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Romero Villela PN, Evans LM, Palviainen T, Border R, Kaprio J, Palmer RHC, Keller MC, Ehringer MA. Loci on chromosome 20 interact with rs16969968 to influence cigarettes per day in European ancestry individuals. Drug Alcohol Depend 2024; 257:111126. [PMID: 38387257 PMCID: PMC11062023 DOI: 10.1016/j.drugalcdep.2024.111126] [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: 10/20/2023] [Revised: 01/12/2024] [Accepted: 02/07/2024] [Indexed: 02/24/2024]
Abstract
BACKGROUND The understanding of the molecular genetic contributions to smoking is largely limited to the additive effects of individual single nucleotide polymorphisms (SNPs), but the underlying genetic risk is likely to also include dominance, epistatic, and gene-environment interactions. METHODS To begin to address this complexity, we attempted to identify genetic interactions between rs16969968, the most replicated SNP associated with smoking quantity, and all SNPs and genes across the genome. RESULTS Using the UK Biobank European subsample, we found one SNP, rs1892967, and two genes, PCNA and TMEM230, that showed a significant genome-wide interaction with rs16969968 for log10 CPD and raw CPD, respectively, in a sample of 116 442 individuals who self-reported currently or previously smoking. We extended these analyses to individuals of South Asian descent and meta-analyzed the combined sample of 117 212 individuals of European and South Asian ancestry. We replicated the gene findings in a meta-analysis of five Finnish samples (N=40 140): FinHealth, FINRISK, Finnish Twin Cohort, GeneRISK, and Health-2000-2011. CONCLUSIONS To our knowledge, this represents the first reliable epistatic association between single nucleotide polymorphisms for smoking behaviors and provides a novel direction for possible future functional studies related to this interaction. Furthermore, this work demonstrates the feasibility of these analyses by pooling multiple datasets across various ancestries, which may be applied to other top SNPs for smoking and/or other phenotypes.
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Affiliation(s)
- Pamela N Romero Villela
- Institute for Behavioral Genetics, University of Colorado, Boulder, USA; Department of Psychology and Neuroscience, University of Colorado, Boulder, USA
| | - Luke M Evans
- Institute for Behavioral Genetics, University of Colorado, Boulder, USA; Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, USA
| | - Teemu Palviainen
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, USA
| | - Richard Border
- Departments of Neurology and Computer Science, University of California, Los Angeles, USA
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, USA
| | - Rohan H C Palmer
- Behavioral Genetics of Addiction Laboratory, Department of Psychology, Emory University, Atlanta, GA, USA
| | - Matthew C Keller
- Institute for Behavioral Genetics, University of Colorado, Boulder, USA; Department of Psychology and Neuroscience, University of Colorado, Boulder, USA
| | - Marissa A Ehringer
- Institute for Behavioral Genetics, University of Colorado, Boulder, USA; Departments of Neurology and Computer Science, University of California, Los Angeles, USA; Department of Integrative Physiology, University of Colorado, Boulder, USA.
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2
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Samuel G, Hardcastle F, Lucassen A. Advocating for a Context Specific Approach to Tackle Inequities. THE AMERICAN JOURNAL OF BIOETHICS : AJOB 2024; 24:109-111. [PMID: 38394004 DOI: 10.1080/15265161.2024.2303168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2024]
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3
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Lappalainen T, Li YI, Ramachandran S, Gusev A. Genetic and molecular architecture of complex traits. Cell 2024; 187:1059-1075. [PMID: 38428388 DOI: 10.1016/j.cell.2024.01.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 12/20/2023] [Accepted: 01/16/2024] [Indexed: 03/03/2024]
Abstract
Human genetics has emerged as one of the most dynamic areas of biology, with a broadening societal impact. In this review, we discuss recent achievements, ongoing efforts, and future challenges in the field. Advances in technology, statistical methods, and the growing scale of research efforts have all provided many insights into the processes that have given rise to the current patterns of genetic variation. Vast maps of genetic associations with human traits and diseases have allowed characterization of their genetic architecture. Finally, studies of molecular and cellular effects of genetic variants have provided insights into biological processes underlying disease. Many outstanding questions remain, but the field is well poised for groundbreaking discoveries as it increases the use of genetic data to understand both the history of our species and its applications to improve human health.
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Affiliation(s)
- Tuuli Lappalainen
- New York Genome Center, New York, NY, USA; Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden.
| | - Yang I Li
- Section of Genetic Medicine, University of Chicago, Chicago, IL, USA; Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Sohini Ramachandran
- Ecology, Evolution and Organismal Biology, Center for Computational Molecular Biology, and the Data Science Institute, Brown University, Providence, RI 029129, USA
| | - Alexander Gusev
- Harvard Medical School and Dana-Farber Cancer Institute, Boston, MA, USA
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4
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Brasher MS, Grotzinger AD, Friedman NP, Smolker HR, Evans LM. Disentangling differing relationships between internalizing disorders and alcohol use. Am J Med Genet B Neuropsychiatr Genet 2024:e32975. [PMID: 38375614 DOI: 10.1002/ajmg.b.32975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 12/14/2023] [Accepted: 02/08/2024] [Indexed: 02/21/2024]
Abstract
Both internalizing disorders and alcohol use have dramatic, wide-spread implications for global health. Previous work has established common phenotypic comorbidity among these disorders, as well as shared genetic variation underlying them both. We used genomic structural equation modeling to investigate the shared genetics of internalizing, externalizing, and alcohol use traits, as well as to explore whether specific domains of internalizing symptoms mediate the contrasting relationships with problematic alcohol use compared to alcohol consumption. We also examined patterns of genetic correlations between similar traits within additional Finnish and East Asian ancestry groups. When the shared genetic influence of externalizing psychopathology was accounted for, the genetic effect of internalizing traits on alcohol use was reduced, suggesting the important role of common genetic factors underlying multiple psychiatric disorders and their genetic influences on comorbidity of internalizing and alcohol use traits. Individual internalizing domains had contrasting effects on frequency of alcohol consumption, which demonstrate the complex system of pleiotropy that exists, even within similar disorders, and can be missed when evaluating only relationships among formal diagnoses. Future work must consider the broad effects of shared psychopathology along with the fine-scale effects of heterogeneity within disorders to more fully understand the biology underlying complex traits.
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Affiliation(s)
- Maizy S Brasher
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, Colorado, USA
- Department of Ecology and Evolutionary Biology, Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, Colorado, USA
| | - Andrew D Grotzinger
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, Colorado, USA
- Department of Psychology and Neuroscience, Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, Colorado, USA
| | - Naomi P Friedman
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, Colorado, USA
- Department of Psychology and Neuroscience, Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, Colorado, USA
| | - Harry R Smolker
- Institute of Cognitive Science, University of Colorado Boulder, Boulder, Colorado, USA
| | - Luke M Evans
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, Colorado, USA
- Department of Ecology and Evolutionary Biology, Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, Colorado, USA
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5
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Kępińska AP, Johnson JS, Huckins LM. Open Science Practices in Psychiatric Genetics: A Primer. BIOLOGICAL PSYCHIATRY GLOBAL OPEN SCIENCE 2024; 4:110-119. [PMID: 38298792 PMCID: PMC10829621 DOI: 10.1016/j.bpsgos.2023.08.007] [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: 05/25/2023] [Revised: 08/04/2023] [Accepted: 08/11/2023] [Indexed: 02/02/2024] Open
Abstract
Open science ensures that research is transparently reported and freely accessible for all to assess and collaboratively build on. Psychiatric genetics has led among the health sciences in implementing some open science practices in common study designs, such as replication as part of genome-wide association studies. However, thorough open science implementation guidelines are limited and largely not specific to data, privacy, and research conduct challenges in psychiatric genetics. Here, we present a primer of open science practices, including selection of a research topic with patients/nonacademic collaborators, equitable authorship and citation practices, design of replicable, reproducible studies, preregistrations, open data, and privacy issues. We provide tips for informative figures and inclusive, precise reporting. We discuss considerations in working with nonacademic collaborators and distributing research through preprints, blogs, social media, and accessible lecture materials. Finally, we provide extra resources to support every step of the research process.
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Affiliation(s)
- Adrianna P. Kępińska
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Psychosis Studies, Institute of Psychiatry, Psychology & Neuroscience, King’s College London, London, United Kingdom
| | - Jessica S. Johnson
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, New York
- Psychiatry Department, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina
| | - Laura M. Huckins
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Psychiatry, Yale University, New Haven, Connecticut
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6
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Sun Y, Wang M, Sun Q, Liu Y, Duan S, Wang Z, Zhou Y, Zhong J, Huang Y, Huang X, Yang Q, Li X, Su H, Cai Y, Jiang X, Chen J, Yan J, Nie S, Hu L, Yang J, Tang R, Wang CC, Liu C, Deng X, Yun L, He G. Distinguished biological adaptation architecture aggravated population differentiation of Tibeto-Burman-speaking people. J Genet Genomics 2023:S1673-8527(23)00210-2. [PMID: 37827489 DOI: 10.1016/j.jgg.2023.10.002] [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: 08/25/2023] [Revised: 09/28/2023] [Accepted: 10/04/2023] [Indexed: 10/14/2023]
Abstract
Tibeto-Burman (TB) people have endeavored to adapt to the hypoxic, cold, and high-UV high-altitude environments in the Tibetan Plateau and complex disease exposures in lowland rainforests since the late Paleolithic period. However, the full landscape of genetic history and biological adaptation of geographically diverse TB-speaking people, as well as their interaction mechanism, remain unknown. Here, we generate a whole-genome meta-database of 500 individuals from 39 TB-speaking populations and present a comprehensive landscape of genetic diversity, admixture history, and differentiated adaptative features of geographically different TB-speaking people. We identify genetic differentiation related to geography and language among TB-speaking people, consistent with their differentiated admixture process with incoming or indigenous ancestral source populations. A robust genetic connection between the Tibetan-Yi corridor and the ancient Yellow River people supports their Northern China origin hypothesis. We finally report substructure-related differentiated biological adaptative signatures between highland Tibetans and Loloish speakers. Adaptative signatures associated with the physical pigmentation (EDAR and SLC24A5) and metabolism (ALDH9A1) are identified in Loloish people, which differed from the high-altitude adaptative genetic architecture in Tibetan. TB-related genomic resources provide new insights into the genetic basis of biological adaptation and better reference for the anthropologically informed sampling design in biomedical and genomic cohort research.
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Affiliation(s)
- Yuntao Sun
- West China School of Basic Science & Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, China; Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, Sichuan 610000, China; Center for Archaeological Science, Sichuan University, Chengdu, Sichuan 610000, China
| | - Mengge Wang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, Sichuan 610000, China; Center for Archaeological Science, Sichuan University, Chengdu, Sichuan 610000, China; Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510275, China; Guangzhou Forensic Science Institute, Guangzhou, Guangdong 510055, China.
| | - Qiuxia Sun
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, Sichuan 610000, China; Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing, 400331, China
| | - Yan Liu
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, Sichuan 610000, China; School of Clinical Medical Sciences, North Sichuan Medical College, Nanchong, Sichuan 637100, China
| | - Shuhan Duan
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, Sichuan 610000, China; School of Basic Medical Sciences, North Sichuan Medical College, Nanchong, Sichuan 637100, China
| | - Zhiyong Wang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, Sichuan 610000, China; School of Forensic Medicine, Kunming Medical University, Kunming, Yunnan 650500, China
| | - Yunyu Zhou
- School of Stomatology, North Sichuan Medical College, Nanchong, Sichuan 637100, China
| | - Jun Zhong
- School of Basic Medical Sciences, North Sichuan Medical College, Nanchong, Sichuan 637100, China
| | - Yuguo Huang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, Sichuan 610000, China
| | - Xinyu Huang
- West China School of Basic Science & Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, China
| | - Qingxin Yang
- School of Forensic Medicine, Kunming Medical University, Kunming, Yunnan 650500, China
| | - Xiangping Li
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, Sichuan 610000, China; School of Forensic Medicine, Kunming Medical University, Kunming, Yunnan 650500, China
| | - Haoran Su
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, Sichuan 610000, China; School of Basic Medical Sciences, North Sichuan Medical College, Nanchong, Sichuan 637100, China
| | - Yan Cai
- School of Basic Medical Sciences, North Sichuan Medical College, Nanchong, Sichuan 637100, China; Department of Medical Laboratory, North Sichuan Medical College, Nanchong, Sichuan 637007, China
| | - Xiucheng Jiang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, Sichuan 610000, China; School of Basic Medical Sciences, North Sichuan Medical College, Nanchong, Sichuan 637100, China
| | - Jing Chen
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, Sichuan 610000, China; School of Forensic Medicine, Shanxi Medical University, Jinzhong, Sichuan 030001, China
| | - Jiangwei Yan
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Sichuan 030001, China
| | - Shengjie Nie
- School of Forensic Medicine, Kunming Medical University, Kunming, Yunnan 650500, China
| | - Liping Hu
- School of Forensic Medicine, Kunming Medical University, Kunming, Yunnan 650500, China
| | - Junbao Yang
- School of Clinical Medical Sciences, North Sichuan Medical College, Nanchong, Sichuan 637100, China
| | - Renkuan Tang
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing, 400331, China
| | - Chuan-Chao Wang
- School of Life Sciences, Xiamen University, Xiamen, Fujian 361005, China
| | - Chao Liu
- Anti-Drug Technology Center of Guangdong Province, Guangzhou, Guangdong 510230, China
| | - Xiaohui Deng
- West China School of Basic Science & Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, China.
| | - Libing Yun
- West China School of Basic Science & Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, China; Center for Archaeological Science, Sichuan University, Chengdu, Sichuan 610000, China.
| | - Guanglin He
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, Sichuan 610000, China; Center for Archaeological Science, Sichuan University, Chengdu, Sichuan 610000, China.
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7
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Wei Y, Zhang T, Wang B, Pan J, Jin S, Fang B, Gu W, Qin X, Dai B, Lin G, Gan H, Wu J, Ye D, Zhu Y. Prospective clinical sequencing of 1016 Chinese prostate cancer patients: uncovering genomic characterization and race disparity. Mol Oncol 2023; 17:2183-2199. [PMID: 37584393 PMCID: PMC10552897 DOI: 10.1002/1878-0261.13511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 07/06/2023] [Accepted: 08/14/2023] [Indexed: 08/17/2023] Open
Abstract
Although there is a well-known disparity in prostate cancer (PC) incidence and mortality between Chinese and Western patients, the underlying genomic differences have been investigated only sparsely. This clinicogenomic study was conducted to reveal the genomic mutations contributing to the PC disparity across ethnicities and investigate the mutational profile of Chinese PC patients. A total of 1016 Chinese PC patients were prospectively enrolled and subjected to targeted sequencing, resulting in usable sequencing data for 41 genes from 859 patients. Genomic data retrieved from The Cancer Genome Atlas (TCGA; locoregional PC), Memorial Sloan Kettering Cancer Center [MSKCC; metastatic castration-sensitive PC (mCSPC)], and Stand Up To Cancer [SU2C; metastatic castration-resistant PC (mCRPC)] cohorts were used as comparators representing Western men. Genomic mutations were analyzed using an integrated bioinformatic strategy. A comparison of the disease stages revealed that mutations in tumor protein 53 (TP53), androgen receptor (AR), forkhead box A1 (FOXA1), and genes involved in the cell cycle pathway were enriched in mCRPC. Mutations in adenomatous polyposis coli (APC) gene were found to be more prevalent in patients with visceral metastasis. Genomic differences between Western and Chinese men were mainly observed in castration-sensitive PC, with tumors from Chinese men having more FOXA1 (11.4% vs. 4.2%) but fewer TP53 (4.8% vs. 13%) mutations in locoregional PC and harboring fewer TP53 (11% vs. 29.2%), phosphatase and tensin homolog (PTEN; 2.5% vs. 10.3%), and APC (1.7% vs. 7.4%) mutations in the mCSPC stage than those of Western men. Patients of both ethnicities with mCRPC had similar mutational spectra. Furthermore, FOXA1 class-2 was less common than FOXA1 class-1 and showed no enrichment in metastasis, contrary to the findings in the Western cohort. Our study provides a valuable resource for a better understanding of PC in China and reveals the genomic alterations associated with PC disparity across races.
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Affiliation(s)
- Yu Wei
- Department of UrologyFudan University Shanghai Cancer CenterChina
- Department of Oncology, Shanghai Medical CollegeFudan UniversityShanghaiChina
- Shanghai Genitourinary Cancer InstituteChina
| | - Tingwei Zhang
- Department of UrologyFudan University Shanghai Cancer CenterChina
- Department of Oncology, Shanghai Medical CollegeFudan UniversityShanghaiChina
- Shanghai Genitourinary Cancer InstituteChina
| | - Beihe Wang
- Department of UrologyFudan University Shanghai Cancer CenterChina
- Department of Oncology, Shanghai Medical CollegeFudan UniversityShanghaiChina
- Shanghai Genitourinary Cancer InstituteChina
| | - Jian Pan
- Department of UrologyFudan University Shanghai Cancer CenterChina
- Department of Oncology, Shanghai Medical CollegeFudan UniversityShanghaiChina
- Shanghai Genitourinary Cancer InstituteChina
| | - Shengming Jin
- Department of UrologyFudan University Shanghai Cancer CenterChina
- Department of Oncology, Shanghai Medical CollegeFudan UniversityShanghaiChina
- Shanghai Genitourinary Cancer InstituteChina
| | - Bangwei Fang
- Department of UrologyFudan University Shanghai Cancer CenterChina
- Department of Oncology, Shanghai Medical CollegeFudan UniversityShanghaiChina
- Shanghai Genitourinary Cancer InstituteChina
| | - Weijie Gu
- Department of UrologyFudan University Shanghai Cancer CenterChina
- Department of Oncology, Shanghai Medical CollegeFudan UniversityShanghaiChina
- Shanghai Genitourinary Cancer InstituteChina
| | - Xiaojian Qin
- Department of UrologyFudan University Shanghai Cancer CenterChina
- Department of Oncology, Shanghai Medical CollegeFudan UniversityShanghaiChina
- Shanghai Genitourinary Cancer InstituteChina
| | - Bo Dai
- Department of UrologyFudan University Shanghai Cancer CenterChina
- Department of Oncology, Shanghai Medical CollegeFudan UniversityShanghaiChina
- Shanghai Genitourinary Cancer InstituteChina
| | - Guowen Lin
- Department of UrologyFudan University Shanghai Cancer CenterChina
- Department of Oncology, Shanghai Medical CollegeFudan UniversityShanghaiChina
- Shanghai Genitourinary Cancer InstituteChina
| | - Hualei Gan
- Department of Oncology, Shanghai Medical CollegeFudan UniversityShanghaiChina
- Department of PathologyFudan University Shanghai Cancer CenterChina
| | - Junlong Wu
- Department of UrologyFudan University Shanghai Cancer CenterChina
- Department of Oncology, Shanghai Medical CollegeFudan UniversityShanghaiChina
- Shanghai Genitourinary Cancer InstituteChina
| | - Dingwei Ye
- Department of UrologyFudan University Shanghai Cancer CenterChina
- Department of Oncology, Shanghai Medical CollegeFudan UniversityShanghaiChina
- Shanghai Genitourinary Cancer InstituteChina
| | - Yao Zhu
- Department of UrologyFudan University Shanghai Cancer CenterChina
- Department of Oncology, Shanghai Medical CollegeFudan UniversityShanghaiChina
- Shanghai Genitourinary Cancer InstituteChina
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Wan D, Yin Y. Trace elements in nutrition and health: a deep dive into essentiality and mechanism of their biological roles. SCIENCE CHINA. LIFE SCIENCES 2023; 66:1949-1951. [PMID: 37646917 DOI: 10.1007/s11427-023-2426-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Indexed: 09/01/2023]
Affiliation(s)
- Dan Wan
- Laboratory of Animal Nutritional Physiology and Metabolic Process, Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China
| | - Yulong Yin
- Laboratory of Animal Nutritional Physiology and Metabolic Process, Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China.
- University of Chinese Academy of Sciences, Beijing, 101408, China.
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9
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Cruz LA, Cooke Bailey JN, Crawford DC. Importance of Diversity in Precision Medicine: Generalizability of Genetic Associations Across Ancestry Groups Toward Better Identification of Disease Susceptibility Variants. Annu Rev Biomed Data Sci 2023; 6:339-356. [PMID: 37196357 PMCID: PMC10720270 DOI: 10.1146/annurev-biodatasci-122220-113250] [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] [Indexed: 05/19/2023]
Abstract
Genome-wide association studies (GWAS) revolutionized our understanding of common genetic variation and its impact on common human disease and traits. Developed and adopted in the mid-2000s, GWAS led to searchable genotype-phenotype catalogs and genome-wide datasets available for further data mining and analysis for the eventual development of translational applications. The GWAS revolution was swift and specific, including almost exclusively populations of European descent, to the neglect of the majority of the world's genetic diversity. In this narrative review, we recount the GWAS landscape of the early years that established a genotype-phenotype catalog that is now universally understood to be inadequate for a complete understanding of complex human genetics. We then describe approaches taken to augment the genotype-phenotype catalog, including the study populations, collaborative consortia, and study design approaches aimed to generalize and then ultimately discover genome-wide associations in non-European descent populations. The collaborations and data resources established in the efforts to diversify genomic findings undoubtedly provide the foundations of the next chapters of genetic association studies with the advent of budget-friendly whole-genome sequencing.
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Affiliation(s)
- Lauren A Cruz
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, USA;
- Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, Ohio, USA
| | - Jessica N Cooke Bailey
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, USA;
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, USA
- Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, Ohio, USA
| | - Dana C Crawford
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, USA;
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, USA
- Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, Ohio, USA
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10
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Koleva-Kolarova R, Vellekoop H, Huygens S, Versteegh M, Mölken MRV, Szilberhorn L, Zelei T, Nagy B, Wordsworth S, Tsiachristas A. Cost-effectiveness of extended DPYD testing before fluoropyrimidine chemotherapy in metastatic breast cancer in the UK. Per Med 2023; 20:339-355. [PMID: 37665240 DOI: 10.2217/pme-2022-0099] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
The aim of this study was to evaluate the cost-effectiveness of ToxNav©, a multivariant genetic test, to screen for DPYD followed by personalized chemotherapy dosing for metastatic breast cancer in the UK compared with no testing followed by standard dose, standard of care. In the main analysis, ToxNav was dominant over standard of care, producing 0.19 additional quality-adjusted life years and savings of £78,000 per patient over a lifetime. The mean additional quality-adjusted life years per person from 1000 simulations was 0.23 savings (95% CI: 0.22-0.24) at £99,000 (95% CI: £95-102,000). Varying input parameters independently by range of 20% was unlikely to change the results in the main analysis. The probabilistic sensitivity analysis showed ~97% probability of the ToxNav strategy to be dominant.
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Affiliation(s)
| | - Heleen Vellekoop
- Institute for Medical Technology Assessment, Erasmus University Rotterdam, Rotterdam, The Netherlands
| | - Simone Huygens
- Institute for Medical Technology Assessment, Erasmus University Rotterdam, Rotterdam, The Netherlands
| | - Matthijs Versteegh
- Institute for Medical Technology Assessment, Erasmus University Rotterdam, Rotterdam, The Netherlands
| | - Maureen Rutten-van Mölken
- Institute for Medical Technology Assessment, Erasmus University Rotterdam, Rotterdam, The Netherlands
- Erasmus School of Health Policy & Management, Erasmus University Rotterdam, Rotterdam, The Netherlands
| | - László Szilberhorn
- Syreon Research Institute, Budapest, Hungary
- Faculty of Social Sciences, Eötvös Loránd University, Budapest, Hungary
| | - Tamás Zelei
- Syreon Research Institute, Budapest, Hungary
| | - Balázs Nagy
- Syreon Research Institute, Budapest, Hungary
| | - Sarah Wordsworth
- Health Economics Research Centre, University of Oxford, Oxford, UK
- National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, Oxford, UK
| | - Apostolos Tsiachristas
- Health Economics Research Centre, University of Oxford, Oxford, UK
- National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, Oxford, UK
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11
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Chen RJ, Wang JJ, Williamson DFK, Chen TY, Lipkova J, Lu MY, Sahai S, Mahmood F. Algorithmic fairness in artificial intelligence for medicine and healthcare. Nat Biomed Eng 2023; 7:719-742. [PMID: 37380750 PMCID: PMC10632090 DOI: 10.1038/s41551-023-01056-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 04/13/2023] [Indexed: 06/30/2023]
Abstract
In healthcare, the development and deployment of insufficiently fair systems of artificial intelligence (AI) can undermine the delivery of equitable care. Assessments of AI models stratified across subpopulations have revealed inequalities in how patients are diagnosed, treated and billed. In this Perspective, we outline fairness in machine learning through the lens of healthcare, and discuss how algorithmic biases (in data acquisition, genetic variation and intra-observer labelling variability, in particular) arise in clinical workflows and the resulting healthcare disparities. We also review emerging technology for mitigating biases via disentanglement, federated learning and model explainability, and their role in the development of AI-based software as a medical device.
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Affiliation(s)
- Richard J Chen
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Cancer Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
- Cancer Data Science Program, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Judy J Wang
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Boston University School of Medicine, Boston, MA, USA
| | - Drew F K Williamson
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Cancer Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Tiffany Y Chen
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Cancer Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jana Lipkova
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Cancer Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ming Y Lu
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Cancer Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
- Cancer Data Science Program, Dana-Farber Cancer Institute, Boston, MA, USA
- Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sharifa Sahai
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Cancer Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Faisal Mahmood
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Cancer Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA.
- Cancer Data Science Program, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
- Harvard Data Science Initiative, Harvard University, Cambridge, MA, USA.
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12
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Richards-Belle A, Austin-Zimmerman I, Wang B, Zartaloudi E, Cotic M, Gracie C, Saadullah Khani N, Wannasuphoprasit Y, Wronska M, Dawda Y, Osborn DP, Bramon E. Associations of antidepressants and antipsychotics with lipid parameters: Do CYP2C19/ CYP2D6 genes play a role? A UK population-based study. J Psychopharmacol 2023; 37:396-407. [PMID: 36772859 PMCID: PMC10101178 DOI: 10.1177/02698811231152748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
BACKGROUND Dyslipidaemia is an important cardiovascular risk factor for people with severe mental illness, contributing to premature mortality. The link between antipsychotics and dyslipidaemia is well established, while evidence on antidepressants is mixed. AIMS To investigate if antidepressant/antipsychotic use was associated with lipid parameters in UK Biobank participants and if CYP2C19 and CYP2D6 genetic variation plays a role. METHODS Review of self-reported prescription medications identified participants taking antidepressants/antipsychotics. Total, low-, and high-density lipoprotein cholesterol (L/HDL-C) and triglycerides derived from blood samples. CYP2C19 and CYP2D6 metabolic phenotypes were assigned from genetic data. Linear regression investigated aims, adjusted for key covariates. RESULTS Of 469,739 participants, 36,043 took antidepressants (53% female, median age 58, 17% taking cholesterol-lowering medications) and 3255 took antipsychotics (58% female, median age 57, 27% taking cholesterol-lowering medications). Significant associations were found between use of each amitriptyline, fluoxetine, citalopram/escitalopram, sertraline, paroxetine and venlafaxine with higher total cholesterol, LDL-C, and triglycerides and lower HDL-C, compared to participants not taking each medication. Venlafaxine was associated with the worst lipid profile (total cholesterol, adjusted mean difference: 0.21 mmol/L, 95% confidence interval (CI): 0.17 to 0.26, p < 0.001). Antipsychotic use was significantly associated with lower HDL-C and higher triglycerides. In participants taking sertraline, CYP2C19 intermediate metabolisers had higher HDL-C (0.05 mmol/L, 95% CI: 0.01 to 0.09, p = 0.007) and lower triglycerides (-0.17 mmol/L, 95% CI: -0.29 to -0.05, p = 0.007), compared to normal metabolisers. CONCLUSIONS Antidepressants were significantly associated with adverse lipid profiles, potentially warranting baseline and regular monitoring. Further research should investigate the mechanistic pathways underlying the protective effects of the CYP2C19 intermediate metaboliser phenotype on HDL-C and triglycerides in people taking sertraline.
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Affiliation(s)
- Alvin Richards-Belle
- Mental Health Neuroscience Research Department, Division of Psychiatry, University College London, London, UK
| | - Isabelle Austin-Zimmerman
- Mental Health Neuroscience Research Department, Division of Psychiatry, University College London, London, UK
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Baihan Wang
- Mental Health Neuroscience Research Department, Division of Psychiatry, University College London, London, UK
| | - Eirini Zartaloudi
- Mental Health Neuroscience Research Department, Division of Psychiatry, University College London, London, UK
| | - Marius Cotic
- Mental Health Neuroscience Research Department, Division of Psychiatry, University College London, London, UK
| | - Caitlin Gracie
- Mental Health Neuroscience Research Department, Division of Psychiatry, University College London, London, UK
| | - Noushin Saadullah Khani
- Mental Health Neuroscience Research Department, Division of Psychiatry, University College London, London, UK
| | - Yanisa Wannasuphoprasit
- Mental Health Neuroscience Research Department, Division of Psychiatry, University College London, London, UK
| | - Marta Wronska
- Mental Health Neuroscience Research Department, Division of Psychiatry, University College London, London, UK
| | - Yogita Dawda
- Department of Pharmacy, Central and North West London NHS Foundation Trust, London, UK
| | - David Pj Osborn
- Epidemiology and Applied Clinical Research Department, Division of Psychiatry, University College London, London, UK
- Camden and Islington NHS Foundation Trust, London, UK
| | - Elvira Bramon
- Mental Health Neuroscience Research Department, Division of Psychiatry, University College London, London, UK
- Camden and Islington NHS Foundation Trust, London, UK
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13
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De Oliveira TC, Secolin R, Lopes-Cendes I. A review of ancestrality and admixture in Latin America and the caribbean focusing on native American and African descendant populations. Front Genet 2023; 14:1091269. [PMID: 36741309 PMCID: PMC9893294 DOI: 10.3389/fgene.2023.1091269] [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: 11/06/2022] [Accepted: 01/09/2023] [Indexed: 01/21/2023] Open
Abstract
Genomics can reveal essential features about the demographic evolution of a population that may not be apparent from historical elements. In recent years, there has been a significant increase in the number of studies applying genomic epidemiological approaches to understand the genetic structure and diversity of human populations in the context of demographic history and for implementing precision medicine. These efforts have traditionally been applied predominantly to populations of European origin. More recently, initiatives in the United States and Africa are including more diverse populations, establishing new horizons for research in human populations with African and/or Native ancestries. Still, even in the most recent projects, the under-representation of genomic data from Latin America and the Caribbean (LAC) is remarkable. In addition, because the region presents the most recent global miscegenation, genomics data from LAC may add relevant information to understand population admixture better. Admixture in LAC started during the colonial period, in the 15th century, with intense miscegenation between European settlers, mainly from Portugal and Spain, with local indigenous and sub-Saharan Africans brought through the slave trade. Since, there are descendants of formerly enslaved and Native American populations in the LAC territory; they are considered vulnerable populations because of their history and current living conditions. In this context, studying LAC Native American and African descendant populations is important for several reasons. First, studying human populations from different origins makes it possible to understand the diversity of the human genome better. Second, it also has an immediate application to these populations, such as empowering communities with the knowledge of their ancestral origins. Furthermore, because knowledge of the population genomic structure is an essential requirement for implementing genomic medicine and precision health practices, population genomics studies may ensure that these communities have access to genomic information for risk assessment, prevention, and the delivery of optimized treatment; thus, helping to reduce inequalities in the Western Hemisphere. Hoping to set the stage for future studies, we review different aspects related to genetic and genomic research in vulnerable populations from LAC countries.
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Affiliation(s)
- Thais C. De Oliveira
- Department of Translational Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil,The Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, Brazil
| | - Rodrigo Secolin
- Department of Translational Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil,The Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, Brazil
| | - Iscia Lopes-Cendes
- Department of Translational Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil,The Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, Brazil,*Correspondence: Iscia Lopes-Cendes,
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14
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Callier SL, Payne PW, Akinniyi D, McPartland K, Richardson TL, Rothstein MA, Royal CDM. Cardiologists' Perspectives on BiDil and the Use of Race in Drug Prescribing. J Racial Ethn Health Disparities 2022; 9:2146-2156. [PMID: 35118611 DOI: 10.1007/s40615-021-01153-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: 11/08/2020] [Revised: 03/04/2021] [Accepted: 09/14/2021] [Indexed: 12/29/2022]
Abstract
OBJECTIVES We explored cardiologists' attitudes and prescribing patterns specific to the use of generic isosorbide dinitrate and hydralazine hydrochloride, and the fixed-dose patented drug, BiDil. BACKGROUND Since the Food and Drug Administration approved BiDil in 2005 with an indication for self-identified black patients, disagreement about the appropriateness of race-based drugs has intensified and led to calls for providers and researchers to abandon race-based delimitations. This paper reports empirical evidence of cardiologists' views on BiDil's race-based indication and their ongoing inertia with respect to the debate about BiDil. METHODS We conducted a 2010 cross-sectional online survey of members of the Association of Black Cardiologists. RESULTS Fifty-nine cardiologists responded to the survey. Most participants (62.7%) prescribed BiDil to their patients. More than 40% of respondents did not prescribe BiDil to any non-African Americans. When considering whether to prescribe BiDil, a patient's race determined by physician assessment was the third most important factor considered by participants. The majority of participants (72.7%) selected symptoms as the most important factor. Most participants (59.2%) perceived race as defining biologically distinct individuals. Respondents prescribed BiDil more often to African American patients than non-African American patients. However, they prescribed the generic components that makeup BiDil to African Americans and non-African American patients similarly. CONCLUSIONS The survey provides useful findings that, when viewed within the context of ongoing debates about race-based medicine, show little progress toward appropriately utilizing BiDil to maximize health outcomes, yet, might inform the development of practical and effective guidelines concerning the use of race in medicine.
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Affiliation(s)
- Shawneequa L Callier
- Department of Clinical Research and Leadership, School of Medicine and Health Sciences, George Washington University, Washington, DC, USA.,Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Perry W Payne
- Department of Clinical Research and Leadership, School of Medicine and Health Sciences, George Washington University, Washington, DC, USA.
| | | | | | | | - Mark A Rothstein
- Institute for Bioethics, Health Policy and Law, School of Medicine, University of Louisville, Louisville, KY, USA
| | - Charmaine D M Royal
- Department of African & African American Studies and Center on Genomics, Race, Identity, Difference, Duke University, NC, Durham, USA
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15
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Wojcik GL. By their powers combined, global initiative joins forces for genomic research. Cell 2022; 185:4256-4258. [PMID: 36288728 DOI: 10.1016/j.cell.2022.10.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 10/07/2022] [Accepted: 10/07/2022] [Indexed: 11/05/2022]
Abstract
Genome-wide association studies (GWASs) can require immense sample sizes to identify variants associated with human health across the frequency spectrum. As the Global Biobank Meta-analysis Initiative (GBMI), Zhou et al. describe a collaborative network across 23 biobanks and 2.2 million participants to address challenges of underrepresentation of diversity in genomic research.
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Affiliation(s)
- Genevieve L Wojcik
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
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16
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Mishra A, Malik R, Hachiya T, Jürgenson T, Namba S, Posner DC, Kamanu FK, Koido M, Le Grand Q, Shi M, He Y, Georgakis MK, Caro I, Krebs K, Liaw YC, Vaura FC, Lin K, Winsvold BS, Srinivasasainagendra V, Parodi L, Bae HJ, Chauhan G, Chong MR, Tomppo L, Akinyemi R, Roshchupkin GV, Habib N, Jee YH, Thomassen JQ, Abedi V, Cárcel-Márquez J, Nygaard M, Leonard HL, Yang C, Yonova-Doing E, Knol MJ, Lewis AJ, Judy RL, Ago T, Amouyel P, Armstrong ND, Bakker MK, Bartz TM, Bennett DA, Bis JC, Bordes C, Børte S, Cain A, Ridker PM, Cho K, Chen Z, Cruchaga C, Cole JW, de Jager PL, de Cid R, Endres M, Ferreira LE, Geerlings MI, Gasca NC, Gudnason V, Hata J, He J, Heath AK, Ho YL, Havulinna AS, Hopewell JC, Hyacinth HI, Inouye M, Jacob MA, Jeon CE, Jern C, Kamouchi M, Keene KL, Kitazono T, Kittner SJ, Konuma T, Kumar A, Lacaze P, Launer LJ, Lee KJ, Lepik K, Li J, Li L, Manichaikul A, Markus HS, Marston NA, Meitinger T, Mitchell BD, Montellano FA, Morisaki T, Mosley TH, Nalls MA, Nordestgaard BG, O'Donnell MJ, Okada Y, Onland-Moret NC, Ovbiagele B, Peters A, Psaty BM, Rich SS, Rosand J, Sabatine MS, Sacco RL, Saleheen D, Sandset EC, Salomaa V, Sargurupremraj M, Sasaki M, Satizabal CL, Schmidt CO, Shimizu A, Smith NL, Sloane KL, Sutoh Y, Sun YV, Tanno K, Tiedt S, Tatlisumak T, Torres-Aguila NP, Tiwari HK, Trégouët DA, Trompet S, Tuladhar AM, Tybjærg-Hansen A, van Vugt M, Vibo R, Verma SS, Wiggins KL, Wennberg P, Woo D, Wilson PWF, Xu H, Yang Q, Yoon K, Millwood IY, Gieger C, Ninomiya T, Grabe HJ, Jukema JW, Rissanen IL, Strbian D, Kim YJ, Chen PH, Mayerhofer E, Howson JMM, Irvin MR, Adams H, Wassertheil-Smoller S, Christensen K, Ikram MA, Rundek T, Worrall BB, Lathrop GM, Riaz M, Simonsick EM, Kõrv J, França PHC, Zand R, Prasad K, Frikke-Schmidt R, de Leeuw FE, Liman T, Haeusler KG, Ruigrok YM, Heuschmann PU, Longstreth WT, Jung KJ, Bastarache L, Paré G, Damrauer SM, Chasman DI, Rotter JI, Anderson CD, Zwart JA, Niiranen TJ, Fornage M, Liaw YP, Seshadri S, Fernández-Cadenas I, Walters RG, Ruff CT, Owolabi MO, Huffman JE, Milani L, Kamatani Y, Dichgans M, Debette S. Stroke genetics informs drug discovery and risk prediction across ancestries. Nature 2022; 611:115-123. [PMID: 36180795 PMCID: PMC9524349 DOI: 10.1038/s41586-022-05165-3] [Citation(s) in RCA: 108] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 07/29/2022] [Indexed: 01/29/2023]
Abstract
Previous genome-wide association studies (GWASs) of stroke - the second leading cause of death worldwide - were conducted predominantly in populations of European ancestry1,2. Here, in cross-ancestry GWAS meta-analyses of 110,182 patients who have had a stroke (five ancestries, 33% non-European) and 1,503,898 control individuals, we identify association signals for stroke and its subtypes at 89 (61 new) independent loci: 60 in primary inverse-variance-weighted analyses and 29 in secondary meta-regression and multitrait analyses. On the basis of internal cross-ancestry validation and an independent follow-up in 89,084 additional cases of stroke (30% non-European) and 1,013,843 control individuals, 87% of the primary stroke risk loci and 60% of the secondary stroke risk loci were replicated (P < 0.05). Effect sizes were highly correlated across ancestries. Cross-ancestry fine-mapping, in silico mutagenesis analysis3, and transcriptome-wide and proteome-wide association analyses revealed putative causal genes (such as SH3PXD2A and FURIN) and variants (such as at GRK5 and NOS3). Using a three-pronged approach4, we provide genetic evidence for putative drug effects, highlighting F11, KLKB1, PROC, GP1BA, LAMC2 and VCAM1 as possible targets, with drugs already under investigation for stroke for F11 and PROC. A polygenic score integrating cross-ancestry and ancestry-specific stroke GWASs with vascular-risk factor GWASs (integrative polygenic scores) strongly predicted ischaemic stroke in populations of European, East Asian and African ancestry5. Stroke genetic risk scores were predictive of ischaemic stroke independent of clinical risk factors in 52,600 clinical-trial participants with cardiometabolic disease. Our results provide insights to inform biology, reveal potential drug targets and derive genetic risk prediction tools across ancestries.
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Affiliation(s)
- Aniket Mishra
- Bordeaux Population Health Research Center, University of Bordeaux, Inserm, UMR 1219, Bordeaux, France
| | - Rainer Malik
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany
| | - Tsuyoshi Hachiya
- Iwate Tohoku Medical Megabank Organization, Iwate Medical University, Iwate, Japan
| | - Tuuli Jürgenson
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
- Institute of Mathematics and Statistics, University of Tartu, Tartu, Estonia
| | - Shinichi Namba
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
| | - Daniel C Posner
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, MA, USA
| | - Frederick K Kamanu
- TIMI Study Group, Boston, MA, USA
- Division of Cardiovascular Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Masaru Koido
- Division of Molecular Pathology, Institute of Medical Sciences, The University of Tokyo, Tokyo, Japan
- Laboratory of Complex Trait Genomics, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Quentin Le Grand
- Bordeaux Population Health Research Center, University of Bordeaux, Inserm, UMR 1219, Bordeaux, France
| | - Mingyang Shi
- Laboratory of Complex Trait Genomics, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Yunye He
- Laboratory of Complex Trait Genomics, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Marios K Georgakis
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and the Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ilana Caro
- Bordeaux Population Health Research Center, University of Bordeaux, Inserm, UMR 1219, Bordeaux, France
| | - Kristi Krebs
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Yi-Ching Liaw
- Laboratory of Clinical Genome Sequencing, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, Taichung, Taiwan
| | - Felix C Vaura
- Department of Internal Medicine, University of Turku, Turku, Finland
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Turku, Finland
| | - Kuang Lin
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Bendik Slagsvold Winsvold
- Department of Research and Innovation, Division of Clinical Neuroscience, Oslo University Hospital, Oslo, Norway
- K. G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Department of Neurology, Oslo University Hospital, Oslo, Norway
| | - Vinodh Srinivasasainagendra
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Livia Parodi
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and the Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Hee-Joon Bae
- Department of Neurology and Cerebrovascular Disease Center, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Republic of Korea
| | | | - Michael R Chong
- Thrombosis and Atherosclerosis Research Institute, David Braley Cardiac, Vascular and Stroke Research Institute, Hamilton, Ontario, Canada
- Department of Pathology and Molecular Medicine, Michael G. DeGroote School of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Liisa Tomppo
- Department of Neurology, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Rufus Akinyemi
- Center for Genomic and Precision Medicine, College of Medicine, University of Ibadan, Ibadan, Nigeria
- Neuroscience and Ageing Research Unit Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Gennady V Roshchupkin
- Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Radiology and Nuclear Medicine, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Naomi Habib
- The Edmond and Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yon Ho Jee
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Jesper Qvist Thomassen
- Department of Clinical Biochemistry, Copenhagen University Hospital-Rigshospitalet, Copenhagen, Denmark
| | - Vida Abedi
- Department of Molecular and Functional Genomics, Weis Center for Research, Geisinger Health System, Danville, VA, USA
- Department of Public Health Sciences, College of Medicine, The Pennsylvania State University, State College, PA, USA
| | - Jara Cárcel-Márquez
- Stroke Pharmacogenomics and Genetics Laboratory, Biomedical Research Institute Sant Pau (IIB Sant Pau), Barcelona, Spain
- Departament de Medicina, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Marianne Nygaard
- The Danish Twin Registry, Department of Public Health, University of Southern Denmark, Odense, Denmark
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Hampton L Leonard
- Center for Alzheimer's and Related Dementias, National Institutes of Health, Bethesda, MD, USA
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Data Tecnica International, Glen Echo, MD, USA
| | - Chaojie Yang
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - Ekaterina Yonova-Doing
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Department of Genetics, Novo Nordisk Research Centre Oxford, Oxford, UK
| | - Maria J Knol
- Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Adam J Lewis
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Renae L Judy
- Department of Surgery, University of Pennsylvania, Philadelphia, PA, USA
| | - Tetsuro Ago
- Department of Medicine and Clinical Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Philippe Amouyel
- University of Lille, INSERM U1167, RID-AGE, LabEx DISTALZ, Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
- CHU Lille, Public Health Department, Lille, France
- Institut Pasteur de Lille, Lille, France
| | - Nicole D Armstrong
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Mark K Bakker
- UMC Utrecht Brain Center, Department of Neurology and Neurosurgery, University Medical Center Utrecht, University Utrecht, Utrecht, The Netherlands
| | - Traci M Bartz
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Joshua C Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Constance Bordes
- Bordeaux Population Health Research Center, University of Bordeaux, Inserm, UMR 1219, Bordeaux, France
| | - Sigrid Børte
- K. G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Research and Communication Unit for Musculoskeletal Health (FORMI), Department of Research and Innovation, Division of Clinical Neuroscience, Oslo University Hospital, Oslo, Norway
| | - Anael Cain
- The Edmond and Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Paul M Ridker
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Kelly Cho
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, MA, USA
| | - Zhengming Chen
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
- MRC Population Health Research Unit, University of Oxford, Oxford, UK
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, Saint Louis, MO, USA
| | - John W Cole
- VA Maryland Health Care System, Baltimore, MD, USA
- Department of Neurology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Phil L de Jager
- Program in Medical and Population Genetics, Broad Institute of Harvard and the Massachusetts Institute of Technology, Cambridge, MA, USA
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Rafael de Cid
- GenomesForLife-GCAT Lab Group, Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain
| | - Matthias Endres
- Klinik und Hochschulambulanz für Neurologie, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Center for Stroke Research Berlin, Berlin, Germany
- German Center for Neurodegenerative Diseases (DZNE), partner site Berlin, Berlin, Germany
- German Centre for Cardiovascular Research (DZHK), partner site Berlin, Berlin, Germany
| | - Leslie E Ferreira
- Post-Graduation Program on Health and Environment, Department of Medicine and Joinville Stroke Biobank, University of the Region of Joinville, Santa Catarina, Brazil
| | - Mirjam I Geerlings
- Department of Epidemiology, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Natalie C Gasca
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Vilmundur Gudnason
- Icelandic Heart Association, Kopavogur, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Jun Hata
- Department of Epidemiology and Public Health, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Jing He
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Alicia K Heath
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - Yuk-Lam Ho
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, MA, USA
| | - Aki S Havulinna
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
- Institute for Molecular Medicine Finland, FIMM-HiLIFE, Helsinki, Finland
| | - Jemma C Hopewell
- Clinical Trial Service and Epidemiological Studies Unit (CTSU), Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Hyacinth I Hyacinth
- Department of Neurology and Rehabilitation Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Michael Inouye
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK
| | - Mina A Jacob
- Department of Neurology, Donders Center for Medical Neuroscience, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Christina E Jeon
- Los Angeles County Department of Public Health, Los Angeles, CA, USA
| | - Christina Jern
- Institute of Biomedicine, Department of Laboratory Medicine, the Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Masahiro Kamouchi
- Department of Health Care Administration and Management, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Keith L Keene
- Department of Biology, Brody School of Medicine Center for Health Disparities, East Carolina University, Greenville, NC, USA
| | - Takanari Kitazono
- Department of Medicine and Clinical Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Steven J Kittner
- Department of Neurology, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Neurology and Geriatric Research and Education Clinical Center, VA Maryland Health Care System, Baltimore, MD, USA
| | - Takahiro Konuma
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
| | - Amit Kumar
- Rajendra Institute of Medical Sciences, Ranchi, India
| | - Paul Lacaze
- Department of Epidemiology and Preventive Medicine, School of Public Health and Preventive Medicine, Monash University, Melbourne, Victoria, Australia
| | - Lenore J Launer
- Intramural Research Program, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Keon-Joo Lee
- Department of Neurology, Korea University Guro Hospital, Seoul, Republic of Korea
| | - Kaido Lepik
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- University Center for Primary Care and Public Health, Lausanne, Switzerland
| | - Jiang Li
- Department of Molecular and Functional Genomics, Weis Center for Research, Geisinger Health System, Danville, VA, USA
| | - Liming Li
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing, China
| | - Ani Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Hugh S Markus
- Stroke Research Group, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Nicholas A Marston
- TIMI Study Group, Boston, MA, USA
- Division of Cardiovascular Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Thomas Meitinger
- Institute of Human Genetics, Technical University of Munich, Munich, Germany
- Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Braxton D Mitchell
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
- Geriatrics Research and Education Clinical Center, Baltimore Veterans Administration Medical Center, Baltimore, MD, USA
| | - Felipe A Montellano
- Institute of Clinical Epidemiology and Biometry, University of Würzburg, Würzburg, Germany
- Department of Neurology, University Hospital Würzburg, Würzburg, Germany
| | - Takayuki Morisaki
- Division of Molecular Pathology, Institute of Medical Sciences, The University of Tokyo, Tokyo, Japan
| | - Thomas H Mosley
- The MIND Center, University of Mississippi Medical Center, Jackson, MS, USA
| | - Mike A Nalls
- Center for Alzheimer's and Related Dementias, National Institutes of Health, Bethesda, MD, USA
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Data Tecnica International, Glen Echo, MD, USA
| | - Børge G Nordestgaard
- Department of Clinical Biochemistry, Copenhagen University Hospital-Herlev and Gentofte, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Martin J O'Donnell
- College of Medicine Nursing and Health Science, NUI Galway, Galway, Ireland
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Department of Genome Informatics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
- Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Japan
| | - N Charlotte Onland-Moret
- Department of Epidemiology, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Bruce Ovbiagele
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Annette Peters
- Institute of Epidemiology, Helmholtz Zentrum München,, German Research Center for Environmental Health, Neuherberg, Germany
- Institute for Medical Information Processing, Biometry and Epidemiology, Ludwig Maximilian University Munich, Munich, Germany
- German Centre for Cardiovascular Research (DZHK), partner site Munich, Munich, Germany
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Department of Health Systems and Population Health, University of Washington, Seattle, WA, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Jonathan Rosand
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and the Massachusetts Institute of Technology, Cambridge, MA, USA
- McCance Center for Brain Health, Massachusetts General Hospital, Boston, MA, USA
| | - Marc S Sabatine
- TIMI Study Group, Boston, MA, USA
- Division of Cardiovascular Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Ralph L Sacco
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, USA
- Evelyn F. McKnight Brain Institute, Gainesville, FL, USA
| | - Danish Saleheen
- Division of Cardiology, Department of Medicine, Columbia University, New York, NY, USA
| | - Else Charlotte Sandset
- Stroke Unit, Department of Neurology, Oslo University Hospital, Oslo, Norway
- Research and Development, The Norwegian Air Ambulance Foundation, Oslo, Norway
| | - Veikko Salomaa
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Muralidharan Sargurupremraj
- Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, University of Texas Health Sciences Center, San Antonio, TX, USA
| | - Makoto Sasaki
- Iwate Tohoku Medical Megabank Organization, Iwate Medical University, Iwate, Japan
| | - Claudia L Satizabal
- Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, University of Texas Health Sciences Center, San Antonio, TX, USA
- Framingham Heart Study, Framingham, MA, USA
| | - Carsten O Schmidt
- University Medicine Greifswald, Institute for Community Medicine, SHIP/KEF, Greifswald, Germany
| | - Atsushi Shimizu
- Iwate Tohoku Medical Megabank Organization, Iwate Medical University, Iwate, Japan
| | - Nicholas L Smith
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Kaiser Permanente Washington Health Research Institute, Kaiser Permanente Washington, Seattle, WA, USA
- Department of Veterans Affairs Office of Research and Development, Seattle Epidemiologic Research and Information Center, Seattle, WA, USA
| | - Kelly L Sloane
- Department of Neurology, University of Pennsylvania, Philadelphia, PA, USA
| | - Yoichi Sutoh
- Iwate Tohoku Medical Megabank Organization, Iwate Medical University, Iwate, Japan
| | - Yan V Sun
- Atlanta VA Health Care System, Decatur, GA, USA
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA, USA
| | - Kozo Tanno
- Iwate Tohoku Medical Megabank Organization, Iwate Medical University, Iwate, Japan
| | - Steffen Tiedt
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany
| | - Turgut Tatlisumak
- Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Unviersity Hospital, Gothenburg, Sweden
| | - Nuria P Torres-Aguila
- Stroke Pharmacogenomics and Genetics Laboratory, Biomedical Research Institute Sant Pau (IIB Sant Pau), Barcelona, Spain
| | - Hemant K Tiwari
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA
| | - David-Alexandre Trégouët
- Bordeaux Population Health Research Center, University of Bordeaux, Inserm, UMR 1219, Bordeaux, France
| | - Stella Trompet
- Department of Internal Medicine, Section of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, The Netherlands
- Department of Cardiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Anil Man Tuladhar
- Department of Neurology, Donders Center for Medical Neuroscience, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Anne Tybjærg-Hansen
- Department of Clinical Biochemistry, Copenhagen University Hospital-Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Marion van Vugt
- Division Heart & Lungs, Department of Cardiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Riina Vibo
- Department of Neurology and Neurosurgery, University of Tartu, Tartu, Estonia
| | - Shefali S Verma
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kerri L Wiggins
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Patrik Wennberg
- Department of Public Health and Clinical Medicine, Umeå University, Umeå, Sweden
| | - Daniel Woo
- Department of Neurology and Rehabilitation Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Peter W F Wilson
- Atlanta VA Health Care System, Decatur, GA, USA
- Department of Medicine, Division of Cardiovascular Disease, Emory University School of Medicine, Atlanta, GA, USA
| | - Huichun Xu
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Qiong Yang
- Framingham Heart Study, Framingham, MA, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Kyungheon Yoon
- Division of Genome Science, Department of Precision Medicine, National Institute of Health, Cheongju, Republic of Korea
| | - Iona Y Millwood
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
- MRC Population Health Research Unit, University of Oxford, Oxford, UK
| | - Christian Gieger
- Research Unit Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Toshiharu Ninomiya
- Department of Epidemiology and Public Health, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Hans J Grabe
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany
- German Center for Neurodegenerative Diseases (DZNE), site Rostock/Greifswald, Rostock, Germany
| | - J Wouter Jukema
- Department of Cardiology, Leiden University Medical Center, Leiden, The Netherlands
- Netherlands Heart Institute, Utrecht, The Netherlands
- Einthoven Laboratory for Experimental Vascular Medicine, LUMC, Leiden, The Netherlands
| | - Ina L Rissanen
- Department of Epidemiology, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Daniel Strbian
- Department of Neurology, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Young Jin Kim
- Division of Genome Science, Department of Precision Medicine, National Institute of Health, Cheongju, Republic of Korea
| | - Pei-Hsin Chen
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, Taichung, Taiwan
| | - Ernst Mayerhofer
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and the Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Joanna M M Howson
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Department of Genetics, Novo Nordisk Research Centre Oxford, Oxford, UK
| | - Marguerite R Irvin
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Hieab Adams
- Department of Clinical Genetics, Department of Radiology and Nuclear Medicine, Erasmus MC, Rotterdam, The Netherlands
- Latin American Brain Health (BrainLat), Universidad Adolfo Ibáñez, Santiago, Chile
| | - Sylvia Wassertheil-Smoller
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, New York, NY, USA
| | - Kaare Christensen
- The Danish Twin Registry, Department of Public Health, University of Southern Denmark, Odense, Denmark
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
- Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, Odense, Denmark
| | - Mohammad A Ikram
- Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Tatjana Rundek
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, USA
- Evelyn F. McKnight Brain Institute, Gainesville, FL, USA
| | - Bradford B Worrall
- Department of Neurology, University of Virginia, Charlottesville, VA, USA
- Department of Public Health Science, University of Virginia, Charlottesville, VA, USA
| | | | - Moeen Riaz
- Department of Epidemiology and Preventive Medicine, School of Public Health and Preventive Medicine, Monash University, Melbourne, Victoria, Australia
| | - Eleanor M Simonsick
- Longitudinal Studies Section, Translational Gerontology Branch, National Institute on Aging, Baltimore, MD, USA
| | - Janika Kõrv
- Department of Neurology and Neurosurgery, University of Tartu, Tartu, Estonia
| | - Paulo H C França
- Post-Graduation Program on Health and Environment, Department of Medicine and Joinville Stroke Biobank, University of the Region of Joinville, Santa Catarina, Brazil
| | - Ramin Zand
- Geisinger Neuroscience Institute, Geisinger Health System, Danville, PA, USA
- Department of Neurology, College of Medicine, The Pennsylvania State University, State College, PA, USA
| | | | - Ruth Frikke-Schmidt
- Department of Clinical Biochemistry, Copenhagen University Hospital-Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Frank-Erik de Leeuw
- Department of Neurology, Donders Center for Medical Neuroscience, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Thomas Liman
- Center for Stroke Research Berlin, Berlin, Germany
- Department of Epidemiology, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Klinik für Neurologie, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | | | - Ynte M Ruigrok
- UMC Utrecht Brain Center, Department of Neurology and Neurosurgery, University Medical Center Utrecht, University Utrecht, Utrecht, The Netherlands
| | - Peter Ulrich Heuschmann
- Institute of Clinical Epidemiology and Biometry, University of Würzburg, Würzburg, Germany
- Comprehensive Heart Failure Center, University Hospital Würzburg, Würzburg, Germany
- Clinical Trial Center, University Hospital Würzburg, Würzburg, Germany
| | - W T Longstreth
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Department of Neurology, University of Washington, Seattle, WA, USA
| | - Keum Ji Jung
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
- Institute for Health Promotion, Graduate School of Public Health, Yonsei University, Seoul, Republic of Korea
| | - Lisa Bastarache
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Guillaume Paré
- Thrombosis and Atherosclerosis Research Institute, David Braley Cardiac, Vascular and Stroke Research Institute, Hamilton, Ontario, Canada
- Department of Pathology and Molecular Medicine, Michael G. DeGroote School of Medicine, McMaster University, Hamilton, Ontario, Canada
- Department of Health Research Methods, Evidence and Impact, McMaster University, Hamilton, Ontario, Canada
- Population Health Research Institute, David Braley Cardiac, Vascular and Stroke Research Institute, Hamilton, Ontario, Canada
| | - Scott M Damrauer
- Department of Surgery and Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
- Corporal Michael Crescenz VA Medical Center, Philadelphia, PA, USA
| | - Daniel I Chasman
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Christopher D Anderson
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and the Massachusetts Institute of Technology, Cambridge, MA, USA
- McCance Center for Brain Health, Massachusetts General Hospital, Boston, MA, USA
- Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA
| | - John-Anker Zwart
- Department of Research and Innovation, Division of Clinical Neuroscience, Oslo University Hospital, Oslo, Norway
- K. G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Teemu J Niiranen
- Department of Internal Medicine, University of Turku, Turku, Finland
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Turku, Finland
- Division of Medicine, Turku University Hospital, Turku, Finland
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Yung-Po Liaw
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, Taichung, Taiwan
- Department of Medical Imaging, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Sudha Seshadri
- Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, University of Texas Health Sciences Center, San Antonio, TX, USA
- Framingham Heart Study, Framingham, MA, USA
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
| | - Israel Fernández-Cadenas
- Stroke Pharmacogenomics and Genetics Laboratory, Biomedical Research Institute Sant Pau (IIB Sant Pau), Barcelona, Spain
| | - Robin G Walters
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
- MRC Population Health Research Unit, University of Oxford, Oxford, UK
| | - Christian T Ruff
- TIMI Study Group, Boston, MA, USA
- Division of Cardiovascular Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Mayowa O Owolabi
- Center for Genomic and Precision Medicine, College of Medicine, University of Ibadan, Ibadan, Nigeria
- Department of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Jennifer E Huffman
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, MA, USA
| | - Lili Milani
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Yoichiro Kamatani
- Laboratory of Complex Trait Genomics, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Martin Dichgans
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany.
- Munich Cluster for Systems Neurology, Munich, Germany.
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany.
| | - Stephanie Debette
- Bordeaux Population Health Research Center, University of Bordeaux, Inserm, UMR 1219, Bordeaux, France.
- Department of Neurology, Institute for Neurodegenerative Diseases, CHU de Bordeaux, Bordeaux, France.
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17
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Murdoch CC, Skaar EP. Nutritional immunity: the battle for nutrient metals at the host-pathogen interface. Nat Rev Microbiol 2022; 20:657-670. [PMID: 35641670 PMCID: PMC9153222 DOI: 10.1038/s41579-022-00745-6] [Citation(s) in RCA: 114] [Impact Index Per Article: 57.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/04/2022] [Indexed: 12/21/2022]
Abstract
Trace metals are essential micronutrients required for survival across all kingdoms of life. From bacteria to animals, metals have critical roles as both structural and catalytic cofactors for an estimated third of the proteome, representing a major contributor to the maintenance of cellular homeostasis. The reactivity of metal ions engenders them with the ability to promote enzyme catalysis and stabilize reaction intermediates. However, these properties render metals toxic at high concentrations and, therefore, metal levels must be tightly regulated. Having evolved in close association with bacteria, vertebrate hosts have developed numerous strategies of metal limitation and intoxication that prevent bacterial proliferation, a process termed nutritional immunity. In turn, bacterial pathogens have evolved adaptive mechanisms to survive in conditions of metal depletion or excess. In this Review, we discuss mechanisms by which nutrient metals shape the interactions between bacterial pathogens and animal hosts. We explore the cell-specific and tissue-specific roles of distinct trace metals in shaping bacterial infections, as well as implications for future research and new therapeutic development.
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Affiliation(s)
- Caitlin C Murdoch
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN, USA
- Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Eric P Skaar
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN, USA.
- Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University School of Medicine, Nashville, TN, USA.
- Vanderbilt Institute for Chemical Biology, Vanderbilt University, Nashville, TN, USA.
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18
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Elghzaly AA, Sun C, Looger LL, Hirose M, Salama M, Khalil NM, Behiry ME, Hegazy MT, Hussein MA, Salem MN, Eltoraby E, Tawhid Z, Alwasefy M, Allam W, El-Shiekh I, Elserafy M, Abdelnaser A, Hashish S, Shebl N, Shahba AA, Elgirby A, Hassab A, Refay K, El-Touchy HM, Youssef A, Shabacy F, Hashim AA, Abdelzaher A, Alshebini E, Fayez D, El-Bakry SA, Elzohri MH, Abdelsalam EN, El-Khamisy SF, Ibrahim S, Ragab G, Nath SK. Genome-wide association study for systemic lupus erythematosus in an egyptian population. Front Genet 2022; 13:948505. [PMID: 36324510 PMCID: PMC9619055 DOI: 10.3389/fgene.2022.948505] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 09/30/2022] [Indexed: 04/11/2024] Open
Abstract
Systemic lupus erythematosus (SLE) susceptibility has a strong genetic component. Genome-wide association studies (GWAS) across trans-ancestral populations show both common and distinct genetic variants of susceptibility across European and Asian ancestries, while many other ethnic populations remain underexplored. We conducted the first SLE GWAS on Egyptians-an admixed North African/Middle Eastern population-using 537 patients and 883 controls. To identify novel susceptibility loci and replicate previously known loci, we performed imputation-based association analysis with 6,382,276 SNPs while accounting for individual admixture. We validated the association analysis using adaptive permutation tests (n = 109). We identified a novel genome-wide significant locus near IRS1/miR-5702 (Pcorrected = 1.98 × 10-8) and eight novel suggestive loci (Pcorrected < 1.0 × 10-5). We also replicated (Pperm < 0.01) 97 previously known loci with at least one associated nearby SNP, with ITGAM, DEF6-PPARD and IRF5 the top three replicated loci. SNPs correlated (r 2 > 0.8) with lead SNPs from four suggestive loci (ARMC9, DIAPH3, IFLDT1, and ENTPD3) were associated with differential gene expression (3.5 × 10-95 < p < 1.0 × 10-2) across diverse tissues. These loci are involved in cellular proliferation and invasion-pathways prominent in lupus and nephritis. Our study highlights the utility of GWAS in an admixed Egyptian population for delineating new genetic associations and for understanding SLE pathogenesis.
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Affiliation(s)
- Ashraf A. Elghzaly
- Department of Clinical Pathology, Faculty of Medicine, Mansoura University, El-Mansoura, Egypt
| | - Celi Sun
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States
| | - Loren L. Looger
- Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, San Diego, CA, United States
| | - Misa Hirose
- Division of Genetics, Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
| | - Mohamed Salama
- Institute of Global Health and Human Ecology, The American University in Cairo, New Cairo, Egypt
| | - Noha M. Khalil
- Rheumatology and Clinical Immunology Unit, Department of Internal Medicine, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Mervat Essam Behiry
- Rheumatology and Clinical Immunology Unit, Department of Internal Medicine, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Mohamed Tharwat Hegazy
- Rheumatology and Clinical Immunology Unit, Department of Internal Medicine, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Mohamed Ahmed Hussein
- Rheumatology and Clinical Immunology Unit, Department of Internal Medicine, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Mohamad Nabil Salem
- Department of Internal Medicine, Faculty of Medicine, Beni-Suef University, Beni Suef, Egypt
| | - Ehab Eltoraby
- Department of Internal Medicine, Faculty of Medicine, Mansoura University, El-Mansoura, Egypt
| | - Ziyad Tawhid
- Department of Clinical Pathology, Faculty of Medicine, Mansoura University, El-Mansoura, Egypt
| | - Mona Alwasefy
- Department of Clinical Pathology, Faculty of Medicine, Mansoura University, El-Mansoura, Egypt
| | - Walaa Allam
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
| | - Iman El-Shiekh
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
| | - Menattallah Elserafy
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
| | - Anwar Abdelnaser
- Institute of Global Health and Human Ecology, The American University in Cairo, New Cairo, Egypt
| | - Sara Hashish
- Institute of Global Health and Human Ecology, The American University in Cairo, New Cairo, Egypt
| | - Nourhan Shebl
- Institute of Global Health and Human Ecology, The American University in Cairo, New Cairo, Egypt
| | | | - Amira Elgirby
- Department of Internal Medicine, Faculty of Medicine, Alexandria University, Bab Sharqi, Egypt
| | - Amina Hassab
- Department of Clinical Pathology, Faculty of Medicine, Alexandria University, Bab Sharqi, Egypt
| | - Khalida Refay
- Department of Internal Medicine, Faculty of Medicine, Al-Azhar University, Cairo, Egypt
| | | | - Ali Youssef
- Department of Rheumatology and Immunology, Faculty of Medicine, Benha University Hospital, Benha, Egypt
| | - Fatma Shabacy
- Department of Rheumatology and Immunology, Faculty of Medicine, Benha University Hospital, Benha, Egypt
| | | | - Asmaa Abdelzaher
- Department of Clinical Pathology, Faculty of Medicine, South Valley University, Qena, Egypt
| | - Emad Alshebini
- Department of Internal Medicine, Faculty of Medicine, Menoufia University, Al Minufiyah, Egypt
| | - Dalia Fayez
- Rheumatology and Clinical Immunology Unit, Department of Internal Medicine, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Samah A. El-Bakry
- Rheumatology and Clinical Immunology Unit, Department of Internal Medicine, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Mona H. Elzohri
- Department of Internal Medicine, Faculty of Medicine, Assiut University, Asyut, Egypt
| | | | - Sherif F. El-Khamisy
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
- The Healthy Lifespan Institute, University of Sheffield, Sheffield, United Kingdom
- The Institute of Cancer Therapeutics, University of Bradford, Bradford, United Kingdom
| | - Saleh Ibrahim
- Division of Genetics, Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
| | - Gaafar Ragab
- Rheumatology and Clinical Immunology Unit, Department of Internal Medicine, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Swapan K. Nath
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States
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19
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Lang M, Zawati MH. Returning individual research results in international direct-to-participant genomic research: results from a 31-country study. Eur J Hum Genet 2022; 30:1132-1137. [PMID: 35478220 PMCID: PMC9553878 DOI: 10.1038/s41431-022-01103-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 03/25/2022] [Accepted: 04/12/2022] [Indexed: 12/15/2022] Open
Abstract
This paper summarizes the results of a 31-country qualitative study of expert perspectives on the regulation of international "direct-to-participant" (DTP) genomic research. We outline how the practice of directly recruiting participants for genomic studies online complicates ethics and regulatory considerations for the return of individual research results. As part of a larger project supported by the National Human Genome Research Institute, National Institutes of Health, we prepared and distributed to 31 global legal experts a questionnaire intended to ascertain opinions and perspectives on the way international DTP genomic research is likely to be regulated. We found significant disagreement across jurisdictions on the most favorable approach to managing such results, with some countries favoring return by default and others preferring to return only with the express consent of research participants. We conclude by outlining policy considerations that should guide researcher practices in this context. As international DTP genomic research evolves, jurists and ethicists should be attentive to the ways novel approaches to subject recruitment align with existing ethical and regulatory norms in research with human participants. This paper is a preliminary step toward documenting such alignment in the context of the return of individual research results.
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Affiliation(s)
- Michael Lang
- grid.14709.3b0000 0004 1936 8649Faculty of Medicine and Health Sciences, Centre of Genomics and Policy, McGill University, Montreal, QC Canada
| | - Ma’n H. Zawati
- grid.14709.3b0000 0004 1936 8649Faculty of Medicine and Health Sciences, Centre of Genomics and Policy, McGill University, Montreal, QC Canada
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20
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Jacobs BM, Peter M, Giovannoni G, Noyce AJ, Morris HR, Dobson R. Towards a global view of multiple sclerosis genetics. Nat Rev Neurol 2022; 18:613-623. [PMID: 36075979 DOI: 10.1038/s41582-022-00704-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/27/2022] [Indexed: 11/09/2022]
Abstract
Multiple sclerosis (MS) is a neuroimmunological disorder of the CNS with a strong heritable component. The genetic architecture of MS susceptibility is well understood in populations of European ancestry. However, the extent to which this architecture explains MS susceptibility in populations of non-European ancestry remains unclear. In this Perspective article, we outline the scientific arguments for studying MS genetics in ancestrally diverse populations. We argue that this approach is likely to yield insights that could benefit individuals with MS from all ancestral groups. We explore the logistical and theoretical challenges that have held back this field to date and conclude that, despite these challenges, inclusion of participants of non-European ancestry in MS genetics studies will ultimately be of value to all patients with MS worldwide.
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Affiliation(s)
- Benjamin Meir Jacobs
- Preventive Neurology Unit, Wolfson Institute of Population Health, Queen Mary University London, London, UK. .,Department of Neurology, Royal London Hospital, London, UK.
| | - Michelle Peter
- NHS North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Gavin Giovannoni
- Preventive Neurology Unit, Wolfson Institute of Population Health, Queen Mary University London, London, UK.,Department of Neurology, Royal London Hospital, London, UK.,Blizard Institute, Queen Mary University London, London, UK
| | - Alastair J Noyce
- Preventive Neurology Unit, Wolfson Institute of Population Health, Queen Mary University London, London, UK.,Department of Neurology, Royal London Hospital, London, UK.,Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Huw R Morris
- Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Ruth Dobson
- Preventive Neurology Unit, Wolfson Institute of Population Health, Queen Mary University London, London, UK.,Department of Neurology, Royal London Hospital, London, UK
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21
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Omics approaches to discover pathophysiological pathways contributing to human pain. Pain 2022; 163:S69-S78. [PMID: 35994593 PMCID: PMC9557800 DOI: 10.1097/j.pain.0000000000002726] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 06/19/2022] [Indexed: 10/26/2022]
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22
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Opportunities and challenges for the use of common controls in sequencing studies. Nat Rev Genet 2022; 23:665-679. [PMID: 35581355 DOI: 10.1038/s41576-022-00487-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/22/2022] [Indexed: 01/02/2023]
Abstract
Genome-wide association studies using large-scale genome and exome sequencing data have become increasingly valuable in identifying associations between genetic variants and disease, transforming basic research and translational medicine. However, this progress has not been equally shared across all people and conditions, in part due to limited resources. Leveraging publicly available sequencing data as external common controls, rather than sequencing new controls for every study, can better allocate resources by augmenting control sample sizes or providing controls where none existed. However, common control studies must be carefully planned and executed as even small differences in sample ascertainment and processing can result in substantial bias. Here, we discuss challenges and opportunities for the robust use of common controls in high-throughput sequencing studies, including study design, quality control and statistical approaches. Thoughtful generation and use of large and valuable genetic sequencing data sets will enable investigation of a broader and more representative set of conditions, environments and genetic ancestries than otherwise possible.
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23
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Martschenko DO, Young JL. Precision Medicine Needs to Think Outside the Box. Front Genet 2022; 13:795992. [PMID: 35559033 PMCID: PMC9086532 DOI: 10.3389/fgene.2022.795992] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 04/07/2022] [Indexed: 11/13/2022] Open
Abstract
Precision medicine offers a precious opportunity to change clinical practice and disrupt medicine’s reliance on crude racial, ethnic, or ancestral categories by focusing on an individual’s unique genetic, environmental, and lifestyle characteristics. However, precision medicine and the genomic studies that are its cornerstone have thus far failed to account for human diversity. This failure is made clearer when looking at individuals who encapsulate a mosaic of different genetic ancestries and do not fit neatly into existing population labels. This piece argues that precision medicine continues to rely on the same forms of crude categorization it seeks to unsettle. Until the scientific community creates inclusive solutions for individuals who fall outside or between our existing population labels, precision medicine will continue to fall short in its aims.
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Affiliation(s)
- Daphne O Martschenko
- Center for Biomedical Ethics, School of Medicine, Stanford University, Stanford, CA, United States
| | - Jennifer L Young
- Center for Biomedical Ethics, School of Medicine, Stanford University, Stanford, CA, United States.,Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
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24
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Enrichment analyses identify shared associations for 25 quantitative traits in over 600,000 individuals from seven diverse ancestries. Am J Hum Genet 2022; 109:871-884. [PMID: 35349783 PMCID: PMC9118115 DOI: 10.1016/j.ajhg.2022.03.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 03/02/2022] [Indexed: 12/12/2022] Open
Abstract
Since 2005, genome-wide association (GWA) datasets have been largely biased toward sampling European ancestry individuals, and recent studies have shown that GWA results estimated from self-identified European individuals are not transferable to non-European individuals because of various confounding challenges. Here, we demonstrate that enrichment analyses that aggregate SNP-level association statistics at multiple genomic scales-from genes to genomic regions and pathways-have been underutilized in the GWA era and can generate biologically interpretable hypotheses regarding the genetic basis of complex trait architecture. We illustrate examples of the robust associations generated by enrichment analyses while studying 25 continuous traits assayed in 566,786 individuals from seven diverse self-identified human ancestries in the UK Biobank and the Biobank Japan as well as 44,348 admixed individuals from the PAGE consortium including cohorts of African American, Hispanic and Latin American, Native Hawaiian, and American Indian/Alaska Native individuals. We identify 1,000 gene-level associations that are genome-wide significant in at least two ancestry cohorts across these 25 traits as well as highly conserved pathway associations with triglyceride levels in European, East Asian, and Native Hawaiian cohorts.
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25
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Gopalan S, Smith SP, Korunes K, Hamid I, Ramachandran S, Goldberg A. Human genetic admixture through the lens of population genomics. Philos Trans R Soc Lond B Biol Sci 2022; 377:20200410. [PMID: 35430881 PMCID: PMC9014191 DOI: 10.1098/rstb.2020.0410] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Over the past 50 years, geneticists have made great strides in understanding how our species' evolutionary history gave rise to current patterns of human genetic diversity classically summarized by Lewontin in his 1972 paper, ‘The Apportionment of Human Diversity’. One evolutionary process that requires special attention in both population genetics and statistical genetics is admixture: gene flow between two or more previously separated source populations to form a new admixed population. The admixture process introduces ancestry-based structure into patterns of genetic variation within and between populations, which in turn influences the inference of demographic histories, identification of genetic targets of selection and prediction of complex traits. In this review, we outline some challenges for admixture population genetics, including limitations of applying methods designed for populations without recent admixture to the study of admixed populations. We highlight recent studies and methodological advances that aim to overcome such challenges, leveraging genomic signatures of admixture that occurred in the past tens of generations to gain insights into human history, natural selection and complex trait architecture. This article is part of the theme issue ‘Celebrating 50 years since Lewontin's apportionment of human diversity’.
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Affiliation(s)
- Shyamalika Gopalan
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA
| | - Samuel Pattillo Smith
- Center for Computational Molecular Biology, Brown University, Providence, RI 02912, USA
- Department of Ecology, Evolution and Organismal Biology, Brown University, Providence, RI 02912, USA
| | - Katharine Korunes
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA
| | - Iman Hamid
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA
| | - Sohini Ramachandran
- Center for Computational Molecular Biology, Brown University, Providence, RI 02912, USA
- Department of Ecology, Evolution and Organismal Biology, Brown University, Providence, RI 02912, USA
- Data Science Initiative, Brown University, Providence, RI 02912, USA
| | - Amy Goldberg
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA
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Abstract
Stroke is the second leading cause of death worldwide and a complex, heterogeneous condition. In this review, we provide an overview of the current knowledge on monogenic and multifactorial forms of stroke, highlighting recent insight into the continuum between these. We describe how, in recent years, large-scale genome-wide association studies have enabled major progress in deciphering the genetic basis for stroke and its subtypes, although more research is needed to interpret these findings. We cover the potential of stroke genetics to reveal novel pathophysiological processes underlying stroke, to accelerate the discovery of new therapeutic approaches, and to identify individuals in the population who are at high risk of stroke and could be targeted for tailored preventative interventions.
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Affiliation(s)
- Stéphanie Debette
- Bordeaux Population Health Research Center, Inserm U1219, University of Bordeaux, France (S.D.).,Department of Neurology, Bordeaux University Hospital, Institute for Neurodegenerative Diseases, France (S.D.)
| | - Hugh S Markus
- Stroke Research Group, Department of Clinical Neurosciences, University of Cambridge, United Kingdom (H.S.M.)
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27
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Schubert R, Geoffroy E, Gregga I, Mulford AJ, Aguet F, Ardlie K, Gerszten R, Clish C, Van Den Berg D, Taylor KD, Durda P, Johnson WC, Cornell E, Guo X, Liu Y, Tracy R, Conomos M, Blackwell T, Papanicolaou G, Lappalainen T, Mikhaylova AV, Thornton TA, Cho MH, Gignoux CR, Lange L, Lange E, Rich SS, Rotter JI, Manichaikul A, Im HK, Wheeler HE. Protein prediction for trait mapping in diverse populations. PLoS One 2022; 17:e0264341. [PMID: 35202437 PMCID: PMC8870552 DOI: 10.1371/journal.pone.0264341] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 02/08/2022] [Indexed: 11/18/2022] Open
Abstract
Genetically regulated gene expression has helped elucidate the biological mechanisms underlying complex traits. Improved high-throughput technology allows similar interrogation of the genetically regulated proteome for understanding complex trait mechanisms. Here, we used the Trans-omics for Precision Medicine (TOPMed) Multi-omics pilot study, which comprises data from Multi-Ethnic Study of Atherosclerosis (MESA), to optimize genetic predictors of the plasma proteome for genetically regulated proteome-wide association studies (PWAS) in diverse populations. We built predictive models for protein abundances using data collected in TOPMed MESA, for which we have measured 1,305 proteins by a SOMAscan assay. We compared predictive models built via elastic net regression to models integrating posterior inclusion probabilities estimated by fine-mapping SNPs prior to elastic net. In order to investigate the transferability of predictive models across ancestries, we built protein prediction models in all four of the TOPMed MESA populations, African American (n = 183), Chinese (n = 71), European (n = 416), and Hispanic/Latino (n = 301), as well as in all populations combined. As expected, fine-mapping produced more significant protein prediction models, especially in African ancestries populations, potentially increasing opportunity for discovery. When we tested our TOPMed MESA models in the independent European INTERVAL study, fine-mapping improved cross-ancestries prediction for some proteins. Using GWAS summary statistics from the Population Architecture using Genomics and Epidemiology (PAGE) study, which comprises ∼50,000 Hispanic/Latinos, African Americans, Asians, Native Hawaiians, and Native Americans, we applied S-PrediXcan to perform PWAS for 28 complex traits. The most protein-trait associations were discovered, colocalized, and replicated in large independent GWAS using proteome prediction model training populations with similar ancestries to PAGE. At current training population sample sizes, performance between baseline and fine-mapped protein prediction models in PWAS was similar, highlighting the utility of elastic net. Our predictive models in diverse populations are publicly available for use in proteome mapping methods at https://doi.org/10.5281/zenodo.4837327.
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Affiliation(s)
- Ryan Schubert
- Department of Mathematics and Statistics, Loyola University Chicago, Chicago, IL, United States of America
- Department of Biology, Loyola University Chicago, Chicago, IL, United States of America
- Program in Bioinformatics, Loyola University Chicago, Chicago, IL, United States of America
| | - Elyse Geoffroy
- Program in Bioinformatics, Loyola University Chicago, Chicago, IL, United States of America
| | - Isabelle Gregga
- Department of Biology, Loyola University Chicago, Chicago, IL, United States of America
| | - Ashley J. Mulford
- Department of Biology, Loyola University Chicago, Chicago, IL, United States of America
- Program in Bioinformatics, Loyola University Chicago, Chicago, IL, United States of America
| | - Francois Aguet
- Broad Institute, Cambridge, MA, United States of America
| | - Kristin Ardlie
- Broad Institute, Cambridge, MA, United States of America
| | - Robert Gerszten
- Beth Israel Deaconess Medical Center, Boston, MA, United States of America
| | - Clary Clish
- Broad Institute, Cambridge, MA, United States of America
| | - David Van Den Berg
- University of Southern California, Los Angeles, CA, United States of America
| | - Kent D. Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, United States of America
| | - Peter Durda
- Laboratory for Clinical Biochemistry Research, University of Vermont, Burlington, VT, United States of America
| | - W. Craig Johnson
- Collaborative Health Studies Coordinating Center, University of Washington, Seattle, WA, United States of America
| | - Elaine Cornell
- Laboratory for Clinical Biochemistry Research, University of Vermont, Burlington, VT, United States of America
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, United States of America
| | - Yongmei Liu
- Department of Medicine, Duke University School of Medicine, Durham, NC, United States of America
| | - Russell Tracy
- Laboratory for Clinical Biochemistry Research, University of Vermont, Burlington, VT, United States of America
| | - Matthew Conomos
- Department of Biostatistics, University of Washington, Seattle, WA, United States of America
| | - Tom Blackwell
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, United States of America
| | - George Papanicolaou
- Epidemiology Branch, National Heart, Lung and Blood Institute, Bethesda, MD, United States of America
| | - Tuuli Lappalainen
- New York Genome Center and Department of Systems Biology, Columbia University, New York, NY United States of America
| | - Anna V. Mikhaylova
- Department of Biostatistics, University of Washington, Seattle, WA, United States of America
| | - Timothy A. Thornton
- Department of Biostatistics, University of Washington, Seattle, WA, United States of America
| | - Michael H. Cho
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA, United States of America
| | - Christopher R. Gignoux
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States of America
| | - Leslie Lange
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States of America
| | - Ethan Lange
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States of America
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States of America
| | - Jerome I. Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, United States of America
| | | | - Ani Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States of America
| | - Hae Kyung Im
- Section of Genetic Medicine, The University of Chicago, Chicago, IL, United States of America
| | - Heather E. Wheeler
- Department of Biology, Loyola University Chicago, Chicago, IL, United States of America
- Program in Bioinformatics, Loyola University Chicago, Chicago, IL, United States of America
- * E-mail:
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28
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Wang B, Giannakopoulou O, Austin-Zimmerman I, Irizar H, Harju-Seppänen J, Zartaloudi E, Bhat A, McQuillin A, Kuchenbäcker K, Bramon E. Adolescent Verbal Memory as a Psychosis Endophenotype: A Genome-Wide Association Study in an Ancestrally Diverse Sample. Genes (Basel) 2022; 13:106. [PMID: 35052446 PMCID: PMC8774761 DOI: 10.3390/genes13010106] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 12/16/2021] [Accepted: 12/29/2021] [Indexed: 02/04/2023] Open
Abstract
Verbal memory impairment is one of the most prominent cognitive deficits in psychosis. However, few studies have investigated the genetic basis of verbal memory in a neurodevelopmental context, and most genome-wide association studies (GWASs) have been conducted in European-ancestry populations. We conducted a GWAS on verbal memory in a maximum of 11,017 participants aged 8.9 to 11.1 years in the Adolescent Brain Cognitive Development Study®, recruited from a diverse population in the United States. Verbal memory was assessed by the Rey Auditory Verbal Learning Test, which included three measures of verbal memory: immediate recall, short-delay recall, and long-delay recall. We adopted a mixed-model approach to perform a joint GWAS of all participants, adjusting for ancestral background and familial relatedness. The inclusion of participants from all ancestries increased the power of the GWAS. Two novel genome-wide significant associations were found for short-delay and long-delay recall verbal memory. In particular, one locus (rs9896243) associated with long-delay recall was mapped to the NSF (N-Ethylmaleimide Sensitive Factor, Vesicle Fusing ATPase) gene, indicating the role of membrane fusion in adolescent verbal memory. Based on the GWAS in the European subset, we estimated the SNP-heritability to be 15% to 29% for the three verbal memory traits. We found that verbal memory was genetically correlated with schizophrenia, providing further evidence supporting verbal memory as an endophenotype for psychosis.
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Affiliation(s)
- Baihan Wang
- Department of Mental Health Neuroscience, Division of Psychiatry, University College London, London W1T 7BN, UK; (O.G.); (I.A.-Z.); (H.I.); (J.H.-S.); (E.Z.); (A.B.); (A.M.); (K.K.)
| | - Olga Giannakopoulou
- Department of Mental Health Neuroscience, Division of Psychiatry, University College London, London W1T 7BN, UK; (O.G.); (I.A.-Z.); (H.I.); (J.H.-S.); (E.Z.); (A.B.); (A.M.); (K.K.)
- UCL Genetics Institute, Division of Biosciences, University College London, London WC1E 6BT, UK
| | - Isabelle Austin-Zimmerman
- Department of Mental Health Neuroscience, Division of Psychiatry, University College London, London W1T 7BN, UK; (O.G.); (I.A.-Z.); (H.I.); (J.H.-S.); (E.Z.); (A.B.); (A.M.); (K.K.)
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 8AF, UK
| | - Haritz Irizar
- Department of Mental Health Neuroscience, Division of Psychiatry, University College London, London W1T 7BN, UK; (O.G.); (I.A.-Z.); (H.I.); (J.H.-S.); (E.Z.); (A.B.); (A.M.); (K.K.)
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jasmine Harju-Seppänen
- Department of Mental Health Neuroscience, Division of Psychiatry, University College London, London W1T 7BN, UK; (O.G.); (I.A.-Z.); (H.I.); (J.H.-S.); (E.Z.); (A.B.); (A.M.); (K.K.)
| | - Eirini Zartaloudi
- Department of Mental Health Neuroscience, Division of Psychiatry, University College London, London W1T 7BN, UK; (O.G.); (I.A.-Z.); (H.I.); (J.H.-S.); (E.Z.); (A.B.); (A.M.); (K.K.)
| | - Anjali Bhat
- Department of Mental Health Neuroscience, Division of Psychiatry, University College London, London W1T 7BN, UK; (O.G.); (I.A.-Z.); (H.I.); (J.H.-S.); (E.Z.); (A.B.); (A.M.); (K.K.)
| | - Andrew McQuillin
- Department of Mental Health Neuroscience, Division of Psychiatry, University College London, London W1T 7BN, UK; (O.G.); (I.A.-Z.); (H.I.); (J.H.-S.); (E.Z.); (A.B.); (A.M.); (K.K.)
| | - Karoline Kuchenbäcker
- Department of Mental Health Neuroscience, Division of Psychiatry, University College London, London W1T 7BN, UK; (O.G.); (I.A.-Z.); (H.I.); (J.H.-S.); (E.Z.); (A.B.); (A.M.); (K.K.)
- UCL Genetics Institute, Division of Biosciences, University College London, London WC1E 6BT, UK
| | - Elvira Bramon
- Department of Mental Health Neuroscience, Division of Psychiatry, University College London, London W1T 7BN, UK; (O.G.); (I.A.-Z.); (H.I.); (J.H.-S.); (E.Z.); (A.B.); (A.M.); (K.K.)
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29
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Jones AV, Curtiss D, Harris C, Southerington T, Hautalahti M, Wihuri P, Mäkelä J, Kallionpää RE, Makkonen E, Knopp T, Mannermaa A, Mäkinen E, Moilanen AM, Tezel TH, Waheed NK. An assessment of prevalence of Type 1 CFI rare variants in European AMD, and why lack of broader genetic data hinders development of new treatments and healthcare access. PLoS One 2022; 17:e0272260. [PMID: 36067162 PMCID: PMC9447915 DOI: 10.1371/journal.pone.0272260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 07/14/2022] [Indexed: 11/19/2022] Open
Abstract
PURPOSE Advanced age-related macular degeneration (AAMD) risk is associated with rare complement Factor I (FI) genetic variants associated with low FI protein levels (termed 'Type 1'), but it is unclear how variant prevalences differ between AMD patients from different ethnicities. METHODS Collective prevalence of Type 1 CFI rare variant genotypes were examined in four European AAMD datasets. Collective minor allele frequencies (MAFs) were sourced from the natural history study SCOPE, the UK Biobank, the International AMD Genomics Consortium (IAMDGC), and the Finnish Biobank Cooperative (FINBB), and compared to paired control MAFs or background population prevalence rates from the Genome Aggregation Database (gnomAD). Due to a lack of available genetic data in non-European AAMD, power calculations were undertaken to estimate the AAMD population sizes required to identify statistically significant association between Type 1 CFI rare variants and disease risk in different ethnicities, using gnomAD populations as controls. RESULTS Type 1 CFI rare variants were enriched in all European AAMD cohorts, with odds ratios (ORs) ranging between 3.1 and 7.8, and a greater enrichment was observed in dry AMD from FINBB (OR 8.9, 95% CI 1.49-53.31). The lack of available non-European AAMD datasets prevented us exploring this relationship more globally, however a statistical association may be detectable by future sequencing studies that sample approximately 2,000 AAMD individuals from Ashkenazi Jewish and Latino/Admixed American ethnicities. CONCLUSIONS The relationship between Type 1 CFI rare variants increasing odds of AAMD are well established in Europeans, however the lack of broader genetic data in AAMD has adverse implications for clinical development and future commercialisation strategies of targeted FI therapies in AAMD. These findings emphasise the importance of generating more diverse genetic data in AAMD to improve equity of access to new treatments and address the bias in health care.
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Affiliation(s)
- Amy V. Jones
- Gyroscope Therapeutics Limited, London, United Kingdom
| | - Darin Curtiss
- Gyroscope Therapeutics Limited, London, United Kingdom
| | - Claire Harris
- Gyroscope Therapeutics Limited, London, United Kingdom
| | - Tom Southerington
- Finnish Biobank Cooperative–FINBB, Turku, Finland
- University of Turku, Turku, Finland
| | | | - Pauli Wihuri
- Finnish Biobank Cooperative–FINBB, Turku, Finland
| | | | - Roosa E. Kallionpää
- Auria Biobank, Turku University Hospital and University of Turku, Turku, Finland
| | | | - Theresa Knopp
- Helsinki Biobank, HUS, Helsinki University Hospital, Helsinki, Finland
| | | | - Erna Mäkinen
- Biobank of Central Finland, Hospital Nova of Central Finland, Jyväskylä, Finland
| | - Anne-Mari Moilanen
- Biobank Borealis of Northern Finland, Oulu University Hospital, Oulu, Finland
| | - Tongalp H. Tezel
- Department of Ophthalmology, Edward S. Harkness Eye Institute, Columbia University College of Physicians and Surgeons, Columbia University Medical Center, New York, NY, United States of America
| | | | - Nadia K. Waheed
- Gyroscope Therapeutics Limited, London, United Kingdom
- Department of Ophthalmology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
- * E-mail:
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30
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Deng L, Pan Y, Wang Y, Chen H, Yuan K, Chen S, Lu D, Lu Y, Mokhtar SS, Rahman TA, Hoh BP, Xu S. Genetic connections and convergent evolution of tropical indigenous peoples in Asia. Mol Biol Evol 2021; 39:6481554. [PMID: 34940850 PMCID: PMC8826522 DOI: 10.1093/molbev/msab361] [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] [Indexed: 11/14/2022] Open
Abstract
Tropical indigenous peoples in Asia (TIA) attract much attention for their unique appearance, whereas their genetic history and adaptive evolution remain mysteries. We conducted a comprehensive study to characterize the genetic distinction and connection of broad geographical TIAs. Despite the diverse genetic makeup and large interarea genetic differentiation between the TIA groups, we identified a basal Asian ancestry (bASN) specifically shared by these populations. The bASN ancestry was relatively enriched in ancient Asian human genomes dated as early as ∼50,000 years before the present and diminished in more recent history. Notably, the bASN ancestry is unlikely to be derived from archaic hominins. Instead, we suggest it may be better modeled as a survived lineage of the initial peopling of Asia. Shared adaptations inherited from the ancient Asian ancestry were detected among the TIA groups (e.g., LIMS1 for hair morphology, and COL24A1 for bone formation), and they are enriched in neurological functions either at an identical locus (e.g., NKAIN3), or different loci in an identical gene (e.g., TENM4). The bASN ancestry could also have formed the substrate of the genetic architecture of the dark pigmentation observed in the TIA peoples. We hypothesize that phenotypic convergence of the dark pigmentation in TIAs could have resulted from parallel (e.g., DDB1/DAK) or genetic convergence driven by admixture (e.g., MTHFD1 and RAD18), new mutations (e.g., STK11), or notably purifying selection (e.g., MC1R). Our results provide new insights into the initial peopling of Asia and an advanced understanding of the phenotypic convergence of the TIA peoples.
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Affiliation(s)
- Lian Deng
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yuwen Pan
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health,University of Chinese Academy of Sciences,Chinese Academy of Sciences, Shanghai 200031, China
| | - Yinan Wang
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health,University of Chinese Academy of Sciences,Chinese Academy of Sciences, Shanghai 200031, China
- Department of Liver Surgery and Transplantation Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Hao Chen
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health,University of Chinese Academy of Sciences,Chinese Academy of Sciences, Shanghai 200031, China
| | - Kai Yuan
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health,University of Chinese Academy of Sciences,Chinese Academy of Sciences, Shanghai 200031, China
| | - Sihan Chen
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai 200438, China
| | - Dongsheng Lu
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health,University of Chinese Academy of Sciences,Chinese Academy of Sciences, Shanghai 200031, China
| | - Yan Lu
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Siti Shuhada Mokhtar
- Institute of Medical Molecular Biotechnology, Faculty of Medicine, Universiti Teknologi MARA, Sungai Buloh Campus, 47000 Sungai Buloh, Selangor, Malaysia
| | - Thuhairah Abdul Rahman
- Clinical Pathology Diagnostic Centre Research Laboratory, Faculty of Medicine, Universiti Teknologi MARA, Sungai Buloh Campus, 47000 Sungai Buloh, Selangor, Malaysia
| | - Boon-Peng Hoh
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health,University of Chinese Academy of Sciences,Chinese Academy of Sciences, Shanghai 200031, China
- Faculty of Medicine and Health Sciences, UCSI University, Jalan Menara Gading, UCSI Heights 56000 Cheras, Kuala Lumpur, Malaysia
| | - Shuhua Xu
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health,University of Chinese Academy of Sciences,Chinese Academy of Sciences, Shanghai 200031, China
- Department of Liver Surgery and Transplantation Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai 200438, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
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31
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Abstract
Clonal haematopoiesis (CH) is a common, age-related expansion of blood cells with somatic mutations that is associated with an increased risk of haematological malignancies, cardiovascular disease and all-cause mortality. CH may be caused by point mutations in genes associated with myeloid neoplasms, chromosomal copy number changes and loss of heterozygosity events. How inherited and environmental factors shape the incidence of CH is incompletely understood. Even though the several varieties of CH may have distinct phenotypic consequences, recent research points to an underlying genetic architecture that is highly overlapping. Moreover, there are numerous commonalities between the inherited variation associated with CH and that which has been linked to age-associated biomarkers and diseases. In this Review, we synthesize what is currently known about how inherited variation shapes the risk of CH and how this genetic architecture intersects with the biology of diseases that occur with ageing.
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Affiliation(s)
- Alexander J Silver
- Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
- Division of Hematology and Oncology, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Alexander G Bick
- Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
- Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
- Center for Immunobiology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Michael R Savona
- Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA.
- Division of Hematology and Oncology, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA.
- Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA.
- Center for Immunobiology, Vanderbilt University School of Medicine, Nashville, TN, USA.
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32
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Majumder MA, Blank ML, Geary J, Bollinger JM, Guerrini CJ, Robinson JO, Canfield I, Cook-Deegan R, McGuire AL. Challenges to Building a Gene Variant Commons to Assess Hereditary Cancer Risk: Results of a Modified Policy Delphi Panel Deliberation. J Pers Med 2021; 11:646. [PMID: 34357113 PMCID: PMC8305920 DOI: 10.3390/jpm11070646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 06/07/2021] [Accepted: 07/03/2021] [Indexed: 11/25/2022] Open
Abstract
Understanding the clinical significance of variants associated with hereditary cancer risk requires access to a pooled data resource or network of resources-a "cancer gene variant commons"-incorporating representative, well-characterized genetic data, metadata, and, for some purposes, pathways to case-level data. Several initiatives have invested significant resources into collecting and sharing cancer gene variant data, but further progress hinges on identifying and addressing unresolved policy issues. This commentary provides insights from a modified policy Delphi process involving experts from a range of stakeholder groups involved in the data-sharing ecosystem. In particular, we describe policy issues and options generated by Delphi participants in five domains critical to the development of an effective cancer gene variant commons: incentives, financial sustainability, privacy and security, equity, and data quality. Our intention is to stimulate wider discussion and lay a foundation for further work evaluating policy options more in-depth and mapping them to those who have the power to bring about change. Addressing issues in these five domains will contribute to a cancer gene variant commons that supports better care for at-risk and affected patients, empowers patient communities, and advances research on hereditary cancers.
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Affiliation(s)
- Mary A. Majumder
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77005, USA; (M.L.B.); (J.M.B.); (C.J.G.); (J.O.R.); (A.L.M.)
| | - Matthew L. Blank
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77005, USA; (M.L.B.); (J.M.B.); (C.J.G.); (J.O.R.); (A.L.M.)
| | - Janis Geary
- School for the Future of Innovation in Society and Consortium for Science, Policy & Outcomes, Arizona State University Barrett & O’Connor Washington Center, 1800 I (Eye) Street, NW, Washington, DC 20006, USA; (J.G.); (R.C.-D.)
| | - Juli M. Bollinger
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77005, USA; (M.L.B.); (J.M.B.); (C.J.G.); (J.O.R.); (A.L.M.)
- Johns Hopkins Berman Institute of Bioethics, Deering Hall, 1809 Ashland Ave, Baltimore, MD 21205, USA
| | - Christi J. Guerrini
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77005, USA; (M.L.B.); (J.M.B.); (C.J.G.); (J.O.R.); (A.L.M.)
| | - Jill Oliver Robinson
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77005, USA; (M.L.B.); (J.M.B.); (C.J.G.); (J.O.R.); (A.L.M.)
| | - Isabel Canfield
- Department of Philosophy, University of Notre Dame, Malloy Hall, Notre Dame, IN 46556, USA;
| | - Robert Cook-Deegan
- School for the Future of Innovation in Society and Consortium for Science, Policy & Outcomes, Arizona State University Barrett & O’Connor Washington Center, 1800 I (Eye) Street, NW, Washington, DC 20006, USA; (J.G.); (R.C.-D.)
| | - Amy L. McGuire
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77005, USA; (M.L.B.); (J.M.B.); (C.J.G.); (J.O.R.); (A.L.M.)
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33
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Amoako E, Jumbam DT, Bediako Y. Unseen and unheard: African children with cancer are consistently excluded from clinical trials. BMJ Glob Health 2021; 6:bmjgh-2020-004750. [PMID: 33472839 PMCID: PMC7818831 DOI: 10.1136/bmjgh-2020-004750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 12/16/2020] [Indexed: 11/04/2022] Open
Affiliation(s)
- Emmanuella Amoako
- Department of Paediatrics and Child Health, Cape Coast Teaching Hospital, Cape Coast, Ghana .,Department of Paediatrics and Child Health, University of Cape Coast, Cape Coast, Ghana.,Yemaachi Biotechnology, Accra, Ghana
| | | | - Yaw Bediako
- Yemaachi Biotechnology, Accra, Ghana.,West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
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34
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Abstract
Immunogenomics studies have been largely limited to individuals of European ancestry, restricting the ability to identify variation in human adaptive immune responses across populations. Inclusion of a greater diversity of individuals in immunogenomics studies will substantially enhance our understanding of human immunology.
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35
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Rare variant contribution to human disease in 281,104 UK Biobank exomes. Nature 2021; 597:527-532. [PMID: 34375979 PMCID: PMC8458098 DOI: 10.1038/s41586-021-03855-y] [Citation(s) in RCA: 164] [Impact Index Per Article: 54.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 07/28/2021] [Indexed: 02/08/2023]
Abstract
Genome-wide association studies have uncovered thousands of common variants associated with human disease, but the contribution of rare variants to common disease remains relatively unexplored. The UK Biobank contains detailed phenotypic data linked to medical records for approximately 500,000 participants, offering an unprecedented opportunity to evaluate the effect of rare variation on a broad collection of traits1,2. Here we study the relationships between rare protein-coding variants and 17,361 binary and 1,419 quantitative phenotypes using exome sequencing data from 269,171 UK Biobank participants of European ancestry. Gene-based collapsing analyses revealed 1,703 statistically significant gene-phenotype associations for binary traits, with a median odds ratio of 12.4. Furthermore, 83% of these associations were undetectable via single-variant association tests, emphasizing the power of gene-based collapsing analysis in the setting of high allelic heterogeneity. Gene-phenotype associations were also significantly enriched for loss-of-function-mediated traits and approved drug targets. Finally, we performed ancestry-specific and pan-ancestry collapsing analyses using exome sequencing data from 11,933 UK Biobank participants of African, East Asian or South Asian ancestry. Our results highlight a significant contribution of rare variants to common disease. Summary statistics are publicly available through an interactive portal ( http://azphewas.com/ ).
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36
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Population-Matched Transcriptome Prediction Increases TWAS Discovery and Replication Rate. iScience 2020; 23:101850. [PMID: 33313492 PMCID: PMC7721644 DOI: 10.1016/j.isci.2020.101850] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 11/12/2020] [Accepted: 11/18/2020] [Indexed: 12/11/2022] Open
Abstract
Most genome-wide association studies (GWAS) and transcriptome-wide association studies (TWAS) focus on European populations; however, these results cannot always be accurately applied to non-European populations due to genetic architecture differences. Using GWAS summary statistics in the Population Architecture using Genomics and Epidemiology study, which comprises ∼50,000 Hispanic/Latinos, African Americans, Asians, Native Hawaiians, and Native Americans, we perform TWAS to determine gene-trait associations. We compared results using three transcriptome prediction models derived from Multi-Ethnic Study of Atherosclerosis populations: the African American and Hispanic/Latino (AFHI) model, the European (EUR) model, and the African American, Hispanic/Latino, and European (ALL) model. We identified 240 unique significant trait-associated genes. We found more significant, colocalized genes that replicate in larger cohorts when applying the AFHI model than the EUR or ALL model. Thus, TWAS with population-matched transcriptome models have more power for discovery and replication, demonstrating the need for more transcriptome studies in diverse populations. TWAS mechanistically extends GWAS findings in diverse populations Population-matched transcriptome models detect more replicable associations Colocalization shows GWAS variants likely act through gene expression regulation More GWAS and transcriptome modeling in diverse populations are needed
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