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New Drug Development and Clinical Trial Design by Applying Genomic Information Management. Pharmaceutics 2022; 14:pharmaceutics14081539. [PMID: 35893795 PMCID: PMC9330622 DOI: 10.3390/pharmaceutics14081539] [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: 07/01/2022] [Revised: 07/19/2022] [Accepted: 07/22/2022] [Indexed: 02/04/2023] Open
Abstract
Depending on the patients’ genotype, the same drug may have different efficacies or side effects. With the cost of genomic analysis decreasing and reliability of analysis methods improving, vast amount of genomic information has been made available. Several studies in pharmacology have been based on genomic information to select the optimal drug, determine the dose, predict efficacy, and prevent side effects. This paper reviews the tissue specificity and genomic information of cancer. If the tissue specificity of cancer is low, cancer is induced in various organs based on a single gene mutation. Basket trials can be performed for carcinomas with low tissue specificity, confirming the efficacy of one drug for a single gene mutation in various carcinomas. Conversely, if the tissue specificity of cancer is high, cancer is induced in only one organ based on a single gene mutation. An umbrella trial can be performed for carcinomas with a high tissue specificity. Some drugs are effective for patients with a specific genotype. A companion diagnostic strategy that prescribes a specific drug for patients selected with a specific genotype is also reviewed. Genomic information is used in pharmacometrics to identify the relationship among pharmacokinetics, pharmacodynamics, and biomarkers of disease treatment effects. Utilizing genomic information, sophisticated clinical trials can be designed that will be better suited to the patients of specific genotypes. Genomic information also provides prospects for innovative drug development. Through proper genomic information management, factors relating to drug response and effects can be determined by selecting the appropriate data for analysis and by understanding the structure of the data. Selecting pre-processing and appropriate machine-learning libraries for use as machine-learning input features is also necessary. Professional curation of the output result is also required. Personalized medicine can be realized using a genome-based customized clinical trial design.
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Barfield R, Qu C, Steinfelder RS, Zeng C, Harrison TA, Brezina S, Buchanan DD, Campbell PT, Casey G, Gallinger S, Giannakis M, Gruber SB, Gsur A, Hsu L, Huyghe JR, Moreno V, Newcomb PA, Ogino S, Phipps AI, Slattery ML, Thibodeau SN, Trinh QM, Toland AE, Hudson TJ, Sun W, Zaidi SH, Peters U. Association between germline variants and somatic mutations in colorectal cancer. Sci Rep 2022; 12:10207. [PMID: 35715570 PMCID: PMC9205954 DOI: 10.1038/s41598-022-14408-2] [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: 11/21/2021] [Accepted: 06/07/2022] [Indexed: 01/11/2023] Open
Abstract
Colorectal cancer (CRC) is a heterogeneous disease with evidence of distinct tumor types that develop through different somatically altered pathways. To better understand the impact of the host genome on somatically mutated genes and pathways, we assessed associations of germline variations with somatic events via two complementary approaches. We first analyzed the association between individual germline genetic variants and the presence of non-silent somatic mutations in genes in 1375 CRC cases with genome-wide SNPs data and a tumor sequencing panel targeting 205 genes. In the second analysis, we tested if germline variants located within previously identified regions of somatic allelic imbalance were associated with overall CRC risk using summary statistics from a recent large scale GWAS (n≃125 k CRC cases and controls). The first analysis revealed that a variant (rs78963230) located within a CNA region associated with TLR3 was also associated with a non-silent mutation within gene FBXW7. In the secondary analysis, the variant rs2302274 located in CDX1/PDGFRB frequently gained/lost in colorectal tumors was associated with overall CRC risk (OR = 0.96, p = 7.50e-7). In summary, we demonstrate that an integrative analysis of somatic and germline variation can lead to new insights about CRC.
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Affiliation(s)
- Richard Barfield
- grid.26009.3d0000 0004 1936 7961Department of Biostatistics and Bioinformatics, Duke University, 11028A Hock Plaza, 2424 Erwin Road Suite 1106, Durham, NC 27705 USA
| | - Conghui Qu
- grid.270240.30000 0001 2180 1622Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA USA
| | - Robert S. Steinfelder
- grid.270240.30000 0001 2180 1622Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA USA
| | - Chenjie Zeng
- grid.280128.10000 0001 2233 9230National Human Genome Research Institute, National Institutes of Health, Bethesda, MD USA
| | - Tabitha A. Harrison
- grid.270240.30000 0001 2180 1622Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA USA
| | - Stefanie Brezina
- grid.22937.3d0000 0000 9259 8492Institute of Cancer Research, Department of Medicine I, Medical University Vienna, Vienna, Austria
| | - Daniel D. Buchanan
- grid.1008.90000 0001 2179 088XColorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, VIC 3010 Australia ,grid.1008.90000 0001 2179 088XUniversity of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC 3010 Australia ,grid.416153.40000 0004 0624 1200Genomic Medicine and Family Cancer Clinic, The Royal Melbourne Hospital, Parkville, VIC Australia
| | - Peter T. Campbell
- grid.251993.50000000121791997Department of Epidemiology and Population Science, Albert Einstein College of Medicine, Bronx, NY USA
| | - Graham Casey
- grid.27755.320000 0000 9136 933XCenter for Public Health Genomics, University of Virginia, Charlottesville, VA USA
| | - Steven Gallinger
- grid.250674.20000 0004 0626 6184Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, ON Canada
| | - Marios Giannakis
- grid.65499.370000 0001 2106 9910Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA USA ,grid.66859.340000 0004 0546 1623The Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Stephen B. Gruber
- grid.42505.360000 0001 2156 6853Department of Medical Oncology and Therapeuytic, University of Southern California, Los Angeles, CA USA
| | - Andrea Gsur
- grid.22937.3d0000 0000 9259 8492Institute of Cancer Research, Department of Medicine I, Medical University Vienna, Vienna, Austria
| | - Li Hsu
- grid.270240.30000 0001 2180 1622Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA USA ,grid.34477.330000000122986657Department of Biostatistics, University of Washington, Seattle, WA USA
| | - Jeroen R. Huyghe
- grid.270240.30000 0001 2180 1622Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA USA
| | - Victor Moreno
- grid.418701.b0000 0001 2097 8389Oncology Data Analytics Program, Catalan Institute of Oncology-IDIBELL, L’Hospitalet de Llobregat, Barcelona, Spain ,grid.466571.70000 0004 1756 6246CIBER Epidemiología Y Salud Pública (CIBERESP), Madrid, Spain ,grid.5841.80000 0004 1937 0247Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain ,grid.418284.30000 0004 0427 2257ONCOBEL Program, Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, Barcelona, Spain
| | - Polly A. Newcomb
- grid.270240.30000 0001 2180 1622Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA USA ,grid.34477.330000000122986657School of Public Health, University of Washington, Seattle, WA USA
| | - Shuji Ogino
- grid.66859.340000 0004 0546 1623The Broad Institute of MIT and Harvard, Cambridge, MA USA ,grid.38142.3c000000041936754XProgram in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA USA ,Cancer Immunology Program, Dana-Farber Harvard Cancer Center, Boston, MA USA ,grid.38142.3c000000041936754XDepartment of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA USA
| | - Amanda I. Phipps
- grid.270240.30000 0001 2180 1622Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA USA ,Department of Epidemiology, Fred Hutchinson Cancer Research Center, University of Washington, 1100 Fairview Ave N, Mail Stop M4-B402, Seattle, WA 98109 USA
| | - Martha L. Slattery
- grid.223827.e0000 0001 2193 0096Department of Internal Medicine, University of Utah, Salt Lake City, UT USA
| | - Stephen N. Thibodeau
- grid.66875.3a0000 0004 0459 167XDivision of Laboratory Genetics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN USA
| | - Quang M. Trinh
- grid.419890.d0000 0004 0626 690XOntario Institute for Cancer Research, Toronto, ON Canada
| | - Amanda E. Toland
- grid.261331.40000 0001 2285 7943Departments of Cancer Biology and Genetics and Internal Medicine, Comprehensive Cancer Center, The Ohio State University, Columbus, OH USA
| | - Thomas J. Hudson
- grid.419890.d0000 0004 0626 690XOntario Institute for Cancer Research, Toronto, ON Canada
| | - Wei Sun
- grid.270240.30000 0001 2180 1622Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA USA ,grid.34477.330000000122986657Department of Biostatistics, University of Washington, Seattle, WA USA ,grid.410711.20000 0001 1034 1720Department of Biostatistics, University of North Carolina, Chapel Hill, NC USA
| | - Syed H. Zaidi
- grid.419890.d0000 0004 0626 690XOntario Institute for Cancer Research, Toronto, ON Canada
| | - Ulrike Peters
- grid.270240.30000 0001 2180 1622Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA USA ,Department of Epidemiology, Fred Hutchinson Cancer Research Center, University of Washington, 1100 Fairview Ave N, Mail Stop M4-B402, Seattle, WA 98109 USA
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Feng G, Feng H, Qi Y, Wang T, Ni N, Wu J, Yuan H. Interaction analysis between germline genetic variants and somatic mutations in head and neck cancer. Oral Oncol 2022; 128:105859. [DOI: 10.1016/j.oraloncology.2022.105859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 03/24/2022] [Accepted: 04/05/2022] [Indexed: 10/18/2022]
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Mao W, Chen R, Lu R, Wang S, Song H, You D, Liu F, He Y, Zheng M. Germline mutation analyses of malignant ground glass opacity nodules in non-smoking lung adenocarcinoma patients. PeerJ 2021; 9:e12048. [PMID: 34540367 PMCID: PMC8415279 DOI: 10.7717/peerj.12048] [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: 01/29/2021] [Accepted: 08/03/2021] [Indexed: 11/20/2022] Open
Abstract
Background Germline mutations play an important role in the pathogenesis of lung cancer. Nonetheless, research on malignant ground glass opacity (GGO) nodules is limited. Methods A total of 13 participants with malignant GGO nodules were recruited in this study. Peripheral blood was used for exome sequencing, and germline mutations were analyzed using InterVar. The whole exome sequencing dataset was analyzed using a filtering strategy. KOBAS 3.0 was used to analyze KEGG pathway to further identify possible deleterious mutations. Results There were seven potentially deleterious germline mutations. NM_001184790:exon8: c.C1070T in PARD3, NM_001170721:exon4:c.C392T in BCAR1 and NM_001127221:exon46: c.G6587A in CACNA1A were present in three cases each; rs756875895 frameshift in MAX, NM_005732: exon13:c.2165_2166insT in RAD50 and NM_001142316:exon2:c.G203C in LMO2, were present in two cases each; one variant was present in NOTCH3. Conclusions Our results expand the germline mutation spectrum in malignant GGO nodules. Importantly, these findings will potentially help screen the high-risk population, guide their health management, and contribute to their clinical treatment and determination of prognosis.
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Affiliation(s)
- Wenjun Mao
- Department of Cardiothoracic Surgery, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi, Jiangsu, China
| | - Ruo Chen
- Department of Cardiothoracic Surgery, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi, Jiangsu, China
| | - Rongguo Lu
- Department of Cardiothoracic Surgery, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi, Jiangsu, China
| | - Shengfei Wang
- Department of Cardiothoracic Surgery, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi, Jiangsu, China
| | - Huizhu Song
- Department of Pharmacy, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi, Jiangsu, China
| | - Dan You
- Department of Pharmacy, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi, Jiangsu, China
| | - Feng Liu
- Department of Cardiothoracic Surgery, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi, Jiangsu, China
| | - Yijun He
- Department of Cardiothoracic Surgery, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi, Jiangsu, China
| | - Mingfeng Zheng
- Department of Cardiothoracic Surgery, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi, Jiangsu, China
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Behrouzfar K, Burton K, Mutsaers SE, Morahan G, Lake RA, Fisher SA. How to Better Understand the Influence of Host Genetics on Developing an Effective Immune Response to Thoracic Cancers. Front Oncol 2021; 11:679609. [PMID: 34235080 PMCID: PMC8256168 DOI: 10.3389/fonc.2021.679609] [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: 03/12/2021] [Accepted: 05/31/2021] [Indexed: 01/02/2023] Open
Abstract
Thoracic cancers pose a significant global health burden. Immune checkpoint blockade therapies have improved treatment outcomes, but durable responses remain limited. Understanding how the host immune system interacts with a developing tumor is essential for the rational development of improved treatments for thoracic malignancies. Recent technical advances have improved our understanding of the mutational burden of cancer cells and changes in cancer-specific gene expression, providing a detailed understanding of the complex biology underpinning tumor-host interactions. While there has been much focus on the genetic alterations associated with cancer cells and how they may impact treatment outcomes, how host genetics affects cancer development is also critical and will greatly determine treatment response. Genome-wide association studies (GWAS) have identified genetic variants associated with cancer predisposition. This approach has successfully identified host genetic risk factors associated with common thoracic cancers like lung cancer, but is less effective for rare cancers like malignant mesothelioma. To assess how host genetics impacts rare thoracic cancers, we used the Collaborative Cross (CC); a powerful murine genetic resource designed to maximize genetic diversity and rapidly identify genes associated with any biological trait. We are using the CC in conjunction with our asbestos-induced MexTAg mouse model, to identify host genes associated with mesothelioma development. Once genes that moderate tumor development and progression are known, human homologues can be identified and human datasets interrogated to validate their association with disease outcome. Furthermore, our CC-MexTAg animal model enables in-depth study of the tumor microenvironment, allowing the correlation of immune cell infiltration and gene expression signatures with disease development. This strategy provides a detailed picture of the underlying biological pathways associated with mesothelioma susceptibility and progression; knowledge that is crucial for the rational development of new diagnostic and therapeutic strategies. Here we discuss the influence of host genetics on developing an effective immune response to thoracic cancers. We highlight current knowledge gaps, and with a focus on mesothelioma, describe the development and application of the CC-MexTAg to overcome limitations and illustrate how the knowledge gained from this unique study will inform the rational design of future treatments of mesothelioma.
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Affiliation(s)
- Kiarash Behrouzfar
- National Centre for Asbestos Related Diseases (NCARD), University of Western Australia, Nedlands, WA, Australia
- School of Biomedical Sciences, University of Western Australia, Nedlands, WA, Australia
| | - Kimberley Burton
- National Centre for Asbestos Related Diseases (NCARD), University of Western Australia, Nedlands, WA, Australia
- School of Biomedical Sciences, University of Western Australia, Nedlands, WA, Australia
| | - Steve E. Mutsaers
- School of Biomedical Sciences, University of Western Australia, Nedlands, WA, Australia
- Institute for Respiratory Health, University of Western Australia, Nedlands, WA, Australia
| | - Grant Morahan
- Centre for Diabetes Research, Harry Perkins Institute of Medical Research, Nedlands, WA, Australia
| | - Richard A. Lake
- National Centre for Asbestos Related Diseases (NCARD), University of Western Australia, Nedlands, WA, Australia
| | - Scott A. Fisher
- National Centre for Asbestos Related Diseases (NCARD), University of Western Australia, Nedlands, WA, Australia
- School of Biomedical Sciences, University of Western Australia, Nedlands, WA, Australia
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Delineation of the Germline and Somatic Mutation Interaction Landscape in Triple-Negative and Non-Triple-Negative Breast Cancer. Int J Genomics 2020; 2020:2641370. [PMID: 32724790 PMCID: PMC7364202 DOI: 10.1155/2020/2641370] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 05/26/2020] [Accepted: 06/09/2020] [Indexed: 11/18/2022] Open
Abstract
Background Breast cancer development and progression involve both germline and somatic mutations. High-throughput genotyping and next-generation sequencing technologies have enabled discovery of genetic risk variants and acquired somatic mutations driving the disease. However, the possible oncogenic interactions between germline genetic risk variants and somatic mutations in triple-negative breast cancer (TNBC) and non-triple-negative breast cancer (non-TNBC) have not been characterized. Here, we delineated the possible oncogenic interactions between genes containing germline and somatic mutations in TNBC and non-TNBC and investigated whether there are differences in gene expression and mutation burden between the two types of breast cancer. Methods We addressed this problem by integrating germline mutation information from genome-wide association studies with somatic mutation information from next-generation sequencing using gene expression data as the intermediated phenotype. We performed network and pathway analyses to discover molecular networks and signalling pathways enriched for germline and somatic mutations. Results The investigation revealed signatures of differentially expressed and differentially somatic mutated genes between TNBC and non-TNBC. Network and pathway analyses revealed functionally related genes interacting in gene regulatory networks and multiple signalling pathways enriched for germline and somatic mutations for each type of breast cancer. Among the signalling pathways discovered included the DNA repair and Androgen and ATM signalling pathways for TNBC and the DNA damage response, molecular mechanisms of cancer, and ATM and GP6 signalling pathways for non-TNBC. Conclusions The results show that integrative genomics is a powerful approach for delineating oncogenic interactions between genes containing germline and genes containing somatic mutations in TNBC and non-TNBC and establishes putative functional bridges between genetic and somatic alterations and the pathways they control in the two types of breast cancer.
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Wang Y, Gorlova OY, Gorlov IP, Zhu M, Dai J, Albanes D, Lam S, Tardon A, Chen C, Goodman GE, Bojesen SE, Landi MT, Johansson M, Risch A, Wichmann HE, Bickeboller H, Christiani DC, Rennert G, Arnold SM, Brennan P, Field JK, Shete S, Le Marchand L, Melander O, Brunnstrom H, Liu G, Hung RJ, Andrew AS, Kiemeney LA, Zienolddiny S, Grankvist K, Johansson M, Caporaso NE, Woll PJ, Lazarus P, Schabath MB, Aldrich MC, Stevens VL, Ma H, Jin G, Hu Z, Amos CI, Shen H. Association Analysis of Driver Gene-Related Genetic Variants Identified Novel Lung Cancer Susceptibility Loci with 20,871 Lung Cancer Cases and 15,971 Controls. Cancer Epidemiol Biomarkers Prev 2020; 29:1423-1429. [PMID: 32277007 PMCID: PMC8120681 DOI: 10.1158/1055-9965.epi-19-1085] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 11/10/2019] [Accepted: 04/07/2020] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND A substantial proportion of cancer driver genes (CDG) are also cancer predisposition genes. However, the associations between genetic variants in lung CDGs and the susceptibility to lung cancer have rarely been investigated. METHODS We selected expression-related single-nucleotide polymorphisms (eSNP) and nonsynonymous variants of lung CDGs, and tested their associations with lung cancer risk in two large-scale genome-wide association studies (20,871 cases and 15,971 controls of European descent). Conditional and joint association analysis was performed to identify independent risk variants. The associations of independent risk variants with somatic alterations in lung CDGs or recurrently altered pathways were investigated using data from The Cancer Genome Atlas (TCGA) project. RESULTS We identified seven independent SNPs in five lung CDGs that were consistently associated with lung cancer risk in discovery (P < 0.001) and validation (P < 0.05) stages. Among these loci, rs78062588 in TPM3 (1q21.3) was a new lung cancer susceptibility locus (OR = 0.86, P = 1.65 × 10-6). Subgroup analysis by histologic types further identified nine lung CDGs. Analysis of somatic alterations found that in lung adenocarcinomas, rs78062588[C] allele (TPM3 in 1q21.3) was associated with elevated somatic copy number of TPM3 (OR = 1.16, P = 0.02). In lung adenocarcinomas, rs1611182 (HLA-A in 6p22.1) was associated with truncation mutations of the transcriptional misregulation in cancer pathway (OR = 0.66, P = 1.76 × 10-3). CONCLUSIONS Genetic variants can regulate functions of lung CDGs and influence lung cancer susceptibility. IMPACT Our findings might help unravel biological mechanisms underlying lung cancer susceptibility.
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Affiliation(s)
- Yuzhuo Wang
- Department of Epidemiology, International Joint Research Center on Environment and Human Health, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Department of Thoracic Surgery, Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & Nanjing Medical University Affiliated Cancer Hospital, Nanjing, China
| | - Olga Y Gorlova
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire
- Department of Medicine, Epidemiology Section, Institute for Clinical and Translational Research, Baylor Medical College, Houston, Texas
| | - Ivan P Gorlov
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire
- Department of Medicine, Epidemiology Section, Institute for Clinical and Translational Research, Baylor Medical College, Houston, Texas
| | - Meng Zhu
- Department of Epidemiology, International Joint Research Center on Environment and Human Health, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Department of Thoracic Surgery, Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & Nanjing Medical University Affiliated Cancer Hospital, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Juncheng Dai
- Department of Epidemiology, International Joint Research Center on Environment and Human Health, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Stephen Lam
- Department of Integrative Oncology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Adonina Tardon
- Department of Public Health IUOPA, University of Oviedo, ISPA and CIBERESP, Oviedo, Spain
| | - Chu Chen
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Gary E Goodman
- Public Health Sciences Division, Swedish Cancer Institute, Seattle, Washington
| | - Stig E Bojesen
- Department of Clinical Biochemistry, Copenhagen University Hospital, Copenhagen, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Mattias Johansson
- Genetic Epidemiology Group, International Agency for Research on Cancer, Lyon, France
| | - Angela Risch
- University of Salzburg, Department of Biosciences, Allergy-Cancer-BioNano Research Centre, Salzburg, Austria
- Division of Epigenomics and Cancer Risk Factors, DKFZ-German Cancer Research Center, Heidelberg, Heidelberg, Germany
- Translational Lung Research Center Heidelberg (TLRC-H), German Center for Lung Research (DZL), Heidelberg, Germany
| | - Heunz-Erich Wichmann
- Institute of Medical Informatics, Biometry and Epidemiology, Chair of Epidemiology, Ludwig Maximilians University, Munich, Bavaria, Germany
- Helmholtz Zentrum Munchen, German Research Center for Environmental Health (GmbH), Institute of Epidemiology, Neuherberg, Germany
- Institute of Medical Statistics and Epidemiology, Technical University Munich, Munich, Germany
| | - Heike Bickeboller
- Department of Genetic Epidemiology, University Medical Center Goettingen, Goettingen, Germany
| | - David C Christiani
- Departments of Environmental Health and Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Gad Rennert
- Technion Faculty of Medicine, Carmel Medical Center, Haifa, Israel
| | - Susanne M Arnold
- Markey Cancer Center, University of Kentucky, Lexington, Kentucky
| | - Paul Brennan
- Genetic Epidemiology Group, International Agency for Research on Cancer, Lyon, France
| | - John K Field
- Molecular and Clinical Cancer Medicine, Roy Castle Lung Cancer Research Programme, The University of Liverpool Institute of Translational Medicine, Liverpool, United Kingdom
| | - Sanjay Shete
- Department of Epidemiology, The University of Texas, MD Anderson Cancer Center, Houston, Texas
| | - Loïc Le Marchand
- Epidemiology Program, University of Hawai'i Cancer Center, Honolulu, Hawai'i
| | - Olle Melander
- Clinical Sciences, Lund University, Lund, Sweden
- Department of Internal Medicine, Skåne University Hospital, Malmö, Sweden
| | | | - Geoffrey Liu
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Rayjean J Hung
- Prosseman Centre for Population Health Research, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Angeline S Andrew
- Department of Neurology, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire
| | - Lambertus A Kiemeney
- Department for Health Evidence, Radboud University Medical Center, Nijmegen, the Netherlands
| | | | - Kjell Grankvist
- Department of Medical Biosciences, Umeå University, Umea, Sweden
| | | | - Neil E Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland
| | - Penella J Woll
- Academic Unit of Clinical Oncology, University of Sheffield, Sheffield, United Kingdom
| | - Philip Lazarus
- Department of Pharmaceutical Sciences, College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, Washington
| | - Matthew B Schabath
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Melinda C Aldrich
- Department of Medicine (Division of Genetic Medicine), Vanderbilt University Medical Center, Nashville, Tennessee
| | - Victoria L Stevens
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, Georgia
| | - Hongxia Ma
- Department of Epidemiology, International Joint Research Center on Environment and Human Health, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Guangfu Jin
- Department of Epidemiology, International Joint Research Center on Environment and Human Health, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Zhibin Hu
- Department of Epidemiology, International Joint Research Center on Environment and Human Health, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Christopher I Amos
- Department of Medicine, Epidemiology Section, Institute for Clinical and Translational Research, Baylor Medical College, Houston, Texas.
| | - Hongbing Shen
- Department of Epidemiology, International Joint Research Center on Environment and Human Health, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China.
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, China
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Wang G, Bai Y, Fu W, Feng Y, Chen W, Li G, Wu X, Meng H, Liu Y, Wei W, Wang S, Wei S, Zhang X, He M, Yang H, Guo H. Daily cooking duration and its joint effects with genetic polymorphisms on lung cancer incidence: Results from a Chinese prospective cohort study. ENVIRONMENTAL RESEARCH 2019; 179:108747. [PMID: 31557604 DOI: 10.1016/j.envres.2019.108747] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 08/30/2019] [Accepted: 09/15/2019] [Indexed: 06/10/2023]
Abstract
OBJECTIVES In this study, we conducted a prospective cohort study to investigate the joint effects of daily cooking duration with single nucleotide polymorphisms (SNPs) on lung cancer incidence. MATERIALS AND METHODS A total of 33,868 individuals recruited in 2013 from Dongfeng-Tongji cohort study were included in our research, in which 5178 participants were genotyped. Daily cooking duration was accessed by questionnaire, and the incident lung cancer cases were confirmed. Fifteen lung cancer related SNPs were selected according to the previous reports. We used the multiple Cox regression models to evaluate the separate and joint effects of daily cooking duration and SNPs on lung cancer incidence. RESULTS Each 1-h increase in daily cooking duration was associated with a 17% elevated risk of lung cancer incidence [hazard ratio (HR) (95%CI) = 1.17(1.03, 1.33)]. Specifically, subjects with daily cooking duration >2 h/day had a 2.05-fold increased incident risk of lung cancer than those without cooking [HR(95%CI) = 2.05(1.20, 3.53)] (Ptrend = 0.011). The rs2395185 and rs3817963, both located at 6p21.32, were significantly associated with lung cancer incidence. Compared with no cooking subjects with rs2395185GG or rs3817963TT genotype, subjects with daily cooking >2 h/day and carrying rs2395185GT + TT genotypes had a 2.48-fold increased risk of lung cancer [HR(95%CI) = 2.48(1.03, 5.97)], and there were significant joint effects of rs3817963TC + CC with daily cooking 1-2 and >2 h/day [HR(95%CI) = 2.23(1.07, 4.64) and 2.22(1.05, 4.68), respectively]. CONCLUSIONS Longer daily cooking duration, especially daily cooking >2 h/day, was associated with increased risk of lung cancer. There were significant joint effects of rs2395185 and rs3817963 with daily cooking duration on lung cancer incidence. This study offered a new indicator of cooking related pollution exposure and added new evidence for the joint effects of environment and genetic factors on lung cancer incidence.
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Affiliation(s)
- Gege Wang
- Department of Occupational and Environmental Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yansen Bai
- Department of Occupational and Environmental Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wenshan Fu
- Department of Occupational and Environmental Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yue Feng
- Department of Occupational and Environmental Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Weilin Chen
- Department of Occupational and Environmental Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Guyanan Li
- Department of Occupational and Environmental Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiulong Wu
- Department of Occupational and Environmental Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hua Meng
- Department of Occupational and Environmental Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuhang Liu
- Department of Occupational and Environmental Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wei Wei
- Department of Occupational and Environmental Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Suhan Wang
- Department of Occupational and Environmental Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Sheng Wei
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaomin Zhang
- Department of Occupational and Environmental Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Meian He
- Department of Occupational and Environmental Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Handong Yang
- Dongfeng Central Hospital, Dongfeng Motor Corporation and Hubei University of Medicine, Shiyan, Hubei, China
| | - Huan Guo
- Department of Occupational and Environmental Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
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Germline Variants Impact Somatic Events during Tumorigenesis. Trends Genet 2019; 35:515-526. [PMID: 31128889 DOI: 10.1016/j.tig.2019.04.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 04/22/2019] [Accepted: 04/23/2019] [Indexed: 01/09/2023]
Abstract
Cancer is characterized by diverse genetic alterations in both germline and somatic genomes that disrupt normal biology and provide a selective advantage to cells during tumorigenesis. Germline and somatic genomes have been extensively studied independently, leading to numerous biological insights. Analyses integrating data from both genomes have identified genetic variants impacting somatic events in tumors, including hotspot driver mutations. Interactions among specific germline variants and somatic events influence cancer subtypes, treatment response, and clinical outcomes. Investigation of these complex interactions is increasing our understanding of aberrant pathways in tumors that may uncover novel therapeutic targets. Here, we review the literature describing the role of germline genetic variants in promoting the selection and generation of specific mutations during tumorigenesis.
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10
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Precision oncology of lung cancer: genetic and genomic differences in Chinese population. NPJ Precis Oncol 2019; 3:14. [PMID: 31069257 PMCID: PMC6499836 DOI: 10.1038/s41698-019-0086-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 03/15/2019] [Indexed: 02/07/2023] Open
Abstract
Knowledge of the lung cancer genome has experienced rapid growth over the past decade. Genome-wide association studies and sequencing studies have identified dozens of genetic variants and somatic mutations implicated in the development of lung cancer in both Chinese and Caucasian populations. With the accumulating evidence, heterogeneities in lung cancer susceptibility were observed in different ethnicities. In this review, the progress on germline-based genetic variants and somatic-based genomic mutations associated with lung cancer and the differences between Chinese and Caucasian populations were systematically summarized. In the analysis of the genetic predisposition to lung cancer, 6 susceptibility loci were shared by Chinese and Caucasian populations (3q28, 5p15, 6p21, 9p21.3, 12q13.13 and 15q25), 14 loci were specific to the Chinese population (1p36.32, 5q31.1, 5q32, 6p21.1, 6q22.2, 6p21.32, 7p15.3, 10p14, 10q25.2, 12q23.1, 13q22, 17q24.3, 20q13.2, and 22q12), and 12 loci were specific to the Caucasian population (1p31.1, 2q32.1, 6q27, 8p21.1, 8p12, 10q24.3, 11q23.3, 12p13.33, 13q13.1, 15q21.1, 20q13.33 and 22q12.1). In the analysis of genomic and somatic alterations, different mutation rates were observed for EGFR (Chinese: 39–59% vs. TCGA: 14%), KRAS (Chinese: 7–11% vs. TCGA: 31%), TP53 (Chinese: 44% vs. TCGA: 53%), CDKN2A (Chinese: 22% vs. TCGA: 15%), NFE2L2 (Chinese: 28% vs. TCGA: 17%), STK11 (Chinese: 4–7% vs. TCGA: 16%), KEAP1 (Chinese: 3–5% vs. TCGA: 18%), and NF1 (Chinese: <2% vs. TCGA: 12%). In addition, frequently amplified regions encompassing genes involved in cytoskeletal organization or focal adhesion were identified only in Chinese patients. These results provide a comprehensive description of the genetic and genomic differences in lung cancer susceptibility between Chinese and Caucasian populations and may contribute to the development of precision medicine for lung cancer treatment and prevention.
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11
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Mamidi TKK, Wu J, Hicks C. Interactions between Germline and Somatic Mutated Genes in Aggressive Prostate Cancer. Prostate Cancer 2019; 2019:4047680. [PMID: 31007957 PMCID: PMC6441536 DOI: 10.1155/2019/4047680] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 01/29/2019] [Accepted: 02/15/2019] [Indexed: 12/13/2022] Open
Abstract
Prostate cancer (PCa) is the most common diagnosed malignancy and the second leading cause of cancer-related deaths among men in the USA. Advances in high-throughput genotyping and next generation sequencing technologies have enabled discovery of germline genetic susceptibility variants and somatic mutations acquired during tumor formation. Emerging evidence indicates that germline variations may interact with somatic events in carcinogenesis. However, the possible oncogenic interactions and cooperation between germline and somatic variation and their role in aggressive PCa remain largely unexplored. Here we investigated the possible oncogenic interactions and cooperation between genes containing germline variation from genome-wide association studies (GWAS) and genes containing somatic mutations from tumor genomes of 305 men with aggressive tumors and 52 control samples from The Cancer Genome Atlas (TCGA). Network and pathway analysis were performed to identify molecular networks and biological pathways enriched for germline and somatic mutations. The analysis revealed 90 functionally related genes containing both germline and somatic mutations. Transcriptome analysis revealed a 61-gene signature containing both germline and somatic mutations. Network analysis revealed molecular networks of functionally related genes and biological pathways including P53, STAT3, NKX3-1, KLK3, and Androgen receptor signaling pathways enriched for germline and somatic mutations. The results show that integrative analysis is a powerful approach to uncovering the possible oncogenic interactions and cooperation between germline and somatic mutations and understanding the broader biological context in which they operate in aggressive PCa.
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Affiliation(s)
- Tarun Karthik Kumar Mamidi
- Department of Genetics, Louisiana State University Health Sciences Center, School of Medicine, 533 Bolivar St., New Orleans, LA 70112, USA
| | - Jiande Wu
- Department of Genetics, Louisiana State University Health Sciences Center, School of Medicine, 533 Bolivar St., New Orleans, LA 70112, USA
| | - Chindo Hicks
- Department of Genetics, Louisiana State University Health Sciences Center, School of Medicine, 533 Bolivar St., New Orleans, LA 70112, USA
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12
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Li H, Xiao L, Wang L, Lin J, Luo M, Chen M, He R, Zhu Y, Zhang C. HLA Polymorphism Affects Risk of de novo Mutation of dystrophin Gene and Clinical Severity of Duchenne Muscular Dystrophy in a Southern Chinese Population. Front Neurol 2018; 9:970. [PMID: 30498470 PMCID: PMC6249334 DOI: 10.3389/fneur.2018.00970] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Accepted: 10/29/2018] [Indexed: 01/08/2023] Open
Abstract
Immune-mediated pathology has been thought to be an important factor contributing to Duchenne muscular dystrophy (DMD). Allele frequencies of certain HLA types are known to differ between patients with dystrophinopathies and healthy controls with low-resolution HLA gene typing data in limit reports. Using Polymerase chain reactionsequence based typing (PCR-SBT) to genotype 64 children with DMD in HLA-A, -B,-C, -DRB1, and -DQB1 locus and 503 healthy controls in HLA-A, -B, -DRB1 locus, this study aimed to investigate associations of specific HLA alleles with, and their possible roles in the development and clinical phenotypic severity of DMD. The χ2 test was used to evaluate the distribution of allele frequencies in HLA-A, -B, -DRB1 locus between the patients and healthy controls. A significantly higher frequency of HLA-B*07:05 was found in children with DMD compared to that in controls (OR = 16.2, 95%CI = 2.9–89.3, P < 0.046). More importantly, significantly higher frequencies of HLA-A*29:01 (OR = 77.308, 95%CI = 6.794–879.731, P < 0.0160) and HLA-B*07:05 (OR = 60.240, 95%CI = 9.637–376.535, P < 2.41*10−3) was found in patients with de novo mutations (n = 14) compared to controls while no difference of HLA alleles frequency ware indicated between patients with inherited mutation and control. The result indicates that HLA alleles is associated with pathogenesis of DMD especially DMD with de novo mutation. We use Vignos scale to estimate the lower limb motor function of patients. The impact of HLA alleles on score of Vignos scale of DMD children was estimated by multiple linear regression. Our study indicates that HLA-A*02:01 may have a dampening effect on the clinical phenotypic severity of DMD, evidenced by the presence of HLA-A*02:01 being associated with lower Vignos score. Our study demonstrates that certain HLA alleles are indeed associated with the pathogenesis and clinical phenotypic severity of DMD.
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Affiliation(s)
- Huan Li
- Department of Neurology, National Key Clinical Department and Key Discipline of Neurology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Lulu Xiao
- Department of Tissue Typing Center, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Liang Wang
- Department of Neurology, National Key Clinical Department and Key Discipline of Neurology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jinfu Lin
- Department of Neurology, National Key Clinical Department and Key Discipline of Neurology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Min Luo
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Menglong Chen
- Department of Neurology, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Ruojie He
- Department of Neurology, National Key Clinical Department and Key Discipline of Neurology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yuling Zhu
- Department of Neurology, National Key Clinical Department and Key Discipline of Neurology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Cheng Zhang
- Department of Neurology, National Key Clinical Department and Key Discipline of Neurology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
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