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Shyr C, Sulieman L, Harris PA. Illuminating the landscape of high-level clinical trial opportunities in the All of Us Research Program. J Am Med Inform Assoc 2024:ocae062. [PMID: 38622899 DOI: 10.1093/jamia/ocae062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 03/02/2024] [Accepted: 03/07/2024] [Indexed: 04/17/2024] Open
Abstract
OBJECTIVE With its size and diversity, the All of Us Research Program has the potential to power and improve representation in clinical trials through ancillary studies like Nutrition for Precision Health. We sought to characterize high-level trial opportunities for the diverse participants and sponsors of future trial investment. MATERIALS AND METHODS We matched All of Us participants with available trials on ClinicalTrials.gov based on medical conditions, age, sex, and geographic location. Based on the number of matched trials, we (1) developed the Trial Opportunities Compass (TOC) to help sponsors assess trial investment portfolios, (2) characterized the landscape of trial opportunities in a phenome-wide association study (PheWAS), and (3) assessed the relationship between trial opportunities and social determinants of health (SDoH) to identify potential barriers to trial participation. RESULTS Our study included 181 529 All of Us participants and 18 634 trials. The TOC identified opportunities for portfolio investment and gaps in currently available trials across federal, industrial, and academic sponsors. PheWAS results revealed an emphasis on mental disorder-related trials, with anxiety disorder having the highest adjusted increase in the number of matched trials (59% [95% CI, 57-62]; P < 1e-300). Participants from certain communities underrepresented in biomedical research, including self-reported racial and ethnic minorities, had more matched trials after adjusting for other factors. Living in a nonmetropolitan area was associated with up to 13.1 times fewer matched trials. DISCUSSION AND CONCLUSION All of Us data are a valuable resource for identifying trial opportunities to inform trial portfolio planning. Characterizing these opportunities with consideration for SDoH can provide guidance on prioritizing the most pressing barriers to trial participation.
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Affiliation(s)
- Cathy Shyr
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37203, United States
| | - Lina Sulieman
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37203, United States
| | - Paul A Harris
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37203, United States
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN 37203, United States
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN 37240, United States
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Haan E, Krebs K, Võsa U, Brikell I, Larsson H, Lehto K. Associations between attention-deficit hyperactivity disorder genetic liability and ICD-10 medical conditions in adults: utilizing electronic health records in a Phenome-Wide Association Study. Psychol Med 2024:1-14. [PMID: 38563284 DOI: 10.1017/s0033291724000606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
BACKGROUND Attention-deficit hyperactivity disorder (ADHD) is often comorbid with other medical conditions in adult patients. However, ADHD is extremely underdiagnosed in adults and little is known about the medical comorbidities in undiagnosed adult individuals with high ADHD liability. In this study we investigated associations between ADHD genetic liability and electronic health record (EHR)-based ICD-10 diagnoses across all diagnostic categories, in individuals without ADHD diagnosis history. METHODS We used data from the Estonian Biobank cohort (N = 111 261) and generated polygenic risk scores (PRS) for ADHD (PRSADHD) based on the ADHD genome-wide association study. We performed a phenome-wide association study (PheWAS) to test for associations between standardized PRSADHD and 1515 EHR-based ICD-10 diagnoses in the full and sex-stratified sample. We compared the observed significant ICD-10 associations to associations with (1) ADHD diagnosis and (2) questionnaire-based high ADHD risk analyses. RESULTS After Bonferroni correction (p = 3.3 × 10-5) we identified 80 medical conditions associated with PRSADHD. The strongest evidence was seen with chronic obstructive pulmonary disease (OR 1.15, CI 1.11-1.18), obesity (OR 1.13, CI 1.11-1.15), and type 2 diabetes (OR 1.11, CI 1.09-1.14). Sex-stratified analysis generally showed similar associations in males and females. Out of all identified associations, 40% and 78% were also observed using ADHD diagnosis or questionnaire-based ADHD, respectively, as the predictor. CONCLUSIONS Overall our findings indicate that ADHD genetic liability is associated with an increased risk of a substantial number of medical conditions in undiagnosed individuals. These results highlight the need for timely detection and improved management of ADHD symptoms in adults.
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Affiliation(s)
- Elis Haan
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
- Viljandi Hospital, Psychiatric Clinic, Viljandi, Estonia
| | - Kristi Krebs
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Urmo Võsa
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Isabell Brikell
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
- Deparment of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Henrik Larsson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- School of Medical Sciences, Örebro University, Örebro, Sweden
| | - Kelli Lehto
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
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Zhao W, Fang P, Lai C, Xu X, Wang Y, Liu H, Jiang H, Liu X, Liu J. Proteome-wide Mendelian randomization identifies therapeutic targets for ankylosing spondylitis. Front Immunol 2024; 15:1366736. [PMID: 38566994 PMCID: PMC10985162 DOI: 10.3389/fimmu.2024.1366736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Accepted: 03/05/2024] [Indexed: 04/04/2024] Open
Abstract
Background Ankylosing Spondylitis (AS) is a chronic inflammatory disorder which can lead to considerable pain and disability. Mendelian randomization (MR) has been extensively applied for repurposing licensed drugs and uncovering new therapeutic targets. Our objective is to pinpoint innovative therapeutic protein targets for AS and assess the potential adverse effects of druggable proteins. Methods We conducted a comprehensive proteome-wide MR study to assess the causal relationships between plasma proteins and the risk of AS. The plasma proteins were sourced from the UK Biobank Pharma Proteomics Project (UKB-PPP) database, encompassing GWAS data for 2,940 plasma proteins. Additionally, GWAS data for AS were extracted from the R9 version of the Finnish database, including 2,860 patients and 270,964 controls. The colocalization analysis was executed to identify shared causal variants between plasma proteins and AS. Finally, we examined the potential adverse effects of druggable proteins for AS therapy by conducting a phenome-wide association study (PheWAS) utilizing the extensive Finnish database in version R9, encompassing 2,272 phenotypes categorized into 46 groups. Results The findings revealed a positive genetic association between the predicted plasma levels of six proteins and an elevated risk of AS, while two proteins exhibited an inverse association with AS risk (P fdr < 0.05). Among these eight plasma proteins, colocalization analysis identified AIF1, TNF, FKBPL, AGER, ALDH5A1, and ACOT13 as shared variation with AS(PPH3+PPH4>0.8), suggesting that they represent potential direct targets for AS intervention. Further phenotype-wide association studies have shown some potential side effects of these six targets (P fdr < 0.05). Conclusion Our investigation examined the causal connections between six plasma proteins and AS, providing a comprehensive understanding of potential therapeutic targets.
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Affiliation(s)
- Wenlong Zhao
- Department of Orthopedics, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Department of Orthopedics, The Affiliated Jinling Hospital of Nanjing Medical University, Nanjing, China
| | - Peng Fang
- Department of Orthopedics, Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Chengteng Lai
- Department of Orthopedics, Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Xiaoyu Xu
- Department of Biology, Wake Forest University, North Carolina, NC, United States
| | - Yang Wang
- Department of Orthopedics, Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Hao Liu
- Department of Orthopedics, Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Hui Jiang
- Department of Orthopedics, Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Xiaozhou Liu
- Department of Orthopedics, Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Jun Liu
- Department of Orthopedics, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
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Ouyang D, Huang C, Liu H, Xie W, Chen C, Su B, Guo L. Comprehensive analysis of genetic associations and single-cell expression profiles reveals potential links between migraine and multiple diseases: a phenome-wide association study. Front Neurol 2024; 15:1301208. [PMID: 38385040 PMCID: PMC10879407 DOI: 10.3389/fneur.2024.1301208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 01/19/2024] [Indexed: 02/23/2024] Open
Abstract
Migraine is a common neurological disorder that affects more than one billion people worldwide. Recent genome-wide association studies have identified 123 genetic loci associated with migraine risk. However, the biological mechanisms underlying migraine and its relationships with other complex diseases remain unclear. We performed a phenome-wide association study (PheWAS) using UK Biobank data to investigate associations between migraine and 416 phenotypes. Mendelian randomization was employed using the IVW method. For loci associated with multiple diseases, pleiotropy was tested using MR-Egger. Single-cell RNA sequencing data was analyzed to profile the expression of 73 migraine susceptibility genes across brain cell types. qPCR was used to validate the expression of selected genes in microglia. PheWAS identified 15 disorders significantly associated with migraine, with one association detecting potential pleiotropy. Single-cell analysis revealed elevated expression of seven susceptibility genes (including ZEB2, RUNX1, SLC24A3, ANKDD1B, etc.) in brain glial cells. And qPCR confirmed the upregulation of these genes in LPS-treated microglia. This multimodal analysis provides novel insights into the link between migraine and other diseases. The single-cell profiling suggests the involvement of specific brain cells and molecular pathways. Validation of gene expression in microglia supports their potential role in migraine pathology. Overall, this study uncovers pleiotropic relationships and the biological underpinnings of migraine susceptibility.
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Affiliation(s)
- Di Ouyang
- Nanjing University of Chinese Medicine, Nanjing, China
- Traditional Chinese Medicine Hospital of Yulin, Yulin, China
| | - Chunying Huang
- Traditional Chinese Medicine Hospital of Yulin, Yulin, China
| | - Huihua Liu
- Traditional Chinese Medicine Hospital of Yulin, Yulin, China
| | | | | | - Ben Su
- Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Lizhong Guo
- Nanjing University of Chinese Medicine, Nanjing, China
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Xia D, Han X, Zeng Y, Wang J, Xu K, Zhang T, Jiang Y, Chen X, Song H, Suo C. Disease trajectory of high neuroticism and the relevance to psychiatric disorders: A retro-prospective cohort study. Acta Psychiatr Scand 2024; 149:133-146. [PMID: 38057974 DOI: 10.1111/acps.13645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 11/06/2023] [Accepted: 11/23/2023] [Indexed: 12/08/2023]
Abstract
BACKGROUND Neuroticism is a psychological personality trait that has a significant impact on public health and is also a potential predisposing factor for adverse disease outcomes; however, comprehensive studies of the subsequently developed conditions are lacking. The starting point of disease trajectory in terms of genetic variation remains unclear. METHOD Our study included 344,609 adult participants from the UK Biobank cohort who were virtually followed up from January 1, 1997. Neuroticism levels were assessed using 12 items from the Eysenck Personality Questionnaire. We performed a phenome-wide association analysis of neuroticism and subsequent diseases. Binomial tests and logistic regression models were used to test the temporal directionality and association between disease pairs to construct disease trajectories. We also investigated the association between polygenic risk scores (PRSs) for five psychiatric traits and high neuroticism. RESULTS The risk for 59 diseases was significantly associated with high neuroticism. Depression, anxiety, irritable bowel syndrome, migraine, spondylosis, and sleep disorders were the most likely to develop, with hazard ratios of 6.13, 3.66, 2.28, 1.74, 1.74, and 1.71, respectively. The disease trajectory network revealed two major disease clusters: cardiometabolic and chronic inflammatory diseases. Medium/high genetic risk groups stratified by the PRSs of four psychiatric traits were associated with an elevated risk of high neuroticism. We further identified eight complete phenotypic trajectory clusters of medium or high genetic risk for psychotic, anxiety-, depression-, and stress-related disorders. CONCLUSION Neuroticism plays an important role in the development of somatic and mental disorders. The full picture of disease trajectories from the genetic risk of psychiatric traits and neuroticism in early life to a series of diseases later provides evidence for future research to explore the etiological mechanisms and precision management.
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Affiliation(s)
- Ding Xia
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China
- Ministry of Education Key Laboratory of Public Health Safety, Fudan University, Shanghai, China
| | - Xin Han
- Mental Health Center and West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, China
- Med-X Center for Informatics, Sichuan University, Chengdu, China
| | - Yu Zeng
- Mental Health Center and West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, China
- Med-X Center for Informatics, Sichuan University, Chengdu, China
| | - Jingru Wang
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China
- Ministry of Education Key Laboratory of Public Health Safety, Fudan University, Shanghai, China
| | - Kelin Xu
- Ministry of Education Key Laboratory of Public Health Safety, Fudan University, Shanghai, China
- Department of Biostatistics, School of Public Health, Shanghai, China
- Taizhou Institute of Health Sciences, Fudan University, Taizhou, China
| | - Tiejun Zhang
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China
- Ministry of Education Key Laboratory of Public Health Safety, Fudan University, Shanghai, China
- Taizhou Institute of Health Sciences, Fudan University, Taizhou, China
| | - Yanfeng Jiang
- Taizhou Institute of Health Sciences, Fudan University, Taizhou, China
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences, Fudan University, Shanghai, China
| | - Xingdong Chen
- Taizhou Institute of Health Sciences, Fudan University, Taizhou, China
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences, Fudan University, Shanghai, China
| | - Huan Song
- Mental Health Center and West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, China
- Med-X Center for Informatics, Sichuan University, Chengdu, China
- Center of Public Health Sciences, Faculty of Medicine, University of Iceland, Reykjavík, Iceland
| | - Chen Suo
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China
- Ministry of Education Key Laboratory of Public Health Safety, Fudan University, Shanghai, China
- Taizhou Institute of Health Sciences, Fudan University, Taizhou, China
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Schraw JM, Jaime E, Shumate CJ, Canfield MA, Lupo PJ. Prevalence of congenital anomalies according to maternal race and ethnicity, Texas, 1999-2018. Birth Defects Res 2024; 116:e2274. [PMID: 38014617 PMCID: PMC10872311 DOI: 10.1002/bdr2.2274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 10/05/2023] [Accepted: 11/08/2023] [Indexed: 11/29/2023]
Abstract
BACKGROUND Few studies of congenital anomalies provide prevalence estimates stratified by maternal race/ethnicity. We sought to determine whether the prevalence of a broad spectrum of anomalies varies among offspring of women from different race/ethnic groups. METHODS We obtained information on cases with anomalies from the population-based Texas Birth Defects Registry, and denominator data on livebirths among Texas residents during 1999-2018 from the Texas Center for Health Statistics. We estimated the prevalence ratio (PR) and 95% confidence interval (CI) of N = 145 anomalies among offspring of Hispanic and non-Hispanic Black relative to non-Hispanic White women using Poisson regression, adjusting for maternal age, education, body mass index, and previous livebirths. We performed a two-stage analysis with a Bonferroni-adjusted p < 1.7 × 10-4 in the initial screening phase to identify anomalies with statistically significant variation. RESULTS There were 7,698,768 livebirths and 1,187,385 anomalies diagnosed in 368,393 cases. The prevalence of any monitored congenital anomaly was similar among offspring of non-Hispanic White (referent), non-Hispanic Black (PR 0.98, CI 0.96-1.00), and Hispanic (PR 0.95, CI 0.93-0.96) women. We observed statistically significant racial/ethnic variation for 42 anomalies. Marked differences were observed when comparing offspring of non-Hispanic Black to non-Hispanic White women with respect to polydactyly (PR 4.38, CI 4.07-4.72), pyloric stenosis (PR 0.34, CI 0.29-0.40), and aortic valve atresia/stenosis (PR 0.51, CI 0.36-0.72). CONCLUSIONS Birth prevalence of many major congenital anomalies varies by maternal race and ethnicity. While the reasons for these differences are likely multifactorial, a thorough understanding of racial and ethnic disparities is useful to stimulate etiologic research.
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Affiliation(s)
- Jeremy M Schraw
- Center for Epidemiology and Population Health, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Elwin Jaime
- Center for Epidemiology and Population Health, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Charles J Shumate
- Birth Defects Epidemiology and Surveillance Branch, Texas Department of State Health Services, Austin, Texas, USA
| | - Mark A Canfield
- Division of Epidemiology, Human Genetics and Environmental Sciences, University of Texas School of Public Health, Austin, Texas, USA
| | - Philip J Lupo
- Center for Epidemiology and Population Health, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
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Borbye-Lorenzen N, Zhu Z, Agerbo E, Albiñana C, Benros ME, Bian B, Børglum AD, Bulik CM, Debost JCPG, Grove J, Hougaard DM, McRae AF, Mors O, Mortensen PB, Musliner KL, Nordentoft M, Petersen LV, Privé F, Sidorenko J, Skogstrand K, Werge T, Wray NR, Vilhjálmsson BJ, McGrath JJ. The correlates of neonatal complement component 3 and 4 protein concentrations with a focus on psychiatric and autoimmune disorders. Cell Genom 2023; 3:100457. [PMID: 38116117 PMCID: PMC10726496 DOI: 10.1016/j.xgen.2023.100457] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 09/03/2023] [Accepted: 11/08/2023] [Indexed: 12/21/2023]
Abstract
Complement components have been linked to schizophrenia and autoimmune disorders. We examined the association between neonatal circulating C3 and C4 protein concentrations in 68,768 neonates and the risk of six mental disorders. We completed genome-wide association studies (GWASs) for C3 and C4 and applied the summary statistics in Mendelian randomization and phenome-wide association studies related to mental and autoimmune disorders. The GWASs for C3 and C4 protein concentrations identified 15 and 36 independent loci, respectively. We found no associations between neonatal C3 and C4 concentrations and mental disorders in the total sample (both sexes combined); however, post-hoc analyses found that a higher C3 concentration was associated with a reduced risk of schizophrenia in females. Mendelian randomization based on C4 summary statistics found an altered risk of five types of autoimmune disorders. Our study adds to our understanding of the associations between C3 and C4 concentrations and subsequent mental and autoimmune disorders.
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Affiliation(s)
- Nis Borbye-Lorenzen
- Center for Neonatal Screening, Department of Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Zhihong Zhu
- National Center for Register-Based Research, Aarhus University, 8210 Aarhus V, Denmark
| | - Esben Agerbo
- National Center for Register-Based Research, Aarhus University, 8210 Aarhus V, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8210 Aarhus V, Denmark
- Center for Integrated Register-based Research, Aarhus University, CIRRAU, 8210 Aarhus V, Denmark
| | - Clara Albiñana
- National Center for Register-Based Research, Aarhus University, 8210 Aarhus V, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8210 Aarhus V, Denmark
| | - Michael E. Benros
- Copenhagen Research Center for Mental Health, Mental Health Center Copenhagen, Copenhagen University Hospital, Hellerup, Denmark
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Beilei Bian
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Anders D. Børglum
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8210 Aarhus V, Denmark
- Department of Biomedicine and the iSEQ Center, Aarhus University, Aarhus, Denmark
- Center for Genomics and Personalized Medicine, CGPM, Aarhus, Denmark
| | - Cynthia M. Bulik
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jean-Christophe Philippe Goldtsche Debost
- National Center for Register-Based Research, Aarhus University, 8210 Aarhus V, Denmark
- Department of Psychosis, Aarhus University Hospital Skejby, Aarhus Nord, Denmark
| | - Jakob Grove
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8210 Aarhus V, Denmark
- Center for Genomics and Personalized Medicine, CGPM, Aarhus, Denmark
- Department of Biomedicine (Human Genetics), Aarhus University, Aarhus, Denmark
- Bioinformatics Research Center, Aarhus University, 8000 Aarhus C, Denmark
| | - David M. Hougaard
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8210 Aarhus V, Denmark
- Department for Congenital Disorders, Statens Serum Institut, 2300 Copenhagen S, Denmark
| | - Allan F. McRae
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Ole Mors
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8210 Aarhus V, Denmark
- Psychosis Research Unit, Aarhus University Hospital – Psychiatry, Aarhus, Denmark
| | - Preben Bo Mortensen
- National Center for Register-Based Research, Aarhus University, 8210 Aarhus V, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8210 Aarhus V, Denmark
- Center for Integrated Register-based Research, Aarhus University, CIRRAU, 8210 Aarhus V, Denmark
| | - Katherine L. Musliner
- Department of Affective Disorders, Aarhus University and Aarhus University Hospital –Psychiatry, Aarhus, Denmark
| | - Merete Nordentoft
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8210 Aarhus V, Denmark
- Mental Health Services in the Capital Region of Denmark, Mental Health Center Copenhagen, University of Copenhagen, 2100 Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Liselotte V. Petersen
- National Center for Register-Based Research, Aarhus University, 8210 Aarhus V, Denmark
| | - Florian Privé
- National Center for Register-Based Research, Aarhus University, 8210 Aarhus V, Denmark
| | - Julia Sidorenko
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Kristin Skogstrand
- Center for Neonatal Screening, Department of Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Thomas Werge
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8210 Aarhus V, Denmark
- Department of Clinical Medicine, University of Copenhagen, 2200 Copenhagen N, Denmark
- Department of Clinical Medicine, Institute of Biological Psychiatry, Mental Health Services, Copenhagen University Hospital, University of Copenhagen, 2200 Copenhagen N, Denmark
- Lundbeck Center for Geogenetics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Naomi R. Wray
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
- Department of Psychiatry, University of Oxford, Oxford OX3 7JX, UK
- Big Data Institute, University of Oxford, Oxford OX3 7LF, UK
| | - Bjarni J. Vilhjálmsson
- National Center for Register-Based Research, Aarhus University, 8210 Aarhus V, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8210 Aarhus V, Denmark
- Bioinformatics Research Center, Aarhus University, 8000 Aarhus C, Denmark
| | - John J. McGrath
- National Center for Register-Based Research, Aarhus University, 8210 Aarhus V, Denmark
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
- Queensland Centre for Mental Health Research, The Park Centre for Mental Health, Brisbane, QLD 4076, Australia
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Dapas M, Lee YL, Wentworth-Sheilds W, Im HK, Ober C, Schoettler N. Revealing polygenic pleiotropy using genetic risk scores for asthma. HGG Adv 2023; 4:100233. [PMID: 37663543 PMCID: PMC10474095 DOI: 10.1016/j.xhgg.2023.100233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 08/11/2023] [Indexed: 09/05/2023] Open
Abstract
In this study we examined how genetic risk for asthma associates with different features of the disease and with other medical conditions and traits. Using summary statistics from two multi-ancestry genome-wide association studies of asthma, we modeled polygenic risk scores (PRSs) and validated their predictive performance in the UK Biobank. We then performed phenome-wide association studies of the asthma PRSs with 371 heritable traits in the UK Biobank. We identified 228 total significant associations across a variety of organ systems, including associations that varied by PRS model, sex, age of asthma onset, ancestry, and human leukocyte antigen region alleles. Our results highlight pervasive pleiotropy between asthma and numerous other traits and conditions and elucidate pathways that contribute to asthma and its comorbidities.
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Affiliation(s)
- Matthew Dapas
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Yu Lin Lee
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
- Biological Sciences Collegiate Division, University of Chicago, Chicago, IL, USA
| | | | - Hae Kyung Im
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Carole Ober
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Nathan Schoettler
- Section of Pulmonary and Critical Care Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
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Hsu WT, Lee YT, Tan J, Chang YH, Qian F, Liu KY, Hsiung JC, Yo CH, Tang SC, Jiang X, Lee CC. Genome-phenome wide association study of broadly defined headache. Brain Commun 2023; 5:fcad167. [PMID: 37288313 PMCID: PMC10243784 DOI: 10.1093/braincomms/fcad167] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 02/13/2023] [Accepted: 05/22/2023] [Indexed: 06/09/2023] Open
Abstract
Until recently, most genetic studies of headache have been conducted on participants with European ancestry. We therefore conducted a large-scale genome-wide association study of self-reported headache in individuals of East Asian ancestry (specifically those who were identified as Han Chinese). In this study, 108 855 participants were enrolled, including 12 026 headache cases from the Taiwan Biobank. For broadly defined headache phenotype, we identified a locus on Chromosome 17, with the lead single-nucleotide polymorphism rs8072917 (odds ratio 1.08, P = 4.49 × 10-8), mapped to two protein-coding genes RNF213 and ENDOV. For severe headache phenotype, we found a strong association on Chromosome 8, with the lead single-nucleotide polymorphism rs13272202 (odds ratio 1.30, P = 1.02 × 10-9), mapped to gene RP11-1101K5.1. We then conducted a conditional analysis and a statistical fine-mapping of the broadly defined headache-associated loci and identified a single credible set of loci with rs8072917 supporting that this lead variant was the true causal variant on RNF213 gene region. RNF213 replicated the result of previous studies and played important roles in the biological mechanism of broadly defined headache. On the basis of the previous results found in the Taiwan Biobank, we conducted phenome-wide association studies for the lead variants using data from the UK Biobank and found that the causal variant (single-nucleotide polymorphism rs8072917) was associated with muscle symptoms, cellulitis and abscess of face and neck, and cardiogenic shock. Our findings foster the genetic architecture of headache in individuals of East Asian ancestry. Our study can be replicated using genomic data linked to electronic health records from a variety of countries, therefore affecting a wide range of ethnicities globally. Our genome-phenome association study may facilitate the development of new genetic tests and novel drug mechanisms.
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Affiliation(s)
| | | | - Jasmine Tan
- Health Data Science Research Group, National Taiwan University Hospital, Taipei 100, Taiwan
| | - Yung-Han Chang
- Department of Emergency Medicine, National Taiwan University Hospital, Taipei 100, Taiwan
- Department of Biostatistics, University of California, Los Angeles, CA 90095, USA
| | - Frank Qian
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Kuei-Yu Liu
- Health Data Science Research Group, National Taiwan University Hospital, Taipei 100, Taiwan
| | - Jo-Ching Hsiung
- Department of Pediatrics, Einstein Medical Center-Philadelphia, National Taiwan University Hospital, Philadelphia, PA 19141, USA
| | - Chia-Hung Yo
- Department of Emergency Medicine, Far Eastern Memorial Hospital, New Taipei City 220, Taiwan
| | - Sung-Chun Tang
- Department of Neurology, National Taiwan University Hospital, Taipei 100, Taiwan
| | - Xia Jiang
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden
| | - Chien-Chang Lee
- Correspondence to: Chien-Chang Lee, MD, ScD The Center for Intelligent Healthcare, Department of Emergency Medicine Health Data Science Research Group, National Taiwan University Hospital No.7, Chung Shan S. Rd., Zhongzheng Dist., Taipei City 100, Taiwan E-mail:
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Wang L, Li X, Montazeri A, MacFarlane AJ, Momoli F, Duthie S, Senekal M, Eguiagaray IM, Munger R, Bennett D, Campbell H, Rubini M, McNulty H, Little J, Theodoratou E. Phenome-wide association study of genetically predicted B vitamins and homocysteine biomarkers with multiple health and disease outcomes: analysis of the UK Biobank. Am J Clin Nutr 2023; 117:564-575. [PMID: 36811473 PMCID: PMC7614280 DOI: 10.1016/j.ajcnut.2023.01.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 01/04/2023] [Accepted: 01/09/2023] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Although a number of health outcomes such as CVDs, metabolic-related outcomes, neurological disorders, pregnancy outcomes, and cancers have been identified in relation to B vitamins, evidence is of uneven quality and volume, and there is uncertainty about putative causal relationships. OBJECTIVES To explore the effects of B vitamins and homocysteine on a wide range of health outcomes based on a large biorepository linking biological samples and electronic medical records. METHODS First, we performed a phenome-wide association study (PheWAS) to investigate the associations of genetically predicted plasma concentrations (genetic component of the circulating concentrations) of folate, vitamin B6, vitamin B12, and their metabolite homocysteine with a wide range of disease outcomes (including both prevalent and incident events) among 385,917 individuals in the UK Biobank. Second, 2-sample Mendelian randomization (MR) analysis was used to replicate any observed associations and detect causality. We considered MR P <0.05 as significant for replication. Third, dose-response, mediation, and bioinformatics analyses were carried out to examine any nonlinear trends and to disentangle the underlying mediating biological mechanisms for the identified associations. RESULTS In total, 1117 phenotypes were tested in each PheWAS analysis. After multiple corrections, 32 phenotypic associations of B vitamins and homocysteine were identified. Two-sample MR analysis supported that 3 of them were causal, including associations of higher plasma vitamin B6 with lower risk of calculus of kidney (OR: 0.64; 95% CI: 0.42, 0.97; P = 0.033), higher homocysteine concentration with higher risk of hypercholesterolemia (OR: 1.28, 95% CI: 1.04, 1.56; P = 0.018), and chronic kidney disease (OR: 1.32, 95% CI: 1.06, 1.63; P = 0.012). Significant nonlinear dose-response relationships were observed for the associations of folate with anemia, vitamin B12 with vitamin B-complex deficiencies, anemia and cholelithiasis, and homocysteine with cerebrovascular disease. CONCLUSIONS This study provides strong evidence for the associations of B vitamins and homocysteine with endocrine/metabolic and genitourinary disorders.
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Affiliation(s)
- Lijuan Wang
- School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China; Centre for Global Health, Usher Institute, The University of Edinburgh, Edinburgh, United Kingdom
| | - Xue Li
- School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Azita Montazeri
- School of Epidemiology and Public Health, University of Ottawa, Ottawa, Ontario, Canada
| | | | - Franco Momoli
- School of Epidemiology and Public Health, University of Ottawa, Ottawa, Ontario, Canada
| | - Susan Duthie
- School of Pharmacy and Life Sciences, Robert Gordon University, Aberdeen, United Kingdom
| | - Marjanne Senekal
- Department of Human Biology, University of Cape Town, Cape Town, South Africa
| | - Ines Mesa Eguiagaray
- Centre for Global Health, Usher Institute, The University of Edinburgh, Edinburgh, United Kingdom
| | - Ron Munger
- Department of Nutrition and Food Sciences and the Center for Epidemiologic Studies, Utah State University, Logan, UT, USA
| | - Derrick Bennett
- Medical Research Council Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | - Harry Campbell
- Centre for Global Health, Usher Institute, The University of Edinburgh, Edinburgh, United Kingdom
| | - Michele Rubini
- Department of Neuroscience and rehabilitation, University of Ferrara, Ferrara, Italy
| | - Helene McNulty
- Nutrition Innovation Centre for Food and Health, Ulster University, Coleraine, Northern Ireland, United Kingdom
| | - Julian Little
- School of Epidemiology and Public Health, University of Ottawa, Ottawa, Ontario, Canada
| | - Evropi Theodoratou
- Centre for Global Health, Usher Institute, The University of Edinburgh, Edinburgh, United Kingdom; Cancer Research UK Edinburgh Centre, The University of Edinburgh MRC Institute of Genetics and Cancer, Edinburgh, United Kingdom.
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Fritsche LG, Jin W, Admon AJ, Mukherjee B. Characterizing and Predicting Post-Acute Sequelae of SARS CoV-2 Infection (PASC) in a Large Academic Medical Center in the US. J Clin Med 2023; 12:1328. [PMID: 36835863 PMCID: PMC9967320 DOI: 10.3390/jcm12041328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/30/2023] [Accepted: 02/04/2023] [Indexed: 02/11/2023] Open
Abstract
BACKGROUND A growing number of Coronavirus Disease-2019 (COVID-19) survivors are affected by post-acute sequelae of SARS CoV-2 infection (PACS). Using electronic health record data, we aimed to characterize PASC-associated diagnoses and develop risk prediction models. METHODS In our cohort of 63,675 patients with a history of COVID-19, 1724 (2.7%) had a recorded PASC diagnosis. We used a case-control study design and phenome-wide scans to characterize PASC-associated phenotypes of the pre-, acute-, and post-COVID-19 periods. We also integrated PASC-associated phenotypes into phenotype risk scores (PheRSs) and evaluated their predictive performance. RESULTS In the post-COVID-19 period, known PASC symptoms (e.g., shortness of breath, malaise/fatigue) and musculoskeletal, infectious, and digestive disorders were enriched among PASC cases. We found seven phenotypes in the pre-COVID-19 period (e.g., irritable bowel syndrome, concussion, nausea/vomiting) and sixty-nine phenotypes in the acute-COVID-19 period (predominantly respiratory, circulatory, neurological) associated with PASC. The derived pre- and acute-COVID-19 PheRSs stratified risk well, e.g., the combined PheRSs identified a quarter of the cohort with a history of COVID-19 with a 3.5-fold increased risk (95% CI: 2.19, 5.55) for PASC compared to the bottom 50%. CONCLUSIONS The uncovered PASC-associated diagnoses across categories highlighted a complex arrangement of presenting and likely predisposing features, some with potential for risk stratification approaches.
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Affiliation(s)
- Lars G. Fritsche
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
- Center for Precision Health Data Science, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Weijia Jin
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
- Center for Precision Health Data Science, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Andrew J. Admon
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
- VA Center for Clinical Management Research, LTC Charles S. Kettles VA Medical Center, Ann Arbor, MI 48109, USA
| | - Bhramar Mukherjee
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
- Center for Precision Health Data Science, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
- Michigan Institute for Data Science, University of Michigan, Ann Arbor, MI 48109, USA
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12
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Li C, Chen Y, Chen Y, Ying Z, Hu Y, Kuang Y, Yang H, Song H, Zeng X. The Causal Association of Irritable Bowel Syndrome with Multiple Disease Outcomes: A Phenome-Wide Mendelian Randomization Study. J Clin Med 2023; 12:jcm12031106. [PMID: 36769754 PMCID: PMC9918111 DOI: 10.3390/jcm12031106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Revised: 01/20/2023] [Accepted: 01/22/2023] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND This study aimed to identify novel associations between irritable bowel syndrome (IBS) and a broad range of outcomes. METHODS In total, 346,352 white participants in the U.K. Biobank were randomly divided into two halves, in which a genome-wide association study (GWAS) of IBS and a polygenic risk score (PRS) analysis of IBS using GWAS summary statistics were conducted, respectively. A phenome-wide association study (PheWAS) based on the PRS of IBS was performed to identify disease outcomes associated with IBS. Then, the causalities of these associations were tested by both one-sample (individual-level data in U.K. Biobank) and two-sample (publicly available summary statistics) Mendelian randomization (MR). Sex-stratified PheWAS-MR analyses were performed in male and female, separately. RESULTS Our PheWAS identified five diseases associated with genetically predicted IBS. Conventional MR confirmed these causal associations between IBS and depression (OR: 1.07, 95%CI: 1.01-1.14, p = 0.02), diverticular diseases of the intestine (OR: 1.13, 95%CI: 1.08-1.19, p = 3.00 × 10-6), gastro-esophageal reflux disease (OR: 1.09, 95%CI: 1.05-1.13, p = 3.72 × 10-5), dyspepsia (OR: 1.21, 95%CI: 1.13-1.30, p = 9.28 × 10-8), and diaphragmatic hernia (OR: 1.10, 95%CI: 1.05-1.15, p = 2.75 × 10-5). The causality of these associations was observed in female only, but not men. CONCLUSIONS Increased risks of IBS is found to cause a series of disease outcomes. Our findings support further investigation on the clinical relevance of increased IBS risks with mental and digestive disorders.
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Affiliation(s)
- Chunyang Li
- Biomedical Big Data Center, West China Hospital, West China School of Medicine, Sichuan University, 37 Guo Xue Xiang, Chengdu 610041, China
- Med-X Center for Informatics, Sichuan University, 17 Ren Min Nan Road 3rd Section, Chengdu 610041, China
| | - Yilong Chen
- Biomedical Big Data Center, West China Hospital, West China School of Medicine, Sichuan University, 37 Guo Xue Xiang, Chengdu 610041, China
- Med-X Center for Informatics, Sichuan University, 17 Ren Min Nan Road 3rd Section, Chengdu 610041, China
| | - Yi Chen
- Department of Gastrointestinal Surgery, West China Hospital, West China School of Medicine, Sichuan University, 37 Guo Xue Xiang, Chengdu 610041, China
| | - Zhiye Ying
- Biomedical Big Data Center, West China Hospital, West China School of Medicine, Sichuan University, 37 Guo Xue Xiang, Chengdu 610041, China
- Med-X Center for Informatics, Sichuan University, 17 Ren Min Nan Road 3rd Section, Chengdu 610041, China
| | - Yao Hu
- Biomedical Big Data Center, West China Hospital, West China School of Medicine, Sichuan University, 37 Guo Xue Xiang, Chengdu 610041, China
- Med-X Center for Informatics, Sichuan University, 17 Ren Min Nan Road 3rd Section, Chengdu 610041, China
| | - Yalan Kuang
- Biomedical Big Data Center, West China Hospital, West China School of Medicine, Sichuan University, 37 Guo Xue Xiang, Chengdu 610041, China
- Med-X Center for Informatics, Sichuan University, 17 Ren Min Nan Road 3rd Section, Chengdu 610041, China
| | - Huazhen Yang
- Biomedical Big Data Center, West China Hospital, West China School of Medicine, Sichuan University, 37 Guo Xue Xiang, Chengdu 610041, China
- Med-X Center for Informatics, Sichuan University, 17 Ren Min Nan Road 3rd Section, Chengdu 610041, China
| | - Huan Song
- Biomedical Big Data Center, West China Hospital, West China School of Medicine, Sichuan University, 37 Guo Xue Xiang, Chengdu 610041, China
- Med-X Center for Informatics, Sichuan University, 17 Ren Min Nan Road 3rd Section, Chengdu 610041, China
| | - Xiaoxi Zeng
- Biomedical Big Data Center, West China Hospital, West China School of Medicine, Sichuan University, 37 Guo Xue Xiang, Chengdu 610041, China
- Med-X Center for Informatics, Sichuan University, 17 Ren Min Nan Road 3rd Section, Chengdu 610041, China
- Correspondence: ; Tel.: +86-28-85422819
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Abstract
Advancements in high-throughput sequencing have yielded vast amounts of genomic data, which are studied using genome-wide association study (GWAS)/phenome-wide association study (PheWAS) methods to identify associations between the genotype and phenotype. The associated findings have contributed to pharmacogenomics and improved clinical decision support at the point of care in many healthcare systems. However, the accumulation of genomic data from sequencing and clinical data from electronic health records (EHRs) poses significant challenges for data scientists. Following the rise of artificial intelligence (AI) technology such as machine learning and deep learning, an increasing number of GWAS/PheWAS studies have successfully leveraged this technology to overcome the aforementioned challenges. In this review, we focus on the application of data science and AI technology in three areas, including risk prediction and identification of causal single-nucleotide polymorphisms, EHR-based phenotyping and CRISPR guide RNA design. Additionally, we highlight a few emerging AI technologies, such as transfer learning and multi-view learning, which will or have started to benefit genomic studies.
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Affiliation(s)
- Jing Lin
- NUHS Corporate Office, National University Health System, Singapore
| | - Kee Yuan Ngiam
- NUHS Corporate Office, National University Health System, Singapore,Department of Surgery, National University of Singapore, Singapore,Correspondence: A/Prof Kee Yuan Ngiam, Group Chief Technology Officer, NUHS Corporate Office, National University Health System, 1E Kent Ridge Road, 119228, Singapore. E-mail:
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14
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Kerchberger VE, Peterson JF, Wei WQ. Scanning the medical phenome to identify new diagnoses after recovery from COVID-19 in a US cohort. J Am Med Inform Assoc 2023; 30:233-244. [PMID: 36005898 PMCID: PMC9452157 DOI: 10.1093/jamia/ocac159] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 06/29/2022] [Accepted: 08/23/2022] [Indexed: 01/20/2023] Open
Abstract
OBJECTIVE COVID-19 survivors are at risk for long-term health effects, but assessing the sequelae of COVID-19 at large scales is challenging. High-throughput methods to efficiently identify new medical problems arising after acute medical events using the electronic health record (EHR) could improve surveillance for long-term consequences of acute medical problems like COVID-19. MATERIALS AND METHODS We augmented an existing high-throughput phenotyping method (PheWAS) to identify new diagnoses occurring after an acute temporal event in the EHR. We then used the temporal-informed phenotypes to assess development of new medical problems among COVID-19 survivors enrolled in an EHR cohort of adults tested for COVID-19 at Vanderbilt University Medical Center. RESULTS The study cohort included 186 105 adults tested for COVID-19 from March 5, 2020 to November 1, 2021; of which 30 088 (16.2%) tested positive. Median follow-up after testing was 412 days (IQR 274-528). Our temporal-informed phenotyping was able to distinguish phenotype chapters based on chronicity of their constituent diagnoses. PheWAS with temporal-informed phenotypes identified increased risk for 43 diagnoses among COVID-19 survivors during outpatient follow-up, including multiple new respiratory, cardiovascular, neurological, and pregnancy-related conditions. Findings were robust to sensitivity analyses, and several phenotypic associations were supported by changes in outpatient vital signs or laboratory tests from the pretesting to postrecovery period. CONCLUSION Temporal-informed PheWAS identified new diagnoses affecting multiple organ systems among COVID-19 survivors. These findings can inform future efforts to enable longitudinal health surveillance for survivors of COVID-19 and other acute medical conditions using the EHR.
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Affiliation(s)
- Vern Eric Kerchberger
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Josh F Peterson
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Wei-Qi Wei
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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Park J, MacLean MT, Lucas AM, Torigian DA, Schneider CV, Cherlin T, Xiao B, Miller JE, Bradford Y, Judy RL, Verma A, Damrauer SM, Ritchie MD, Witschey WR, Rader DJ. Exome-wide association analysis of CT imaging-derived hepatic fat in a medical biobank. Cell Rep Med 2022; 3:100855. [PMID: 36513072 PMCID: PMC9798024 DOI: 10.1016/j.xcrm.2022.100855] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 08/22/2022] [Accepted: 11/17/2022] [Indexed: 12/14/2022]
Abstract
Nonalcoholic fatty liver disease is common and highly heritable. Genetic studies of hepatic fat have not sufficiently addressed non-European and rare variants. In a medical biobank, we quantitate hepatic fat from clinical computed tomography (CT) scans via deep learning in 10,283 participants with whole-exome sequences available. We conduct exome-wide associations of single variants and rare predicted loss-of-function (pLOF) variants with CT-based hepatic fat and perform cross-modality replication in the UK Biobank (UKB) by linking whole-exome sequences to MRI-based hepatic fat. We confirm single variants previously associated with hepatic fat and identify several additional variants, including two (FGD5 H600Y and CITED2 S198_G199del) that replicated in UKB. A burden of rare pLOF variants in LMF2 is associated with increased hepatic fat and replicates in UKB. Quantitative phenotypes generated from clinical imaging studies and intersected with genomic data in medical biobanks have the potential to identify molecular pathways associated with human traits and disease.
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Affiliation(s)
- Joseph Park
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Matthew T MacLean
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Anastasia M Lucas
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Drew A Torigian
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Carolin V Schneider
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Tess Cherlin
- Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Brenda Xiao
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jason E Miller
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yuki Bradford
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Renae L Judy
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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- Regeneron Genetics Center, Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | - Anurag Verma
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Scott M Damrauer
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Surgery, Corporal Michael Crescenz VA Medical Center, Philadelphia, PA, USA
| | - Marylyn D Ritchie
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Walter R Witschey
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Daniel J Rader
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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Fritsche LG, Jin W, Admon AJ, Mukherjee B. Characterizing and Predicting Post-Acute Sequelae of SARS CoV-2 infection (PASC) in a Large Academic Medical Center in the US. medRxiv 2022:2022.10.21.22281356. [PMID: 36415469 PMCID: PMC9681058 DOI: 10.1101/2022.10.21.22281356] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Objective A growing number of Coronavirus Disease-2019 (COVID-19) survivors are affected by Post-Acute Sequelae of SARS CoV-2 infection (PACS). Using electronic health records data, we aimed to characterize PASC-associated diagnoses and to develop risk prediction models. Methods In our cohort of 63,675 COVID-19 positive patients, 1,724 (2.7 %) had a recorded PASC diagnosis. We used a case control study design and phenome-wide scans to characterize PASC-associated phenotypes of the pre-, acute-, and post-COVID-19 periods. We also integrated PASC-associated phenotypes into Phenotype Risk Scores (PheRSs) and evaluated their predictive performance. Results In the post-COVID-19 period, known PASC symptoms (e.g., shortness of breath, malaise/fatigue) and musculoskeletal, infectious, and digestive disorders were enriched among PASC cases. We found seven phenotypes in the pre-COVID-19 period (e.g., irritable bowel syndrome, concussion, nausea/vomiting) and 69 phenotypes in the acute-COVID-19 period (predominantly respiratory, circulatory, neurological) associated with PASC. The derived pre- and acute-COVID-19 PheRSs stratified risk well, e.g., the combined PheRSs identified a quarter of the COVID-19 positive cohort with an at least 2.9-fold increased risk for PASC. Conclusions The uncovered PASC-associated diagnoses across categories highlighted a complex arrangement of presenting and likely predisposing features, some with a potential for risk stratification approaches.
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Affiliation(s)
- Lars G. Fritsche
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, Michigan 48109, United States of America,Center for Precision Health Data Science, University of Michigan School of Public Health, Ann Arbor, Michigan 48109, United States of America,Correspondence: ,
| | - Weijia Jin
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, Michigan 48109, United States of America,Center for Precision Health Data Science, University of Michigan School of Public Health, Ann Arbor, Michigan 48109, United States of America
| | - Andrew J. Admon
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States of America,Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, Michigan 48109, United States of America,VA Center for Clinical Management Research, LTC Charles S. Kettles VA Medical Center, Ann Arbor, Michigan 48109, United States of America
| | - Bhramar Mukherjee
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, Michigan 48109, United States of America,Center for Precision Health Data Science, University of Michigan School of Public Health, Ann Arbor, Michigan 48109, United States of America,Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, Michigan 48109, United States of America,Michigan Institute for Data Science, University of Michigan, Ann Arbor, Michigan 48109, United States of America,Correspondence: ,
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Pathak GA, De Lillo A, Wendt FR, De Angelis F, Koller D, Mendoza BC, Jacoby D, Miller EJ, Buxbaum JN, Polimanti R. The integration of genetically-regulated transcriptomics and electronic health records highlights a pattern of medical outcomes related to increased hepatic transthyretin expression. Amyloid 2022; 29:110-119. [PMID: 34935565 PMCID: PMC9213571 DOI: 10.1080/13506129.2021.2018678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Transthyretin (TTR) is the precursor of the fibrils that compromise organ function in hereditary and sporadic systemic amyloidoses (ATTR). RNA-interference and anti-sense therapeutics targeting TTR hepatic transcription have been shown to reduce TTR amyloid formation. In the present study, we leveraged genetic and phenotypic information from the UK Biobank and transcriptomic profiles from the Genotype-Tissue Expression project to test the association of genetically regulated TTR gene expression with 7149 traits assessed in 420,531 individuals. We conducted a multi-tissue analysis of TTR transcription and identified an association with a operational procedure related to bone fracture (p = 5.46×10-6). Using tissue-specific TTR expression information, we demonstrated that the association is driven by the genetic regulation of TTR hepatic expression (odds ratio [OR] = 3.46, p = 9.51×10-5). Using the UK Biobank electronic health records (EHRs), we investigated the comorbidities affecting individuals undergoing this surgical procedure. Excluding bone fracture EHRs, we identified a pattern of health outcomes previously associated with ATTR manifestations. These included osteoarthritis (OR = 3.18, p = 9.18×10-8), carpal tunnel syndrome (OR = 2.15, p = .002), and a history of gastrointestinal diseases (OR = 2.01, p = 8.07×10-4). In conclusion, our study supports that TTR hepatic expression can affect health outcomes linked to physiological and pathological processes presumably related to the encoded protein.
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Affiliation(s)
- Gita A. Pathak
- Department of Psychiatry, Yale School of Medicine, West Haven, CT 06516, USA
- VA CT Healthcare Center, West Haven, CT 06516, USA
| | - Antonella De Lillo
- Department of Psychiatry, Yale School of Medicine, West Haven, CT 06516, USA
- Department of Biology, University of Rome Tor Vergata, Rome 00133, Italy
| | - Frank R. Wendt
- Department of Psychiatry, Yale School of Medicine, West Haven, CT 06516, USA
- VA CT Healthcare Center, West Haven, CT 06516, USA
| | - Flavio De Angelis
- Department of Psychiatry, Yale School of Medicine, West Haven, CT 06516, USA
- VA CT Healthcare Center, West Haven, CT 06516, USA
- Department of Biology, University of Rome Tor Vergata, Rome 00133, Italy
| | - Dora Koller
- Department of Psychiatry, Yale School of Medicine, West Haven, CT 06516, USA
- VA CT Healthcare Center, West Haven, CT 06516, USA
| | - Brenda Cabrera Mendoza
- Department of Psychiatry, Yale School of Medicine, West Haven, CT 06516, USA
- VA CT Healthcare Center, West Haven, CT 06516, USA
| | - Daniel Jacoby
- Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06510, USA
| | - Edward J. Miller
- Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06510, USA
| | | | - Renato Polimanti
- Department of Psychiatry, Yale School of Medicine, West Haven, CT 06516, USA
- VA CT Healthcare Center, West Haven, CT 06516, USA
- Corresponding author: Renato Polimanti, Ph.D., Yale University School of Medicine, Department of Psychiatry. VA CT 116A2, 950 Campbell Avenue, West Haven, CT 06516, USA. Phone: +1 (203) 932-5711 x5745. Fax: +1 (203) 937-3897.
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18
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Dumancas GG, Harrison D, Rico JA, Zamora PRFC, Liwag AG, Villaruz JF, Guanzon MLVV, Ferraris HFD, Jalandoni PJB, Padernal WF, Villareal BNL, Maculada RA, Fernandez RMA, Villa FR, de Castro R. Are phenome-wide association studies feasible in a developing country? Trends Genet 2022; 38:885-888. [PMID: 35660028 DOI: 10.1016/j.tig.2022.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 05/02/2022] [Accepted: 05/03/2022] [Indexed: 11/18/2022]
Abstract
Phenome-wide association studies (PheWASs), a powerful approach that examines phenotypes associated with a genetic marker, have been used extensively in highly developed countries. Although there may be a clear need for PheWAS in a developing country such as the Philippines, limitations related to resources and practicality would make conducting them a challenge.
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Affiliation(s)
- Gerard G Dumancas
- Department of Chemistry, Loyola Science Center, The University of Scranton, Scranton, PA 18510, USA; Balik Scientist Program, Department of Science and Technology-Philippine Council for Health Research and Development, Bicutan, Taguig City, 1631, Philippines.
| | - Destiny Harrison
- Department of Mathematics and Physical Sciences, Louisiana State University - Alexandria, Alexandria, LA 71302, USA
| | - Jonathan Adam Rico
- Center for Informatics, University of San Agustin, Gen. Luna St, Iloilo City, 5000, Philippines
| | | | - Aretha G Liwag
- West Visayas State University, Luna St, Lapaz, Iloilo City, 5000, Philippines
| | - Joselito F Villaruz
- West Visayas State University, Luna St, Lapaz, Iloilo City, 5000, Philippines
| | - Ma Luz Vicenta V Guanzon
- Corazon Locsin Montelibano Memorial Regional Hospital, Lacson St, Bacolod, Negros Occidental, 6100, Philippines
| | - Hans Francis D Ferraris
- Corazon Locsin Montelibano Memorial Regional Hospital, Lacson St, Bacolod, Negros Occidental, 6100, Philippines
| | | | | | | | | | | | | | - Romulo de Castro
- Center for Informatics, University of San Agustin, Gen. Luna St, Iloilo City, 5000, Philippines; Balik Scientist Program, Department of Science and Technology-Philippine Council for Health Research and Development, Bicutan, Taguig City, 1631, Philippines
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19
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Zuber V, Grinberg NF, Gill D, Manipur I, Slob EAW, Patel A, Wallace C, Burgess S. Combining evidence from Mendelian randomization and colocalization: Review and comparison of approaches. Am J Hum Genet 2022; 109:767-782. [PMID: 35452592 PMCID: PMC7612737 DOI: 10.1016/j.ajhg.2022.04.001] [Citation(s) in RCA: 80] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Mendelian randomization and colocalization are two statistical approaches that can be applied to summarized data from genome-wide association studies (GWASs) to understand relationships between traits and diseases. However, despite similarities in scope, they are different in their objectives, implementation, and interpretation, in part because they were developed to serve different scientific communities. Mendelian randomization assesses whether genetic predictors of an exposure are associated with the outcome and interprets an association as evidence that the exposure has a causal effect on the outcome, whereas colocalization assesses whether two traits are affected by the same or distinct causal variants. When considering genetic variants in a single genetic region, both approaches can be performed. While a positive colocalization finding typically implies a non-zero Mendelian randomization estimate, the reverse is not generally true: there are several scenarios which would lead to a non-zero Mendelian randomization estimate but lack evidence for colocalization. These include the existence of distinct but correlated causal variants for the exposure and outcome, which would violate the Mendelian randomization assumptions, and a lack of strong associations with the outcome. As colocalization was developed in the GWAS tradition, typically evidence for colocalization is concluded only when there is strong evidence for associations with both traits. In contrast, a non-zero estimate from Mendelian randomization can be obtained despite only nominally significant genetic associations with the outcome at the locus. In this review, we discuss how the two approaches can provide complementary information on potential therapeutic targets.
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Affiliation(s)
- Verena Zuber
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK; MRC Centre for Environment and Health, School of Public Health, Imperial College London, London, UK; UK Dementia Research Institute at Imperial College, Imperial College London, London, UK
| | | | - Dipender Gill
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK; Clinical Pharmacology and Therapeutics Section, Institute of Medical and Biomedical Education and Institute for Infection and Immunity, St George's, University of London, London, UK; Clinical Pharmacology Group, Pharmacy and Medicines Directorate, St George's University Hospitals NHS Foundation Trust, London, UK; Genetics Department, Novo Nordisk Research Centre Oxford, Oxford, UK
| | - Ichcha Manipur
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, University of Cambridge, Cambridge, UK; Department of Medicine, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Eric A W Slob
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
| | - Ashish Patel
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
| | - Chris Wallace
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, University of Cambridge, Cambridge, UK; Department of Medicine, School of Clinical Medicine, University of Cambridge, Cambridge, UK; MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
| | - Stephen Burgess
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK; Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.
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20
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Fu M, Chang TS. Phenome-Wide Association Study of Polygenic Risk Score for Alzheimer's Disease in Electronic Health Records. Front Aging Neurosci 2022; 14:800375. [PMID: 35370621 PMCID: PMC8965623 DOI: 10.3389/fnagi.2022.800375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 02/04/2022] [Indexed: 11/13/2022] Open
Abstract
Alzheimer's disease (AD) is the most common form of dementia and a growing public health burden in the United States. Significant progress has been made in identifying genetic risk for AD, but limited studies have investigated how AD genetic risk may be associated with other disease conditions in an unbiased fashion. In this study, we conducted a phenome-wide association study (PheWAS) by genetic ancestry groups within a large academic health system using the polygenic risk score (PRS) for AD. PRS was calculated using LDpred2 with genome-wide association study (GWAS) summary statistics. Phenotypes were extracted from electronic health record (EHR) diagnosis codes and mapped to more clinically meaningful phecodes. Logistic regression with Firth's bias correction was used for PRS phenotype analyses. Mendelian randomization was used to examine causality in significant PheWAS associations. Our results showed a strong association between AD PRS and AD phenotype in European ancestry (OR = 1.26, 95% CI: 1.13, 1.40). Among a total of 1,515 PheWAS tests within the European sample, we observed strong associations of AD PRS with AD and related phenotypes, which include mild cognitive impairment (MCI), memory loss, and dementias. We observed a phenome-wide significant association between AD PRS and gouty arthropathy (OR = 0.90, adjusted p = 0.05). Further causal inference tests with Mendelian randomization showed that gout was not causally associated with AD. We concluded that genetic predisposition of AD was negatively associated with gout, but gout was not a causal risk factor for AD. Our study evaluated AD PRS in a real-world EHR setting and provided evidence that AD PRS may help to identify individuals who are genetically at risk of AD and other related phenotypes. We identified non-neurodegenerative diseases associated with AD PRS, which is essential to understand the genetic architecture of AD and potential side effects of drugs targeting genetic risk factors of AD. Together, these findings expand our understanding of AD genetic and clinical risk factors, which provide a framework for continued research in aging with the growing number of real-world EHR linked with genetic data.
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Affiliation(s)
- Mingzhou Fu
- Movement Disorders Program, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States.,Medical Informatics Home Area, Department of Bioinformatics, University of California, Los Angeles, Los Angeles, CA, United States
| | | | | | - Timothy S Chang
- Movement Disorders Program, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
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21
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Schlauch KA, Read RW, Koning SM, Neveux I, Grzymski JJ. Using phenome-wide association studies and the SF-12 quality of life metric to identify profound consequences of adverse childhood experiences on adult mental and physical health in a Northern Nevadan population. Front Psychiatry 2022; 13:984366. [PMID: 36276335 PMCID: PMC9583677 DOI: 10.3389/fpsyt.2022.984366] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 09/15/2022] [Indexed: 11/13/2022] Open
Abstract
In this research, we examine and identify the implications of Adverse Childhood Experiences (ACEs) on a range of health outcomes, with particular focus on a number of mental health disorders. Many previous studies observed that traumatic childhood events are linked to long-term adult diseases using the standard Adverse Childhood Experience Questionnaire. The study cohort was derived from the Healthy Nevada Project, a volunteer-based population health study in which each adult participant is invited to take a retrospective questionnaire that includes the Adverse Childhood Experience Questionnaire, the 12-item Short Form Survey measuring quality of life, and self-reported incidence of nine mental disorders. Using participant's cross-referenced electronic health records, a phenome-wide association analysis of 1,703 phenotypes and the incidence of ACEs examined links between traumatic events in childhood and adult disease. These analyses showed that many mental disorders were significantly associated with ACEs in a dose-response manner. Similarly, a dose response between ACEs and obesity, chronic pain, migraine, and other physical phenotypes was identified. An examination of the prevalence of self-reported mental disorders and incidence of ACEs showed a positive relationship. Furthermore, participants with less adverse childhood events experienced a higher quality of life, both physically and mentally. The whole-phenotype approach confirms that ACEs are linked with many negative adult physical and mental health outcomes. With the nationwide prevalence of ACEs as high as 67%, these findings suggest a need for new public health resources: ACE-specific interventions and early childhood screenings.
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Affiliation(s)
- Karen A Schlauch
- Center for Genomic Medicine, Desert Research Institute, Reno, NV, United States
| | - Robert W Read
- Center for Genomic Medicine, Desert Research Institute, Reno, NV, United States
| | | | - Iva Neveux
- Center for Genomic Medicine, Desert Research Institute, Reno, NV, United States
| | - Joseph J Grzymski
- Center for Genomic Medicine, Desert Research Institute, Reno, NV, United States.,Renown Health, Reno, NV, United States
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22
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Hartwell EE, Merikangas AK, Verma SS, Ritchie MD, Kranzler HR, Kember RL. Genetic liability for substance use associated with medical comorbidities in electronic health records of African- and European-ancestry individuals. Addict Biol 2022; 27:e13099. [PMID: 34611967 PMCID: PMC9254745 DOI: 10.1111/adb.13099] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 07/17/2021] [Accepted: 09/01/2021] [Indexed: 01/03/2023]
Abstract
Polygenic risk scores (PRS) represent an individual's summed genetic risk for a trait and can serve as biomarkers for disease. Less is known about the utility of PRS as a means to quantify genetic risk for substance use disorders (SUDs) than for many other traits. Nonetheless, the growth of large, electronic health record-based biobanks makes it possible to evaluate the association of SUD PRS with other traits. We calculated PRS for smoking initiation, alcohol use disorder (AUD), and opioid use disorder (OUD) using summary statistics from the Million Veteran Program sample. We then tested the association of each PRS with its primary phenotype in the Penn Medicine BioBank (PMBB) using all available genotyped participants of African or European ancestry (AFR and EUR, respectively) (N = 18,612). Finally, we conducted phenome-wide association analyses (PheWAS) separately by ancestry and sex to test for associations across disease categories. Tobacco use disorder was the most common SUD in the PMBB, followed by AUD and OUD, consistent with the population prevalence of these disorders. All PRS were associated with their primary phenotype in both ancestry groups. PheWAS results yielded cross-trait associations across multiple domains, including psychiatric disorders and medical conditions. SUD PRS were associated with their primary phenotypes; however, they are not yet predictive enough to be useful diagnostically. The cross-trait associations of the SUD PRS are indicative of a broader genetic liability. Future work should extend findings to additional population groups and for other substances of abuse.
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Affiliation(s)
- Emily E. Hartwell
- Mental Illness Research, Education and Clinical Center, Crescenz VAMC, Philadelphia, PA,Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Alison K. Merikangas
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA
| | - Shefali S. Verma
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Marylyn D. Ritchie
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA,Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA
| | | | - Henry R. Kranzler
- Mental Illness Research, Education and Clinical Center, Crescenz VAMC, Philadelphia, PA,Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Rachel L. Kember
- Mental Illness Research, Education and Clinical Center, Crescenz VAMC, Philadelphia, PA,Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
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23
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Soccio RE. Galectin-3 in NAFLD: Therapeutic Target or Noncausal Biomarker? J Clin Endocrinol Metab 2021; 106:e3773-e3774. [PMID: 34019644 PMCID: PMC8372627 DOI: 10.1210/clinem/dgab363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Indexed: 02/02/2023]
Affiliation(s)
- Raymond E Soccio
- Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism; Institute for Diabetes, Obesity and Metabolism; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Correspondence: Raymond E Soccio, MD, PhD, University of Pennsylvania Perelman School of Medicine, 3400 Civic Center Blvd, Philadelphia, PA 19104, USA.
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24
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Tremblay M, Perrot N, Ghodsian N, Gobeil É, Couture C, Mitchell PL, Thériault S, Arsenault BJ. Circulating Galectin-3 Levels Are Not Associated With Nonalcoholic Fatty Liver Disease: A Mendelian Randomization Study. J Clin Endocrinol Metab 2021; 106:e3178-e3184. [PMID: 33693708 DOI: 10.1210/clinem/dgab144] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Indexed: 02/01/2023]
Abstract
CONTEXT The impact of galectin-3 inhibitors on nonalcoholic fatty liver diseases (NAFLD)-related outcomes is currently under investigation in randomized clinical trials. Whether there is a causal association between plasma galectin-3 levels and NAFLD is unknown. OBJECTIVE To evaluate the causal effect of circulating galectin-3 levels on NAFLD as well as >800 other human diseases. DESIGN Inverse variance-weighted (IVW) Mendelian randomization (MR) and phenome-wide MR. SETTING Summary statistics of genome-wide association studies. PATIENTS Participants of the UK Biobank, Electronic Medical Records and Genomics (eMERGE), FinnGen, Prevention of Renal and Vascular End-Stage Disease (PREVEND), and IMPROVE cohorts. INTERVENTION Identification of independent single-nucleotide polymorphisms (SNPs) associated with galectin-3 levels (P < 5 × 10-8) in the PREVEND (14 SNPs) and IMPROVE (3 SNPs) cohorts. MAIN OUTCOME MEASURES Presence of NAFLD in a meta-analysis of genome-wide association study of the eMERGE, UK Biobank, and FinnGen cohorts (3042 NAFLD cases and 504 853 controls), as well as >800 other human diseases in the UK Biobank and FinnGen. RESULTS Using IVW-MR, we found no causal association between galectin-3 levels and NAFLD in the meta-analysis of the 3 cohorts or in each individual cohort. After correction for multiple testing, we found no causal association between galectin-3 levels and >800 human disease-related traits. CONCLUSIONS This MR study revealed no causal associations between circulating galectin-3 levels and NAFLD or any other disease traits, suggesting that plasma galectin-3 levels may not be directly implicated in the pathogenesis of NAFLD or other human diseases.
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Affiliation(s)
- Maxime Tremblay
- Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec, Québec, Canada
- Department of Medicine, Faculty of Medicine, Université Laval, Québec, Canada
| | - Nicolas Perrot
- Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec, Québec, Canada
- Department of Medicine, Faculty of Medicine, Université Laval, Québec, Canada
| | - Nooshin Ghodsian
- Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec, Québec, Canada
| | - Émilie Gobeil
- Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec, Québec, Canada
- Department of Medicine, Faculty of Medicine, Université Laval, Québec, Canada
| | - Christian Couture
- Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec, Québec, Canada
| | - Patricia L Mitchell
- Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec, Québec, Canada
| | - Sébastien Thériault
- Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec, Québec, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Université Laval, Québec, Canada
| | - Benoit J Arsenault
- Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec, Québec, Canada
- Department of Medicine, Faculty of Medicine, Université Laval, Québec, Canada
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25
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Actkins KV, Beasley HK, Faucon AB, Davis LK, Sakwe AM. Calcium-Sensing Receptor Polymorphisms at rs1801725 Are Associated with Increased Risk of Secondary Malignancies. J Pers Med 2021; 11:642. [PMID: 34357109 PMCID: PMC8304025 DOI: 10.3390/jpm11070642] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 06/07/2021] [Accepted: 07/02/2021] [Indexed: 12/19/2022] Open
Abstract
Dysregulation of systemic calcium homeostasis during malignancy is common in most patients with high-grade tumors. However, it remains unclear whether single nucleotide polymorphisms (SNPs) that alter the sensitivity of the calcium-sensing receptor (CaSR) to circulating calcium are associated with primary and/or secondary neoplasms at specific pathological sites in patients of European and African ancestry. Multivariable logistic regression models were used to analyze the association of CASR SNPs with circulating calcium, parathyroid hormone, vitamin D, and primary and secondary neoplasms. Circulating calcium is associated with an increased risk for breast, prostate, and skin cancers. In patients of European descent, the rs1801725 CASR SNP is associated with bone-related cancer phenotypes, deficiency of humoral immunity, and a higher risk of secondary neoplasms in the lungs and bone. Interestingly, circulating calcium levels are higher in homozygous patients for the inactivating CASR variant at rs1801725 (TT genotype), and this is associated with a higher risk of secondary malignancies. Our data suggest that expression of CaSR variants at rs1801725 is associated with a higher risk of developing secondary neoplastic lesions in the lungs and bone, due in part to cancer-induced hypercalcemia and/or tumor immune suppression. Screening of patients for CASR variants at this locus may lead to improved management of high calcium associated tumor progression.
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Affiliation(s)
- Ky’Era V. Actkins
- Department of Microbiology, Immunology and Physiology, School of Graduate Studies and Research, Meharry Medical College, Nashville, TN 37208, USA;
| | - Heather K. Beasley
- Department of Biochemistry, Cancer Biology, Neuroscience and Pharmacology, School of Graduate Studies and Research, Meharry Medical College, Nashville, TN 37208, USA; (H.K.B.); (L.K.D.)
| | - Annika B. Faucon
- Vanderbilt University Medical Center, Vanderbilt Genetics Institute, Nashville, TN 37232, USA;
| | - Lea K. Davis
- Department of Biochemistry, Cancer Biology, Neuroscience and Pharmacology, School of Graduate Studies and Research, Meharry Medical College, Nashville, TN 37208, USA; (H.K.B.); (L.K.D.)
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Amos M. Sakwe
- Department of Biochemistry, Cancer Biology, Neuroscience and Pharmacology, School of Graduate Studies and Research, Meharry Medical College, Nashville, TN 37208, USA; (H.K.B.); (L.K.D.)
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26
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Xie L, McKenzie CI, Qu X, Mu Y, Wang Q, Bing N, Naidoo K, Alam MJ, Yu D, Gong F, Ang C, Robert R, Marques FZ, Furlotte N, Hinds D, Gasser O, Xavier RJ, Mackay CR. pH and Proton Sensor GPR65 Determine Susceptibility to Atopic Dermatitis. J Immunol 2021; 207:101-109. [PMID: 34135065 PMCID: PMC8674371 DOI: 10.4049/jimmunol.2001363] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 04/15/2021] [Indexed: 12/15/2022]
Abstract
pH sensing by GPR65 regulates various inflammatory conditions, but its role in skin remains unknown. In this study, we performed a phenome-wide association study and report that the T allele of GPR65-intronic single-nucleotide polymorphism rs8005161, which reduces GPR65 signaling, showed a significant association with atopic dermatitis, in addition to inflammatory bowel diseases and asthma, as previously reported. Consistent with this genetic association in humans, we show that deficiency of GPR65 in mice resulted in markedly exacerbated disease in the MC903 experimental model of atopic dermatitis. Deficiency of GPR65 also increased neutrophil migration in vitro. Moreover, GPR65 deficiency in mice resulted in higher expression of the inflammatory cytokine TNF-α by T cells. In humans, CD4+ T cells from rs8005161 heterozygous individuals expressed higher levels of TNF-α after PMA/ionomycin stimulation, particularly under pH 6 conditions. pH sensing by GPR65 appears to be important for regulating the pathogenesis of atopic dermatitis.
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Affiliation(s)
- Liang Xie
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Hypertension Research Laboratory, School of Biological Sciences, Monash University, Clayton, Victoria, Australia
| | - Craig I McKenzie
- Department of Immunology and Pathology, Central Clinical School, Monash University, Melbourne, Victoria, Australia
- Department of Allergy, Immunology and Respiratory Medicine, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Xinyan Qu
- School of Pharmaceutical Sciences, Shandong Analysis and Test Center, Qilu University of Technology, Shandong Academy of Sciences, Jinan, China
| | - Yan Mu
- School of Pharmaceutical Sciences, Shandong Analysis and Test Center, Qilu University of Technology, Shandong Academy of Sciences, Jinan, China
| | - Quanbo Wang
- School of Pharmaceutical Sciences, Shandong Analysis and Test Center, Qilu University of Technology, Shandong Academy of Sciences, Jinan, China
| | | | - Karmella Naidoo
- Malaghan Institute of Medical Research, Victoria University of Wellington, Wellington, New Zealand
| | - Md Jahangir Alam
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Di Yu
- School of Pharmaceutical Sciences, Shandong Analysis and Test Center, Qilu University of Technology, Shandong Academy of Sciences, Jinan, China
- The University of Queensland Diamantina Institute, Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
| | - Fang Gong
- Department of Laboratory Medicine, Wuxi Hospital of Integrated Traditional Chinese and Western Medicine, Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Caroline Ang
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Remy Robert
- Department of Physiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Francine Z Marques
- Hypertension Research Laboratory, School of Biological Sciences, Monash University, Clayton, Victoria, Australia
- Heart Failure Research Laboratory, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | | | | | - Olivier Gasser
- Malaghan Institute of Medical Research, Victoria University of Wellington, Wellington, New Zealand
| | - Ramnik J Xavier
- Broad Institute, MA
- Center for Computational and Integrative Biology, Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA; and
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA
| | - Charles R Mackay
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia;
- School of Pharmaceutical Sciences, Shandong Analysis and Test Center, Qilu University of Technology, Shandong Academy of Sciences, Jinan, China
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27
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Katsevich E, Sabatti C, Bogomolov M. Filtering the rejection set while preserving false discovery rate control. J Am Stat Assoc 2021; 118:165-176. [PMID: 37346227 PMCID: PMC10281705 DOI: 10.1080/01621459.2021.1920958] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 04/14/2021] [Accepted: 04/18/2021] [Indexed: 12/28/2022]
Abstract
Scientific hypotheses in a variety of applications have domain-specific structures, such as the tree structure of the International Classification of Diseases (ICD), the directed acyclic graph structure of the Gene Ontology (GO), or the spatial structure in genome-wide association studies. In the context of multiple testing, the resulting relationships among hypotheses can create redundancies among rejections that hinder interpretability. This leads to the practice of filtering rejection sets obtained from multiple testing procedures, which may in turn invalidate their inferential guarantees. We propose Focused BH, a simple, flexible, and principled methodology to adjust for the application of any pre-specified filter. We prove that Focused BH controls the false discovery rate under various conditions, including when the filter satisfies an intuitive monotonicity property and the p-values are positively dependent. We demonstrate in simulations that Focused BH performs well across a variety of settings, and illustrate this method's practical utility via analyses of real datasets based on ICD and GO.
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Affiliation(s)
| | - Chiara Sabatti
- Departments of Statistics and Biomedical Data Science, Stanford University
| | - Marina Bogomolov
- Faculty of Industrial Engineering and Management, Technion - Israel Institute of Technology
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28
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Dashti HS, Cade BE, Stutaite G, Saxena R, Redline S, Karlson EW. Sleep health, diseases, and pain syndromes: findings from an electronic health record biobank. Sleep 2021; 44:5909423. [PMID: 32954408 DOI: 10.1093/sleep/zsaa189] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 08/28/2020] [Indexed: 02/02/2023] Open
Abstract
STUDY OBJECTIVES Implementation of electronic health record biobanks has facilitated linkage between clinical and questionnaire data and enabled assessments of relationships between sleep health and diseases in phenome-wide association studies (PheWAS). In the Mass General Brigham Biobank, a large health system-based study, we aimed to systematically catalog associations between time in bed, sleep timing, and weekly variability with clinical phenotypes derived from ICD-9/10 codes. METHODS Self-reported habitual bed and wake times were used to derive variables: short (<7 hours) and long (≥9 hours) time in bed, sleep midpoint, social jetlag, and sleep debt. Logistic regression and Cox proportional hazards models were used to test cross-sectional and prospective associations, respectively, adjusted for age, gender, race/ethnicity, and employment status and further adjusted for body mass index. RESULTS In cross-sectional analysis (n = 34,651), sleep variable associations were most notable for circulatory system, mental disorders, and endocrine/metabolic phenotypes. We observed the strongest associations for short time in bed with obesity, for long time in bed and sleep midpoint with major depressive disorder, for social jetlag with hypercholesterolemia, and for sleep debt with acne. In prospective analysis (n = 24,065), we observed short time in bed associations with higher incidence of acute pain and later sleep midpoint and higher sleep debt and social jetlag associations with higher incidence of major depressive disorder. CONCLUSIONS Our analysis reinforced that sleep health is a multidimensional construct, corroborated robust known findings from traditional cohort studies, and supported the application of PheWAS as a promising tool for advancing sleep research. Considering the exploratory nature of PheWAS, careful interrogation of novel findings is imperative.
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Affiliation(s)
- Hassan S Dashti
- Center for Genomic Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA.,Broad Institute, Cambridge, MA.,Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Brian E Cade
- Broad Institute, Cambridge, MA.,Division of Sleep and Circadian Disorders, Department of Medicine, Brigham and Women's Hospital, Boston, MA.,Division of Sleep Medicine, Harvard Medical School, Boston, MA
| | - Gerda Stutaite
- Mass General Brigham Personalized Medicine, Mass General Brigham, Boston, MA
| | - Richa Saxena
- Center for Genomic Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA.,Broad Institute, Cambridge, MA.,Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA.,Division of Sleep Medicine, Harvard Medical School, Boston, MA
| | - Susan Redline
- Division of Sleep and Circadian Disorders, Department of Medicine, Brigham and Women's Hospital, Boston, MA.,Division of Sleep Medicine, Harvard Medical School, Boston, MA.,Department of Medicine, Brigham and Women's Hospital and Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA
| | - Elizabeth W Karlson
- Mass General Brigham Personalized Medicine, Mass General Brigham, Boston, MA.,Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Boston, MA
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29
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Langlois PH, Schraw JM, Hoyt AT, Lupo PJ. Leveraging a phenome-wide approach to identify novel exposure-birth defect associations: A proof of concept using maternal smoking and a spectrum of birth defects. Birth Defects Res 2020; 113:439-445. [PMID: 33275842 DOI: 10.1002/bdr2.1851] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 11/07/2020] [Accepted: 11/08/2020] [Indexed: 11/06/2022]
Abstract
BACKGROUND There are often questions about the impact of exposures on a range of birth defects, but there are few rigorous approaches for evaluating these associations. Using maternal smoking as an example we applied a phenome-wide association study (PheWAS) approach to evaluate the impact of this exposure on a comprehensive range of birth defects. METHODS Cases were obtained from the Texas Birth Defects Registry for the period 1999-2015. A total of 127 birth defects were examined. Maternal smoking at any time during the pregnancy was ascertained from the vital record. Data were randomly divided into discovery (60%) and replication (40%) partitions. Poisson regression models were run in the discovery partition, using a Bonferroni threshold of p < 3.9×10-4 . Birth defects passing that threshold in adjusted models were evaluated in the replication partition using p < 0.05 to determine statistical significance. RESULTS Four birth defects were positively and significantly associated with maternal smoking in both partitions: cleft palate, anomalies of the pulmonary artery, other specified anomalies of the mouth and pharynx, and congenital hypertrophic pyloric stenosis. Obstructive defects of the renal pelvis and ureter showed consistent negative associations. All five defects exhibited significant dose-response relationships. CONCLUSIONS We demonstrated that a statistically rigorous approach can be applied to birth defects registry data to examine the association between specified exposures and a range of birth defects. While we confirmed previously reported associations, others were not validated, likely due to misclassification in exposure based on vital records.
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Affiliation(s)
- Peter H Langlois
- Division of Epidemiology, Human Genetics, and Environmental Sciences, University of Texas School of Public Health - Austin Regional Campus, Austin, Texas, USA
| | - Jeremy M Schraw
- Center for Epidemiology and Population Health, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA.,Section of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA.,Texas Children's Cancer and Hematology Centers, Texas Children's Hospital, Houston, Texas, USA
| | - Adrienne T Hoyt
- University of Texas School of Public Health - Austin Regional Campus, Austin, Texas, USA
| | - Philip J Lupo
- Center for Epidemiology and Population Health, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA.,Section of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA.,Texas Children's Cancer and Hematology Centers, Texas Children's Hospital, Houston, Texas, USA
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30
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Zhou J, Liu C, Francis M, Sun Y, Ryu MS, Grider A, Ye K. The Causal Effects of Blood Iron and Copper on Lipid Metabolism Diseases: Evidence from Phenome-Wide Mendelian Randomization Study. Nutrients 2020; 12:E3174. [PMID: 33080795 PMCID: PMC7603077 DOI: 10.3390/nu12103174] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/13/2020] [Accepted: 10/14/2020] [Indexed: 02/07/2023] Open
Abstract
Blood levels of iron and copper, even within their normal ranges, have been associated with a wide range of clinical outcomes. The available epidemiological evidence for these associations is often inconsistent and suffers from confounding and reverse causation. This study aims to examine the causal clinical effects of blood iron and copper with Mendelian randomization (MR) analyses. Genetic instruments for the blood levels of iron and copper were curated from existing genome-wide association studies. Candidate clinical outcomes were identified based on a phenome-wide association study (PheWAS) between these genetic instruments and a wide range of phenotypes in 310,999 unrelated individuals of European ancestry from the UK Biobank. All signals passing stringent correction for multiple testing were followed by MR analyses, with replication in independent data sources where possible. We found that genetically predicted higher blood levels of iron and copper are both associated with lower risks of iron deficiency anemia (odds ratio (OR) = 0.75, 95% confidence interval (CI): 0.67-0.85, p = 1.90 × 10-6 for iron; OR = 0.88, 95% CI: 0.78-0.98, p = 0.032 for copper), lipid metabolism disorders, and its two subcategories, hyperlipidemia (OR = 0.90, 95% CI: 0.85-0.96, p = 6.44 × 10-4; OR = 0.92, 95% CI: 0.87-0.98, p = 5.51 × 10-3) and hypercholesterolemia (OR = 0.90, 95% CI: 0.84-0.95, p = 5.34 × 10-4; OR = 0.93, 95% CI: 0.89-0.99, p = 0.022). Consistently, they are also associated with lower blood levels of total cholesterol and low-density lipoprotein cholesterol. Multiple sensitivity tests were applied to assess the presence of pleiotropy and the robustness of causal estimates. Regardless of the approaches, consistent evidence was obtained. Moreover, the unique clinical effects of each blood mineral were identified. Notably, genetically predicated higher blood iron is associated with an enhanced risk of varicose veins (OR = 1.28, 95% CI: 1.15-1.42, p = 4.34 × 10-6), while blood copper is positively associated with the risk of osteoarthrosis (OR = 1.07, 95% CI: 1.02-1.13, p = 0.010). Sex-stratified MR analysis further revealed some degree of sex differences in their clinical effects. Our comparative PheWAS-MR study of iron and copper comprehensively characterized their shared and unique clinical effects, highlighting their potential causal roles in hyperlipidemia and hypercholesterolemia. Given the modifiable nature of blood mineral status and the potential for clinical intervention, these findings warrant further investigation.
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Affiliation(s)
- Jingqi Zhou
- Department of Genetics, University of Georgia, Athens, GA 30602, USA; (J.Z.); (C.L.); (Y.S.)
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Chang Liu
- Department of Genetics, University of Georgia, Athens, GA 30602, USA; (J.Z.); (C.L.); (Y.S.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Michael Francis
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA;
| | - Yitang Sun
- Department of Genetics, University of Georgia, Athens, GA 30602, USA; (J.Z.); (C.L.); (Y.S.)
| | - Moon-Suhn Ryu
- Department of Food Science and Nutrition, University of Minnesota, St. Paul, MN 55108, USA;
| | - Arthur Grider
- Department of Foods and Nutrition, University of Georgia, Athens, GA 30602, USA;
| | - Kaixiong Ye
- Department of Genetics, University of Georgia, Athens, GA 30602, USA; (J.Z.); (C.L.); (Y.S.)
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA;
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31
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Benavides E, Lupo PJ, Langlois PH, Schraw JM. A Comprehensive Assessment of the Associations Between Season of Conception and Birth Defects, Texas, 1999-2015. Int J Environ Res Public Health 2020; 17:E7120. [PMID: 33003294 DOI: 10.3390/ijerph17197120] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 09/25/2020] [Accepted: 09/26/2020] [Indexed: 12/23/2022]
Abstract
Birth defects prevalence may vary seasonally, but previous studies have focused on a few commonly occurring phenotypes. We performed a phenome-wide association study (PheWAS) in order to evaluate the associations between season of conception and a broad range of birth defects. Date of conception was estimated for all livebirths and birth defect cases in Texas from 1999-2015 using data from vital records, provided by the Texas Department of State Health Services Center for Health Statistics. Birth defects diagnoses were obtained from the Texas Birth Defects Registry, a statewide, active surveillance system. We estimated prevalence ratios (PRs) for phenotypes with ≥50 cases according to conception in spring (March-May), summer (June-August) or fall (September-November) relative to winter (December-February), using Poisson regression. Season of conception was associated with 5% of birth defects studied in models adjusted for maternal age, education, race/ethnicity, and number of previous livebirths. Specifically, summer conception was associated with any monitored birth defect (PR 1.03, 95% CI 1.02-1.04) and five specific phenotypes, most notably Hirschsprung disease (PR 1.46, 95% CI 1.22-1.75). These findings suggest that seasonally variable exposures influence the development of several birth defects and may assist in identifying novel environmental risk factors.
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32
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Kuo CL, Pilling LC, Atkins JL, Kuchel GA, Melzer D. ApoE e2 and aging-related outcomes in 379,000 UK Biobank participants. Aging (Albany NY) 2020; 12:12222-12233. [PMID: 32511104 PMCID: PMC7343499 DOI: 10.18632/aging.103405] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 05/25/2020] [Indexed: 01/07/2023]
Abstract
The Apolipoprotein E (APOE) e4 allele is associated with reduced longevity and increased Coronary Artery Disease (CAD) and Alzheimer’s disease, with e4e4 having markedly larger effect sizes than e3e4. The e2 longevity promoting variant is less studied. We conducted a phenome-wide association study of ApoE e2e3 and e2e2 with aging phenotypes, to assess their potential as targets for anti-aging interventions. Data were from 379,000 UK Biobank participants, aged 40 to 70 years. e2e3 (n=46,535) had mostly lower lipid-related biomarker levels including reduced total and LDL-cholesterol, and lower risks of CAD (Odds Ratio=0.87, 95% CI: 0.83 to 0.90, p=4.92×10-14) and hypertension (OR=0.94, 95% CI: 0.92 to 0.97, p=7.28×10-7) versus e3e3. However, lipid changes in e2e2 (n=2,398) were more extreme, including a marked increase in triglyceride levels (0.41 Standard Deviations, 95% CI: 0.37 to 0.45, p=5.42×10-92), with no associated changes in CAD risks. There were no associations with biomarkers of kidney function. The effects of both e2e2 and e2e3 were minimal on falls, muscle mass, grip strength or frailty. In conclusion, e2e3 has protective effects on some health outcomes, but the effects of e2e2 are not similar, complicating the potential usefulness of e2 as a target for anti-aging intervention.
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Affiliation(s)
- Chia-Ling Kuo
- Department of Public Health Sciences, University of Connecticut Health, Farmington, CT 06032, USA.,Connecticut Convergence Institute for Translation in Regenerative Engineering, University of Connecticut Health, Farmington, CT 06032, USA.,Center on Aging, School of Medicine, University of Connecticut Health, Farmington, CT 06030, USA
| | - Luke C Pilling
- Center on Aging, School of Medicine, University of Connecticut Health, Farmington, CT 06030, USA.,College of Medicine and Health, University of Exeter, Exeter, Devon, UK
| | - Janice L Atkins
- College of Medicine and Health, University of Exeter, Exeter, Devon, UK
| | - George A Kuchel
- Center on Aging, School of Medicine, University of Connecticut Health, Farmington, CT 06030, USA
| | - David Melzer
- Center on Aging, School of Medicine, University of Connecticut Health, Farmington, CT 06030, USA.,College of Medicine and Health, University of Exeter, Exeter, Devon, UK
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33
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Kibinge NK, Relton CL, Gaunt TR, Richardson TG. Characterizing the Causal Pathway for Genetic Variants Associated with Neurological Phenotypes Using Human Brain-Derived Proteome Data. Am J Hum Genet 2020; 106:885-892. [PMID: 32413284 PMCID: PMC7273531 DOI: 10.1016/j.ajhg.2020.04.007] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 04/06/2020] [Indexed: 01/09/2023] Open
Abstract
Leveraging high-dimensional molecular datasets can help us develop mechanistic insight into associations between genetic variants and complex traits. In this study, we integrated human proteome data derived from brain tissue to evaluate whether targeted proteins putatively mediate the effects of genetic variants on seven neurological phenotypes (Alzheimer disease, amyotrophic lateral sclerosis, depression, insomnia, intelligence, neuroticism, and schizophrenia). Applying the principles of Mendelian randomization (MR) systematically across the genome highlighted 43 effects between genetically predicted proteins derived from the dorsolateral prefrontal cortex and these outcomes. Furthermore, genetic colocalization provided evidence that the same causal variant at 12 of these loci was responsible for variation in both protein and neurological phenotype. This included genes such as DCC, which encodes the netrin-1 receptor and has an important role in the development of the nervous system (p = 4.29 × 10-11 with neuroticism), as well as SARM1, which has been previously implicated in axonal degeneration (p = 1.76 × 10-08 with amyotrophic lateral sclerosis). We additionally conducted a phenome-wide MR study for each of these 12 genes to assess potential pleiotropic effects on 700 complex traits and diseases. Our findings suggest that genes such as SNX32, which was initially associated with increased risk of Alzheimer disease, may potentially influence other complex traits in the opposite direction. In contrast, genes such as CTSH (which was also associated with Alzheimer disease) and SARM1 may make worthwhile therapeutic targets because they did not have genetically predicted effects on any of the other phenotypes after correcting for multiple testing.
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Affiliation(s)
- Nelson K Kibinge
- Medical Research Council (MRC) Integrative Epidemiology Unit (IEU), Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, United Kingdom
| | - Caroline L Relton
- Medical Research Council (MRC) Integrative Epidemiology Unit (IEU), Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, United Kingdom
| | - Tom R Gaunt
- Medical Research Council (MRC) Integrative Epidemiology Unit (IEU), Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, United Kingdom
| | - Tom G Richardson
- Medical Research Council (MRC) Integrative Epidemiology Unit (IEU), Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, United Kingdom.
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34
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Joo YY, Actkins K, Pacheco JA, Basile AO, Carroll R, Crosslin DR, Day F, Denny JC, Velez Edwards DR, Hakonarson H, Harley JB, Hebbring SJ, Ho K, Jarvik GP, Jones M, Karaderi T, Mentch FD, Meun C, Namjou B, Pendergrass S, Ritchie MD, Stanaway IB, Urbanek M, Walunas TL, Smith M, Chisholm RL, Kho AN, Davis L, Hayes MG. A Polygenic and Phenotypic Risk Prediction for Polycystic Ovary Syndrome Evaluated by Phenome-Wide Association Studies. J Clin Endocrinol Metab 2020; 105:dgz326. [PMID: 31917831 PMCID: PMC7453038 DOI: 10.1210/clinem/dgz326] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 01/07/2020] [Indexed: 11/19/2022]
Abstract
CONTEXT As many as 75% of patients with polycystic ovary syndrome (PCOS) are estimated to be unidentified in clinical practice. OBJECTIVE Utilizing polygenic risk prediction, we aim to identify the phenome-wide comorbidity patterns characteristic of PCOS to improve accurate diagnosis and preventive treatment. DESIGN, PATIENTS, AND METHODS Leveraging the electronic health records (EHRs) of 124 852 individuals, we developed a PCOS risk prediction algorithm by combining polygenic risk scores (PRS) with PCOS component phenotypes into a polygenic and phenotypic risk score (PPRS). We evaluated its predictive capability across different ancestries and perform a PRS-based phenome-wide association study (PheWAS) to assess the phenomic expression of the heightened risk of PCOS. RESULTS The integrated polygenic prediction improved the average performance (pseudo-R2) for PCOS detection by 0.228 (61.5-fold), 0.224 (58.8-fold), 0.211 (57.0-fold) over the null model across European, African, and multi-ancestry participants respectively. The subsequent PRS-powered PheWAS identified a high level of shared biology between PCOS and a range of metabolic and endocrine outcomes, especially with obesity and diabetes: "morbid obesity", "type 2 diabetes", "hypercholesterolemia", "disorders of lipid metabolism", "hypertension", and "sleep apnea" reaching phenome-wide significance. CONCLUSIONS Our study has expanded the methodological utility of PRS in patient stratification and risk prediction, especially in a multifactorial condition like PCOS, across different genetic origins. By utilizing the individual genome-phenome data available from the EHR, our approach also demonstrates that polygenic prediction by PRS can provide valuable opportunities to discover the pleiotropic phenomic network associated with PCOS pathogenesis.
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Affiliation(s)
- Yoonjung Yoonie Joo
- Division of Endocrinology, Metabolism, and Molecular Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Ky'Era Actkins
- Department of Microbiology, Immunology, and Physiology, Meharry Medical College, Nashville, Tennessee
| | - Jennifer A Pacheco
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Anna O Basile
- Department of Biomedical Informatics, Columbia University New York, New York
| | - Robert Carroll
- Departments of Biomedical Informatics and Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - David R Crosslin
- Department of Biomedical Informatics and Medical Education, University of Washington School of Medicine, Seattle, Wahington
| | - Felix Day
- MRC Epidemiology Unit, Cambridge Biomedical Campus, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
| | - Joshua C Denny
- Departments of Biomedical Informatics and Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Digna R Velez Edwards
- Departments of Biomedical Informatics and Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
- Division of Quantitative Sciences, Department of Obstetrics and Gynecology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - John B Harley
- Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
- Department of Pediatrics, University of Cincinnati College of Medicine; US Department of Veterans Affairs, Cincinnati, Ohio
| | - Scott J Hebbring
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, Wisconsin, USA
| | - Kevin Ho
- Biomedical and Translational Informatics, Geisinger, Danville, Pennsylvania
| | - Gail P Jarvik
- Division of Medical Genetics, Department of Medicine (Medical Genetics) and Genome Sciences, University of Washington Medical School, Seattle, Wahington
| | - Michelle Jones
- Center for Bioinformatics & Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California
| | - Tugce Karaderi
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Frank D Mentch
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Cindy Meun
- Department of Obstetrics and Gynecology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Bahram Namjou
- Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Sarah Pendergrass
- Biomedical and Translational Informatics, Geisinger, Danville, Pennsylvania
| | - Marylyn D Ritchie
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Ian B Stanaway
- Department of Biomedical Informatics and Medical Education, University of Washington School of Medicine, Seattle, Wahington
| | - Margrit Urbanek
- Division of Endocrinology, Metabolism, and Molecular Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Theresa L Walunas
- Division of General Internal Medicine and Geriatrics, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Maureen Smith
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Rex L Chisholm
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Abel N Kho
- Division of General Internal Medicine and Geriatrics, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Lea Davis
- Departments of Biomedical Informatics and Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - M Geoffrey Hayes
- Division of Endocrinology, Metabolism, and Molecular Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
- Department of Anthropology, Northwestern University, Evanston, Illinois
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35
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Hsiung CN, Chang YC, Lin CW, Chang CW, Chou WC, Chu HW, Su MW, Wu PE, Shen CY. The Causal Relationship of Circulating Triglyceride and Glycated Hemoglobin: A Mendelian Randomization Study. J Clin Endocrinol Metab 2020; 105:5648095. [PMID: 31784746 DOI: 10.1210/clinem/dgz243] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 11/29/2019] [Indexed: 12/20/2022]
Abstract
CONTEXT The association between circulating triglyceride (TG) and glycated hemoglobin A1c (HbA1c), a biomarker for type 2 diabetes, has been widely addressed, but the causal direction of the relationship is still ambiguous. OBJECTIVE To confirm the causal relationship between TG and HbA1c by using bidirectional and 2-step Mendelian randomization (MR) approaches. METHODS We carried out a bidirectional MR approach using the summarized results from the public database to examine any potential causal effects between serum TG and HbA1c in 16 000 individuals of the Taiwan Biobank cohort. We used the MR estimate and the MR inverse variance-weighted method to reveal that relationship between TG and HbA1c. To further determine whether the DNA methylation at specific sequences mediate the causal pathway between TG and HbA1c, using the 2-step MR approach. RESULTS We identified that a single-unit increase in TG measured via log transformation of mg/dL data was associated with a significant increase of 10 units of HbA1c (95% CI = 1.05-18.95, P = 0.029). In contrast, the genetic determinants of HbA1c do not contribute to the amount of circulating TG (beta = 1.75, 95% CI = -11.50 to 14.90). Sensitivity analyses, included the weighted-median approach and MR-Egger regression, were performed to confirm no pleiotropic effect among these instrumental variables. Furthermore, we identified the genetic variant, rs1823200, is associated with both methylation of the CpG site adjacent to CADPS gene and HbA1c level. CONCLUSION Our study suggests that higher circulating TG can have an affect on genomic methylation status, ultimately causing elevated level of circulating HbA1c.
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Affiliation(s)
- Chia-Ni Hsiung
- Institute of Bioinformatics and Structure Biology, National Tsing Hua University, Hsinchu, Taiwan
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Yi-Cheng Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University, Taipei, Taiwan
| | | | | | - Wen-Cheng Chou
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Hou-Wei Chu
- Taiwan Biobank, Academia Sinica, Taipei, Taiwan
| | - Ming-Wei Su
- Taiwan Biobank, Academia Sinica, Taipei, Taiwan
| | - Pei-Ei Wu
- Taiwan Biobank, Academia Sinica, Taipei, Taiwan
| | - Chen-Yang Shen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
- College of Public Health, China Medical University, Taichung, Taiwan
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Wu P, Gifford A, Meng X, Li X, Campbell H, Varley T, Zhao J, Carroll R, Bastarache L, Denny JC, Theodoratou E, Wei WQ. Mapping ICD-10 and ICD-10-CM Codes to Phecodes: Workflow Development and Initial Evaluation. JMIR Med Inform 2019; 7:e14325. [PMID: 31553307 PMCID: PMC6911227 DOI: 10.2196/14325] [Citation(s) in RCA: 234] [Impact Index Per Article: 46.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 08/03/2019] [Accepted: 09/24/2019] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND The phecode system was built upon the International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM) for phenome-wide association studies (PheWAS) using the electronic health record (EHR). OBJECTIVE The goal of this paper was to develop and perform an initial evaluation of maps from the International Classification of Diseases, 10th Revision (ICD-10) and the International Classification of Diseases, 10th Revision, Clinical Modification (ICD-10-CM) codes to phecodes. METHODS We mapped ICD-10 and ICD-10-CM codes to phecodes using a number of methods and resources, such as concept relationships and explicit mappings from the Centers for Medicare & Medicaid Services, the Unified Medical Language System, Observational Health Data Sciences and Informatics, Systematized Nomenclature of Medicine-Clinical Terms, and the National Library of Medicine. We assessed the coverage of the maps in two databases: Vanderbilt University Medical Center (VUMC) using ICD-10-CM and the UK Biobank (UKBB) using ICD-10. We assessed the fidelity of the ICD-10-CM map in comparison to the gold-standard ICD-9-CM phecode map by investigating phenotype reproducibility and conducting a PheWAS. RESULTS We mapped >75% of ICD-10 and ICD-10-CM codes to phecodes. Of the unique codes observed in the UKBB (ICD-10) and VUMC (ICD-10-CM) cohorts, >90% were mapped to phecodes. We observed 70-75% reproducibility for chronic diseases and <10% for an acute disease for phenotypes sourced from the ICD-10-CM phecode map. Using the ICD-9-CM and ICD-10-CM maps, we conducted a PheWAS with a Lipoprotein(a) genetic variant, rs10455872, which replicated two known genotype-phenotype associations with similar effect sizes: coronary atherosclerosis (ICD-9-CM: P<.001; odds ratio (OR) 1.60 [95% CI 1.43-1.80] vs ICD-10-CM: P<.001; OR 1.60 [95% CI 1.43-1.80]) and chronic ischemic heart disease (ICD-9-CM: P<.001; OR 1.56 [95% CI 1.35-1.79] vs ICD-10-CM: P<.001; OR 1.47 [95% CI 1.22-1.77]). CONCLUSIONS This study introduces the beta versions of ICD-10 and ICD-10-CM to phecode maps that enable researchers to leverage accumulated ICD-10 and ICD-10-CM data for PheWAS in the EHR.
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Affiliation(s)
- Patrick Wu
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, United States
- Medical Scientist Training Program, Vanderbilt University School of Medicine, Nashville, TN, United States
| | - Aliya Gifford
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Xiangrui Meng
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, The University of Edinburgh, Edinburgh, United Kingdom
| | - Xue Li
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, The University of Edinburgh, Edinburgh, United Kingdom
| | - Harry Campbell
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, The University of Edinburgh, Edinburgh, United Kingdom
| | - Tim Varley
- Public Health and Intelligence Strategic Business Unit, National Services Scotland, Edinburgh, United Kingdom
| | - Juan Zhao
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Robert Carroll
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Lisa Bastarache
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Joshua C Denny
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, United States
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Evropi Theodoratou
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, The University of Edinburgh, Edinburgh, United Kingdom
- Edinburgh Cancer Research Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Wei-Qi Wei
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, United States
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Richardson TG, Harrison S, Hemani G, Davey Smith G. An atlas of polygenic risk score associations to highlight putative causal relationships across the human phenome. eLife 2019; 8:e43657. [PMID: 30835202 PMCID: PMC6400585 DOI: 10.7554/elife.43657] [Citation(s) in RCA: 115] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 02/01/2019] [Indexed: 12/12/2022] Open
Abstract
The age of large-scale genome-wide association studies (GWAS) has provided us with an unprecedented opportunity to evaluate the genetic liability of complex disease using polygenic risk scores (PRS). In this study, we have analysed 162 PRS (p<5×10-05) derived from GWAS and 551 heritable traits from the UK Biobank study (N = 334,398). Findings can be investigated using a web application (http://mrcieu.mrsoftware.org/PRS_atlas/), which we envisage will help uncover both known and novel mechanisms which contribute towards disease susceptibility. To demonstrate this, we have investigated the results from a phenome-wide evaluation of schizophrenia genetic liability. Amongst findings were inverse associations with measures of cognitive function which extensive follow-up analyses using Mendelian randomization (MR) provided evidence of a causal relationship. We have also investigated the effect of multiple risk factors on disease using mediation and multivariable MR frameworks. Our atlas provides a resource for future endeavours seeking to unravel the causal determinants of complex disease.
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Affiliation(s)
- Tom G Richardson
- MRC Integrative Epidemiology Unit (IEU), Population Health Sciences, Bristol Medical SchoolUniversity of BristolBristolUnited Kingdom
| | - Sean Harrison
- MRC Integrative Epidemiology Unit (IEU), Population Health Sciences, Bristol Medical SchoolUniversity of BristolBristolUnited Kingdom
| | - Gibran Hemani
- MRC Integrative Epidemiology Unit (IEU), Population Health Sciences, Bristol Medical SchoolUniversity of BristolBristolUnited Kingdom
| | - George Davey Smith
- MRC Integrative Epidemiology Unit (IEU), Population Health Sciences, Bristol Medical SchoolUniversity of BristolBristolUnited Kingdom
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Barnado A, Carroll RJ, Casey C, Wheless L, Denny JC, Crofford LJ. Phenome-wide association study identifies dsDNA as a driver of major organ involvement in systemic lupus erythematosus. Lupus 2018; 28:66-76. [PMID: 30477398 DOI: 10.1177/0961203318815577] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
In systemic lupus erythematosus (SLE), dsDNA antibodies are associated with renal disease. Less is known about comorbidities in patients without dsDNA or other autoantibodies. Using an electronic health record (EHR) SLE cohort, we employed a phenome-wide association study (PheWAS) that scans across billing codes to compare comorbidities in SLE patients with and without autoantibodies. We used our validated algorithm to identify SLE subjects. Autoantibody status was defined as ever positive for dsDNA, RNP, Smith, SSA and SSB. PheWAS was performed in antibody positive vs. negative SLE patients adjusting for age and race and using a false discovery rate of 0.05. We identified 1097 SLE subjects. In the PheWAS of dsDNA positive vs. negative subjects, dsDNA positive subjects were more likely to have nephritis ( p = 2.33 × 10-9) and renal failure ( p = 1.85 × 10-5). After adjusting for sex, race, age and other autoantibodies, dsDNA was independently associated with nephritis and chronic kidney disease. Those patients negative for dsDNA, RNP, SSA and SSB negative subjects were all more likely to have billing codes for sleep, pain and mood disorders. PheWAS uncovered a hierarchy within SLE-specific autoantibodies with dsDNA having the greatest impact on major organ involvement.
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Affiliation(s)
- A Barnado
- 1 Department of Medicine, Vanderbilt University Medical Center, Nashville, USA
| | - R J Carroll
- 2 Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, USA
| | - C Casey
- 3 Department of Medicine, Lehigh Valley Health Network, Allentown, USA
| | - L Wheless
- 4 Department of Dermatology, Vanderbilt University Medical Center, Nashville, USA
| | - J C Denny
- 1 Department of Medicine, Vanderbilt University Medical Center, Nashville, USA.,2 Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, USA
| | - L J Crofford
- 1 Department of Medicine, Vanderbilt University Medical Center, Nashville, USA
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Abstract
The field of human genomics has changed dramatically over time. Initial genomic studies were predominantly restricted to rare disorders in small families. Over the past decade, researchers changed course from family-based studies and instead focused on common diseases and traits in populations of unrelated individuals. With further advancements in biobanking, computer science, electronic health record (EHR) data, and more affordable high-throughput genomics, we are experiencing a new paradigm in human genomic research. Rapidly changing technologies and resources now make it possible to study thousands of diseases simultaneously at the genomic level. This review will focus on these advancements as scientists begin to incorporate phenome-wide strategies in human genomic research to understand the etiology of human diseases and develop new drugs to treat them.
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Rhoades SD, Bastarache L, Denny JC, Hughey JJ. Pulling the covers in electronic health records for an association study with self-reported sleep behaviors. Chronobiol Int 2018; 35:1702-1712. [PMID: 30183400 DOI: 10.1080/07420528.2018.1508152] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The electronic health record (EHR) contains rich histories of clinical care, but has not traditionally been mined for information related to sleep habits. Here, we performed a retrospective EHR study based on a cohort of 3,652 individuals with self-reported sleep behaviors documented from visits to the sleep clinic. These individuals were obese (mean body mass index 33.6 kg/m2) and had a high prevalence of sleep apnea (60.5%), however we found sleep behaviors largely concordant with prior prospective cohort studies. In our cohort, average wake time was 1 hour later and average sleep duration was 40 minutes longer on weekends than on weekdays (p < 10-12). Sleep duration varied considerably as a function of age and tended to be longer in females and in whites. Additionally, through phenome-wide association analyses, we found an association of long weekend sleep with depression, and an unexpectedly large number of associations of long weekday sleep with mental health and neurological disorders (q < 0.05). We then sought to replicate previously published genetic associations with morning/evening preference on a subset of our cohort with extant genotyping data (n = 555). While those findings did not replicate in our cohort, a polymorphism (rs3754214) in high linkage disequilibrium with a previously published polymorphism near TARS2 was associated with long sleep duration (p < 0.01). Collectively, our results highlight the potential of the EHR for uncovering the correlates of human sleep in real-world populations.
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Affiliation(s)
- Seth D Rhoades
- a Department of Biomedical Informatics , Vanderbilt University Medical Center , Nashville , Tennessee , USA
| | - Lisa Bastarache
- a Department of Biomedical Informatics , Vanderbilt University Medical Center , Nashville , Tennessee , USA
| | - Joshua C Denny
- a Department of Biomedical Informatics , Vanderbilt University Medical Center , Nashville , Tennessee , USA.,b Department of Medicine , Vanderbilt University Medical Center , Nashville , Tennessee , USA
| | - Jacob J Hughey
- a Department of Biomedical Informatics , Vanderbilt University Medical Center , Nashville , Tennessee , USA.,c Department of Biological Sciences , Vanderbilt University , Nashville , Tennessee , USA
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Fritsche LG, Gruber SB, Wu Z, Schmidt EM, Zawistowski M, Moser SE, Blanc VM, Brummett CM, Kheterpal S, Abecasis GR, Mukherjee B. Association of Polygenic Risk Scores for Multiple Cancers in a Phenome-wide Study: Results from The Michigan Genomics Initiative. Am J Hum Genet 2018; 102:1048-1061. [PMID: 29779563 DOI: 10.1016/j.ajhg.2018.04.001] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 03/26/2018] [Indexed: 12/11/2022] Open
Abstract
Health systems are stewards of patient electronic health record (EHR) data with extraordinarily rich depth and breadth, reflecting thousands of diagnoses and exposures. Measures of genomic variation integrated with EHRs offer a potential strategy to accurately stratify patients for risk profiling and discover new relationships between diagnoses and genomes. The objective of this study was to evaluate whether polygenic risk scores (PRS) for common cancers are associated with multiple phenotypes in a phenome-wide association study (PheWAS) conducted in 28,260 unrelated, genotyped patients of recent European ancestry who consented to participate in the Michigan Genomics Initiative, a longitudinal biorepository effort within Michigan Medicine. PRS for 12 cancer traits were calculated using summary statistics from the NHGRI-EBI catalog. A total of 1,711 synthetic case-control studies was used for PheWAS analyses. There were 13,490 (47.7%) patients with at least one cancer diagnosis in this study sample. PRS exhibited strong association for several cancer traits they were designed for, including female breast cancer, prostate cancer, melanoma, basal cell carcinoma, squamous cell carcinoma, and thyroid cancer. Phenome-wide significant associations were observed between PRS and many non-cancer diagnoses. To differentiate PRS associations driven by the primary trait from associations arising through shared genetic risk profiles, the idea of "exclusion PRS PheWAS" was introduced. Further analysis of temporal order of the diagnoses improved our understanding of these secondary associations. This comprehensive PheWAS used PRS instead of a single variant.
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Affiliation(s)
- Lars G Fritsche
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA; Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA; K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Norwegian University of Science and Technology, 7491 Trondheim, Sør-Trøndelag, Norway
| | - Stephen B Gruber
- USC Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA
| | - Zhenke Wu
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA; Michigan Institute for Data Science, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ellen M Schmidt
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Matthew Zawistowski
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA; Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Stephanie E Moser
- Division of Pain Medicine, Department of Anesthesiology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Victoria M Blanc
- Central Biorepository, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Chad M Brummett
- Division of Pain Medicine, Department of Anesthesiology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Institute for Healthcare Policy and Innovation, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sachin Kheterpal
- Division of Pain Medicine, Department of Anesthesiology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Institute for Healthcare Policy and Innovation, University of Michigan, Ann Arbor, MI 48109, USA
| | - Gonçalo R Abecasis
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA; Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Bhramar Mukherjee
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA; Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA; Michigan Institute for Data Science, University of Michigan, Ann Arbor, MI 48109, USA; Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA; University of Michigan Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA.
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Emdin CA, Khera AV, Natarajan P, Klarin D, Won HH, Peloso GM, Stitziel NO, Nomura A, Zekavat SM, Bick AG, Gupta N, Asselta R, Duga S, Merlini PA, Correa A, Kessler T, Wilson JG, Bown MJ, Hall AS, Braund PS, Samani NJ, Schunkert H, Marrugat J, Elosua R, McPherson R, Farrall M, Watkins H, Willer C, Abecasis GR, Felix JF, Vasan RS, Lander E, Rader DJ, Danesh J, Ardissino D, Gabriel S, Saleheen D, Kathiresan S. Phenotypic Characterization of Genetically Lowered Human Lipoprotein(a) Levels. J Am Coll Cardiol 2016; 68:2761-2772. [PMID: 28007139 PMCID: PMC5328146 DOI: 10.1016/j.jacc.2016.10.033] [Citation(s) in RCA: 155] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 09/21/2016] [Accepted: 10/04/2016] [Indexed: 02/02/2023]
Abstract
BACKGROUND Genomic analyses have suggested that the LPA gene and its associated plasma biomarker, lipoprotein(a) (Lp[a]), represent a causal risk factor for coronary heart disease (CHD). As such, lowering Lp(a) levels has emerged as a therapeutic strategy. Beyond target identification, human genetics may contribute to the development of new therapies by defining the full spectrum of beneficial and adverse consequences and by developing a dose-response curve of target perturbation. OBJECTIVES The goal of this study was to establish the full phenotypic impact of LPA gene variation and to estimate a dose-response curve between genetically altered plasma Lp(a) and risk for CHD. METHODS We leveraged genetic variants at the LPA gene from 3 data sources: individual-level data from 112,338 participants in the U.K. Biobank; summary association results from large-scale genome-wide association studies; and LPA gene sequencing results from case subjects with CHD and control subjects free of CHD. RESULTS One SD genetically lowered Lp(a) level was associated with a 29% lower risk of CHD (odds ratio [OR]: 0.71; 95% confidence interval [CI]: 0.69 to 0.73), a 31% lower risk of peripheral vascular disease (OR: 0.69; 95% CI: 0.59 to 0.80), a 13% lower risk of stroke (OR: 0.87; 95% CI: 0.79 to 0.96), a 17% lower risk of heart failure (OR: 0.83; 95% CI: 0.73 to 0.94), and a 37% lower risk of aortic stenosis (OR: 0.63; 95% CI: 0.47 to 0.83). We observed no association with 31 other disorders, including type 2 diabetes and cancer. Variants that led to gain of LPA gene function increased the risk for CHD, whereas those that led to loss of gene function reduced the CHD risk. CONCLUSIONS Beyond CHD, genetically lowered Lp(a) levels are associated with a lower risk of peripheral vascular disease, stroke, heart failure, and aortic stenosis. As such, pharmacological lowering of plasma Lp(a) may influence a range of atherosclerosis-related diseases.
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Affiliation(s)
- Connor A Emdin
- Center for Human Genetic Research, Cardiovascular Research Center and Cardiology Division, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts; Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts
| | - Amit V Khera
- Center for Human Genetic Research, Cardiovascular Research Center and Cardiology Division, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts; Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts
| | - Pradeep Natarajan
- Center for Human Genetic Research, Cardiovascular Research Center and Cardiology Division, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts; Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts
| | - Derek Klarin
- Center for Human Genetic Research, Cardiovascular Research Center and Cardiology Division, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts; Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts
| | - Hong-Hee Won
- Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Samsung Medical Center, Seoul, Republic of Korea
| | - Gina M Peloso
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts; Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
| | - Nathan O Stitziel
- Departments of Medicine, Genetics, and the McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri
| | - Akihiro Nomura
- Center for Human Genetic Research, Cardiovascular Research Center and Cardiology Division, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts; Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts
| | - Seyedeh M Zekavat
- Center for Human Genetic Research, Cardiovascular Research Center and Cardiology Division, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts; Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts
| | - Alexander G Bick
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts
| | - Namrata Gupta
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts
| | - Rosanna Asselta
- Department of Biomedical Sciences, Humanitas University and Humanitas Clinical and Research Center, Milan, Italy
| | - Stefano Duga
- Department of Biomedical Sciences, Humanitas University and Humanitas Clinical and Research Center, Milan, Italy
| | | | - Adolfo Correa
- Jackson Heart Study, Department of Medicine, University of Mississippi Medical Center, Jackson, Mississippi
| | - Thorsten Kessler
- Deutsches Herzzentrum München, Technische Universität München, Deutsches Zentrum für Herz-Kreislauf-Forschung, München, Germany; Munich Heart Alliance, München, Germany
| | - James G Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, Mississippi
| | - Matthew J Bown
- Departments of Cardiovascular Sciences and NIHR Leicester Cardiovascular Biomedical Research Unit, University of Leicester, Leicester, United Kingdom
| | - Alistair S Hall
- Leeds Institute of Cardiovascular and Metabolic Medicine, Leeds University, Leeds, United Kingdom
| | - Peter S Braund
- Departments of Cardiovascular Sciences and NIHR Leicester Cardiovascular Biomedical Research Unit, University of Leicester, Leicester, United Kingdom
| | - Nilesh J Samani
- Departments of Cardiovascular Sciences and NIHR Leicester Cardiovascular Biomedical Research Unit, University of Leicester, Leicester, United Kingdom
| | - Heribert Schunkert
- Deutsches Herzzentrum München, Technische Universität München, Deutsches Zentrum für Herz-Kreislauf-Forschung, München, Germany
| | - Jaume Marrugat
- Cardiovascular Epidemiology & Genetics, IMIM (Hospital del Mar Research Institute), Barcelona, Spain
| | - Roberto Elosua
- Cardiovascular Epidemiology & Genetics, IMIM (Hospital del Mar Research Institute), Barcelona, Spain
| | - Ruth McPherson
- University of Ottawa Heart Institute, Ottawa, Ontario, Canada
| | - Martin Farrall
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine and the Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Hugh Watkins
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine and the Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Cristen Willer
- Department of Computational Medicine and Bioinformatics, Department of Human Genetics, and Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Gonçalo R Abecasis
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, Michigan
| | - Janine F Felix
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Ramachandran S Vasan
- National Heart, Lung, and Blood Institute's and Boston University's Framingham Heart Study, Framingham, Massachusetts; Sections of Cardiology, Preventive Medicine and Epidemiology, Department of Medicine, Boston University Schools of Medicine and Public Health, Boston, Massachusetts
| | - Eric Lander
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts
| | - Daniel J Rader
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - John Danesh
- Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom; National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Diego Ardissino
- Division of Cardiology, Azienda Ospedaliero-Universitaria di Parma, University of Parma, Parma, Italy; ASTC: Associazione per lo Studio Della Trombosi in Cardiologia, Pavia, Italy
| | - Stacey Gabriel
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts
| | - Danish Saleheen
- Biostatistics and Epidemiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Sekar Kathiresan
- Center for Human Genetic Research, Cardiovascular Research Center and Cardiology Division, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts; Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts.
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Oetjens MT, Bush WS, Denny JC, Birdwell K, Kodaman N, Verma A, Dilks HH, Pendergrass SA, Ritchie MD, Crawford DC. Evidence for extensive pleiotropy among pharmacogenes. Pharmacogenomics 2016; 17:853-66. [PMID: 27249515 DOI: 10.2217/pgs-2015-0007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
AIM We sought to identify potential pleiotropy involving pharmacogenes. METHODS We tested 184 functional variants in 34 pharmacogenes for associations using a custom grouping of International Classification and Disease, Ninth Revision billing codes extracted from deidentified electronic health records of 6892 patients. RESULTS We replicated several associations including ABCG2 (rs2231142) and gout (p = 1.73 × 10(-7); odds ratio [OR]: 1.73; 95% CI: 1.40-2.12); and SLCO1B1 (rs4149056) and jaundice (p = 2.50 × 10(-4); OR: 1.67; 95% CI: 1.27-2.20). CONCLUSION In this systematic screen for phenotypic associations with functional variants, several novel genotype-phenotype combinations also achieved phenome-wide significance, including SLC15A2 rs1143672 and renal osteodystrophy (p = 2.67 × 10(-) (6); OR: 0.61; 95% CI: 0.49-0.75).
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Affiliation(s)
- Matthew T Oetjens
- Center for Human Genetics Research, Vanderbilt University, Nashville, TN 37232, USA
| | - William S Bush
- Department of Epidemiology & Biostatistics, Institute for Computational Biology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Joshua C Denny
- Department of Biomedical Informatics, Vanderbilt University, Nashville, TN 37203, USA
| | - Kelly Birdwell
- Department of Medicine, Vanderbilt University, Nashville, TN 37232, USA
| | - Nuri Kodaman
- Center for Human Genetics Research, Vanderbilt University, Nashville, TN 37232, USA
| | - Anurag Verma
- Center for Systems Genomics, Department of Biochemistry & Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Holli H Dilks
- Sarah Cannon Research Institute, Nashville, TN 37203 USA
| | - Sarah A Pendergrass
- Center for Systems Genomics, Department of Biochemistry & Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Marylyn D Ritchie
- Center for Systems Genomics, Department of Biochemistry & Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Dana C Crawford
- Department of Epidemiology & Biostatistics, Institute for Computational Biology, Case Western Reserve University, Cleveland, OH 44106, USA
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Abstract
Beginning in the early 2000s, the accumulation of biospecimens linked to electronic health records (EHRs) made possible genome-phenome studies (i.e., comparative analyses of genetic variants and phenotypes) using only data collected as a by-product of typical health care. In addition to disease and trait genetics, EHRs proved a valuable resource for analyzing pharmacogenetic traits and developing reverse genetics approaches such as phenome-wide association studies (PheWASs). PheWASs are designed to survey which of many phenotypes may be associated with a given genetic variant. PheWAS methods have been validated through replication of hundreds of known genotype-phenotype associations, and their use has differentiated between true pleiotropy and clinical comorbidity, added context to genetic discoveries, and helped define disease subtypes, and may also help repurpose medications. PheWAS methods have also proven to be useful with research-collected data. Future efforts that integrate broad, robust collection of phenotype data (e.g., EHR data) with purpose-collected research data in combination with a greater understanding of EHR data will create a rich resource for increasingly more efficient and detailed genome-phenome analysis to usher in new discoveries in precision medicine.
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Affiliation(s)
- Joshua C Denny
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee 37203; .,Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
| | - Lisa Bastarache
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee 37203;
| | - Dan M Roden
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee 37203; .,Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee 37232.,Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
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Hebbring SJ. The challenges, advantages and future of phenome-wide association studies. Immunology 2014; 141:157-65. [PMID: 24147732 PMCID: PMC3904236 DOI: 10.1111/imm.12195] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Revised: 10/16/2013] [Accepted: 10/17/2013] [Indexed: 12/11/2022] Open
Abstract
Over the last decade, significant technological breakthroughs have revolutionized human genomic research in the form of genome-wide association studies (GWASs). GWASs have identified thousands of statistically significant genetic variants associated with hundreds of human conditions including many with immunological aetiologies (e.g. multiple sclerosis, ankylosing spondylitis and rheumatoid arthritis). Unfortunately, most GWASs fail to identify clinically significant associations. Identifying biologically significant variants by GWAS also presents a challenge. The GWAS is a phenotype-to-genotype approach. As a complementary/alternative approach to the GWAS, investigators have begun to exploit extensive electronic medical record systems to conduct a genotype-to-phenotype approach when studying human disease – specifically, the phenome-wide association study (PheWAS). Although the PheWAS approach is in its infancy, this method has already demonstrated its capacity to rediscover important genetic associations related to immunological diseases/conditions. Furthermore, PheWAS has the advantage of identifying genetic variants with pleiotropic properties. This is particularly relevant for HLA variants. For example, PheWAS results have demonstrated that the HLA-DRB1 variant associated with multiple sclerosis may also be associated with erythematous conditions including rosacea. Likewise, PheWAS has demonstrated that the HLA-B genotype is not only associated with spondylopathies, uveitis, and variability in platelet count, but may also play an important role in other conditions, such as mastoiditis. This review will discuss and compare general PheWAS methodologies, describe both the challenges and advantages of the PheWAS, and provide insight into the potential directions in which PheWAS may lead.
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Affiliation(s)
- Scott J Hebbring
- Center for Human Genetics, Marshfield Clinic Research Foundation, Marshfield, WI, USA
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