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Bouwman HB, Guchelaar HJ. The efficacy and safety of eculizumab in patients and the role of C5 polymorphisms. Drug Discov Today 2024; 29:104134. [PMID: 39111540 DOI: 10.1016/j.drudis.2024.104134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 07/11/2024] [Accepted: 07/31/2024] [Indexed: 08/13/2024]
Abstract
Eculizumab is an orphan drug with indications for extremely rare autoimmune disorders. It is primarily prescribed for use in patients with paroxysmal nocturnal hemoglobinuria and atypical hemolytic uremic syndrome; but is also highly effective in the treatment of myasthenia gravis, among others. By binding to the C5 protein in the complement system, eculizumab effectively inhibits cellular hemolysis and autoimmune reactions. Despite this effective treatment, some patients reported no improvement in symptoms. Genetic sequencing revealed three distinct C5 mutations in the non-responders and these polymorphisms appeared to be most prevalent among Japanese, Korean and African populations. Here, we present an overview of the current and potential future applications of eculizumab, as well as the disadvantages of eculizumab treatment in patients with C5 polymorphisms.
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Affiliation(s)
| | - Henk-Jan Guchelaar
- Clinical Pharmacy and Toxicology, Leiden University Medical Center, PO Box 9600, 2300 RC Leiden, the Netherlands.
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Koo YK, Kwon SS, Suh EJ, Kim NH, Kim HK, Cho YK, Choi SJ, Kim S, Lee KA. Evaluating the TaqMan Jr a-Genotyping Method for Rapidly Predicting the Presence of Anti-Jr a Antibodies. Ann Lab Med 2024; 44:418-425. [PMID: 38373791 PMCID: PMC11169768 DOI: 10.3343/alm.2023.0325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 11/14/2023] [Accepted: 02/06/2024] [Indexed: 02/21/2024] Open
Abstract
Background The Jra antigen is a high-prevalence red blood cell (RBC) antigen. Reports on cases of fatal hemolytic disease of the fetus and newborn and acute hemolytic transfusion reactions suggest that antibodies against Jra (anti-Jra) have potential clinical significance. Identifying anti-Jra is challenging owing to a lack of commercially available antisera. We developed an alternative approach to rapidly predict the presence of anti-Jra using the TaqMan single-nucleotide polymorphism (SNP)-genotyping method. Methods Residual peripheral blood samples from 10 patients suspected of having the anti-Jra were collected. Two samples with confirmed Jr(a-) RBCs and anti-Jra were used to validate the TaqMan genotyping assay by comparing the genotyping results with direct sequencing. The accuracy of the assay in predicting the presence of anti-Jra was verified through crossmatching with in-house Jr(a-) O+ RBCs. Results The TaqMan-genotyping method was validated with two Jr(a-) RBC- and anti-Jra-confirmed samples that showed concordant Jra genotyping and direct sequencing results. Jra genotyping for the remaining samples and crossmatching the serum samples with inhouse Jr(a-) O+ RBCs showed consistent results. Conclusions We validated a rapid, simple, accurate, and cost-effective method for predicting the presence of anti-Jra using a TaqMan-based SNP-genotyping assay. Implementing this method in routine practice in clinical laboratories will assist in solving difficult problems regarding alloantibodies to high-prevalence RBC antigens and ultimately aid in providing safe and timely transfusions and proper patient care.
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Affiliation(s)
- Yu-Kyung Koo
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Soon Sung Kwon
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Eun Jung Suh
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Na Hyeong Kim
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Hyun Kyung Kim
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Youn Keong Cho
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Seung Jun Choi
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Sinyoung Kim
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Kyung-A Lee
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
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Kim YJ, Park HS, Youk J, Han JW, Byeon SH, Kim SS, Ju YS, Lee CS. Subset of retinoblastoma tumours is associated with BRCA1/2 mutations. Br J Ophthalmol 2024; 108:1011-1017. [PMID: 37833038 DOI: 10.1136/bjo-2023-323388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 09/11/2023] [Indexed: 10/15/2023]
Abstract
BACKGROUND We investigated the potential association between pathogenic BRCA1/2 variants and retinoblastoma pathogenicity. METHODS In this single-centre, retrospective case series, we performed hereditary cancer panel tests using blood samples for patients with retinoblastoma diagnosed between March 2017 and October 2021. Bioinformatics prediction tools were then used to conduct in silico pathogenicity assessments for patients with BRCA1/2 family variants, in addition to the American College of Medical Genetics and Genomics (ACMG) variant classification. One patient with a germline BRCA1 variant was analysed with whole-genome sequencing (WGS), mutational signature analysis and methylation analysis for RB1 and BRCA using the patient's tumour and blood samples. RESULTS Of 30 retinoblastoma patients who underwent panel sequencing, six (20%) were found to carry germline variants in the BRCA1/2 or BRIP1 genes. Among these six patients, two had pathogenic or likely pathogenic variants as per the ACMG variant classification. Additionally, three patients showed potential pathogenic BRCA1/2 family variants through further analysis with alternative bioinformatics prediction tools. In the WGS analysis of a tumour from a patient with a germline likely pathogenic BRCA1 variant in one allele, we observed the loss of one RB1 allele due to a large deletion. No somatic non-synonymous mutations or frameshift indels were detected in the RB1 locus of the remaining allele. This sample also showed BRCA1 gene promoter hypermethylation in the tumour, indicating additional epigenetic silencing. CONCLUSION This study demonstrated that some retinoblastoma patients harboured germline BRCA1/2 family variants, which may be associated with the development of retinoblastoma along with RB1 mutations.
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Affiliation(s)
- Yong Joon Kim
- Department of Ophthalmology, Institute of Vision Research, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Hyo Song Park
- Department of Ophthalmology, Soonchunhyang University College of Medicine, Cheonan, Republic of Korea
- Department of Ophthalmology, Soonchunhyang University Hospital Bucheon, Bucheon, Republic of Korea
| | - Jeonghwan Youk
- Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jung Woo Han
- Department of Pediatrics, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Suk Ho Byeon
- Department of Ophthalmology, Institute of Vision Research, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Sung Soo Kim
- Department of Ophthalmology, Institute of Vision Research, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Young Seok Ju
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
- GENOME INSIGHT Inc, San Diego, CA 92121, USA
| | - Christopher Seungkyu Lee
- Department of Ophthalmology, Institute of Vision Research, Yonsei University College of Medicine, Seoul, Republic of Korea
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Lee JY, Moon J, Hu HJ, Ryu CS, Ko EJ, Ahn EH, Kim YR, Kim JH, Kim NK. Discovery of Pathogenic Variants Associated with Idiopathic Recurrent Pregnancy Loss Using Whole-Exome Sequencing. Int J Mol Sci 2024; 25:5447. [PMID: 38791485 PMCID: PMC11121708 DOI: 10.3390/ijms25105447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 05/08/2024] [Accepted: 05/15/2024] [Indexed: 05/26/2024] Open
Abstract
Idiopathic recurrent pregnancy loss (RPL) is defined as at least two pregnancy losses before 20 weeks of gestation. Approximately 5% of pregnant couples experience idiopathic RPL, which is a heterogeneous disease with various causes including hormonal, chromosomal, and intrauterine abnormalities. Although how pregnancy loss occurs is still unknown, numerous biological factors are associated with the incidence of pregnancy loss, including genetic variants. Whole-exome sequencing (WES) was conducted on blood samples from 56 Korean patients with RPL and 40 healthy controls. The WES data were aligned by means of bioinformatic analysis, and the detected variants were annotated using machine learning tools to predict the pathogenicity of protein alterations. Each indicated variant was confirmed using Sanger sequencing. A replication study was also conducted in 112 patients and 114 controls. The Variant Effect Scoring Tool, Combined Annotation Dependent Depletion tool, Sorting Intolerant from Tolerant annotation tool, and various databases detected 10 potential variants previously associated with spontaneous abortion genes in patients by means of a bioinformatic analysis of WES data. Several variants were detected in more than one patient. Interestingly, several of the detected genes were functionally clustered, including some with a secretory function (mucin 4; MUC4; rs200737893 G>A and hyaluronan-binding protein 2; HABP2; rs542838125 G>T), in which growth arrest-specific 2 Like 2 (GAS2L2; rs140842796 C>T) and dynamin 2 (DNM2; rs763894364 G>A) are functionally associated with cell protrusion and the cytoskeleton. ATP Binding Cassette Subfamily C Member 6 (ABCC6) was the only gene with two variants. HABP2 (rs542838125 G>T), MUC4 (rs200737893 G>A), and GAS2L2 (rs140842796 C>T) were detected in only the patient group in the replication study. The combination of WES and machine learning tools is a useful method to detect potential variants associated with RPL. Using bioinformatic tools, we found 10 potential variants in 9 genes. WES data from patients are needed to better understand the causes of RPL.
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Affiliation(s)
- Jeong Yong Lee
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Republic of Korea; (J.Y.L.); (C.S.R.); (E.J.K.)
| | - JaeWoo Moon
- Endomics, Inc., Seongnam-si 13595, Republic of Korea; (J.M.); (H.-J.H.)
| | - Hae-Jin Hu
- Endomics, Inc., Seongnam-si 13595, Republic of Korea; (J.M.); (H.-J.H.)
| | - Chang Soo Ryu
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Republic of Korea; (J.Y.L.); (C.S.R.); (E.J.K.)
| | - Eun Ju Ko
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Republic of Korea; (J.Y.L.); (C.S.R.); (E.J.K.)
| | - Eun Hee Ahn
- Department of Obstetrics and Gynecology, CHA Bundang Medical Center, School of Medicine, CHA University, Seongnam 13596, Republic of Korea; (E.H.A.); (Y.R.K.)
| | - Young Ran Kim
- Department of Obstetrics and Gynecology, CHA Bundang Medical Center, School of Medicine, CHA University, Seongnam 13596, Republic of Korea; (E.H.A.); (Y.R.K.)
| | - Ji Hyang Kim
- Department of Obstetrics and Gynecology, CHA Bundang Medical Center, School of Medicine, CHA University, Seongnam 13596, Republic of Korea; (E.H.A.); (Y.R.K.)
| | - Nam Keun Kim
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Republic of Korea; (J.Y.L.); (C.S.R.); (E.J.K.)
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Park K, Do AR, Chung Y, Kim MJ, Rhee SJ, Yoon DH, Choi SH, Cho SJ, Kim HN, Ahn YM, Won S. Genome-wide association study implicates the role of TBXAS1 in the pathogenesis of depressive symptoms among the Korean population. Transl Psychiatry 2024; 14:80. [PMID: 38320993 PMCID: PMC10847124 DOI: 10.1038/s41398-024-02777-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 01/09/2024] [Accepted: 01/12/2024] [Indexed: 02/08/2024] Open
Abstract
Although depression is an emerging disorder affecting many people worldwide, most genetic studies have been performed in European descent populations. Herein, a genome-wide association study (GWAS) was conducted in Korean population to elucidate the genomic loci associated with depressive symptoms. Two independent cohorts were used as discovery datasets, which consisted of 6474 (1484 cases and 4990 controls) and 1654 (557 cases and 1097 controls) Korean participants, respectively. The participants were divided into case and control groups based on the Beck Depression Inventory (BDI). Meta-analysis using the two cohorts revealed that rs6945590 was significantly associated with the risk of depressive symptoms [P = 2.83 × 10-8; odds ratio (OR) = 1.23; 95% confidence interval (CI): 1.15-1.33]. This association was validated in other independent cohorts which were another Korean cohort (258 cases and 1757 controls) and the East Asian study of the Psychiatric Genomics Consortium (PGC) (12,455 cases and 85,548 controls). The predicted expression levels of thromboxane A synthase 1 gene (TBXAS1), which encodes the enzyme thromboxane A synthase 1 and participates in the arachidonic acid (AA) cascade, was significantly decreased in the whole blood tissues of the participants with depressive symptoms. Furthermore, Mendelian randomization (MR) analysis showed a causal association between TBXAS1 expression and the risk of depressive symptoms. In conclusion, as the number of risk alleles (A) of rs6945590 increased, TBXAS1 expression decreased, which subsequently caused an increase in the risk of depressive symptoms.
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Grants
- 20000134 Ministry of Trade, Industry and Energy (Ministry of Trade, Industry and Energy, Korea)
- 20000134 Ministry of Trade, Industry and Energy (Ministry of Trade, Industry and Energy, Korea)
- 20000134 Ministry of Trade, Industry and Energy (Ministry of Trade, Industry and Energy, Korea)
- 20000134 Ministry of Trade, Industry and Energy (Ministry of Trade, Industry and Energy, Korea)
- Ministry of Science and ICT (MSIT, Korea) / NRF-2021R1A5A1033157
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Affiliation(s)
- Kyungtaek Park
- Institute of Health and Environment, Seoul National University, Seoul, Republic of Korea
| | - Ah Ra Do
- Interdisciplinary Program of Bioinformatics, College of Natural Sciences, Seoul National University, Seoul, Republic of Korea
| | - Yuree Chung
- Department of Public Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea
| | - Min Ji Kim
- Department of Neuropsychiatry, Seoul National University Hospital, Seoul, Republic of Korea
- Department of Psychiatry, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sang Jin Rhee
- Department of Psychiatry, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Dae Hyun Yoon
- Department of Psychiatry, Seoul National University Hospital Healthcare System Gangnam Center, Seoul, Republic of Korea
| | - Seung Ho Choi
- Department of Internal Medicine, Healthcare Research Institute, Healthcare System Gangnam Center, Seoul National University Hospital, Seoul, Republic of Korea
| | - Sung Joon Cho
- Department of Psychiatry, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
- Workplace Mental Health Institute, Kangbuk Samsung Hospital, Seoul, Republic of Korea
| | - Han-Na Kim
- Department of Clinical Research Design and Evaluation, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul, Republic of Korea.
- Biomedical Statistics Center, Research Institute for Future Medicine, Samsung Medical Center, Seoul, Republic of Korea.
| | - Yong Min Ahn
- Department of Neuropsychiatry, Seoul National University Hospital, Seoul, Republic of Korea.
- Department of Psychiatry, Seoul National University College of Medicine, Seoul, Republic of Korea.
- Institute of Human Behavioral Medicine, Seoul National University Medical Research Center, Seoul, Republic of Korea.
| | - Sungho Won
- Institute of Health and Environment, Seoul National University, Seoul, Republic of Korea.
- Interdisciplinary Program of Bioinformatics, College of Natural Sciences, Seoul National University, Seoul, Republic of Korea.
- Department of Public Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea.
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Park JE, Lee T, Ha K, Cho EH, Ki CS. Carrier frequency and incidence of alpha-mannosidosis: population database-based study-focus on the East Asian and Korean population. Front Genet 2023; 14:1297543. [PMID: 38107468 PMCID: PMC10725197 DOI: 10.3389/fgene.2023.1297543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 11/23/2023] [Indexed: 12/19/2023] Open
Abstract
Background: Alpha-mannosidosis caused by mutations in the MAN2B1 gene is a rare genetic disorder characterized by physical abnormalities and intellectual disabilities. The objective of this study was to analyze the carrier frequency and estimated incidence of alpha-mannosidosis in East Asian populations, as limited data exists on its incidence in this group. Methods: In this study, a total of 125,748 exomes from the gnomAD database was analyzed. Additionally, 5,305 data from the KOVA and 1,722 data from the KRGDB, both representing Korean populations, were included. Results: The global carrier frequency of alpha-mannosidosis in gnomAD was 0.23%; the highest carrier frequency was observed in the Finnish at 0.49%, and East Asians had the second highest carrier frequency at 0.30%. Globally, the approximate incidence of alpha-mannosidosis was calculated at 1 in 784,535, l in 166,801 Europeans (Finnish), and l in 431,689 East Asians. By integrating the data from the 8,936 Koreans in gnomAD Korean, KOVA and KRGDB, the carrier frequency of alpha-mannosidosis in the Korean population was 0.04% and estimated incidence was 1 in 19,963,024. Conclusion: This study is the first to investigate the carrier frequencies of alpha-mannosidosis in East Asians and Koreans, including specific subpopulations, utilizing gnomAD and the Korean genomic database. The variant spectrum of MAN2B1 genes in East Asians showed significant differences compared to other ethnic groups. Our data provide valuable reference information for future investigations into alpha-mannosidosis, aiding in understanding the genetic diversity and specific variants associated with the condition in East Asian populations.
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Affiliation(s)
- Jong Eun Park
- Department of Laboratory Medicine, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri, Republic of Korea
| | | | | | - Eun Hye Cho
- Department of Laboratory Medicine, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
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Ye W, Yu Y, Zhu X, Wan W, Liu Y, Zou H, Zhu Z. A Common Functional Variant at the Enhancer of the Rheumatoid Arthritis Risk Gene ORMDL3 Regulates its Expression Through Allele-Specific JunD Binding. PHENOMICS (CHAM, SWITZERLAND) 2023; 3:485-495. [PMID: 37881318 PMCID: PMC10593690 DOI: 10.1007/s43657-023-00107-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 03/27/2023] [Accepted: 03/29/2023] [Indexed: 10/27/2023]
Abstract
Genome-wide association studies (GWASs) have identified over 100 loci associated with rheumatoid arthritis (RA); however, the functionally affected genes and the underlying molecular mechanisms contributing to these associations are often unknown. In this study, we conducted an integrative genomic analysis incorporating multiple "omics" data and identified a functional regulatory DNA variant, rs56199421, and a plausible mechanism by which it regulates the expression of a putative RA risk gene, ORMDL Sphingolipid Biosynthesis Regulator 3 (ORMDL3). The T allele of rs56199421, located in the enhancer region of ORMDL3, exhibited stronger direct binding ability than the other C allele of rs56199421 did in vitro with the transcription factor JunD and demonstrated higher transcriptional activity. Moreover, the T allele of rs56199421 is associated with elevated RA risk, and ORMDL3 expression is increased in RA patients. Thus, these findings suggest that the T allele of rs56199421 enhances JunD transcription factor binding, increases enhancer activity, and elevates the expression of the RA risk gene ORMDL3. Supplementary Information The online version contains supplementary material available at 10.1007/s43657-023-00107-z.
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Affiliation(s)
- Wenjing Ye
- Division of Rheumatology and Immunology, Huashan Hospital, Fudan University, Shanghai, 200040 China
- Institute of Rheumatology, Immunology and Allergy, Fudan University, Shanghai, 200040 China
| | - Yiyun Yu
- Division of Rheumatology and Immunology, Huashan Hospital, Fudan University, Shanghai, 200040 China
- Institute of Rheumatology, Immunology and Allergy, Fudan University, Shanghai, 200040 China
| | - Xiaoxia Zhu
- Division of Rheumatology and Immunology, Huashan Hospital, Fudan University, Shanghai, 200040 China
- Institute of Rheumatology, Immunology and Allergy, Fudan University, Shanghai, 200040 China
| | - Weiguo Wan
- Division of Rheumatology and Immunology, Huashan Hospital, Fudan University, Shanghai, 200040 China
- Institute of Rheumatology, Immunology and Allergy, Fudan University, Shanghai, 200040 China
| | - Yun Liu
- The Ministry of Education Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032 China
| | - Hejian Zou
- Division of Rheumatology and Immunology, Huashan Hospital, Fudan University, Shanghai, 200040 China
- Institute of Rheumatology, Immunology and Allergy, Fudan University, Shanghai, 200040 China
| | - Zaihua Zhu
- Division of Rheumatology and Immunology, Huashan Hospital, Fudan University, Shanghai, 200040 China
- Institute of Rheumatology, Immunology and Allergy, Fudan University, Shanghai, 200040 China
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Kim H, Lee K, Shim YM, Kim EE, Kim SK, Phi JH, Park CK, Choi SH, Park SH. Epigenetic Alteration of H3K27me3 as a Possible Oncogenic Mechanism of Central Neurocytoma. J Transl Med 2023; 103:100159. [PMID: 37088465 DOI: 10.1016/j.labinv.2023.100159] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 04/11/2023] [Accepted: 04/13/2023] [Indexed: 04/25/2023] Open
Abstract
Central neurocytoma (CN) is a low-grade neuronal tumor that mainly arises from the lateral ventricle (LV). This tumor remains poorly understood in the sense that no driver gene aberrations have been identified thus far. We investigated immunomarkers in fetal and adult brains and 45 supratentorial periventricular tumors to characterize the biomarkers, cell of origin, and tumorigenesis of CN. All CNs occurred in the LV. A minority involved the third ventricle, but none involved the fourth ventricle. As expected, next-generation sequencing performed using a brain-tumor-targeted gene panel in 7 CNs and whole exome sequencing in 5 CNs showed no driver mutations. Immunohistochemically, CNs were robustly positive for FGFR3 (100%), SSTR2 (92%), TTF-1 (Nkx2.1) (88%), GLUT-1 (84%), and L1CAM (76%), in addition to the well-known markers of CN, synaptophysin (100%) and NeuN (96%). TTF-1 was also positive in subependymal giant cell astrocytomas (100%, 5/5) and the pituicyte tumor family, including pituicytoma and spindle cell oncocytoma (100%, 5/5). Interestingly, 1 case of LV subependymoma (20%, 1/5) was positive for TTF-1, but all LV ependymomas were negative (0/5 positive). Because TTF-1-positive cells were detected in the medial ganglionic eminence around the foramen of Monro of the fetal brain and in the subventricular zone of the LV of the adult brain, CN may arise from subventricular TTF-1-positive cells undergoing neuronal differentiation. H3K27me3 loss was observed in all CNs and one case (20%) of LV subependymoma, suggesting that chromatin remodeling complexes or epigenetic alterations may be involved in the tumorigenesis of all CNs and some ST-subependymomas. Further studies are required to determine the exact tumorigenic mechanism of CN.
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Affiliation(s)
- Hyunhee Kim
- Department of Pathology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Kwanghoon Lee
- Department of Pathology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Yu-Mi Shim
- Department of Pathology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Eric Eunshik Kim
- Department of Pathology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Seung-Ki Kim
- Department of Neurosurgery, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Ji Hoon Phi
- Department of Neurosurgery, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Chul-Kee Park
- Department of Neurosurgery, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Seung Hong Choi
- Department of Radiology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sung-Hye Park
- Department of Pathology, Seoul National University College of Medicine, Seoul, Republic of Korea; Neuroscience Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea.
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Lee D, Koo T, Park J, Shin HT. Comparison of Risk Allele Frequencies of Psoriasis-Associated Single-Nucleotide Polymorphisms in Different Population Groups. Ann Dermatol 2023; 35:32-37. [PMID: 36750456 PMCID: PMC9905865 DOI: 10.5021/ad.22.110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 08/18/2022] [Accepted: 10/12/2022] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND The prevalence of psoriasis differs by population, and it appears to be more common among Europeans than in East Asians. Recent genome-wide association studies (GWAS) have identified alleles that increase the risk of psoriasis, and these alleles may present different frequencies in different geographic regions. OBJECTIVE We aimed to gain insights into the causes of differences in disease frequencies according to populations and the factors affecting prevalence and pattern differences. METHODS We collected a total of 147 psoriasis-associated single-nucleotide polymorphisms (SNPs) from the GWAS catalog and compared the allele frequency differences in 27 populations using public population frequency in the 1000 Genomes Project phase 3 (n=2,504) and the Korean Reference Genome Database (n=1,722). Additionally, we calculated the composited genetic risk scores across the population groups. RESULTS There were distinct patterns of allele frequencies in different population groups. In many cases, East Asians exhibited allele frequencies opposite to that of Europeans. The genetic risk score was higher in Europeans (average: 0.487) and Americans (average: 0.492) than in East Asians (average: 0.471). The prevalence of psoriasis correlated with the average genetic risk score of the population. CONCLUSION We observed a difference in the allele frequencies of psoriasis-associated SNPs between the studied populations. This result suggests that the difference in the prevalence of psoriasis between population groups can be interpreted to some extent by the genotype.
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Affiliation(s)
- Donghoon Lee
- Department of Dermatology, Veterans Health Service Medical Center, Seoul, Korea
| | - Taehan Koo
- Department of Dermatology, Veterans Health Service Medical Center, Seoul, Korea
| | - Jiho Park
- Oaro Dermatology Clinic, Seoul, Korea
| | - Hyun-Tae Shin
- Department of Dermatology, Inha University College of Medicine, Incheon, Korea.,Research Center for Controlling Intercellular Communication (RCIC), Inha University College of Medicine, Incheon, Korea.
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Aschenbrenner D, Ye Z, Zhou Y, Hu W, Brooks I, Williams I, Capitani M, Gartner L, Kotlarz D, Snapper SB, Klein C, Muise AM, Marsden BD, Huang Y, Uhlig HH. Pathogenic Interleukin-10 Receptor Alpha Variants in Humans - Balancing Natural Selection and Clinical Implications. J Clin Immunol 2023; 43:495-511. [PMID: 36370291 PMCID: PMC9892166 DOI: 10.1007/s10875-022-01366-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 09/09/2022] [Indexed: 11/15/2022]
Abstract
Balancing natural selection is a process by which genetic variants arise in populations that are beneficial to heterozygous carriers, but pathogenic when homozygous. We systematically investigated the prevalence, structural, and functional consequences of pathogenic IL10RA variants that are associated with monogenic inflammatory bowel disease. We identify 36 non-synonymous and non-sense variants in the IL10RA gene. Since the majority of these IL10RA variants have not been functionally characterized, we performed a systematic screening of their impact on STAT3 phosphorylation upon IL-10 stimulation. Based on the geographic accumulation of confirmed pathogenic IL10RA variants in East Asia and in Northeast China, the distribution of infectious disorders worldwide, and the functional evidence of IL-10 signaling in the pathogenesis, we identify Schistosoma japonicum infection as plausible selection pressure driving variation in IL10RA. Consistent with this is a partially augmented IL-10 response in peripheral blood mononuclear cells from heterozygous variant carriers. A parasite-driven heterozygote advantage through reduced IL-10 signaling has implications for health care utilization in regions with high allele frequencies and potentially indicates pathogen eradication strategies that target IL-10 signaling.
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Affiliation(s)
- Dominik Aschenbrenner
- Translational Gastroenterology Unit, Experimental Medicine, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, UK
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Ziqing Ye
- Translational Gastroenterology Unit, Experimental Medicine, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, UK
- Department of Gastroenterology, National Children's Medical Center, Children's Hospital of Fudan University, 399 Wanyuan Road, Shanghai, 201102, China
| | - Ying Zhou
- Translational Gastroenterology Unit, Experimental Medicine, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, UK
- Department of Gastroenterology, National Children's Medical Center, Children's Hospital of Fudan University, 399 Wanyuan Road, Shanghai, 201102, China
| | - Wenhui Hu
- Department of Gastroenterology, National Children's Medical Center, Children's Hospital of Fudan University, 399 Wanyuan Road, Shanghai, 201102, China
| | - Isabel Brooks
- Translational Gastroenterology Unit, Experimental Medicine, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, UK
| | - Isabelle Williams
- Translational Gastroenterology Unit, Experimental Medicine, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, UK
| | - Melania Capitani
- Translational Gastroenterology Unit, Experimental Medicine, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, UK
- SenTcell Ltd., London, UK
| | - Lisa Gartner
- Translational Gastroenterology Unit, Experimental Medicine, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, UK
| | - Daniel Kotlarz
- Dr. von Hauner Children's Hospital, Department of Pediatrics, University Hospital, Ludwig-Maximilians-Universität Munich, Munich, Germany
- Institute of Translational Genomics, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Scott B Snapper
- Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Christoph Klein
- Dr. von Hauner Children's Hospital, Department of Pediatrics, University Hospital, Ludwig-Maximilians-Universität Munich, Munich, Germany
- Gene Center, LMU Munich, Munich, Germany
- Deutsche Zentrum für Infektionsforschung (DZIF) and Deutsches Zentrum für Kinder- und Jugendgesundheit, Partner site Munich, Munich, Germany
| | - Aleixo M Muise
- SickKids Inflammatory Bowel Disease Centre and Cell Biology Program, Research Institute, The Hospital for Sick Children, Toronto, Canada
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Toronto, Canada
- The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Brian D Marsden
- Centre of Medicines Discovery, NDM, University of Oxford, Oxford, OX3 7DQ, UK
- Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Oxford, OX3 7FY, UK
| | - Ying Huang
- Department of Gastroenterology, National Children's Medical Center, Children's Hospital of Fudan University, 399 Wanyuan Road, Shanghai, 201102, China.
| | - Holm H Uhlig
- Translational Gastroenterology Unit, Experimental Medicine, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, UK.
- Department of Pediatrics, University of Oxford, Oxford, UK.
- Biomedical Research Center, University of Oxford, Oxford, UK.
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11
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Lee J, Han JH, Lee CH, Park HS, Min SK, Lee H, Cho U, Yoon SE, Kim SJ, Kim WS, Cho J. Comparison of histological and molecular features of pediatric-type follicular lymphoma and pediatric nodal marginal zone lymphoma. Virchows Arch 2023; 482:849-858. [PMID: 36656392 DOI: 10.1007/s00428-023-03493-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 01/09/2023] [Accepted: 01/11/2023] [Indexed: 01/20/2023]
Abstract
Pediatric-type follicular lymphoma and pediatric nodal marginal zone lymphoma are pediatric B cell lymphomas with similar clinical characteristics but distinct histological features. We investigated the differences between pediatric-type follicular lymphoma and pediatric nodal marginal zone lymphoma by comparing their histological and molecular characteristics. A total of 5 pediatric-type follicular lymphoma and 11 pediatric nodal marginal zone lymphoma patients were included in the study. In the histological review, 5 of the 16 cases showed overlapping morphological features of pediatric-type follicular lymphoma and pediatric nodal marginal zone lymphoma; hence, they were reclassified as "mixed type." In molecular analysis, using panel-based massively parallel sequencing, MAP2K1, TNFRSF14, and IRF8 mutations were found in 6, 3, and 2 of the 11 pediatric nodal marginal zone lymphoma patients, respectively, and IRF8 mutation was found in one of the five pediatric-type follicular lymphoma patients. There were no significant differences in genetic alterations established from the histologically reclassified diagnosis as well as the initial diagnosis. Pediatric-type follicular lymphoma and pediatric nodal marginal zone lymphoma showed morphological overlap in some cases, and no difference between the two was found upon molecular analysis. These findings suggest the possibility that pediatric-type follicular lymphoma and pediatric nodal marginal zone lymphoma are single entity pediatric B-cell lymphoma with broad morphological spectrum.
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Affiliation(s)
- Jiyeon Lee
- Department of Pathology, Korea University Guro Hospital, Seoul, Korea.,Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, #81, Irwon-ro, Gangnam-Gu, Seoul, 06351, Korea
| | - Jae-Ho Han
- Department of Pathology, Ajou University School of Medicine, Suwon, Korea
| | - Chang Hun Lee
- Department of Pathology, Pusan National University Hospital, Pusan National University School of Medicine, Busan, Korea
| | - Ho-Sung Park
- Department of Pathology, Jeonbuk National University Hospital, Jeonbuk National University Medical School, Jeonju, Korea
| | - Soo Kee Min
- Department of Pathology, Hallym University Sacred Heart Hospital, Anyang, Korea
| | - Hojung Lee
- Department of Pathology, Nowon Eulji Medical Center, Eulji University, Seoul, Korea
| | - Uiju Cho
- Department of Pathology, St. Vincent's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Sang Eun Yoon
- Division of Hematology and Oncology, Department of Medicine Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Seok Jin Kim
- Division of Hematology and Oncology, Department of Medicine Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Won Seog Kim
- Division of Hematology and Oncology, Department of Medicine Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Junhun Cho
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, #81, Irwon-ro, Gangnam-Gu, Seoul, 06351, Korea.
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12
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Cho EH, Park JE, Lee T, Ha K, Ki CS. Carrier frequency and incidence estimation of RPE65-associated inherited retinal diseases in East Asian population by population database-based analysis. Orphanet J Rare Dis 2022; 17:409. [PMID: 36352427 PMCID: PMC9644481 DOI: 10.1186/s13023-022-02566-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 10/07/2022] [Accepted: 10/30/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Inherited retinal diseases (IRDs) are clinically and genetically heterogenous disorders leading to visual impairment and blindness. Because gene therapy for RPE65-associated IRDs was recently approved, it is necessary to predict the carrier frequency and prevalence for RPE65-associated IRDs. This study aimed to analyze the carrier frequency and expected incidence of RPE65-associated IRDs in East Asians and Koreans using exome data from the Genome Aggregation Database (gnomAD) and the Korean Reference Genome Database (KRGDB). METHODS We analyzed 9,197 exomes for East Asian populations from gnomAD comprising 1,909 Korean and 1,722 Korean genomes from KRGDB. All identified RPE65 variants were classified according to the 2015 American College of Medical Genetics and Genomics and the Association for Molecular Pathology guidelines. RESULTS The total carrier frequencies of East Asians and Koreans from both gnomAD and KRGDB were 0.10% (11/10,919) and 0.06% (2/3,631), respectively. The estimated incidence of RPE65-associated IRDs was 1/3,941,308 in East Asians and 1/13,184,161 in Koreans. CONCLUSION This study identified carrier frequencies of RPE65-associated IRDs in East Asians and Koreans using gnomAD and KRGDB. We confirmed that the carrier frequency of RPE65-associated IRDs patients was low in Koreans among all East Asian populations, and the incidence was also predicted to be lower than in other East Asian populations. The variant spectrum of RPE65 gene in East Asian and Korean populations differed greatly from those of other ethnic groups.
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Affiliation(s)
- Eun Hye Cho
- Department of Laboratory Medicine, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Jong Eun Park
- Department of Laboratory Medicine, Hanyang University Guri Hospital, Hanyang University College of Medicine, Hanyang University Guri Hospital, 153, Gyeongchun-ro, 11923, Guri-si, Gyeonggi-do, Republic of Korea.
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13
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Kim IY, Kim JH, Choi JE, Yu SJ, Kim JH, Kim SR, Choi MS, Kim MH, Hong KW, Park BC. The first broad replication study of SNPs and a pilot genome-wide association study for androgenetic alopecia in Asian populations. J Cosmet Dermatol 2022; 21:6174-6183. [PMID: 35754308 DOI: 10.1111/jocd.15187] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/10/2022] [Accepted: 06/15/2022] [Indexed: 12/27/2022]
Abstract
BACKGROUND Many candidate genes for androgenetic alopecia (AGA) have been identified in studies of the Caucasians and some Asian populations. AIMS This study aimed to confirm the known susceptibility genes reported in previous studies and find additional candidate genes for high-risk individuals for AGA in Korean population. PATIENTS/METHODS We recapitulated the previously reported SNPs and identified the novel Korean AGA risk genetic variants using a Korean hospital-based AGA case and control samples. The population was consisting of 494 individuals (275 AGA cases and 146 controls). Using the 800 K SNPs of precision medical research array (PMRA SNP microarray chip) and imputation-based SNPs, 12 previous GWAS reports for AGA and a total of 62 160 SNPs were examined in our study samples. Also, we conducted the genome-wide association study (GWAS) by the logistic regression analyses for AGA cases and controls with controlling the age as the covariates. RESULTS Among the 62 160 SNPs, a total of 1143 SNPs in 76 gene regions showed weak replication tendency with the p-values <0.05 and same direction of effects. Additionally, the GWAS results showed 110 SNPs in 13 independent regions with the suggestive p-values <1.00 × 10-5 . The most significantly replicated SNP resided on chromosome 20, which were similar to other AGA replication studies including Chinese study. The GWAS identified two SNPs (rs11010734 and rs2420640) increasing the risk for AGA in our study population. CONCLUSIONS Our study would be a reference of the non-European studies to better understand AGA in different populations and ancestral contexts.
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Affiliation(s)
- In-Young Kim
- Division of Personal Genome Service, Theragen Bio Co., Ltd., Seongnam, Gyeonggi, Korea
| | - Ji-Hye Kim
- Division of Personal Genome Service, Theragen Bio Co., Ltd., Seongnam, Gyeonggi, Korea
| | - Ja-Eun Choi
- Division of Personal Genome Service, Theragen Bio Co., Ltd., Seongnam, Gyeonggi, Korea
| | - So-Jin Yu
- Division of Personal Genome Service, Theragen Bio Co., Ltd., Seongnam, Gyeonggi, Korea
| | - Joo Hee Kim
- Department of Dermatology, College of Medicine, Dankook University, Cheonan, Korea.,Basic and Clinical Hair Institute, Dankook University, Cheonan, Korea
| | - Soon Rye Kim
- Department of Dermatology, College of Medicine, Dankook University, Cheonan, Korea.,Basic and Clinical Hair Institute, Dankook University, Cheonan, Korea
| | - Mi Soo Choi
- Department of Dermatology, College of Medicine, Dankook University, Cheonan, Korea
| | - Myung Hwa Kim
- Department of Dermatology, College of Medicine, Dankook University, Cheonan, Korea
| | - Kyung-Won Hong
- Division of Personal Genome Service, Theragen Bio Co., Ltd., Seongnam, Gyeonggi, Korea
| | - Byung-Cheol Park
- Department of Dermatology, College of Medicine, Dankook University, Cheonan, Korea.,Basic and Clinical Hair Institute, Dankook University, Cheonan, Korea
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14
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Lee CK, Rha SY, Kim HS, Jung M, Kang B, Che J, Kwon WS, Park S, Bae WK, Koo DH, Shin SJ, Kim H, Jeung HC, Zang DY, Lee SK, Nam CM, Chung HC. A single arm phase Ib/II trial of first-line pembrolizumab, trastuzumab and chemotherapy for advanced HER2-positive gastric cancer. Nat Commun 2022; 13:6002. [PMID: 36224176 PMCID: PMC9556512 DOI: 10.1038/s41467-022-33267-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 09/09/2022] [Indexed: 12/24/2022] Open
Abstract
In this multi-center phase II trial, we evaluated the efficacy and safety of a quadruplet regimen (pembrolizumab, trastuzumab, and doublet chemotherapy) as first-line therapy for unresectable or metastatic human epidermal growth factor receptor 2 (HER2)-positive advanced gastric cancer (AGC) (NCT02901301). The primary endpoints were recommended phase 2 dose (RP2D) for phase Ib and objective response rate (ORR) for phase II. The secondary endpoints included progression-free survival (PFS), overall survival (OS), duration of response, time to response and safety. Without dose-limiting or unexpected toxicities, the starting dose in the phase Ib trial was selected as RP2D. In 43 patients, the primary endpoint was achieved: the objective response rate was 76.7% (95% confidence interval [CI]: 61.4-88.2), with complete and partial responses in 14% and 62.8% of patients, respectively. The median progression-free survival, overall survival, and duration of response were 8.6 months, 19.3 months, and 10.8 months, respectively. No patients discontinued pembrolizumab because of immune-related adverse events. Programmed death ligand-1 status was not related to survival. Post hoc analyses of pretreatment tumor specimens via targeted sequencing indicated that ERBB2 amplification, RTK/RAS pathway alterations, and high neoantigen load corrected by HLA-B were positively related to survival. The current quadruplet regimen shows durable efficacy and safety for patients with HER2-positive AGC.
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Affiliation(s)
- Choong-Kun Lee
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, South Korea
- Sondang Institute for Cancer Research, Yonsei University College of Medicine, Seoul, South Korea
| | - Sun Young Rha
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, South Korea
- Sondang Institute for Cancer Research, Yonsei University College of Medicine, Seoul, South Korea
| | - Hyo Song Kim
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, South Korea
- Sondang Institute for Cancer Research, Yonsei University College of Medicine, Seoul, South Korea
| | - Minkyu Jung
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, South Korea
- Sondang Institute for Cancer Research, Yonsei University College of Medicine, Seoul, South Korea
| | - Beodeul Kang
- Department of Medical Oncology, CHA Bundang Medical Center, CHA University, Seongnam, South Korea
| | - Jingmin Che
- Sondang Institute for Cancer Research, Yonsei University College of Medicine, Seoul, South Korea
| | - Woo Sun Kwon
- Sondang Institute for Cancer Research, Yonsei University College of Medicine, Seoul, South Korea
| | - Sejung Park
- Sondang Institute for Cancer Research, Yonsei University College of Medicine, Seoul, South Korea
- Department of Biostatistics and Computing, Yonsei University College of Medicine, Seoul, South Korea
| | - Woo Kyun Bae
- Division of Hematology-Oncology, Department of Internal Medicine, Chonnam National University Medical School and Hwasun Hospital, Jeollanam-do, South Korea
| | - Dong-Hoe Koo
- Division of Hematology/Oncology, Department of Internal Medicine, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Su-Jin Shin
- Department of Pathology, Yonsei University College of Medicine, Seoul, South Korea
| | - Hyunki Kim
- Department of Pathology, Yonsei University College of Medicine, Seoul, South Korea
| | - Hei-Cheul Jeung
- Department of Internal Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
| | - Dae Young Zang
- Division of Hematology-Oncology, Department of Internal Medicine, Hallym University Medical Center, Hallym University College of Medicine, Anyang, South Korea
| | - Sang Kil Lee
- Division of Gastroenterology, Department of Internal Medicine, Yonsei University College of Medicine, Seoul, South Korea
| | - Chung Mo Nam
- Department of Preventive Medicine, Yonsei University College of Medicine, Seoul, South Korea
| | - Hyun Cheol Chung
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, South Korea.
- Sondang Institute for Cancer Research, Yonsei University College of Medicine, Seoul, South Korea.
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15
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Kim EJ, Na DL, Kim HJ, Park KW, Lee JH, Roh JH, Kwon JC, Yoon SJ, Jung NY, Jeong JH, Jang JW, Kim HJ, Park KH, Choi SH, Kim S, Park YH, Kim BC, Youn YC, Ki CS, Kim SH, Seo SW, Kim YE. Genetic Screening in Korean Patients with Frontotemporal Dementia Syndrome. J Alzheimers Dis Rep 2022; 6:651-662. [DOI: 10.3233/adr-220030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 09/04/2022] [Indexed: 11/15/2022] Open
Abstract
Background: Frontotemporal dementia (FTD) syndrome is a genetically heterogeneous group of diseases. However, pathogenic variants in the chromosome 9 open reading frame 72 (C9orf72), microtubule-associated protein tau (MAPT), and progranulin (GRN) genes are mainly associated with genetic FTD in Caucasian populations. Objective: To understand the genetic background of Korean patients with FTD syndrome. Methods: We searched for pathogenic variants of 52 genes related to FTD, amyotrophic lateral sclerosis, familial Alzheimer’s disease, and other dementias, and hexanucleotide repeats of the C9orf72 gene in 72 Korean patients with FTD using whole exome sequencing and the repeat-primed polymerase chain reaction, respectively. Results: One likely pathogenic variant, p.G706R of MAPT, in a patient with behavioral variant FTD (bvFTD) and 13 variants of uncertain significance (VUSs) in nine patients with FTD were identified. Of these VUSs, M232R of the PRNP gene, whose role in pathogenicity is controversial, was also found in two patients with bvFTD. Conclusions: These results indicate that known pathogenic variants of the three main FTD genes (MAPT, GRN, and C9orf72) in Western countries are rare in Korean FTD patients.
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Affiliation(s)
- Eun-Joo Kim
- Department of Neurology, Pusan National University Hospital, Pusan National University School of Medicine and Medical Research Institute, Busan, Korea
| | - Duk L. Na
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Hee-Jin Kim
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Kyung Won Park
- Department of Neurology, Dong-A Medical Center, Dong-A University College of Medicine, Busan, Korea
| | - Jae-Hong Lee
- Department of Neurology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Jee Hoon Roh
- Department of Biomedical Sciences and Department of Physiology, Korea University College of Medicine, Seoul, Republic of Korea
| | - Jay C. Kwon
- Department of Neurology, Changwon Fatima Hospital, Changwon, Korea
| | - Soo Jin Yoon
- Department of Neurology, Eulji University Hospital, Daejeon
| | - Na-Yeon Jung
- Department of Neurology, Pusan National University Yangsan Hospital, Research Institute for Convergence of Biomedical Science and Technology, Busan, Korea
| | - Jee H. Jeong
- Department of Neurology, Ewha Womans University Hospital, Seoul
| | - Jae-Won Jang
- Department of Neurology, Kangwon National University Hospital, Chuncheon
| | - Hee-Jin Kim
- Department of Neurology, Hanyang University College of Medicine, Seoul, Korea
| | - Kee Hyung Park
- Department of Neurology, Gachon University Gil Hospital, Incheon, Korea
| | - Seong Hye Choi
- Department of Neurology, Inha University School of Medicine, Incheon, Korea
| | - SangYun Kim
- Department of Neurology, Seoul National University College of Medicine and Clinical Neuroscience Center, Seoul National University Bundang Hospital, Gyeonggi-do, Korea
| | - Young Ho Park
- Department of Neurology, Seoul National University College of Medicine and Clinical Neuroscience Center, Seoul National University Bundang Hospital, Gyeonggi-do, Korea
| | - Byeong C. Kim
- Department of Neurology, Chonnam National University Medical School, Gwangju, Korea
| | - Young Chul Youn
- Department of Neurology, Chung-Ang University Hospital, Chung-Ang University College of Medicine, Seoul, Korea
| | | | - Seung-Hyun Kim
- Department of Neurology, Hanyang University College of Medicine, Seoul, Korea
| | - Sang Won Seo
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
- Department of Neurology, Gachon University Gil Hospital, Incheon, Korea
| | - Young-Eun Kim
- Department of Laboratory Medicine, Hanyang University College of Medicine, Seoul, Korea
- Department of Neurology, Gachon University Gil Hospital, Incheon, Korea
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16
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Shigemizu D, Asanomi Y, Akiyama S, Higaki S, Sakurai T, Ito K, Niida S, Ozaki K. Network-based meta-analysis and the candidate gene association studies reveal novel ethnicity-specific variants in MFSD3 and MRPL43 associated with dementia with Lewy bodies. Am J Med Genet B Neuropsychiatr Genet 2022; 189:139-150. [PMID: 35765761 PMCID: PMC9543256 DOI: 10.1002/ajmg.b.32908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 01/18/2022] [Accepted: 06/14/2022] [Indexed: 11/06/2022]
Abstract
Dementia with Lewy bodies (DLB) is the second most common form of neurodegenerative dementia in elderly people, following Alzheimer's disease. Only three genes, SNCA (α-synuclein), APOE (apolipoprotein E), and GBA (glucosylceramidase), have been convincingly demonstrated to be associated with DLB. Here, we applied whole-genome sequencing to blood samples from 61 DLB patients and 45 cognitively normal controls. We used accumulation of candidate mutations to detect novel DLB-associated genes. Subsequent single nucleotide polymorphism (SNP) genotyping and association studies in a large number of samples from Japanese individuals revealed novel heterozygous variants in MFSD3 (rs143475431, c.888T>A:p.C296*; n = 5,421, p = 0.00063) and MRPL43 (chr10:102746730, c.241A>C:p.N81H; n = 4,782, p = 0.0029). We further found that the MFSD3 variant increased plasma levels of butyrylcholinesterase (n = 1,206, p = 0.029). We believe that our findings will contribute to the understanding of DLB and provide insight into its pathogenic mechanism for future studies.
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Affiliation(s)
- Daichi Shigemizu
- Medical Genome Center, Research InstituteNational Center for Geriatrics and GerontologyObuAichiJapan
- RIKEN Center for Integrative Medical SciencesYokohamaKanagawaJapan
| | - Yuya Asanomi
- Medical Genome Center, Research InstituteNational Center for Geriatrics and GerontologyObuAichiJapan
| | - Shintaro Akiyama
- Medical Genome Center, Research InstituteNational Center for Geriatrics and GerontologyObuAichiJapan
| | - Sayuri Higaki
- Medical Genome Center, Research InstituteNational Center for Geriatrics and GerontologyObuAichiJapan
| | - Takashi Sakurai
- Department of Prevention and Care Science, Center for Development of Advanced Medicine for Dementia, Research InstituteNational Center for Geriatrics and GerontologyObuAichiJapan
- Department of Cognitive and Behavioral ScienceNagoya University Graduate School of MedicineNagoyaAichiJapan
| | - Kengo Ito
- National Center for Geriatrics and GerontologyObuAichiJapan
| | - Shumpei Niida
- Core Facility Administration, Research InstituteNational Center for Geriatrics and GerontologyObuAichiJapan
| | - Kouichi Ozaki
- Medical Genome Center, Research InstituteNational Center for Geriatrics and GerontologyObuAichiJapan
- RIKEN Center for Integrative Medical SciencesYokohamaKanagawaJapan
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17
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CD47 overexpression is common in intestinal non-GCB type diffuse large B-cell lymphoma and associated with 18q21 gain. Blood Adv 2022; 6:6120-6130. [PMID: 35475881 PMCID: PMC9768246 DOI: 10.1182/bloodadvances.2021006305] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 03/22/2022] [Accepted: 03/26/2022] [Indexed: 12/30/2022] Open
Abstract
The CD47/signal regulatory protein α pathway is an emerging immune checkpoint that is a new therapeutic target. We investigated CD47 expression in diffuse large B-cell lymphoma (DLBCL) of various subtypes and organs. Moreover, the relationship between CD47 expression and genetic alterations was analyzed using panel-based massively parallel sequencing (next-generation sequencing [NGS]). CD8, CD68, and CD47 immunohistochemical staining were performed on 238 patients with DLBCL. CD47 was scored according to intensity on a 5-level scale, and CD8 and CD68 were quantitatively evaluated using QuPath software. Panel-based NGS was performed in 37 patients. In CD8 and CD68 quantitative analyses by organs, intestinal DLBCL showed significantly lower cytotoxic T-cell infiltration than that in others (P < .001). The CD47-high group comprised 24 of 58 (41.4%) patients in the group with DLBCL from intestine and 15 of 180 (8.3%) patients in the group with DLBCL from other organs (P < .001). The 18q21 gain/amplification was found in 10 of 37 patients, and all of them were CD47-high. Intestinal CD47-high DLBCL occurred in terminal ileum to ascending colon and was restricted to nongerminal center B-cell type. In the survival analyses, the prognosis of nonintestinal CD47-high DLBCL was poorer than that of intestinal CD47-high DLBCL (P = .025). CD47-high DLBCL was closely associated with 18q21 gain/amplification and showed a high prevalence in intestine. We propose to classify CD47-high DLBCL into intestinal and nonintestinal types. Further studies are necessary to assess whether the constellation of features seen here is reproducible and sufficient to consider primary intestinal DLBCL as a distinct biological entity.
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Yang HJ, Park G, Nam-Goong IS, Ahn JW, Weon YC. The First Korean Siblings With Adult-Onset 4H Leukodystrophy Related to Nonsynonymous POLR3B Mutations. NEUROLOGY GENETICS 2022; 8:e667. [PMID: 35434302 PMCID: PMC9007423 DOI: 10.1212/nxg.0000000000000667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 02/07/2022] [Indexed: 11/21/2022]
Abstract
Objectives 4H leukodystrophy is a rare autosomal recessive hypomyelinating disorder characterized by several combinations of motor dysfunction, abnormal dentition, and ophthalmic and endocrine abnormalities. To date, only a single Korean case report of pediatric leukodystrophy caused by the POLR1C sequence variation has been published, while there are no reports on the POLR3B, POLR3A, or POLR3K variants. Methods Genetic tests of Korean sibling pairs with primary amenorrhea due to normosmic isolated hypogonadotropic hypogonadism and cognitive or behavioral symptoms were performed by whole-exome sequencing (WES). The WES results were validated by direct Sanger sequencing. Results We identified biallelic variations in the POLR3B gene of p.Tyr685* and p.Tyr746Cys, which have not been associated with 4H leukodystrophy. Both sequence variants lie in the hybrid-binding domain of the protein RPC2. The protein structure analysis predicted that cysteine substitution of the phylogenetically conserved amino acid tyrosine can cause destabilization. Discussion The siblings reported are the first POLR3B-related hypomyelinating leukodystrophy cases in Korea. Our report expands the mutational spectrum of 4H leukodystrophy and suggests that it is mandatory to consider its diagnostic possibility in adult patients presenting with primary amenorrhea and mild cognitive or behavioral symptoms.
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Affiliation(s)
- Hui-Jun Yang
- Department of Neurology (H.-J.Y.), Department of Radiology (G.P., Y.C.W.), Department of Internal Medicine (I.S.N.-G.), and Department of Obstetrics and Gynecology (J.-W.A.), Ulsan University Hospital, University of Ulsan College of Medicine, South Korea
| | - Gyeongmin Park
- Department of Neurology (H.-J.Y.), Department of Radiology (G.P., Y.C.W.), Department of Internal Medicine (I.S.N.-G.), and Department of Obstetrics and Gynecology (J.-W.A.), Ulsan University Hospital, University of Ulsan College of Medicine, South Korea
| | - Il Seong Nam-Goong
- Department of Neurology (H.-J.Y.), Department of Radiology (G.P., Y.C.W.), Department of Internal Medicine (I.S.N.-G.), and Department of Obstetrics and Gynecology (J.-W.A.), Ulsan University Hospital, University of Ulsan College of Medicine, South Korea
| | - Jun-Woo Ahn
- Department of Neurology (H.-J.Y.), Department of Radiology (G.P., Y.C.W.), Department of Internal Medicine (I.S.N.-G.), and Department of Obstetrics and Gynecology (J.-W.A.), Ulsan University Hospital, University of Ulsan College of Medicine, South Korea
| | - Young Cheol Weon
- Department of Neurology (H.-J.Y.), Department of Radiology (G.P., Y.C.W.), Department of Internal Medicine (I.S.N.-G.), and Department of Obstetrics and Gynecology (J.-W.A.), Ulsan University Hospital, University of Ulsan College of Medicine, South Korea
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Kang CH, Kim YM, Kim YJ, Hong SJ, Kim DY, Woo HG, Kim YR, Kim JG, Lee JS, Kong MH, Kim HJ, Choi JC. Pathogenic NOTCH3 Variants Are Frequent Among the Korean General Population. Neurol Genet 2021; 7:e639. [PMID: 34881353 PMCID: PMC8650050 DOI: 10.1212/nxg.0000000000000639] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 10/05/2021] [Indexed: 01/22/2023]
Abstract
OBJECTIVE This study aimed to determine the frequency of pathogenic NOTCH3 variants among Koreans. METHODS In this cross-sectional study, we queried for pathogenic NOTCH3 variants in 2 Korean public genome databases: the Korean Reference Genome Database (KRGDB) and the Korean Genome Project (Korea1K). In addition, we screened the 3 most common pathogenic NOTCH3 variants (p.Arg75Pro, p.Arg544Cys, and p.Arg578Cys) for 1,000 individuals on Jeju Island, where the largest number of patients with cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) have been reported in Korea. RESULTS The pathogenic NOTCH3 variant (p.Arg544Cys) was found in 0.12% of sequences in the KRGDB, and 3 pathogenic variants (p.Arg75Pro, p.Arg182Cys, and p.Arg544Cys) were present in 0.44% of the Korea1K database. Of the 1,000 individuals on Jeju Island, we found 2 cysteine-altering NOTCH3 variants (p.Arg544Cys variant in 9 and p.Arg578Cys in 1 individual) in 1.00% of the participants (95% confidence interval: 0.48%-1.83%). The presence of cysteine-altering NOTCH3 variants was significantly associated with a history of stroke (p < 0.001). DISCUSSION Pathogenic NOTCH3 variants are frequently found in the general Korean population. Such a high prevalence of pathogenic variants could threaten the brain health of tens of thousands to hundreds of thousands of older adults in Korea.
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Affiliation(s)
| | | | - Yang-Ji Kim
- From the Department of Neurology (C.-H.K., J.-G.K., J.S.L., J.C.C.), Jeju National University Hospital, Jeju National University School of Medicine; Department of Biochemistry (Y.M.K.), School of Medicine; Institute of Medical Science (Y.-J.K., S.-J.H., J.C.C.), Jeju National University, Korea; Department of Physiology (D.Y.K., H.G.W.), School of Medicine; Department of Biomedical Science (D.Y.K., H.G.W.), Graduate School, Ajou University, Suwon, Republic of Korea; Department of Laboratory Medicine (Y.R.K.), School of Medicine, Jeju National University; Department of Family Medicine (M.H.K., H.J.K.), Jeju National University Hospital; and Department of Family Medicine (M.H.K., H.J.K.), School of Medicine, Jeju National University, Korea
| | - Su-Jeong Hong
- From the Department of Neurology (C.-H.K., J.-G.K., J.S.L., J.C.C.), Jeju National University Hospital, Jeju National University School of Medicine; Department of Biochemistry (Y.M.K.), School of Medicine; Institute of Medical Science (Y.-J.K., S.-J.H., J.C.C.), Jeju National University, Korea; Department of Physiology (D.Y.K., H.G.W.), School of Medicine; Department of Biomedical Science (D.Y.K., H.G.W.), Graduate School, Ajou University, Suwon, Republic of Korea; Department of Laboratory Medicine (Y.R.K.), School of Medicine, Jeju National University; Department of Family Medicine (M.H.K., H.J.K.), Jeju National University Hospital; and Department of Family Medicine (M.H.K., H.J.K.), School of Medicine, Jeju National University, Korea
| | - Do Yoon Kim
- From the Department of Neurology (C.-H.K., J.-G.K., J.S.L., J.C.C.), Jeju National University Hospital, Jeju National University School of Medicine; Department of Biochemistry (Y.M.K.), School of Medicine; Institute of Medical Science (Y.-J.K., S.-J.H., J.C.C.), Jeju National University, Korea; Department of Physiology (D.Y.K., H.G.W.), School of Medicine; Department of Biomedical Science (D.Y.K., H.G.W.), Graduate School, Ajou University, Suwon, Republic of Korea; Department of Laboratory Medicine (Y.R.K.), School of Medicine, Jeju National University; Department of Family Medicine (M.H.K., H.J.K.), Jeju National University Hospital; and Department of Family Medicine (M.H.K., H.J.K.), School of Medicine, Jeju National University, Korea
| | - Hyun Goo Woo
- From the Department of Neurology (C.-H.K., J.-G.K., J.S.L., J.C.C.), Jeju National University Hospital, Jeju National University School of Medicine; Department of Biochemistry (Y.M.K.), School of Medicine; Institute of Medical Science (Y.-J.K., S.-J.H., J.C.C.), Jeju National University, Korea; Department of Physiology (D.Y.K., H.G.W.), School of Medicine; Department of Biomedical Science (D.Y.K., H.G.W.), Graduate School, Ajou University, Suwon, Republic of Korea; Department of Laboratory Medicine (Y.R.K.), School of Medicine, Jeju National University; Department of Family Medicine (M.H.K., H.J.K.), Jeju National University Hospital; and Department of Family Medicine (M.H.K., H.J.K.), School of Medicine, Jeju National University, Korea
| | - Young Ree Kim
- From the Department of Neurology (C.-H.K., J.-G.K., J.S.L., J.C.C.), Jeju National University Hospital, Jeju National University School of Medicine; Department of Biochemistry (Y.M.K.), School of Medicine; Institute of Medical Science (Y.-J.K., S.-J.H., J.C.C.), Jeju National University, Korea; Department of Physiology (D.Y.K., H.G.W.), School of Medicine; Department of Biomedical Science (D.Y.K., H.G.W.), Graduate School, Ajou University, Suwon, Republic of Korea; Department of Laboratory Medicine (Y.R.K.), School of Medicine, Jeju National University; Department of Family Medicine (M.H.K., H.J.K.), Jeju National University Hospital; and Department of Family Medicine (M.H.K., H.J.K.), School of Medicine, Jeju National University, Korea
| | - Joong-Goo Kim
- From the Department of Neurology (C.-H.K., J.-G.K., J.S.L., J.C.C.), Jeju National University Hospital, Jeju National University School of Medicine; Department of Biochemistry (Y.M.K.), School of Medicine; Institute of Medical Science (Y.-J.K., S.-J.H., J.C.C.), Jeju National University, Korea; Department of Physiology (D.Y.K., H.G.W.), School of Medicine; Department of Biomedical Science (D.Y.K., H.G.W.), Graduate School, Ajou University, Suwon, Republic of Korea; Department of Laboratory Medicine (Y.R.K.), School of Medicine, Jeju National University; Department of Family Medicine (M.H.K., H.J.K.), Jeju National University Hospital; and Department of Family Medicine (M.H.K., H.J.K.), School of Medicine, Jeju National University, Korea
| | - Jung Seok Lee
- From the Department of Neurology (C.-H.K., J.-G.K., J.S.L., J.C.C.), Jeju National University Hospital, Jeju National University School of Medicine; Department of Biochemistry (Y.M.K.), School of Medicine; Institute of Medical Science (Y.-J.K., S.-J.H., J.C.C.), Jeju National University, Korea; Department of Physiology (D.Y.K., H.G.W.), School of Medicine; Department of Biomedical Science (D.Y.K., H.G.W.), Graduate School, Ajou University, Suwon, Republic of Korea; Department of Laboratory Medicine (Y.R.K.), School of Medicine, Jeju National University; Department of Family Medicine (M.H.K., H.J.K.), Jeju National University Hospital; and Department of Family Medicine (M.H.K., H.J.K.), School of Medicine, Jeju National University, Korea
| | - Mi Hee Kong
- From the Department of Neurology (C.-H.K., J.-G.K., J.S.L., J.C.C.), Jeju National University Hospital, Jeju National University School of Medicine; Department of Biochemistry (Y.M.K.), School of Medicine; Institute of Medical Science (Y.-J.K., S.-J.H., J.C.C.), Jeju National University, Korea; Department of Physiology (D.Y.K., H.G.W.), School of Medicine; Department of Biomedical Science (D.Y.K., H.G.W.), Graduate School, Ajou University, Suwon, Republic of Korea; Department of Laboratory Medicine (Y.R.K.), School of Medicine, Jeju National University; Department of Family Medicine (M.H.K., H.J.K.), Jeju National University Hospital; and Department of Family Medicine (M.H.K., H.J.K.), School of Medicine, Jeju National University, Korea
| | - Hyeon Ju Kim
- From the Department of Neurology (C.-H.K., J.-G.K., J.S.L., J.C.C.), Jeju National University Hospital, Jeju National University School of Medicine; Department of Biochemistry (Y.M.K.), School of Medicine; Institute of Medical Science (Y.-J.K., S.-J.H., J.C.C.), Jeju National University, Korea; Department of Physiology (D.Y.K., H.G.W.), School of Medicine; Department of Biomedical Science (D.Y.K., H.G.W.), Graduate School, Ajou University, Suwon, Republic of Korea; Department of Laboratory Medicine (Y.R.K.), School of Medicine, Jeju National University; Department of Family Medicine (M.H.K., H.J.K.), Jeju National University Hospital; and Department of Family Medicine (M.H.K., H.J.K.), School of Medicine, Jeju National University, Korea
| | - Jay Chol Choi
- From the Department of Neurology (C.-H.K., J.-G.K., J.S.L., J.C.C.), Jeju National University Hospital, Jeju National University School of Medicine; Department of Biochemistry (Y.M.K.), School of Medicine; Institute of Medical Science (Y.-J.K., S.-J.H., J.C.C.), Jeju National University, Korea; Department of Physiology (D.Y.K., H.G.W.), School of Medicine; Department of Biomedical Science (D.Y.K., H.G.W.), Graduate School, Ajou University, Suwon, Republic of Korea; Department of Laboratory Medicine (Y.R.K.), School of Medicine, Jeju National University; Department of Family Medicine (M.H.K., H.J.K.), Jeju National University Hospital; and Department of Family Medicine (M.H.K., H.J.K.), School of Medicine, Jeju National University, Korea
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20
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Kang S, Jeong JH, Yoon S, Yoo C, Kim KP, Cho H, Ryoo BY, Jung J, Kim JE. Real-world data analysis of patients with cancer of unknown primary. Sci Rep 2021; 11:23074. [PMID: 34845302 PMCID: PMC8630084 DOI: 10.1038/s41598-021-02543-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 10/15/2021] [Indexed: 01/08/2023] Open
Abstract
Cancer of unknown primary (CUP) is a heterogeneous malignancy in which the primary site of the tumor cannot be identified through standard work-up. The survival outcome of CUP is generally poor, and there is no consensus for treatment. Here, we comprehensively analyzed the real-world data of 218 patients with CUP (median age, 62 years [range, 19-91]; male, 62.3%). Next-generation sequencing was conducted in 22 (10%) patients, one of whom showed level 1 genetic alteration. Most (60.3%) patients were treated with empirical cytotoxic chemotherapy, and two patients received targeted therapy based on the NGS results. The median OS was 8.3 months (95% confidence interval [CI] 6.2-11.4), and the median progression-free survival of patients treated with chemotherapy was 4.4 months (95% CI 3.4-5.3). In multivariate Cox regression analysis, Eastern Cooperative Oncology Group performance status (ECOG PS) of 0 or 1 and localized disease were significantly associated with favorable survival outcomes. Collectively, we found that CUP patients had a poor prognosis after standard treatment, and those with localized disease who received local treatment and those with better PS treated with multiple lines of chemotherapy had better survival outcomes. Targeted therapies based on NGS results are expected to improve survival outcomes.
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Affiliation(s)
- Sora Kang
- Department of Medical Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Jae Ho Jeong
- Department of Medical Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Shinkyo Yoon
- Department of Medical Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Changhoon Yoo
- Department of Medical Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Kyu-Pyo Kim
- Department of Medical Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Hyungwoo Cho
- Department of Medical Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Baek-Yeol Ryoo
- Department of Medical Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Jinhong Jung
- Department of Radiation Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Jeong Eun Kim
- Department of Medical Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea.
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21
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Lee Y, Yun J, Jeong D, Ryu S, Kwon SR, Yun H, Kim SM, Park JH, Lee DS. Genetic profile of primary plasma cell leukemia in Korea: comparison with plasma cell myeloma. Leuk Lymphoma 2021; 63:385-394. [PMID: 34592901 DOI: 10.1080/10428194.2021.1983568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Plasma cell leukemia (PCL) is clinically and genetically distinct from multiple myeloma (MM), despite controversies regarding the disease definition. To determine the distinct features of PCL, the genetic property of primary PCL (pPCL) was compared with that of secondary PCL (sPCL) and MM. In patients with pPCL, Eighty-nine non-synonymous mutations were observed in 68 genes. The most frequently mutated genes were TP53, TSC2, and TYK2. In comparison with genetic abnormalities of sPCL and MM, 45 genes were present only in pPCL while 28 genes were only in sPCL and 22 genes only in MM. Among the common genes between pPCL and MM, a higher prevalence of TP53 was observed in pPCL, compared to MM (p < 0.05), while similar, compared to sPCL (p = 0.64). In summary, pPCL patients showed a higher level of genetic heterogeneity and distinctive genetic signature in their mutational profile compared to patients with MM and sPCL.
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Affiliation(s)
- Youngeun Lee
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, South Korea
| | - Jiwon Yun
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, South Korea
| | - Dajeong Jeong
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, South Korea
| | - Sohee Ryu
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, South Korea
| | - Seok Ryun Kwon
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, South Korea
| | - Hongseok Yun
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, South Korea
| | - Sung Min Kim
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, South Korea
| | - Jae Hyeon Park
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, South Korea
| | - Dong Soon Lee
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, South Korea.,Cancer Research Institute, Seoul National University College of Medicine, Seoul, South Korea
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22
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Cho J, Yoon SE, Kim SJ, Ko YH, Kim WS. Comparison of tumor mutation burden of 300 various non-Hodgkin lymphomas using panel based massively parallel sequencing. BMC Cancer 2021; 21:972. [PMID: 34461835 PMCID: PMC8404326 DOI: 10.1186/s12885-021-08695-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 08/17/2021] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Tumor mutation burden is an emerging biomarker for immunotherapy. Although several clinical trials for immunotherapy in lymphoma have been carried out, the mutation burden of various lymphomas is not well known yet. Thus, the objective of this study was to compare tumor mutation burden of various non-Hodgkin lymphomas using panel based massively parallel sequencing. METHODS We conducted 405 gene panel based massively parallel sequencing of 300 non-Hodgkin lymphomas and investigate the number of SNV/Indel in each lymphoma. RESULTS The number of SNV/Indel was higher in mature B-cell lymphoma than in mature T- and NK-cell lymphoma. (P < 0.001) The number of SNV/Indel in primary mediastinal large B-cell lymphoma and primary diffuse large B-cell lymphoma of the central nervous system was the highest, which was significantly higher than that in diffuse large B-cell lymphoma, not otherwise specified (DLBCL NOS).(P = 0.030 and P = 0.008, respectively) The SNV/Indel number in EBV-positive DLBCL NOS was significantly lower than that in DLBCL NOS. (P = 0.048) Peripheral T-cell lymphoma, NOS showed no significant difference in the number of SNV/Indel from extranodal NK/T-cell lymphoma, nasal type (P = 0.942) or angioimmunoblastic T-cell lymphoma (P = 0.739). The number of SNV/Indel in anaplastic large cell lymphoma, ALK-positive was significantly lower than that in anaplastic large cell lymphoma, ALK-negative (P = 0.049). It was the lowest among all the lymphomas considered. CONCLUSION Various lymphomas have different mutation burdens. Thus, tumor mutation burden can be used as a promising biomarker for immunotherapy in lymphomas.
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Affiliation(s)
- Junhun Cho
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Sang Eun Yoon
- Division of Hematology and Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, #81, Irwon-ro, Gangnam-Gu, Seoul, 06351, South Korea
| | - Seok Jin Kim
- Division of Hematology and Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, #81, Irwon-ro, Gangnam-Gu, Seoul, 06351, South Korea
| | - Young Hyeh Ko
- Department of Pathology, Korea University Guro hospital, #148, Gurodong-ro, Guro-gu, Seoul, 08308, South Korea.
- Department of Pathology, Hanyang University hospital, #222-1, Wangsimni-ro, Seongdong-gu, Seoul, 04763, South Korea.
| | - Won Seog Kim
- Division of Hematology and Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, #81, Irwon-ro, Gangnam-Gu, Seoul, 06351, South Korea.
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Sirivarasai J, Chanprasertyothin S, Kongtip P, Woskie S. Genetic Polymorphisms of Pesticide-Metabolizing Enzymes and Transporters in Agricultural Workers and Thyroid Hormone Levels. Risk Manag Healthc Policy 2021; 14:3435-3451. [PMID: 34434063 PMCID: PMC8380960 DOI: 10.2147/rmhp.s314510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 07/22/2021] [Indexed: 11/23/2022] Open
Abstract
PURPOSE Chronic exposure to pesticides has been associated with thyroid dysfunction owing to their endocrine disruption ability. Genetic variations in genes encoding phase I and II enzymes and phase III transporters are partly responsible for individual responses to chemical pesticides. This study investigated the association between variations in genes involved in pesticide metabolism and altered thyroid hormone concentrations. METHODS We assessed thyroid-stimulating hormone (TSH), free triiodothyronine (FT3), and free thyroxine (FT4) in organic agriculture workers (n = 216) and workers who used chemical pesticides (n = 229). A questionnaire was used to collect sociodemographic, pesticide exposure, and health status data. Blood samples were analyzed for TSH, FT3, and FT4. Genomic DNA was extracted and genotyped using the TaqMan real-time PCR genotyping assay and restriction fragment length polymorphism method for 15 metabolically related genes. RESULTS Significant differences in the TSH (1.58 vs 1.12 µIU/mL) and FT3 (0.34 vs 0.31 ng/dL) concentrations between the chemical and organic worker groups were observed. The frequencies of all single nucleotide polymorphisms were in Hardy-Weinberg equilibrium and were mostly consistent with Asian populations. The findings showed the association between SNPs of enzymes and transporters and TSH, FT3, and FT4. The odd ratio and adjusted odd ratio (with sex, age, smoking status, alcohol consumption and exposure parameters) for subclinical thyroid disease by the variant alleles CYP1A1 rs1048943, CYP2B6 rs2279343, CYP2C19 rs4244285, NAT2 rs1799931, and PON1 rs662 in the chemical workers compared with the organic workers were found (P values < 0.05). CONCLUSION This is the first study to assess gene-environment interactions in Thai agricultural workers by investigating disruptions of the hypothalamic-pituitary-thyroid axis. The investigated SNP profiles revealed several gene-thyroid hormone associations in which even low levels of pesticide exposure could disturb thyroid homeostasis. These findings provide a foundation for planning future studies investigating associations between complex diseases and occupational pesticide exposure.
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Affiliation(s)
- Jintana Sirivarasai
- Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Suwanee Chanprasertyothin
- Research and Innovation Center, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Pornpimol Kongtip
- Department of Occupational Health and Safety, Faculty of Public Health, Mahidol University, Bangkok, Thailand
| | - Susan Woskie
- Department of Public Health, University of Massachusetts Lowell, Lowell, MA, USA
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Jia J, Li J, Qu H, Li M, Zhang S, Hao J, Gao X, Meng X, Sun Y, Hakonarson H, Zeng X, Xia Q, Li J. New insights into hallux valgus by whole exome sequencing study. Exp Biol Med (Maywood) 2021; 246:1607-1616. [PMID: 33926255 PMCID: PMC8326439 DOI: 10.1177/15353702211008641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 03/13/2021] [Indexed: 11/16/2022] Open
Abstract
The traditional view is that the occurrence and development of hallux valgus (HV) are mainly due to environmental factors. Recent studies have suggested the large contribution of genetic heritability to HV, but it remains elusive about the genetic variants underlying the development of HV. To gain knowledge about the molecular mechanisms of HV pathogenesis by genetic approach, whole exome sequencing studies were performed in 10 individuals (7 affected by HV and 3 unaffected) from three independent families. Specific mutations were found to be related to the pathogenesis of HV and conform to the laws of inheritance. A total of 36 genes with functional candidate single nucleotide variants were identified. Genetic predisposition plays an important role in the development of HV. Interestingly, some of these genes are related to chronic arthritis, such as the complement encoding gene C7, or are related to long toe or long fingers, such as TTN, COL6A3, LARS, FIG4, and CBS. This study identified rare potentially pathogenic mutations represented by genes related to digital anomalies and chronic arthritis underlying the familial types of HV, which acquired new insights into the genetic and physiological foundations of HV, thereby might improve accurate prevention and drug development for HV.
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Affiliation(s)
- Jun Jia
- Department of Surgery of Foot and Ankle, Tianjin Hospital,
Tianjin 300211, China
| | - Junyi Li
- Department of Cell Biology, the Province and Ministry
Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of
Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Huiqi Qu
- Center for Applied Genomics, Children’s Hospital of
Philadelphia, Philadelphia, PA 19104-4399, USA
| | - Mengyu Li
- Department of Cell Biology, the Province and Ministry
Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of
Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Sipeng Zhang
- Department of Cell Biology, the Province and Ministry
Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of
Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Jun Hao
- Tianjin University of Traditional Chinese Medicine, Tianjin
301617, China
| | - Xinyi Gao
- Department of Cell Biology, the Province and Ministry
Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of
Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Xinyi Meng
- Department of Cell Biology, the Province and Ministry
Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of
Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Yan Sun
- Department of Cell Biology, the Province and Ministry
Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of
Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Hakon Hakonarson
- Center for Applied Genomics, Children’s Hospital of
Philadelphia, Philadelphia, PA 19104-4399, USA
- Division of Human Genetics, Children’s Hospital of Philadelphia,
Philadelphia, PA 19104-4399, USA
- Department of Pediatrics, Perelman School of Medicine,
University of Pennsylvania, Philadelphia, PA 19104-6243, USA
| | - Xiantie Zeng
- Department of Surgery of Foot and Ankle, Tianjin Hospital,
Tianjin 300211, China
| | - Qianghua Xia
- Department of Cell Biology, the Province and Ministry
Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of
Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Jin Li
- Department of Cell Biology, the Province and Ministry
Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of
Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
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Georgiou M, Robson AG, Fujinami K, Leo SM, Vincent A, Nasser F, Cabral De Guimarães TA, Khateb S, Pontikos N, Fujinami-Yokokawa Y, Liu X, Tsunoda K, Hayashi T, Vargas ME, Thiadens AAHJ, de Carvalho ER, Nguyen XTA, Arno G, Mahroo OA, Martin-Merida MI, Jimenez-Rolando B, Gordo G, Carreño E, Ayuso C, Sharon D, Kohl S, Huckfeldt RM, Wissinger B, Boon CJF, Banin E, Pennesi ME, Khan AO, Webster AR, Zrenner E, Héon E, Michaelides M. KCNV2-Associated Retinopathy: Genetics, Electrophysiology, and Clinical Course-KCNV2 Study Group Report 1. Am J Ophthalmol 2021; 225:95-107. [PMID: 33309813 PMCID: PMC8186730 DOI: 10.1016/j.ajo.2020.11.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 11/18/2020] [Accepted: 11/25/2020] [Indexed: 12/01/2022]
Abstract
PURPOSE To investigate genetics, electrophysiology, and clinical course of KCNV2-associated retinopathy in a cohort of children and adults. STUDY DESIGN This was a multicenter international clinical cohort study. METHODS Review of clinical notes and molecular genetic testing. Full-field electroretinography (ERG) recordings, incorporating the international standards, were reviewed and quantified and compared with age and recordings from control subjects. RESULTS In total, 230 disease-associated alleles were identified from 117 patients, corresponding to 75 different KCNV2 variants, with 28 being novel. The mean age of onset was 3.9 years old. All patients were symptomatic before 12 years of age (range, 0-11 years). Decreased visual acuity was present in all patients, and 4 other symptoms were common: reduced color vision (78.6%), photophobia (53.5%), nyctalopia (43.6%), and nystagmus (38.6%). After a mean follow-up of 8.4 years, the mean best-corrected visual acuity (BCVA ± SD) decreased from 0.81 ± 0.27 to 0.90 ± 0.31 logarithm of minimal angle of resolution. Full-field ERGs showed pathognomonic waveform features. Quantitative assessment revealed a wide range of ERG amplitudes and peak times, with a mean rate of age-associated reduction indistinguishable from the control group. Mean amplitude reductions for the dark-adapted 0.01 ERG, dark-adapted 10 ERG a-wave, and LA 3.0 30 Hz and LA3 ERG b-waves were 55%, 21%, 48%, and 74%, respectively compared with control values. Peak times showed stability across 6 decades. CONCLUSION In KCNV2-associated retinopathy, full-field ERGs are diagnostic and consistent with largely stable peripheral retinal dysfunction. Report 1 highlights the severity of the clinical phenotype and established a large cohort of patients, emphasizing the unmet need for trials of novel therapeutics.
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Affiliation(s)
- Michalis Georgiou
- Moorfields Eye Hospital, London, United Kingdom; University College London Institute of Ophthalmology, London, United Kingdom
| | - Anthony G Robson
- Moorfields Eye Hospital, London, United Kingdom; University College London Institute of Ophthalmology, London, United Kingdom
| | - Kaoru Fujinami
- Moorfields Eye Hospital, London, United Kingdom; University College London Institute of Ophthalmology, London, United Kingdom; Laboratory of Visual Physiology, Division of Vision Research, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Tokyo, Japan; Department of Ophthalmology, Keio University School of Medicine, Tokyo, Ontario, Japan
| | - Shaun M Leo
- Moorfields Eye Hospital, London, United Kingdom; University College London Institute of Ophthalmology, London, United Kingdom
| | - Ajoy Vincent
- Department of Ophthalmology and Vision Sciences, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Fadi Nasser
- Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Tübingen, Germany
| | | | - Samer Khateb
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Nikolas Pontikos
- Moorfields Eye Hospital, London, United Kingdom; University College London Institute of Ophthalmology, London, United Kingdom
| | - Yu Fujinami-Yokokawa
- University College London Institute of Ophthalmology, London, United Kingdom; Department of Health Policy and Management, Keio University School of Medicine, Tokyo, Japan
| | - Xiao Liu
- Laboratory of Visual Physiology, Division of Vision Research, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Tokyo, Japan; Department of Ophthalmology, Keio University School of Medicine, Tokyo, Ontario, Japan
| | - Kazushige Tsunoda
- Laboratory of Visual Physiology, Division of Vision Research, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Tokyo, Japan; Department of Ophthalmology, Keio University School of Medicine, Tokyo, Ontario, Japan
| | - Takaaki Hayashi
- Department of Ophthalmology, Katsushika Medical Center, The Jikei University School of Medicine, Tokyo, Japan
| | - Mauricio E Vargas
- Department of Ophthalmology, Oregon Health and Science University, Casey Eye Institute, Portland, Oregon, USA
| | | | - Emanuel R de Carvalho
- University College London Institute of Ophthalmology, London, United Kingdom; Department of Ophthalmology, Amsterdam UMC, Academic Medical Center, Amsterdam, the Netherlands
| | - Xuan-Thanh-An Nguyen
- Department of Ophthalmology, Leiden University Medical Center, Leiden, the Netherlands
| | - Gavin Arno
- Moorfields Eye Hospital, London, United Kingdom; University College London Institute of Ophthalmology, London, United Kingdom
| | - Omar A Mahroo
- Moorfields Eye Hospital, London, United Kingdom; University College London Institute of Ophthalmology, London, United Kingdom
| | - Maria Inmaculada Martin-Merida
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital-Universidad Autónoma de Madrid, Madrid, Spain; Center for Biomedical Network Research on Rare Diseases, Instituto de Salud Carlos III, Madrid, Spain
| | - Belen Jimenez-Rolando
- Department of Ophthalmology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital-Universidad Autónoma de Madrid, Madrid, Spain
| | - Gema Gordo
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital-Universidad Autónoma de Madrid, Madrid, Spain; Center for Biomedical Network Research on Rare Diseases, Instituto de Salud Carlos III, Madrid, Spain
| | - Ester Carreño
- Department of Ophthalmology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital-Universidad Autónoma de Madrid, Madrid, Spain
| | - Carmen Ayuso
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital-Universidad Autónoma de Madrid, Madrid, Spain; Center for Biomedical Network Research on Rare Diseases, Instituto de Salud Carlos III, Madrid, Spain
| | - Dror Sharon
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Susanne Kohl
- Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - Rachel M Huckfeldt
- Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, USA
| | - Bernd Wissinger
- Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - Camiel J F Boon
- Department of Ophthalmology, Amsterdam UMC, Academic Medical Center, Amsterdam, the Netherlands; Department of Ophthalmology, Leiden University Medical Center, Leiden, the Netherlands
| | - Eyal Banin
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Mark E Pennesi
- Department of Ophthalmology, Oregon Health and Science University, Casey Eye Institute, Portland, Oregon, USA
| | - Arif O Khan
- Department of Ophthalmology, Cleveland Clinic Lerner College of Medicine of Case Western University, Cleveland, Ohio, USA; Eye Institute, Cleveland Clinic Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Andrew R Webster
- Moorfields Eye Hospital, London, United Kingdom; University College London Institute of Ophthalmology, London, United Kingdom
| | - Eberhart Zrenner
- Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - Elise Héon
- Department of Ophthalmology and Vision Sciences, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Michel Michaelides
- Moorfields Eye Hospital, London, United Kingdom; University College London Institute of Ophthalmology, London, United Kingdom.
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Kim JH, Park S, Park HS, Park JS, Lee ST, Kim SW, Lee JW, Lee MH, Park SK, Noh WC, Choi DH, Han W, Jung SH. Analysis of BRCA1/2 variants of unknown significance in the prospective Korean Hereditary Breast Cancer study. Sci Rep 2021; 11:8485. [PMID: 33875706 PMCID: PMC8055990 DOI: 10.1038/s41598-021-87792-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 04/05/2021] [Indexed: 11/12/2022] Open
Abstract
Genetic testing for BRCA1 and BRCA2 is crucial in diagnosing hereditary breast and ovarian cancer syndromes and has increased with the development of multigene panel tests. However, results classified as variants of uncertain significance (VUS) present challenges to clinicians in attempting to choose an appropriate management plans. We reviewed a total of 676 breast cancer patients included in the Korean Hereditary Breast Cancer (KOHBRA) study with a VUS on BRCA mutation tests between November 2007 and April 2013. These results were compared to the ClinVar database. We calculated the incidence and odds ratios for these variants using the Korean Reference Genome Database. A total of 58 and 91 distinct VUS in BRCA1 and BRCA2 were identified in the KOHBRA study (comprising 278 and 453 patients, respectively). A total of 27 variants in the KOHBRA study were not registered in the Single Nucleotide Polymorphism database. Among BRCA1 VUSs, 20 were reclassified as benign or likely benign, four were reclassified as pathogenic or likely pathogenic, and eight remained as VUSs according to the ClinVar database. Of the BRCA2 VUSs, 25 were reclassified as benign or likely benign, two were reclassified as pathogenic or likely pathogenic, and 33 remained as VUS according to the ClinVar database. There were 12 variants with conflicting interpretations of pathogenicity for BRCA1 and 18 for BRCA2. Among them, p.Leu1780Pro showed a particularly high odds ratio. Six pathogenic variants and one conflicting variant identified using ClinVar could be reclassified as pathogenic variants in this study. Using updated ClinVar information and calculating odds ratios can be helpful when reclassifying VUSs in BRCA1/2.
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Affiliation(s)
- Joo Heung Kim
- Department of Surgery, Yongin Severance Hospital, Yonsei University College of Medicine, Yongin, Gyeonggi, Republic of Korea
| | - Sunggyun Park
- Department of Laboratory Medicine, Keimyung University School of Medicine, Daegu, Republic of Korea
| | - Hyung Seok Park
- Department of Surgery, Yonsei University College of Medicine, 50-1 Yonseiro, Seodaemun-gu, Seoul, 03722, Republic of Korea.
| | - Ji Soo Park
- Hereditary Cancer Clinic, Cancer Prevention Center, Yonsei Cancer Center, Yonsei University College of Medicine, 50-1 Yonseiro, Seodaemun-gu, Seoul, 03722, Republic of Korea.
| | - Seung-Tae Lee
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Sung-Won Kim
- Department of Surgery, Daerim St. Mary's Hospital, Seoul, Republic of Korea
| | - Jong Won Lee
- Department of Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Min Hyuk Lee
- Department of Surgery, Soonchunhyang University Seoul Hospital, Seoul, Republic of Korea
| | - Sue K Park
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
- Cancer Research Institute, Seoul National University, Seoul, Republic of Korea
| | - Woo-Chul Noh
- Department of Surgery, Korea Institute of Radiological & Medical Science, Korea Cancer Center Hospital, Seoul, Republic of Korea
| | - Doo Ho Choi
- Department of Radiation Oncology, Samsung Medical Center, Sungkyunkwan University, Seoul, Republic of Korea
| | - Wonshik Han
- Department of Surgery, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sung Hoo Jung
- Department of Surgery, Chonbuk National University Hospital, Jeonju, Jeollabuk, Republic of Korea
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Lee JW, Lee IH, Sato T, Kong SW, Iimura T. Genetic variation analyses indicate conserved SARS-CoV-2-host interaction and varied genetic adaptation in immune response factors in modern human evolution. Dev Growth Differ 2021; 63:219-227. [PMID: 33595856 PMCID: PMC8013644 DOI: 10.1111/dgd.12717] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 02/10/2021] [Accepted: 02/11/2021] [Indexed: 01/11/2023]
Abstract
Coronavirus disease 2019 (COVID‐19), caused by severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2), is a pandemic as of early 2020. Upon infection, SARS‐CoV‐2 attaches to its receptor, that is, angiotensin‐converting enzyme 2 (ACE2), on the surface of host cells and is then internalized into host cells via enzymatic machineries. This subsequently stimulates immune response factors. Since the host immune response and severity of COVID‐19 vary among individuals, genetic risk factors for severe COVID‐19 cases have been investigated. Our research group recently conducted a survey of genetic variants among SARS‐CoV‐2‐interacting molecules across populations, noting near absence of difference in allele frequency spectrum between populations in these genes. Recent genome‐wide association studies have identified genetic risk factors for severe COVID‐19 cases in a segment of chromosome 3 that involves six genes encoding three immune‐regulatory chemokine receptors and another three molecules. The risk haplotype seemed to be inherited from Neanderthals, suggesting genetic adaptation against pathogens in modern human evolution. Therefore, SARS‐CoV‐2 uses highly conserved molecules as its virion interaction, whereas its immune response appears to be genetically biased in individuals to some extent. We herein review the molecular process of SARS‐CoV‐2 infection as well as our further survey of genetic variants of its related immune effectors. We also discuss aspects of modern human evolution.
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Affiliation(s)
- Ji-Won Lee
- Department of Pharmacology, Faculty and Graduate School of Dental Medicine, Hokkaido University, Sapporo, Japan
| | - In-Hee Lee
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA
| | - Takanori Sato
- Department of Pharmacology, Faculty and Graduate School of Dental Medicine, Hokkaido University, Sapporo, Japan
| | - Sek Won Kong
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Tadahiro Iimura
- Department of Pharmacology, Faculty and Graduate School of Dental Medicine, Hokkaido University, Sapporo, Japan
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Cho SB, Jang JH, Chung MG, Kim SC. Exome Chip Analysis of 14,026 Koreans Reveals Known and Newly Discovered Genetic Loci Associated with Type 2 Diabetes Mellitus. Diabetes Metab J 2021; 45:231-240. [PMID: 32794382 PMCID: PMC8024163 DOI: 10.4093/dmj.2019.0163] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Accepted: 02/10/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Most loci associated with type 2 diabetes mellitus (T2DM) discovered to date are within noncoding regions of unknown functional significance. By contrast, exonic regions have advantages for biological interpretation. METHODS We analyzed the association of exome array data from 14,026 Koreans to identify susceptible exonic loci for T2DM. We used genotype information of 50,543 variants using the Illumina exome array platform. RESULTS In total, 7 loci were significant with a Bonferroni adjusted P=1.03×10-6. rs2233580 in paired box gene 4 (PAX4) showed the highest odds ratio of 1.48 (P=1.60×10-10). rs11960799 in membrane associated ring-CH-type finger 3 (MARCH3) and rs75680863 in transcobalamin 2 (TCN2) were newly identified loci. When we built a model to predict the incidence of diabetes with the 7 loci and clinical variables, area under the curve (AUC) of the model improved significantly (AUC=0.72, P<0.05), but marginally in its magnitude, compared with the model using clinical variables (AUC=0.71, P<0.05). When we divided the entire population into three groups-normal body mass index (BMI; <25 kg/m2), overweight (25≤ BMI <30 kg/m2), and obese (BMI ≥30 kg/m2) individuals-the predictive performance of the 7 loci was greatest in the group of obese individuals, where the net reclassification improvement was highly significant (0.51; P=8.00×10-5). CONCLUSION We found exonic loci having a susceptibility for T2DM. We found that such genetic information is advantageous for predicting T2DM in a subgroup of obese individuals.
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Affiliation(s)
- Seong Beom Cho
- Division of Biomedical Informatics, Center for Genome Science, National Institute of Health, Korea Center for Disease Control and Prevention, Cheongju, Korea
| | - Jin Hwa Jang
- Division of Biomedical Informatics, Center for Genome Science, National Institute of Health, Korea Center for Disease Control and Prevention, Cheongju, Korea
| | - Myung Guen Chung
- Division of Biomedical Informatics, Center for Genome Science, National Institute of Health, Korea Center for Disease Control and Prevention, Cheongju, Korea
| | - Sang Cheol Kim
- Division of Biomedical Informatics, Center for Genome Science, National Institute of Health, Korea Center for Disease Control and Prevention, Cheongju, Korea
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Park S, Hur YJ, Yoon JS, Jang MA. Distinctive Severe Ocular Abnormalities and Epilepsy Accompanied by a Novel ZEB2 Mutation in a Child with Mowat-Wilson Syndrome. ANNALS OF CHILD NEUROLOGY 2021. [DOI: 10.26815/acn.2021.00486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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30
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Lee IH, Lee JW, Kong SW. A survey of genetic variants in SARS-CoV-2 interacting domains of ACE2, TMPRSS2 and TLR3/7/8 across populations. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2020; 85:104507. [PMID: 32858233 PMCID: PMC7448771 DOI: 10.1016/j.meegid.2020.104507] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 07/28/2020] [Accepted: 08/18/2020] [Indexed: 12/21/2022]
Abstract
The COVID-19 pandemic highlighted healthcare disparities in multiple countries. As such morbidity and mortality vary significantly around the globe between populations and ethnic groups. Underlying medical conditions and environmental factors contribute higher incidence in some populations and a genetic predisposition may play a role for severe cases with respiratory failure. Here we investigated whether genetic variation in the key genes for viral entry to host cells-ACE2 and TMPRSS2-and sensing of viral genomic RNAs (i.e., TLR3/7/8) could explain the variation in incidence across diverse ethnic groups. Overall, these genes are under strong selection pressure and have very few nonsynonymous variants in all populations. Genetic determinant for the binding affinity between SARS-CoV-2 and ACE2 does not show significant difference between populations. Non-genetic factors are likely to contribute differential population characteristics affected by COVID-19. Nonetheless, a systematic mutagenesis study on the receptor binding domain of ACE2 is required to understand the difference in host-viral interaction across populations.
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Affiliation(s)
- In-Hee Lee
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA 02115, USA
| | - Ji-Won Lee
- Department of Nephrology, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pharmacology, Graduate School of Dental Medicine, Hokkaido University, Sapporo 060-8549, Japan
| | - Sek Won Kong
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA.
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Fasham J, Leslie JS, Harrison JW, Deline J, Williams KB, Kuhl A, Scott Schwoerer J, Cross HE, Crosby AH, Baple EL. No association between SCN9A and monogenic human epilepsy disorders. PLoS Genet 2020; 16:e1009161. [PMID: 33216760 PMCID: PMC7717534 DOI: 10.1371/journal.pgen.1009161] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 12/04/2020] [Accepted: 09/28/2020] [Indexed: 11/27/2022] Open
Abstract
Many studies have demonstrated the clinical utility and importance of epilepsy gene panel testing to confirm the specific aetiology of disease, enable appropriate therapeutic interventions, and inform accurate family counselling. Previously, SCN9A gene variants, in particular a c.1921A>T p.(Asn641Tyr) substitution, have been identified as a likely autosomal dominant cause of febrile seizures/febrile seizures plus and other monogenic seizure phenotypes indistinguishable from those associated with SCN1A, leading to inclusion of SCN9A on epilepsy gene testing panels. Here we present serendipitous findings of genetic studies that identify the SCN9A c.1921A>T p.(Asn641Tyr) variant at high frequency in the Amish community in the absence of such seizure phenotypes. Together with findings in UK Biobank these data refute an association of SCN9A with epilepsy, which has important clinical diagnostic implications.
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Affiliation(s)
- James Fasham
- RILD Wellcome Wolfson Centre, University of Exeter Medical School, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter, United Kingdom
- Peninsula Clinical Genetics Service, Royal Devon & Exeter Hospital, Gladstone Road, Exeter, United Kingdom
| | - Joseph S. Leslie
- RILD Wellcome Wolfson Centre, University of Exeter Medical School, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter, United Kingdom
| | - Jamie W. Harrison
- RILD Wellcome Wolfson Centre, University of Exeter Medical School, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter, United Kingdom
- University of Exeter, Department of Biosciences, Exeter, United Kingdom
| | - James Deline
- Center for Special Children, La Farge Medical Clinic-VMH, La Farge, Wisconsin, United States of America
| | - Katie B. Williams
- Department of Pediatrics, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Ashley Kuhl
- Department of Pediatrics, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Jessica Scott Schwoerer
- Department of Pediatrics, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Harold E. Cross
- Department of Ophthalmology, University of Arizona College of Medicine, Tucson, Arizona, United States of America
| | - Andrew H. Crosby
- RILD Wellcome Wolfson Centre, University of Exeter Medical School, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter, United Kingdom
| | - Emma L. Baple
- RILD Wellcome Wolfson Centre, University of Exeter Medical School, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter, United Kingdom
- Peninsula Clinical Genetics Service, Royal Devon & Exeter Hospital, Gladstone Road, Exeter, United Kingdom
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