was 22.8-fold higher in IPF fibroblasts. The levels of CCL8 mRNA and protein were 3 and 9-fold higher in 14 IPF fibroblasts than those in 10 control fibroblasts by real-time PCR and ELISA (p = 0.022 and p = 0.026, respectively). The CCL8 concentrations in BAL fluid was significantly higher in 86 patients with IPF than those in 41 controls, and other interstitial lung diseases including non-specific interstitial pneumonia (n = 22), hypersensitivity pneumonitis (n = 20) and sarcoidosis (n = 19) (p < 0.005, respectively). Cut-off values of 2.29 pg/mL and 0.43 pg/mL possessed 80.2 and 70.7% accuracy for the discrimination of IPF from NC and the other lung diseases, respectively. IPF subjects with CCL8 levels >28.61 pg/mL showed shorter survival compared to those with lower levels (p = 0.012). CCL8 was expressed by α-SMA-positive cells in the interstitium of IPF. Conclusions Transcriptome analysis identified several novel IPF-related genes. Among them, CCL8 is a candidate molecule for the differential diagnosis and prediction of survival. Electronic supplementary material The online version of this article (doi:10.1186/s12931-016-0493-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jong-Uk Lee
- Department of Interdisciplinary Program in Biomedical Science Major, Soonchunhyang Graduate School, Bucheon, Korea
| | - Hyun Sub Cheong
- Department of Genetic Epidemiology, SNP Genetics, Inc., Sogang University, Seoul, Korea
| | - Eun-Young Shim
- Department of Interdisciplinary Program in Biomedical Science Major, Soonchunhyang Graduate School, Bucheon, Korea
| | - Da-Jeong Bae
- Department of Interdisciplinary Program in Biomedical Science Major, Soonchunhyang Graduate School, Bucheon, Korea
| | - Hun Soo Chang
- Department of Interdisciplinary Program in Biomedical Science Major, Soonchunhyang Graduate School, Bucheon, Korea.,Division of Allergy and Respiratory Medicine, Department of Internal Medicine, Soonchunhyang, University Bucheon Hospital, Bucheon, Korea
| | - Soo-Taek Uh
- Division of Respiratory and Allergy Medicine, Department of Internal Medicine, Soonchunhyang University Seoul Hospital, 1174, Jung Dong, Wonmi-Gu, Bucheon, Gyeonggi Do, 420-021, Korea
| | - Young Hoon Kim
- Division of Respiratory Medicine, Department of Internal Medicine, Soonchunhyang University, Chunan Hospital, Cheonan, Korea
| | - Jong-Sook Park
- Division of Allergy and Respiratory Medicine, Department of Internal Medicine, Soonchunhyang, University Bucheon Hospital, Bucheon, Korea
| | - Bora Lee
- Department of Biostatistic Consulting, Soon Chun Hyang Medical Center, Bucheon, Korea
| | - Hyoung Doo Shin
- Department of Genetic Epidemiology, SNP Genetics, Inc., Sogang University, Seoul, Korea.,Department of Life Science, Sogang University, Seoul, Korea
| | - Choon-Sik Park
- Department of Interdisciplinary Program in Biomedical Science Major, Soonchunhyang Graduate School, Bucheon, Korea. .,Division of Allergy and Respiratory Medicine, Department of Internal Medicine, Soonchunhyang, University Bucheon Hospital, Bucheon, Korea.
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Kim LH, Chang H, Namgoong S, Kim JO, Cheong HS, Lee SG, Park JS, Baek AR, Koo SM, Choi IS, Kim MK, Park HS, Park CS, Shin HD. Genetic variants of the gasdermin B gene associated with the development of aspirin-exacerbated respiratory diseases. Allergy Asthma Proc 2017; 38:4-12. [PMID: 28052796 DOI: 10.2500/aap.2017.38.4014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
BACKGROUND Aspirin-exacerbated respiratory disease (AERD) is characterized by a severe and sudden asthma attack after aspirin ingestion in patients with asthma. We studied associations with six common single nucleotide polymorphisms (SNP) of the gasdermin B gene (GSDMB). OBJECTIVE DNA obtained from 572 patients with asthma (with AERD, n = 165; and with aspirin-tolerant asthma, n = 407) and 391 normal controls was subjected to genotyping of six SNPs of GSDMB. METHODS An association analysis between GSDMB variants and AERD, with a fall rate of the forced expiratory volume in the first second of expiration (FEV1), was performed by using logistic and regression models. RESULTS Two SNPs in the intron (rs870830, rs7216389) showed significant associations with AERD (minimum p = 7.00 × 10-4 in the dominant model), even after Bonferroni correction (pcorr = 0.01 for the rs870830). Regression analysis of the genetic variants with FEV1 revealed significant associations with rs870830 and the haplotype 2 (pcorr = 4.71 × 10-4 for rs870830 and pcorr = 1.14 × 10-3 for haplotype 2, respectively). CONCLUSION We found strong associations among GSDMB polymorphisms and the presence of AERD and FEV1 in Korean patients with asthma. Our findings indicated that genetic variations of GSDMB may be associated with the development of AERD and aspirin-induced bronchospasm.
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Lee JS, Cheong HS, Koh Y, Ahn KS, Shin HD, Yoon SS. MCM7 polymorphisms associated with the AML relapse and overall survival. Ann Hematol 2016; 96:93-98. [PMID: 27837251 DOI: 10.1007/s00277-016-2844-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 09/25/2016] [Indexed: 11/30/2022]
Abstract
The minichromosome maintenance complex component 7 (MCM7) encodes a member of MCM complex, which plays a critical role in the initiation of gene replication. Due to the importance of MCM complex, MCM7 gene has been regarded as a candidate gene for cancer development. In the present study, seven MCM7 polymorphisms were genotyped in 344 subjects composed of 103 acute myeloid leukemia (AML) patients and 241 normal controls to examine the possible associations between MCM7 polymorphisms and the risk of AML. MCM7 polymorphisms were not associated with the risk of AML (P > 0.05). However, MCM7 polymorphisms were significantly related to the relapse of AML and overall survival. The rs2070215 (N144S) showed a protective effect to the risk of AML relapse (OR = 0.37; P corr = 0.02). In haplotype analyses, the ht1 and ht2 showed significant associations with the risk of AML relapse (P corr = 0.02-0.03). In addition, rs1534309 showed an association with the overall survival of AML patients. Patients with major homozygote genotype (CC) of rs1534309 showed a higher survival rate than the patients with other genotypes (CG and GG). The results of the present study indicate that MCM7 polymorphisms may be able to predict the prognosis of AML patients.
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MESH Headings
- Adolescent
- Adult
- Aged
- Female
- Humans
- Leukemia, Myeloid, Acute/diagnosis
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/mortality
- Male
- Middle Aged
- Minichromosome Maintenance Complex Component 7/genetics
- Neoplasm Recurrence, Local/diagnosis
- Neoplasm Recurrence, Local/genetics
- Neoplasm Recurrence, Local/mortality
- Polymorphism, Single Nucleotide/genetics
- Survival Rate/trends
- Young Adult
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Affiliation(s)
- Jin Sol Lee
- Research Institute for Basic Science, Sogang University, Seoul, 121-742, Republic of Korea
- Department of Life Science, Sogang University, Seoul, 121-742, Republic of Korea
| | - Hyun Sub Cheong
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, South Korea
- Department of Genetic Epidemiology, SNP Genetics Inc., Seoul, South Korea
| | - Youngil Koh
- Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, 101 Daehang-ro, Jongno-gu, Seoul, 110-744, South Korea
| | - Kwang-Sung Ahn
- Functional Genome Institute, PDXen Biosystem Inc., Seoul, South Korea
| | - Hyoung Doo Shin
- Department of Life Science, Sogang University, Seoul, 121-742, Republic of Korea
- Department of Genetic Epidemiology, SNP Genetics Inc., Seoul, South Korea
| | - Sung-Soo Yoon
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, South Korea.
- Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, 101 Daehang-ro, Jongno-gu, Seoul, 110-744, South Korea.
- Clinical Research Institute, Seoul National University Hospital, Seoul, South Korea.
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Bae JS, Koh I, Cheong HS, Seo JM, Kim DY, Oh JT, Kim HY, Jung K, Sul JH, Park WY, Kim JH, Shin HD. A genome-wide association analysis of chromosomal aberrations and Hirschsprung disease. Transl Res 2016; 177:31-40.e6. [PMID: 27370899 DOI: 10.1016/j.trsl.2016.06.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [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] [Received: 12/10/2015] [Revised: 05/12/2016] [Accepted: 06/06/2016] [Indexed: 12/12/2022]
Abstract
Hirschsprung disease (HSCR) is a neurocristopathy characterized by the absence of intramural ganglion cells along variable lengths of the gastrointestinal tract. Although the RET proto-oncogene is considered to be the main risk factor for HSCR, only about 30% of the HSCR cases can be explained by variations in previously known genes including RET. Recently, copy number variation (CNV) and loss of heterozygosity (LOH) have emerged as new ways to understand human genomic variation. The goal of this present study is to identify new HSCR genetic factors related to CNV in Korean patients. In the genome-wide genotyping, using Illumina's HumanOmni1-Quad BeadChip (1,140,419 markers), of 123 HSCR patients and 432 unaffected subjects (total n = 555), a total of 8,188 CNVs (1 kb ∼ 1 mb) were identified by CNVpartition. As a result, 16 CNV regions and 13 LOH regions were identified as associated with HSCR (minimum P = 0.0005). Two top CNV regions (deletions at chr6:32675155-32680480 and chr22:20733495-21607293) were successfully validated by additional real-time quantitative polymerase chain reaction analysis. In addition, 2 CNV regions (6p21.32 and 22q11.21) and 2 LOH regions (3p22.2 and 14q23.3) were discovered to be unique to the HSCR patients group. Regarding the large-scale chromosomal aberrations (>1 mb), 11 large aberrations in the HSCR patients group were identified, which suggests that they may be a risk factor for HSCR. Although further replication in a larger cohort is needed, our findings may contribute to the understanding of the etiology of HSCR.
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Affiliation(s)
- Joon Seol Bae
- Laboratory of Translational Genomics, Samsung Genome Institute, Samsung Medical Center, Seoul, Republic of Korea
| | - InSong Koh
- Department of Physiology, College of Medicine, Hanyang University, Seoul, Republic of Korea
| | - Hyun Sub Cheong
- Department of Genetic Epidemiology, SNP Genetics, Inc., Seoul, Republic of Korea
| | - Jeong-Meen Seo
- Division of Pediatric Surgery, Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Dae-Yeon Kim
- Department of Pediatric Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Jung-Tak Oh
- Department of Pediatric Surgery, Severance Children's Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Hyun-Young Kim
- Department of Pediatric Surgery, Seoul National University Children's Hospital, Seoul, Republic of Korea
| | - Kyuwhan Jung
- Department of Surgery, Jeju National University Hospital, Aran 13gil 15, Jeju, Republic of Korea
| | - Jae Hoon Sul
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, Calif, USA; Semel Center for Informatics and Personalized Genomics, University of California, Los Angeles, Calif, USA
| | - Woong-Yang Park
- Laboratory of Translational Genomics, Samsung Genome Institute, Samsung Medical Center, Seoul, Republic of Korea
| | - Jeong-Hyun Kim
- Research Institute for Basic Science, Sogang University, Seoul, Republic of Korea.
| | - Hyoung Doo Shin
- Research Institute for Basic Science, Sogang University, Seoul, Republic of Korea; Department of Life Science, Sogang University, Seoul, Republic of Korea.
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Lee MK, Cheong HS, Koh Y, Ahn KS, Yoon SS, Shin HD. Genetic Association of PARP15 Polymorphisms with Clinical Outcome of Acute Myeloid Leukemia in a Korean Population. Genet Test Mol Biomarkers 2016; 20:696-701. [PMID: 27610459 DOI: 10.1089/gtmb.2016.0007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [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: 01/09/2023] Open
Abstract
AIMS Some members of the poly ADP-ribose polymerase (PARP) protein family have been regarded as targets for the therapeutic inhibition of cancer. Among these PARP genes, poly ADP-ribose polymerase family, member 15 (PARP15) is a candidate gene for cancer development due to its ability to regulate gene transcription and its reported association with apoptosis. The current study investigated the possible association between PARP15 single-nucleotide polymorphisms and the risk of acute myeloid leukemia (AML). In addition, we analyzed the effects of the PARP15 polymorphisms on the clinical phenotypes associated with cytosine arabinose (AraC) chemotherapy in AML patients. METHODS Ten PARP15 polymorphisms were genotyped via TaqMan assay in a total of 344 Korean subjects, including 103 AML patients and 241 normal controls. The genetic effects of the polymorphisms on the risk of AML and the clinical phenotypes were analyzed using Statistical Analysis System (SAS) software. RESULTS The results from a Cox regression analysis for overall survival revealed that two polymorphisms were associated with increased overall survival and the signal for rs17208928 was retained after correcting for multiple tests (pcorr < 0.05). CONCLUSIONS These results suggest the possibility that the PARP15 gene may be a potential therapeutic target in AML patients although much larger scale studies are needed for validation.
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Affiliation(s)
- Min Kyung Lee
- 1 Department of Life Science, Sogang University , Seoul, Republic of Korea
| | - Hyun Sub Cheong
- 2 Cancer Research Institute, Seoul National University Hospital , Seoul, Republic of Korea.,3 Department of Genetic Epidemiology, SNP Genetics, Inc. , Seoul, Republic of Korea
| | - Youngil Koh
- 4 Department of Internal Medicine, Seoul National University College of Medicine , Seoul, Republic of Korea
| | - Kwang-Sung Ahn
- 5 Functional Genome Institute , PDXen Biosystem, Inc., Seoul, Republic of Korea
| | - Sung-Soo Yoon
- 2 Cancer Research Institute, Seoul National University Hospital , Seoul, Republic of Korea.,4 Department of Internal Medicine, Seoul National University College of Medicine , Seoul, Republic of Korea.,6 Clinical Research Institute, Seoul National University Hospital , Seoul, Republic of Korea
| | - Hyoung Doo Shin
- 1 Department of Life Science, Sogang University , Seoul, Republic of Korea.,3 Department of Genetic Epidemiology, SNP Genetics, Inc. , Seoul, Republic of Korea
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Kim JH, Lee C, Cheong HS, Koh Y, Ahn KS, Kim HL, Shin HD, Yoon SS. SLC29A1 (ENT1) polymorphisms and outcome of complete remission in acute myeloid leukemia. Cancer Chemother Pharmacol 2016; 78:533-40. [DOI: 10.1007/s00280-016-3103-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 07/06/2016] [Indexed: 02/08/2023]
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32
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Kim LH, Park BL, Cheong HS, Namgoong S, Kim JO, Kim JH, Shin JG, Park CS, Kim BJ, Kim JW, Choi IG, Hwang J, Shin HD, Woo SI. Genome-wide association study with the risk of schizophrenia in a Korean population. Am J Med Genet B Neuropsychiatr Genet 2016; 171B:257-65. [PMID: 26531332 DOI: 10.1002/ajmg.b.32400] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 10/23/2015] [Indexed: 11/10/2022]
Abstract
Schizophrenia is regarded as a multifactorial and polygenic brain disorder that is attributed to different combinations of genetic and environmental risk factors. Recently, several genome-wide association studies (GWASs) of schizophrenia have identified numerous risk factors, but the replication results remain controversial and ambiguous. To identify schizophrenia susceptibility loci in the Korean population, we performed a GWAS using the Illumina HumanOmni1-Quad V1.0 Microarray. We genotyped 1,140,419 single nucleotide polymorphisms (SNPs) in 350 Korea schizophrenia patients and 700 control subjects, and approximately 620,001 autosomal SNPs were passed our quality control. In the case-control analysis, the rs9607195 A>G on intergenic area 250 kb away from the ISX gene and the rs12738007 A>G on the intron of the MECR gene were the most strongly associated SNPs with the risk of schizophrenia (P = 6.2 × 10(-8) , OR = 0.50 and P = 3.7 × 10(-7) , OR = 2.39, respectively). In subsequent fine-mapping analysis, 6 SNPs of MECR were genotyped with 310 schizophrenia patients and 604 control subjects. The association of the MECR rs12738007, a top ranked-SNP in GWAS, was replicated (P = 1.5 × 10(-2) , OR = 1.53 in fine mapping analysis, P = 1.5 × 10(-6) , OR = 1.90 in combined analysis). The identification of putative schizophrenia susceptibility loci could provide new insights into genetic factors related with schizophrenia and clues for the development of diagnosis strategies.
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Affiliation(s)
- Lyoung Hyo Kim
- Department of Genetic Epidemiology, SNP Genetics, Inc., Mapo-gu, Seoul, Republic of Korea.,Department of Life Science, Sogang University, Mapo-gu, Seoul, Republic of Korea
| | - Byung Lae Park
- Department of Genetic Epidemiology, SNP Genetics, Inc., Mapo-gu, Seoul, Republic of Korea
| | - Hyun Sub Cheong
- Department of Genetic Epidemiology, SNP Genetics, Inc., Mapo-gu, Seoul, Republic of Korea
| | - Suhg Namgoong
- Department of Genetic Epidemiology, SNP Genetics, Inc., Mapo-gu, Seoul, Republic of Korea.,Department of Life Science, Sogang University, Mapo-gu, Seoul, Republic of Korea
| | - Ji On Kim
- Department of Genetic Epidemiology, SNP Genetics, Inc., Mapo-gu, Seoul, Republic of Korea
| | - Jeong-Hyun Kim
- Department of Life Science, Sogang University, Mapo-gu, Seoul, Republic of Korea
| | - Joong-Gon Shin
- Department of Life Science, Sogang University, Mapo-gu, Seoul, Republic of Korea
| | - Chul Soo Park
- Department of Psychiatry, College of Medicine, Gyeongsang National University, Gyeongsang Nam Do, Republic of Korea
| | - Bong-Jo Kim
- Department of Psychiatry, College of Medicine, Gyeongsang National University, Gyeongsang Nam Do, Republic of Korea
| | - Jae Won Kim
- Division of Life Science, Research Institute of Life Science, Gyeongsang National University, Jinju-ro, Gyeongsang Nam Do, Republic of Korea
| | - Ihn-Geun Choi
- Department of Neuropsychiatry, Hallym University, Han-Gang Sacred Heart Hospital, Yeongdeungpo-gu, Seoul, Republic of Korea
| | - Jaeuk Hwang
- Department of Neuropsychiatry, Soonchunhyang University Hospital, Yongsan-gu, Seoul, Republic of Korea
| | - Hyoung Doo Shin
- Department of Genetic Epidemiology, SNP Genetics, Inc., Mapo-gu, Seoul, Republic of Korea.,Department of Life Science, Sogang University, Mapo-gu, Seoul, Republic of Korea
| | - Sung-Il Woo
- Department of Neuropsychiatry, Soonchunhyang University Hospital, Yongsan-gu, Seoul, Republic of Korea
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Namgoong S, Cheong HS, Kim JO, Kim LH, Na HS, Koh IS, Chung MW, Shin HD. Comparison of genetic variations of the SLCO1B1, SLCO1B3, and SLCO2B1 genes among five ethnic groups. Environ Toxicol Pharmacol 2015; 40:692-697. [PMID: 26409184 DOI: 10.1016/j.etap.2015.08.033] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 08/30/2015] [Accepted: 08/31/2015] [Indexed: 06/05/2023]
Abstract
Organic anion-transporting polypeptide (OATP; gene symbol, SLCO) transporters are generally involved in the uptake of multiple drugs and their metabolites at most epithelial barriers. The pattern of single-nucleotide polymorphisms (SNPs) in these transporters may be determinants of interindividual variability in drug disposition and response. The objective of this study was to define the distribution of SNPs of three SLCO genes, SLCO1B1, SLCO1B3, and SLCO2B1, in a Korean population and other ethnic groups. The study was screened using the Illumina GoldenGate assay for genomic DNA from 450 interethnic subjects, including 11 pharmacogenetic core variants and 76 HapMap tagging SNPs. The genotype distribution of the Korean population was similar to East Asian populations, but significantly different from African American and European American cohorts. These interethnic differences will be useful information for prospective studies, including genetic association and pharmacogenetic studies of drug metabolism by SLCO families.
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Affiliation(s)
- Suhg Namgoong
- Department of Life Science, Sogang University, Seoul, Republic of Korea; Research Institute for Basic Science, Sogang University, Seoul, Republic of Korea
| | - Hyun Sub Cheong
- Research Institute for Basic Science, Sogang University, Seoul, Republic of Korea
| | - Ji On Kim
- Department of Life Science, Sogang University, Seoul, Republic of Korea; Research Institute for Basic Science, Sogang University, Seoul, Republic of Korea
| | - Lyoung Hyo Kim
- Department of Life Science, Sogang University, Seoul, Republic of Korea; Research Institute for Basic Science, Sogang University, Seoul, Republic of Korea
| | - Han Sung Na
- Clinical Research Division, Toxicological Evaluation and Research Department, National Institute of Food and Drug Safety Evaluation, Osong Health Technology Administration Complex, Osong, Chungcheongbuk-do, Republic of Korea
| | - In Song Koh
- Department of Physiology, College of Medicine, Hanyang University, Seoul, Republic of Korea
| | - Myeon Woo Chung
- Clinical Research Division, Toxicological Evaluation and Research Department, National Institute of Food and Drug Safety Evaluation, Osong Health Technology Administration Complex, Osong, Chungcheongbuk-do, Republic of Korea.
| | - Hyoung Doo Shin
- Department of Life Science, Sogang University, Seoul, Republic of Korea; Research Institute for Basic Science, Sogang University, Seoul, Republic of Korea.
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Kim LH, Cheong HS, Shin JG, Seo JM, Kim DY, Oh JT, Kim HY, Jung K, Koh I, Kim JH, Shin HD. Genetic variants of IL-11 associated with risk of Hirschsprung disease. Neurogastroenterol Motil 2015; 27:1371-7. [PMID: 26172388 DOI: 10.1111/nmo.12629] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [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: 01/16/2015] [Accepted: 06/15/2015] [Indexed: 02/08/2023]
Abstract
BACKGROUND Hirschsprung disease (HSCR) is a congenital and heterogeneous disorder characterized by the absence of enteric ganglia during enteric nervous system (ENS) development. Our recent genome-wide association study has identified a variant (rs6509940) of interleukin-11 (IL-11) as a potential susceptible locus for HSCR. As interleukins play important roles in the ENS, we further studied associations with HSCR of nine common single nucleotide polymorphisms (SNPs) on IL-11. METHODS Biopsy specimens or surgical materials from all patients that were tested for histological examination based on the absence of the enteric ganglia were collected. A total of nine SNPs on IL-11 were genotyped in 187 HSCR patients and 283 unaffected controls using TaqMan genotyping assay. KEY RESULTS Combined analysis revealed that several SNPs (minimum p = 1.57 × 10(-7) ) showed statistically significant associations with HSCR, even after Bonferroni correction (pcorr = 1.73 × 10(-6) for the SNP). Moreover, the most common haplotype was strongly associated with HSCR (pcorr = 2.20 × 10(-6) ). In further analysis among three HSCR subtypes (short segment, S-HSCR; long segment, L-HSCR; total colonic aganglionosis, TCA) based on the extent of aganglionic segment, the result showed a different association pattern depending on the subtypes (minimum pcorr = 6.12 × 10(-5) for rs6509940 in S-HSCR; but no significant SNP in L-HSCR and TCA). CONCLUSIONS & INFERENCES Although further replication in a larger cohort and functional evaluations are needed, our findings suggest that genetic variations of IL-11 may be associated with the risk of HSCR and/or the mechanisms related to ENS development.
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Affiliation(s)
- L H Kim
- Department of Life Science, Sogang University, Seoul, Korea
| | - H S Cheong
- Department of Genetic Epidemiology, SNP Genetics, Inc., Seoul, Korea
| | - J-G Shin
- Department of Life Science, Sogang University, Seoul, Korea
| | - J-M Seo
- Division of Pediatric Surgery, Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - D-Y Kim
- Department of Pediatric Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - J-T Oh
- Department of Pediatric Surgery, Severance Children's Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - H-Y Kim
- Department of Pediatric Surgery, Seoul National University Children's Hospital, Seoul, Korea
| | - K Jung
- Department of Surgery, Seoul National University Bundang Hospital, Seongnam, Gyeonggi, Korea
| | - I Koh
- Department of Physiology, College of Medicine, Hanyang University, Seoul, Korea
| | - J-H Kim
- Research Institute for Basic Science, Sogang University, Seoul, Korea
| | - H D Shin
- Department of Life Science, Sogang University, Seoul, Korea.,Research Institute for Basic Science, Sogang University, Seoul, Korea
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35
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Jung K, Kim JH, Cheong HS, Shin E, Kim SH, Hwang JY, Lee E, Yoon MO, Kim SH, Sio CA, Shin HD, Jung SE. Gene expression profile of necrotizing enterocolitis model in neonatal mice. Int J Surg 2015; 23:28-34. [PMID: 26403067 DOI: 10.1016/j.ijsu.2015.09.049] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 09/11/2015] [Accepted: 09/14/2015] [Indexed: 12/17/2022]
Abstract
BACKGROUND Necrotizing enterocolitis (NEC) characterized by intestinal necrosis is one of the most common gastrointestinal emergencies in newborns. The main purpose of this study was to evaluate the whole genome expression levels in a NEC mouse model controlled with breast milk. METHODS This study induced a NEC model in mice of gestational ages of 18-21 days by intensive hypoxic insult and permitted breast-feeding instead of formula feeding. After evaluating the NEC status in the small intestines of neonatal mice by histological examination, a genome-wide gene expression profile study was completed using microarray analysis. RESULTS A total of 72 genes (38 down-regulated and 34 up-regulated) were observed to have significantly different expression profiles in the NEC mouse model compared with the normal control animals, based on a significance at fold change ≥ 2 and P < 0.05. In particular, down-regulated Hist1h2aa and up-regulated Ube2i showed the most significant signals (P = 0.0008 for both genes). In an additional gene ontology analysis, the endopeptidase related categories (specifically, serine-type endopeptidase inhibitor activity, P = 8.95 × 10(-5); Pcorr = 0.008) appeared to affect NEC development in the mouse model. CONCLUSION Although replications and functional evaluations are needed, our results suggest that several genes may have different expression profiles in the NEC mouse model. In particular, endopeptidase related genes (which are also known to be relevant to NEC), as identified through gene ontology analysis, may represent attractive targets for future research.
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Affiliation(s)
- Kyuwhan Jung
- Department of Surgery, Seoul National University Bundang Hospital, Seongnam, Gyeonggi, 463-707, Republic of Korea
| | - Jeong-Hyun Kim
- Research Institute for Basic Science, Sogang University, Seoul, 121-742, Republic of Korea
| | - Hyun Sub Cheong
- Department of Genetic Epidemiology, SNP Genetics, Inc., Seoul 153-803, Republic of Korea
| | - Eun Shin
- Department of Pathology, Seoul National University Bundang Hospital, Seongnam, Gyeonggi, 463-707, Republic of Korea
| | - Seong-Ho Kim
- Department of Surgery, Seoul National University Bundang Hospital, Seongnam, Gyeonggi, 463-707, Republic of Korea
| | - Ji-Yeon Hwang
- Preclinical Experimental Center, Seoul National University Bundang Hospital, Seongnam, Gyeonggi, 463-707, Republic of Korea
| | - Eunyoung Lee
- Department of Surgery, Seoul National University Bundang Hospital, Seongnam, Gyeonggi, 463-707, Republic of Korea
| | - Mi-Ok Yoon
- Department of Surgery, Seoul National University Bundang Hospital, Seongnam, Gyeonggi, 463-707, Republic of Korea
| | - Seong-Hee Kim
- Department of Surgery, Seoul National University Bundang Hospital, Seongnam, Gyeonggi, 463-707, Republic of Korea
| | - Cherry Ann Sio
- Department of Surgery, Seoul National University Bundang Hospital, Seongnam, Gyeonggi, 463-707, Republic of Korea
| | - Hyoung Doo Shin
- Research Institute for Basic Science, Sogang University, Seoul, 121-742, Republic of Korea; Department of Life Science, Sogang University, Seoul 121-742, Republic of Korea.
| | - Sung-Eun Jung
- Department of Surgery, Seoul National University Children's Hospital, Seoul 110-773, Republic of Korea.
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Hyo Kim L, Sub Cheong H, Koh Y, Ahn KS, Lee C, Kim HL, Doo Shin H, Yoon SS. Cytidine deaminase polymorphisms and worse treatment response in normal karyotype AML. J Hum Genet 2015; 60:749-54. [PMID: 26354033 DOI: 10.1038/jhg.2015.105] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 07/20/2015] [Accepted: 07/30/2015] [Indexed: 11/09/2022]
Abstract
The cytidine deaminase (CDA) catalyzes the irreversible hydrolytic deamination of the cytarabine (AraC) into a 1-β-D-arabinofuranosyluracil (AraU), an inactive metabolite that plays a crucial role in lowering the amount of AraC, a key chemotherapeutic drug, in the treatment of patients with acute myeloid leukemia (AML). In this study, we hypothesized that CDA polymorphisms were associated with the AraC metabolism for AML treatment and/or related clinical phenotypes. We analyzed 16 polymorphisms of CDA among 50 normal karyotype AML (NK-AML) patients, 45 abnormal karyotype AML (AK-AML) patients and 241 normal controls (NC). Several polymorphisms and haplotypes, rs532545, rs2072671, rs471760, rs4655226, rs818194 and CDA-ht3, were found to have a strong correlation with NK-AML compared with NC and these polymorphisms also revealed strong linkage disequilibrium with each other. Among them, rs2072671 (79A>C), which is located in a coding region and the resultant amino acid change K27Q, showed significant associations with NK-AML compared with NC (P=0.009 and odds ratio=2.44 in the dominant model). The AC and CC genotypes of rs2072671 (79A>C) were significantly correlated with shorter overall survival rates (P=0.03, hazard ratio=1.84) and first complete remission duration (P=0.007, hazard ratio=3.24) compared with the AA genotype in the NK-AML patients. Our results indicate that rs2072671 in CDA may be an important prognostic marker in NK-AML patients.
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Affiliation(s)
- Lyoung Hyo Kim
- Department of Life Science, Sogang University, Seoul, Republic of Korea.,Department of Genetic Epidemiology, SNP Genetics, Seoul, Republic of Korea
| | - Hyun Sub Cheong
- Department of Genetic Epidemiology, SNP Genetics, Seoul, Republic of Korea.,Cancer Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
| | - Youngil Koh
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Kwang-Sung Ahn
- Functional Genome Institute, PDXen Biosystem, Seoul, Republic of Korea
| | - Chansu Lee
- Cancer Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
| | - Hyung-Lae Kim
- Department of Biochemistry, School of Medicine, Ewha Womans University, Seoul, Republic of Korea
| | - Hyoung Doo Shin
- Department of Life Science, Sogang University, Seoul, Republic of Korea.,Department of Genetic Epidemiology, SNP Genetics, Seoul, Republic of Korea
| | - Sung-Soo Yoon
- Cancer Research Institute, Seoul National University Hospital, Seoul, Republic of Korea.,Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea.,Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
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Cheong HS, Lee JH, Yu SJ, Yoon JH, Lee HS, Cheong JY, Cho SW, Park NH, Park BL, Namgoong S, Kim LH, Shin HD, Kim YJ. Association of VARS2-SFTA2 polymorphisms with the risk of chronic hepatitis B in a Korean population. Liver Int 2015; 35:1934-40. [PMID: 25404243 DOI: 10.1111/liv.12740] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [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: 07/17/2014] [Accepted: 11/13/2014] [Indexed: 12/12/2022]
Abstract
BACKGROUND & AIMS Hepatitis B virus (HBV) infection is the most serious risk factor for chronic hepatitis B (CHB), cirrhosis, and hepatocellular carcinoma. Recently, several genome-wide association studies (GWASs) identified important variants associated with the risk of CHB in Asian populations. Specifically, our previous GWAS identified the VARS2-SFTA2 gene region as one of the genetic risk loci for CHB. METHODS To further characterize this association and to isolate possible causal variants within it, we performed an additional association study by genotyping more SNPs in the vicinity of the VARS2 and SFTA2 genes. In all, 14 SNPs of VARS2-SFTA2 were analysed among a total of 3902 subjects (1046 cases and 2856 controls). RESULTS Logistic regression analysis revealed that six SNPs, including the previously reported rs2532932, were significantly associated with the risk of CHB (P = 1.7 × 10(-10) ~0.002). Further linkage disequilibrium and conditional analysis identified two variants (rs9394021 and rs2517459) as new markers of genetic risk factors for CHB rather than the reported SNP from our previous study (rs2532932). To evaluate the cumulative risk for CHB based on all known genetic factors, genetic risk score (GRS) were calculated. As anticipated, the distribution of the number of risk alleles in cases vs. controls clearly differed according to the GRS. Similarly, the odds ratios (ORs) were increased (OR = 0.32-3.97). CONCLUSION Our findings show that common variants in the VARS2-SFTA2 gene region are significantly associated with CHB in a Korean population, which may be useful in further understanding genetic susceptibility to CHB.
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Affiliation(s)
- Hyun Sub Cheong
- Department of Genetic Epidemiology, SNP Genetics Inc., Sogang University, Seoul, Korea
| | - Jeong-Hoon Lee
- Department of Internal Medicine and Liver Research Institute, Seoul National University, Seoul, Korea
| | - Su Jong Yu
- Department of Internal Medicine and Liver Research Institute, Seoul National University, Seoul, Korea
| | - Jung-Hwan Yoon
- Department of Internal Medicine and Liver Research Institute, Seoul National University, Seoul, Korea
| | - Hyo-Suk Lee
- Department of Internal Medicine and Liver Research Institute, Seoul National University, Seoul, Korea
| | - Jae Youn Cheong
- Department of Gastroenterology, Ajou University School of Medicine, Suwon, Korea
| | - Sung Won Cho
- Department of Gastroenterology, Ajou University School of Medicine, Suwon, Korea
| | - Neung Hwa Park
- Department of Internal Medicine, Ulsan University Hospital, Ulsan, Korea
| | - Byung Lae Park
- Department of Genetic Epidemiology, SNP Genetics Inc., Sogang University, Seoul, Korea
| | - Suhg Namgoong
- Department of Genetic Epidemiology, SNP Genetics Inc., Sogang University, Seoul, Korea.,Department of Life Science, Sogang University, Seoul, Korea
| | - Lyoung Hyo Kim
- Department of Genetic Epidemiology, SNP Genetics Inc., Sogang University, Seoul, Korea.,Department of Life Science, Sogang University, Seoul, Korea
| | - Hyoung Doo Shin
- Department of Genetic Epidemiology, SNP Genetics Inc., Sogang University, Seoul, Korea.,Department of Life Science, Sogang University, Seoul, Korea
| | - Yoon-Jun Kim
- Department of Internal Medicine and Liver Research Institute, Seoul National University, Seoul, Korea
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Bae JS, Park BL, Cheong HS, Kim JH, Kim JY, Namgoong S, Kim JO, Park CS, Kim BJ, Lee CS, Kim JW, Choi WH, Shin TM, Hwang J, Koh IS, Shin HD, Woo SI. Association analysis of PDE4B polymorphisms with schizophrenia and smooth pursuit eye movement abnormality in a Korean population. Gen Physiol Biophys 2015; 34:277-84. [PMID: 25926551 DOI: 10.4149/gpb_2015004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 02/06/2015] [Indexed: 11/08/2022]
Abstract
Schizophrenia is a debilitating mental disorder with a high heritability rate. Located on chromosome 1p31.3, the human cAMP-specific 3',5'-cyclic phosphodiesterase 4B (PDE4B) gene has been considered as an important candidate gene for the risk of schizophrenia. Several genetic association studies reported the association between PDE4B polymorphisms and the risk of schizophrenia in Caucasian, African American, Indian, and Japanese populations. The aim of this study is to examine the association of PDE4B variations with schizophrenia and smooth pursuit eye movement (SPEM) abnormality in a Korean population. A case-control association analysis was carried out by comparing the genotype distribution of eight PDE4B polymorphisms between 457 schizophrenia patients and 386 normal healthy subjects. Differences in the frequency distribution of PDE4B single nucleotide polymorphisms (SNPs) and haplotypes were analyzed by logistic regression analyses controlling for age as a covariate. Statistical analyses revealed nominal significant associations of rs1040716, rs472952, rs1321177, and rs2144719 with the risk of schizophrenia (p = 0.02~0.05). The rs11208756 polymorphism showed a nominal significant association with SPEM abnormality (p = 0.05). In a meta-analysis with Japanese and Korean populations, three SNPs (rs472952, rs1040716, and rs2180335) revealed significant associations with schizophrenia (meta-p value = 0.0038~0.019). Our results support previously reported association of PDE4B variations with schizophrenia in other populations. The findings in this study add a new evidence for the involvement of PDE4B gene in schizophrenia etiology.
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Affiliation(s)
- Joon Seol Bae
- Laboratory of Translational Genomics, Samsung Genome Institute, Samsung Medical Center, Seoul 135-710, Republic of Korea
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39
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Kim LH, Cheong HS, Namgoong S, Kim JO, Kim JH, Park BL, Cho SW, Park NH, Cheong JY, Koh I, Shin HD, Kim YJ. Replication of genome wide association studies on hepatocellular carcinoma susceptibility loci of STAT4 and HLA-DQ in a Korean population. Infect Genet Evol 2015; 33:72-6. [PMID: 25913043 DOI: 10.1016/j.meegid.2015.04.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 04/03/2015] [Accepted: 04/15/2015] [Indexed: 12/14/2022]
Abstract
A recent genome-wide association study (GWAS) for hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC) identified two loci (rs7574865 in STAT4 and rs9275319 in HLA-DQ) in a Chinese population. We attempted to replicate the associations between the two SNP loci and the risk of HCC in a Korean population. The rs7574865 in STAT4 and rs9275319 in HLA-DQ were genotyped in a total of 3838 Korean subjects composed of 287 HBV-related hepatocellular carcinoma patients, 671 chronic hepatitis B virus (CHB) patients, and 2880 population controls using TaqMan genotyping assay. Gene expression was measured by microarray. A logistic regression analysis revealed that rs7574865 in STAT4 and rs9275319 in HLA-DQ were associated with the risk of CHB (OR = 1.25, P = 0.0002 and OR = 1.57, P= 1.44 × 10(-10), respectively). However, these loci were no association with the risk of HBV-related HCC among CHB patients. In the gene expression analyses, although no significant differences in mRNA expression of nearby genes according to genotypes were detected, a significantly decreased mRNA expression in HCC subjects was observed in STAT4, HLA-DQA1, and HLA-DQB1. Although the genetic effects of two HCC susceptibility loci were not replicated, the two loci were found to exert susceptibility effects on the risk of CHB in a Korean population. In addition, the decreased mRNA expression of STAT4, HLA-DQA1, and HLA-DQB1 in HCC tissue might provide a clue to understanding their role in the progression to HCC.
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Affiliation(s)
- Lyoung Hyo Kim
- Department of Life Science, Sogang University, Republic of Korea; Department of Genetic Epidemiology, SNP Genetics, Inc., Republic of Korea
| | - Hyun Sub Cheong
- Department of Genetic Epidemiology, SNP Genetics, Inc., Republic of Korea
| | - Suhg Namgoong
- Department of Life Science, Sogang University, Republic of Korea; Department of Genetic Epidemiology, SNP Genetics, Inc., Republic of Korea
| | - Ji On Kim
- Department of Genetic Epidemiology, SNP Genetics, Inc., Republic of Korea
| | - Jeong-Hyun Kim
- Department of Life Science, Sogang University, Republic of Korea
| | - Byung Lae Park
- Department of Genetic Epidemiology, SNP Genetics, Inc., Republic of Korea
| | - Sung Won Cho
- Department of Gastroenterology, Ajou University School of Medicine, Republic of Korea
| | - Neung Hwa Park
- Department of Internal Medicine, Ulsan University Hospital, Republic of Korea
| | - Jae Youn Cheong
- Department of Gastroenterology, Ajou University School of Medicine, Republic of Korea
| | - InSong Koh
- Department of Physiology, College of Medicine, Han Yang University, Republic of Korea
| | - Hyoung Doo Shin
- Department of Life Science, Sogang University, Republic of Korea; Department of Genetic Epidemiology, SNP Genetics, Inc., Republic of Korea.
| | - Yoon-Jun Kim
- Department of Internal Medicine and Liver Research Institute, Seoul National University, Republic of Korea.
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Kim JH, Cheong HS, Kim LH, Shin HJ, Na HS, Chung MW, Shin HD. Direct sequencing for comprehensive screening of LDLR genetic polymorphisms among five ethnic populations. Genes Genomics 2015. [DOI: 10.1007/s13258-014-0244-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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41
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Choi SY, Kim HJ, Cheong HS, Myung SC. The association of 5-alpha reductase type 2 (SRD5A2) gene polymorphisms with prostate cancer in a Korean population. Korean J Urol 2015; 56:19-30. [PMID: 25598933 PMCID: PMC4294851 DOI: 10.4111/kju.2015.56.1.19] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 11/27/2014] [Indexed: 11/23/2022] Open
Abstract
Purpose Steroid 5-alpha reductase type 2 (SRD5A2) modifies testosterone to dihydrotestosterone (DHT) in the prostate. Single-nucleotide polymorphisms (SNPs) of the SRD5A2 gene might affect DHT. We sought to understand the relationship of SRD5A2 SNPs to prostate cancer in the Korean population. Materials and Methods Twenty-six common SNPs in the SRD5A2 gene were assessed in 272 prostate cancer cases and 173 controls. Single-locus analyses were conducted by using conditional logistic regression. Additionally, we performed a haplotype analysis for the SRD5A2 SNPs tested. Results Among the 20 SNPs and 4 haplotypes, there were no statistically significant results in the prostate cancer patients and the controls. In the logistic analysis of SRD5A2 polymorphisms with prostate-specific antigen (PSA) criteria, two SNPs (rs508562, rs11675297) and haplotype 1 displayed significant results (odds ratio [OR], 1.76; p=0.05; OR, 1.88-2.02; p=0.01-0.04; OR, 0.59; p=0.02, respectively). rs508562, rs11675297, rs2208532, and haplotype 1 (OR, 1.49; p=0.05; OR, 2.02; p=0.05; OR, 2.01; p=0.04; OR, 0.56-0.64, p=0.03-0.04, respectively) had significant associations with Gleason score. rs508562, rs11675297, and haplotype 1 (OR, 1.41-2.34; p=0.004-0.05; OR, 1.74-1.82; p=0.03-0.05; OR, 0.42-0.67; p=0.0005-0.03, respectively) were significantly associated with clinical stage. Conclusions We conclude that there was no significant association between SRD5A2 SNPs and the risk of prostate cancer in the Korean population. However, we found that some SNPs and 1 haplotype influenced PSA level, Gleason score, and clinical stage.
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Affiliation(s)
- Se Young Choi
- Department of Urology, Chung-Ang University College of Medicine, Seoul, Korea
| | - Hae Jong Kim
- Future Fusion Research Division, Korea Institute of Science and Technology, Department of Genetic Epidemiology, Seoul, Korea
| | | | - Soon Chul Myung
- Department of Urology, Chung-Ang University College of Medicine, Seoul, Korea
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42
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Kim JH, Cheong HS, Sul JH, Seo JM, Kim DY, Oh JT, Park KW, Kim HY, Jung SM, Jung K, Cho MJ, Bae JS, Shin HD. A genome-wide association study identifies potential susceptibility loci for Hirschsprung disease. PLoS One 2014; 9:e110292. [PMID: 25310821 PMCID: PMC4195606 DOI: 10.1371/journal.pone.0110292] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [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: 05/26/2014] [Accepted: 09/11/2014] [Indexed: 12/30/2022] Open
Abstract
Hirschsprung disease (HSCR) is a congenital and heterogeneous disorder characterized by the absence of intramural nervous plexuses along variable lengths of the hindgut. Although RET is a well-established risk factor, a recent genome-wide association study (GWAS) of HSCR has identified NRG1 as an additional susceptibility locus. To discover additional risk loci, we performed a GWAS of 123 sporadic HSCR patients and 432 unaffected controls using a large-scale platform with coverage of over 1 million polymorphic markers. The result was that our study replicated the findings of RET-CSGALNACT2-RASGEF1A genomic region (rawP = 5.69×10−19 before a Bonferroni correction; corrP = 4.31×10−13 after a Bonferroni correction) and NRG1 as susceptibility loci. In addition, this study identified SLC6A20 (adjP = 2.71×10−6), RORA (adjP = 1.26×10−5), and ABCC9 (adjP = 1.86×10−5) as new potential susceptibility loci under adjusting the already known loci on the RET-CSGALNACT2-RASGEF1A and NRG1 regions, although none of the SNPs in these genes passed the Bonferroni correction. In further subgroup analysis, the RET-CSGALNACT2-RASGEF1A genomic region was observed to have different significance levels among subgroups: short-segment (S-HSCR, corrP = 1.71×10−5), long-segment (L-HSCR, corrP = 6.66×10−4), and total colonic aganglionosis (TCA, corrP>0.05). This differential pattern in the significance level suggests that other genomic loci or mechanisms may affect the length of aganglionosis in HSCR subgroups during enteric nervous system (ENS) development. Although functional evaluations are needed, our findings might facilitate improved understanding of the mechanisms of HSCR pathogenesis.
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Affiliation(s)
- Jeong-Hyun Kim
- Research Institute for Basic Science, Sogang University, Seoul, Republic of Korea; Department of Life Science, Sogang University, Seoul, Republic of Korea
| | - Hyun Sub Cheong
- Department of Genetic Epidemiology, SNP Genetics, Inc., Seoul, Republic of Korea
| | - Jae Hoon Sul
- Department of Computer Science, University of California Los Angeles, Los Angeles, California, United States of America
| | - Jeong-Meen Seo
- Division of Pediatric Surgery, Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Dae-Yeon Kim
- Department of Pediatric Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Jung-Tak Oh
- Department of Pediatric Surgery, Severance Children's Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Kwi-Won Park
- Department of Pediatric Surgery, Seoul National University Children's Hospital, Seoul, Republic of Korea
| | - Hyun-Young Kim
- Department of Pediatric Surgery, Seoul National University Children's Hospital, Seoul, Republic of Korea
| | - Soo-Min Jung
- Division of Pediatric Surgery, Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Kyuwhan Jung
- Department of Surgery, Seoul National University Bundang Hospital, Seongnam, Gyeonggi, Republic of Korea
| | - Min Jeng Cho
- Department of Surgery, Konkuk University Medical Center, Seoul, Republic of Korea
| | - Joon Seol Bae
- Laboratory of Translational Genomics, Samsung Genome Institute, Samsung Medical Center, Seoul, Republic of Korea
| | - Hyoung Doo Shin
- Research Institute for Basic Science, Sogang University, Seoul, Republic of Korea; Department of Life Science, Sogang University, Seoul, Republic of Korea; Department of Genetic Epidemiology, SNP Genetics, Inc., Seoul, Republic of Korea
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Kim HJ, Lee J, Lee SY, Cheong HS, Kye YS, Kim W, Byun SS, Myung SC. The association between KL polymorphism and prostate cancer risk in Korean patients. Mol Biol Rep 2014; 41:7595-606. [PMID: 25120167 DOI: 10.1007/s11033-014-3647-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Accepted: 07/27/2014] [Indexed: 02/07/2023]
Abstract
The Klotho (KL) gene is a classical "aging suppressor" gene. Although recent studies have shown that KL participates in the progression of several types of human cancers, the relationship between KL polymorphism and prostate cancer was unknown. The present study aimed to investigate the association between KL genetic polymorphisms and prostate cancer. Twenty-five common single nucleotide polymorphisms (SNPs) in KL gene (including KL gene polymorphism C1818T in exon 4) were assessed in 272 prostate cancer cases and 173 controls. Single-locus analyses were conducted using unconditional logistic regression. In addition, we did a haplotype analysis for the 25 KL SNPs tested. CC genotype of C1548T KL polymorphism had approximately twofold increased prostate cancer risk compared with the homozygous genotype TT and heterozygote CT (odds ratio 1.85 [95% CI, 1.09-3.12], P = 0.02). We also found that non-T allele carriers had significantly higher prostate cancer risk associated with the prostate cancer clinical characteristics (tumor stage or Gleason score). Our findings suggested that the C1548T polymorphism of KL gene is associated with the prostate cancer and may act as a risk factor for the development of prostate cancer.
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Affiliation(s)
- Hae Jong Kim
- Advanced Urogenital Disease Research Center, Chung-Ang University College of Medicine, Seoul, 156-756, Korea
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44
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Kim JH, Park BL, Cheong HS, Bae JS, Kim LH, Kim JW, Lee BC, Seo CH, Kang TC, Park SH, Choi IG, Shin HD. Association BetweenHTR7Genetic Polymorphisms and Alcohol Dependence, Using the Alcohol Use Disorders Identification Test (AUDIT). Alcohol Clin Exp Res 2014; 38:2354-61. [DOI: 10.1111/acer.12482] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Accepted: 05/05/2014] [Indexed: 12/16/2022]
Affiliation(s)
- Jeong-Hyun Kim
- Department of Life Science; Sogang University; Seoul Korea
- Research Institute for Basic Science; Sogang University; Seoul Korea
| | - Byung-Lae Park
- Department of Genetic Epidemiology; SNP Genetics, Inc.; Seoul Korea
| | - Hyun Sub Cheong
- Department of Genetic Epidemiology; SNP Genetics, Inc.; Seoul Korea
| | - Joon Seol Bae
- Laboratory of Translational Genomics; Samsung Medical Center; Samsung Genome Institute; Seoul Korea
| | - Lyoung Hyo Kim
- Department of Life Science; Sogang University; Seoul Korea
- Department of Genetic Epidemiology; SNP Genetics, Inc.; Seoul Korea
| | - Jee Wook Kim
- Department of Neuropsychiatry; Hallym University Dongtan Sacred Heart Hospital; Hwaseong Korea
- Burn Institute; Hallym University; Seoul Korea
| | - Byoung Chul Lee
- Burn Institute; Hallym University; Seoul Korea
- Department of Neuropsychiatry; Hangang Sacred Heart Hospital; Hallym University; Seoul Korea
| | - Cheong Hoon Seo
- Burn Institute; Hallym University; Seoul Korea
- Department of Rehabilitation Medicine; Hangang Sacred Heart Hospital; Hallym University; Seoul Korea
| | - Tae-Cheon Kang
- Department of Anatomy and Neurobiology; Institute of Epilepsy Research; College of Medicine; Hallym University; Chuncheon Korea
| | - Sun-Hee Park
- Keyo Medical Foundation; Keyo Hospital; Uiwang Korea
| | - Ihn-Geun Choi
- Burn Institute; Hallym University; Seoul Korea
- Department of Neuropsychiatry; Hallym University Kangnam Sacred Heart Hospital; Seoul Korea
| | - Hyoung Doo Shin
- Department of Life Science; Sogang University; Seoul Korea
- Research Institute for Basic Science; Sogang University; Seoul Korea
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Lee JS, Bae JS, Park BL, Cheong HS, Kim JH, Kim JY, Namgoong S, Kim JO, Park CS, Shin HD. Association Analysis of TEC Polymorphisms with Aspirin-Exacerbated Respiratory Disease in a Korean Population. Genomics Inform 2014; 12:58-63. [PMID: 25031568 PMCID: PMC4099349 DOI: 10.5808/gi.2014.12.2.58] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Revised: 05/20/2014] [Accepted: 05/26/2014] [Indexed: 11/30/2022] Open
Abstract
The tyrosine-protein kinase Tec (TEC) is a member of non-receptor tyrosine kinases and has critical roles in cell signaling transmission, calcium mobilization, gene expression, and transformation. TEC is also involved in various immune responses, such as mast cell activation. Therefore, we hypothesized that TEC polymorphisms might be involved in aspirin-exacerbated respiratory disease (AERD) pathogenesis. We genotyped 38 TEC single nucleotide polymorphisms in a total of 592 subjects, which comprised 163 AERD cases and 429 aspirin-tolerant asthma controls. Logistic regression analysis was performed to examine the associations between TEC polymorphisms and the risk of AERD in a Korean population. The results revealed that TEC polymorphisms and major haplotypes were not associated with the risk of AERD. In another regression analysis for the fall rate of forced expiratory volume in 1 second (FEV1) by aspirin provocation, two variations (rs7664091 and rs12500534) and one haplotype (TEC_BL2_ht4) showed nominal associations with FEV1 decline (p = 0.03-0.04). However, the association signals were not retained after performing corrections for multiple testing. Despite TEC playing an important role in immune responses, the results from the present study suggest that TEC polymorphisms do not affect AERD susceptibility. Findings from the present study might contribute to the genetic etiology of AERD pathogenesis.
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Affiliation(s)
- Jin Sol Lee
- Research Institute for Basic Science, Sogang University, Seoul 121-742, Korea. ; Department of Life Science, Sogang University, Seoul 121-742, Korea
| | - Joon Seol Bae
- Laboratory of Translational Genomics, Samsung Genome Institute, Samsung Medical Center, Seoul 135-710, Korea
| | - Byung-Lae Park
- Department of Genetic Epidemiology, SNP Genetics, Inc., Seoul 153-801, Korea
| | - Hyun Sub Cheong
- Department of Genetic Epidemiology, SNP Genetics, Inc., Seoul 153-801, Korea
| | - Jeong-Hyun Kim
- Research Institute for Basic Science, Sogang University, Seoul 121-742, Korea
| | - Jason Yongha Kim
- Department of Life Science, Sogang University, Seoul 121-742, Korea
| | - Suhg Namgoong
- Department of Life Science, Sogang University, Seoul 121-742, Korea. ; Department of Genetic Epidemiology, SNP Genetics, Inc., Seoul 153-801, Korea
| | - Ji-On Kim
- Department of Life Science, Sogang University, Seoul 121-742, Korea. ; Department of Genetic Epidemiology, SNP Genetics, Inc., Seoul 153-801, Korea
| | - Choon-Sik Park
- Division of Allergy and Respiratory Medicine, Soonchunhyang University Seoul Hospital, Seoul 140-743, Korea
| | - Hyoung Doo Shin
- Department of Life Science, Sogang University, Seoul 121-742, Korea. ; Department of Genetic Epidemiology, SNP Genetics, Inc., Seoul 153-801, Korea
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Kim JY, Cheong HS, Park TJ, Shin HJ, Seo DW, Na HS, Chung MW, Shin HD. Screening for 392 polymorphisms in 141 pharmacogenes. Biomed Rep 2014; 2:463-476. [PMID: 24944790 DOI: 10.3892/br.2014.272] [Citation(s) in RCA: 10] [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: 02/17/2014] [Accepted: 03/28/2014] [Indexed: 11/05/2022] Open
Abstract
Pharmacogenomics is the study of the association between inter-individual genetic differences and drug responses. Researches in pharmacogenomics have been performed in compliance with the use of several genotyping technologies. In this study, a total of 392 single-nucleotide polymorphisms (SNPs) located in 141 pharmacogenes, including 21 phase I, 13 phase II, 18 transporter and 5 modifier genes, were selected and genotyped in 150 subjects using the GoldenGate assay or the SNaPshot technique. These variants were in Hardy-Weinberg equilibrium (HWE) (P>0.05), except for 22 SNPs. Genotyping of the 392 SNPs revealed that the minor allele frequencies of 47 SNPs were <0.05, 105 SNPs were monomorphic and 22 variants were not in HWE. Also, based on previous studies, we predicted the association between the polymorphisms of certain pharmacogenes, such as cytochrome P450 2D6, cytochrome P450 2C9, vitamin K epoxide reductase complex, subunit 1, cytochrome P450 2C19, human leukocyte antigen, class I, B and thiopurine S-methyltransferase, and drug efficacy. In conclusion, our study demonstrated the allele distribution of SNPs in 141 pharmacogenes as determined by high-throughput screening. Our results may be helpful in developing personalized medicines by using pharmacogene polymorphisms.
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Affiliation(s)
- Jason Yongha Kim
- Department of Life Science, Sogang University, SNP Genetics, Inc., Seoul 121-742, Republic of Korea
| | - Hyun Sub Cheong
- Department of Genetic Epidemiology, SNP Genetics, Inc., Seoul 121-742, Republic of Korea
| | - Tae-Joon Park
- Department of Life Science, Sogang University, SNP Genetics, Inc., Seoul 121-742, Republic of Korea
| | - Hee Jung Shin
- Division of Clinical Reaserch, Department of Toxicological Evaluation and Research, National Institute of Food and Drug Safety Evaluation, Osong Health Technology Administration Complex, Osong, Chungcheongbuk 363-700, Republic of Korea
| | - Doo Won Seo
- Division of Clinical Reaserch, Department of Toxicological Evaluation and Research, National Institute of Food and Drug Safety Evaluation, Osong Health Technology Administration Complex, Osong, Chungcheongbuk 363-700, Republic of Korea
| | - Han Sung Na
- Division of Clinical Reaserch, Department of Toxicological Evaluation and Research, National Institute of Food and Drug Safety Evaluation, Osong Health Technology Administration Complex, Osong, Chungcheongbuk 363-700, Republic of Korea
| | - Myeon Woo Chung
- Division of Clinical Reaserch, Department of Toxicological Evaluation and Research, National Institute of Food and Drug Safety Evaluation, Osong Health Technology Administration Complex, Osong, Chungcheongbuk 363-700, Republic of Korea
| | - Hyoung Doo Shin
- Department of Life Science, Sogang University, SNP Genetics, Inc., Seoul 121-742, Republic of Korea ; Department of Genetic Epidemiology, SNP Genetics, Inc., Seoul 121-742, Republic of Korea
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Wi YM, Kim SW, Chang HH, Jung SI, Kim YS, Cheong HS, Ki HK, Son JS, Kwon KT, Heo ST, Yeom JS, Ko KS, Kang CI, Chung DR, Peck KR, Song JH. Predictors of uropathogens other than Escherichia coli in patients with community-onset acute pyelonephritis. Int J Clin Pract 2014; 68:749-55. [PMID: 24447335 DOI: 10.1111/ijcp.12368] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
AIM A constant reduction in the incidence of community-onset acute pyelonephritis (CO-APN) caused by Escherichia coli has been shown with a parallel increase incidence caused by other organisms. Therefore, we evaluated the risk factors and outcome of non-E. coli as uropathogens in patients with community-onset APN. METHODS As a part of a nationwide multicentre surveillance study conducted in Korea, a total of 416 patients with CO-APN were collected with their epidemiological, antibiotic treatment and outcome data. RESULTS The risk factors and outcomes of non-E. coli as uropathogens were evaluated in a total of 416 patients with culture-confirmed CO-APN. Non-E. coli caused 127 cases (30.5%) of CO-APN. CO-APN caused by non-E. coli resulted in higher inappropriate empirical therapy (38.6% vs. 20.1%, p < 0.001), longer hospital stay (12.6 days vs. 6.7 days, p = 0.005) and higher 30-day mortality (9.4% vs. 3.8% p = 0.020) compared with CO-APN caused by E. coli. Multivariate analyses showed that male gender (OR, 3.48; CI, 2.13-5.67; p < 0.001), underlying haematological disease (OR, 5.32; CI, 1.17-24.254; p = 0.031), underlying benign prostate hyperplasia (OR, 2.61; CI, 1.02-6.74; p = 0.046), chronic indwelling urethral catheter (OR, 6.34; CI, 1.26-31.84; p = 0.025) and admission history in the previous 6 months (OR, 2.12; CI, 1.23-3.58; p = 0.005) were predictors for CO-APN caused by a non-E. coli isolate. CONCLUSIONS Community-onset APN caused by non-E. coli represents a distinct subset of urinary tract infections with worse outcomes. The defined risk factors related with non-E. coli should be taken into consideration when empirical antibiotic therapy is prescribed in patients with community-onset APN.
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Affiliation(s)
- Y M Wi
- Division of Infectious Diseases, Samsung Changwon Hospital, Sungkyunkwan University School of Medicine, Seoul, Korea
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Park TJ, Park JS, Cheong HS, Park BL, Kim LH, Heo JS, Kim YK, Kim KU, Uh ST, Lee HS, Na JO, Seo KH, Choi JS, Kim YH, Kim MS, Park CS, Shin HD. Genome-wide association study identifies ALLC polymorphisms correlated with FEV₁ change by corticosteroid. Clin Chim Acta 2014; 436:20-6. [PMID: 24792382 DOI: 10.1016/j.cca.2014.04.023] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2014] [Revised: 04/16/2014] [Accepted: 04/18/2014] [Indexed: 12/14/2022]
Abstract
OBJECTIVES Asthma can be suppressed by inhaled corticosteroids (ICS). However, response to ICS shows marked inter-individual variability. This study is aimed to identify the genetic variants associated with the change in the percentage of forced expiratory volume in 1second (%ΔFEV1) following ICS treatment. METHODS A genome-wide association study was performed in a Korean asthmatic cohort. To further investigate these genetic associations, 11 additional single-nucleotide polymorphisms (SNPs) on the allantoicase (ALLC) gene were selected from the HapMap database and genotyped in the same asthmatic patients in the follow-up study. RESULTS In a genome-wide study, we identified the lowest P-value in ALLC, but none of the SNPs met the genome-wide association criteria (P<1.0×10(-8)). However, among 25 SNPs on ALLC in the follow-up study, 6 variants showed significant associations with the mean %ΔFEV1 in the study subjects (P<3.73×10(-6)). CONCLUSIONS Although the associated signals could not overcome the genome-wide multiple correction due to small sample size (n=189), our results suggest that associated SNPs of ALLC might be genetic predictors of response to ICS, at least with respect to ΔFEV1 in Korean asthmatics.
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Affiliation(s)
- Tae-Joon Park
- Department of Life Science, Sogang University, 35, Baekbeom-ro, Mapo-gu, Seoul 121-742, Republic of Korea
| | - Jong-Sook Park
- Division of Allergy and Respiratory Medicine, Soonchunhyang University Bucheon Hospital, 1174, Jung-dong, Wonmi-gu, Gyeonggi-do 420-020, Republic of Korea
| | - Hyun Sub Cheong
- Department of Genetic Epidemiology, SNP Genetics, Inc., 35, Baekbeom-ro, Mapo-gu, Seoul 121-742, Republic of Korea
| | - Byung-Lae Park
- Department of Genetic Epidemiology, SNP Genetics, Inc., 35, Baekbeom-ro, Mapo-gu, Seoul 121-742, Republic of Korea
| | - Lyoung Hyo Kim
- Department of Genetic Epidemiology, SNP Genetics, Inc., 35, Baekbeom-ro, Mapo-gu, Seoul 121-742, Republic of Korea
| | - Jeong Seok Heo
- Division of Allergy and Respiratory Medicine, Soonchunhyang University Bucheon Hospital, 1174, Jung-dong, Wonmi-gu, Gyeonggi-do 420-020, Republic of Korea
| | - Yang Ki Kim
- Division of Allergy and Respiratory Medicine, Soonchunhyang University Seoul Hospital, 59, Daesagwan-ro, Yongsan-gu, Seoul 140-887, Republic of Korea
| | - Ki-Up Kim
- Division of Allergy and Respiratory Medicine, Soonchunhyang University Seoul Hospital, 59, Daesagwan-ro, Yongsan-gu, Seoul 140-887, Republic of Korea
| | - Soo-Taek Uh
- Division of Allergy and Respiratory Medicine, Soonchunhyang University Seoul Hospital, 59, Daesagwan-ro, Yongsan-gu, Seoul 140-887, Republic of Korea
| | - Ho Sung Lee
- Division of Allergy and Respiratory Medicine, Soonchunhyang University Cheonan Hospital, 23-20, Byeongmyeong-dong, Dongnam-gu, Cheonan, Chungcheongnam-do 330-721, Republic of Korea
| | - Joo-Ock Na
- Division of Allergy and Respiratory Medicine, Soonchunhyang University Cheonan Hospital, 23-20, Byeongmyeong-dong, Dongnam-gu, Cheonan, Chungcheongnam-do 330-721, Republic of Korea
| | - Ki-Hyun Seo
- Division of Allergy and Respiratory Medicine, Soonchunhyang University Cheonan Hospital, 23-20, Byeongmyeong-dong, Dongnam-gu, Cheonan, Chungcheongnam-do 330-721, Republic of Korea
| | - Jae-Sung Choi
- Division of Allergy and Respiratory Medicine, Soonchunhyang University Cheonan Hospital, 23-20, Byeongmyeong-dong, Dongnam-gu, Cheonan, Chungcheongnam-do 330-721, Republic of Korea
| | - Yong Hoon Kim
- Division of Allergy and Respiratory Medicine, Soonchunhyang University Cheonan Hospital, 23-20, Byeongmyeong-dong, Dongnam-gu, Cheonan, Chungcheongnam-do 330-721, Republic of Korea
| | - Myung-Sin Kim
- Division of Allergy and Respiratory Medicine, Soonchunhyang University Gumi Hospital, 250, Gongdan-dong, Gumi, Kyungsangbook-do 730-706, Republic of Korea
| | - Choon-Sik Park
- Division of Allergy and Respiratory Medicine, Soonchunhyang University Bucheon Hospital, 1174, Jung-dong, Wonmi-gu, Gyeonggi-do 420-020, Republic of Korea.
| | - Hyoung Doo Shin
- Department of Life Science, Sogang University, 35, Baekbeom-ro, Mapo-gu, Seoul 121-742, Republic of Korea; Department of Genetic Epidemiology, SNP Genetics, Inc., 35, Baekbeom-ro, Mapo-gu, Seoul 121-742, Republic of Korea.
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Park SK, Park CS, Lee HS, Park KS, Park BL, Cheong HS, Shin HD. Functional polymorphism in aldehyde dehydrogenase-2 gene associated with risk of tuberculosis. BMC Med Genet 2014; 15:40. [PMID: 24690209 PMCID: PMC3975138 DOI: 10.1186/1471-2350-15-40] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Accepted: 03/27/2014] [Indexed: 11/29/2022]
Abstract
Background The well-known genetic polymorphisms in ADH1B(His47Arg) and ALDH2(Glu487Lys) have dramatic effects on the rate of metabolizing alcohol and acetaldehyde. We investigated possible involvement of these functional polymorphisms in other common complex-trait diseases. Methods The genetic effects of these two polymorphisms on hepatitis, asthma, type-2 diabetes mellitus (T2DM), and tuberculosis (TB) were examined in a Korean population. Results We demonstrated that the well-known functional polymorphism of a primary alcohol-metabolizing enzyme (ALDH2 Glu487Lys) has a strong genetic association with the risk of TB. The frequency of the minor allele (ALDH2*487Lys) was found to be much lower in TB patients (freq. = 0.099/n = 477) than among controls (freq. = 0.162/n = 796) (P = 0.00001, OR (95% confidential interval) = 0.57 (0.45-0.74)). Our data may indicate that TB was once an endemic disease, which exerted selection pressure for higher frequencies of ALDH2*487Lys in Asian populations. In addition, the calculated attributable fraction (AF) indicates that 39.5% of TB patients can attribute their disease to the detrimental effects of ALDH2Glu487Glu. Conclusion Our results suggest that this polymorphism is one of the genetic components of TB, at least in the Korean population.
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Affiliation(s)
| | | | | | | | | | | | - Hyoung Doo Shin
- Department of Genetic Epidemiology, SNP Genetics, Inc,, 1 Shinsu-dong, Mapo-gu, Seoul 121-742, Republic of Korea.
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Park TJ, Kim HJ, Kim JH, Bae JS, Cheong HS, Park BL, Shin HD. Associations of CD6, TNFRSF1A and IRF8 polymorphisms with risk of inflammatory demyelinating diseases. Neuropathol Appl Neurobiol 2014; 39:519-30. [PMID: 22994200 DOI: 10.1111/j.1365-2990.2012.01304.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Accepted: 09/18/2012] [Indexed: 11/29/2022]
Abstract
AIMS Multiple sclerosis (MS) and neuromyelitis optica (NMO) are inflammatory autoimmune diseases that affect the central nervous system. Several genome-wide and candidate gene studies have identified genetic polymorphisms associated with the risk of MS or NMO. In particular, two recently published studies of meta-analysis in European-origin populations have suggested associations of single-nucleotide polymorphisms (SNPs) in CD6, TNFRSF1A and IRF8 with MS. The aim of our study was to assess the associations between SNPs in these three genes and the risk of inflammatory demyelinating disease (IDD) including MS and NMO. To the best of our knowledge, this is the first time such a study has been performed in an Asian population. METHODS A total of 21 SNPs of CD6, TNFRSF1A and IRF8 were genotyped in 178 IDD cases (79 MS and 99 NMO patients) and 237 normal controls in a Korean population. RESULTS Logistic analyses revealed that one SNP in CD6 (rs12288280, P = 0.04) and three SNPs in TNFRSF1A (rs767455, rs4149577 and rs1800693, P = 0.01-0.03) were associated with NMO. However, there was no association of IRF8 polymorphisms with IDD, including MS and NMO. Using further information from the SNP Function Prediction website, two exonic splicing enhancers (ESEs), including the polymorphic site of rs767455, were predicted to be binding sites for splicing factors (SRp55, SF2/ASF2 and SF2/ASF1). CONCLUSION Although additional studies are needed, our findings could provide information regarding the genetic aetiology of IDD in the Korean population.
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Affiliation(s)
- T-J Park
- Department of Life Science, Sogang University, Seoul, Korea
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