1
|
Ruíz-Patiño A, Rojas L, Zuluaga J, Arrieta O, Corrales L, Martín C, Franco S, Raez L, Rolfo C, Sánchez N, Cardona AF. Genomic ancestry and cancer among Latin Americans. Clin Transl Oncol 2024:10.1007/s12094-024-03415-6. [PMID: 38581481 DOI: 10.1007/s12094-024-03415-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 02/20/2024] [Indexed: 04/08/2024]
Abstract
Latin American populations, characterized by intricate admixture patterns resulting from the intermingling of ancestries from European, Native American (NA) Asian, and African ancestries which result in a vast and complex genetic landscape, harboring unique combinations of novel variants. This genetic diversity not only poses challenges in traditional population genetics methods but also opens avenues for a deeper understanding of its implications in health. In cancer, the interplay between genetic ancestry, lifestyle factors, and healthcare disparities adds a layer of complexity to the varying incidence and mortality rates observed across different Latin American subpopulations. This complex interdependence has been unveiled through numerous studies, whether conducted on Latin American patients residing on the continent or abroad, revealing discernible differences in germline composition that influence divergent disease phenotypes such as higher incidence of Luminal B and Her2 breast tumors, EGFR and KRAS mutated lung adenocarcinomas in addition to an enrichment in BRCA1/2 pathogenic variants and a higher than expected prevalence of variants in colorectal cancer associated genes such as APC and MLH1. In prostate cancer novel risk variants have also been solely identified in Latin American populations. Due to the complexity of genetic divergence, inputs from each individual ancestry seem to carry independent contributions that interplay in the development of these complex disease phenotypes. By understanding these unique population characteristics, genomic ancestries hold a promising avenue for tailoring prognostic assessments and optimizing responses to oncological interventions.
Collapse
Affiliation(s)
- Alejandro Ruíz-Patiño
- Clinical Genetics, Luis Carlos Sarmiento Angulo Cancer Treatment and Research Center (CTIC), Bogotá, Colombia
- Foundation for Clinical and Applied Cancer Research - FICMAC, Bogotá, Colombia
- GIGA/TERA Research Group, CTIC/Universidad El Bosque, Bogotá, Colombia
| | - Leonardo Rojas
- GIGA/TERA Research Group, CTIC/Universidad El Bosque, Bogotá, Colombia
- Thoracic Oncology Unit, Luis Carlos Sarmiento Angulo Cancer Treatment and Research Center (CTIC), Bogotá, Colombia
| | - Jairo Zuluaga
- GIGA/TERA Research Group, CTIC/Universidad El Bosque, Bogotá, Colombia
- Thoracic Oncology Unit, Luis Carlos Sarmiento Angulo Cancer Treatment and Research Center (CTIC), Bogotá, Colombia
| | - Oscar Arrieta
- Instituto Nacional de Cancerología -INCaN, Mexico City, Mexico
| | - Luis Corrales
- Thoracic Oncology Unit, Centro de Investigación y Manejo del Cáncer (CIMCA), San José, Costa Rica
| | - Claudio Martín
- Thoracic Oncology Unit, Instituto Alexander Fleming, Buenos Aires, Argentina
| | - Sandra Franco
- GIGA/TERA Research Group, CTIC/Universidad El Bosque, Bogotá, Colombia
- Breast Cancer Unit, Luis Carlos Sarmiento Angulo Cancer Treatment and Research Center (CTIC), Bogotá, Colombia
| | - Luis Raez
- Oncology Department, Memorial Cancer Institute (MCI), Memorial Healthcare System, Miami, FL, USA
| | - Christian Rolfo
- Center for Thoracic Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Natalia Sánchez
- GIGA/TERA Research Group, CTIC/Universidad El Bosque, Bogotá, Colombia
- Institute of Research, Science and Education, Luis Carlos Sarmiento Angulo Cancer Treatment and Research Center (CTIC), Bogotá, Colombia
| | - Andrés Felipe Cardona
- GIGA/TERA Research Group, CTIC/Universidad El Bosque, Bogotá, Colombia.
- Thoracic Oncology Unit, Luis Carlos Sarmiento Angulo Cancer Treatment and Research Center (CTIC), Bogotá, Colombia.
- Institute of Research, Science and Education, Luis Carlos Sarmiento Angulo Cancer Treatment and Research Center (CTIC), Bogotá, Colombia.
- Direction of Research and Education, Luis Carlos Sarmiento Angulo Cancer Treatment and Research Center (CTIC), Cra. 14 #169-49, Bogotá, Colombia.
| |
Collapse
|
2
|
Li B, Lin Y, Yang Y, Wang Z, Shi R, Zheng T, Liao B, Liao G, Huang J. Patients with periodontitis might increase the risk of urologic cancers: a bidirectional two-sample Mendelian randomization study. Int Urol Nephrol 2024; 56:1243-1251. [PMID: 38015384 PMCID: PMC10923993 DOI: 10.1007/s11255-023-03858-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 10/14/2023] [Indexed: 11/29/2023]
Abstract
BACKGROUND Numerous observational epidemiological studies have reported a bidirectional relationship between periodontitis and urological cancers. However, the causal link between these two phenotypes remains uncertain. This study aimed to examine the bidirectional causal association between periodontitis and four types of urological tumors, specifically kidney cancer (KC), prostate cancer (PC), bladder cancer (BC), and testis cancer (TC). METHODS Based on large-scale genome-wide association study (GWAS) data, we utilized the two-sample Mendelian randomization (MR) approach to evaluate causal relationships between periodontitis and urological cancers. Several MR methods covering various consistency assumptions were applied in this study, including contamination mixture and Robust Adjusted Profile Score to obtain robust results. Summary-level data of individuals with European ancestry were extracted from the UK Biobank, the Kaiser GERA cohorts, and the FinnGen consortium. RESULTS Our findings revealed significant positive genetic correlations between periodontitis and kidney cancer (OR 1.287; 95% CI 1.04, 1.594; P = 0.020). We did not find a significant association of periodontitis on prostate cancer, bladder cancer, and testis cancer. In reverse MR, no significant results were observed supporting the effect of urologic cancers on periodontitis (all P > 0.05). CONCLUSION Our study provides the evidence of a potential causal relationship between periodontitis and kidney cancer. However, large-scale studies are warranted to confirm and elucidate the underlying mechanisms of this association.
Collapse
Affiliation(s)
- Bojia Li
- Health Management Center, General Practice Medical Center, Medical Device Regulatory Research and Evaluation Center, West China Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China
- West China School of Public Health, West China Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Yifei Lin
- Health Management Center, General Practice Medical Center, Medical Device Regulatory Research and Evaluation Center, West China Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Yong Yang
- Health Management Center, General Practice Medical Center, Medical Device Regulatory Research and Evaluation Center, West China Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Zeng Wang
- Engineering Research Center of Medical Information Technology, Ministry of Education, West China Hospital of Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Rui Shi
- Engineering Research Center of Medical Information Technology, Ministry of Education, West China Hospital of Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Tao Zheng
- Engineering Research Center of Medical Information Technology, Ministry of Education, West China Hospital of Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Banghua Liao
- Department of Urology, Institute of Urology (Laboratory of Reconstructive Urology), West China Hospital, Sichuan University, Chengdu, Sichuan, 610044, People's Republic of China.
| | - Ga Liao
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, People's Republic of China.
| | - Jin Huang
- Health Management Center, General Practice Medical Center, Medical Device Regulatory Research and Evaluation Center, West China Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China.
| |
Collapse
|
3
|
Wang Q, Cai B, Zhong L, Intirach J, Chen T. Causal relationship between diabetes mellitus, glycemic traits and Parkinson's disease: a multivariable mendelian randomization analysis. Diabetol Metab Syndr 2024; 16:59. [PMID: 38438892 PMCID: PMC10913216 DOI: 10.1186/s13098-024-01299-8] [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] [Received: 11/18/2023] [Accepted: 02/23/2024] [Indexed: 03/06/2024] Open
Abstract
BACKGROUND Observational studies have indicated an association between diabetes mellitus (DM), glycemic traits, and the occurrence of Parkinson's disease (PD). However, the complex interactions between these factors and the presence of a causal relationship remain unclear. Therefore, we aim to systematically assess the causal relationship between diabetes, glycemic traits, and PD onset, risk, and progression. METHOD We used two-sample Mendelian randomization (MR) to investigate potential associations between diabetes, glycemic traits, and PD. We used summary statistics from genome-wide association studies (GWAS). In addition, we employed multivariable Mendelian randomization to evaluate the mediating effects of anti-diabetic medications on the relationship between diabetes, glycemic traits, and PD. To ensure the robustness of our findings, we performed a series of sensitivity analyses. RESULTS In our univariable Mendelian randomization (MR) analysis, we found evidence of a causal relationship between genetic susceptibility to type 1 diabetes (T1DM) and a reduced risk of PD (OR = 0.9708; 95% CI: 0.9466, 0.9956; P = 0.0214). In our multivariable MR analysis, after considering the conditions of anti-diabetic drug use, this correlation disappeared with adjustment for potential mediators, including anti-diabetic medications, insulin use, and metformin use. CONCLUSION Our MR study confirms a potential protective causal relationship between genetically predicted type 1 diabetes and reduced risk of PD, which may be mediated by factors related to anti-diabetic medications.
Collapse
Affiliation(s)
- Qitong Wang
- Department of Neurology, Hainan General Hospital, Hainan Afliated Hospital of Hainan Medical University, 570311, Haikou, Hainan, China
| | - Benchi Cai
- Department of Neurology, Hainan General Hospital, Hainan Afliated Hospital of Hainan Medical University, 570311, Haikou, Hainan, China
| | - Lifan Zhong
- Department of Neurology, Hainan General Hospital, Hainan Afliated Hospital of Hainan Medical University, 570311, Haikou, Hainan, China
| | - Jitrawadee Intirach
- Department of Neurology, Hainan General Hospital, Hainan Afliated Hospital of Hainan Medical University, 570311, Haikou, Hainan, China
| | - Tao Chen
- Department of Neurology, Hainan General Hospital, Hainan Afliated Hospital of Hainan Medical University, 570311, Haikou, Hainan, China.
- Hainan Provincial Bureau of Disease Prevention and Control, 570100, Haikou, China.
| |
Collapse
|
4
|
Wang X, Zhang Z, Ding Y, Chen T, Mucci L, Albanes D, Landi MT, Caporaso NE, Lam S, Tardon A, Chen C, Bojesen SE, Johansson M, Risch A, Bickeböller H, Wichmann HE, Rennert G, Arnold S, Brennan P, McKay JD, Field JK, Shete SS, Le Marchand L, Liu G, Andrew AS, Kiemeney LA, Zienolddiny-Narui S, Behndig A, Johansson M, Cox A, Lazarus P, Schabath MB, Aldrich MC, Hung RJ, Amos CI, Lin X, Christiani DC. Impact of individual level uncertainty of lung cancer polygenic risk score (PRS) on risk stratification. Genome Med 2024; 16:22. [PMID: 38317189 PMCID: PMC10840262 DOI: 10.1186/s13073-024-01298-4] [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: 01/19/2023] [Accepted: 01/26/2024] [Indexed: 02/07/2024] Open
Abstract
BACKGROUND Although polygenic risk score (PRS) has emerged as a promising tool for predicting cancer risk from genome-wide association studies (GWAS), the individual-level accuracy of lung cancer PRS and the extent to which its impact on subsequent clinical applications remains largely unexplored. METHODS Lung cancer PRSs and confidence/credible interval (CI) were constructed using two statistical approaches for each individual: (1) the weighted sum of 16 GWAS-derived significant SNP loci and the CI through the bootstrapping method (PRS-16-CV) and (2) LDpred2 and the CI through posteriors sampling (PRS-Bayes), among 17,166 lung cancer cases and 12,894 controls with European ancestry from the International Lung Cancer Consortium. Individuals were classified into different genetic risk subgroups based on the relationship between their own PRS mean/PRS CI and the population level threshold. RESULTS Considerable variances in PRS point estimates at the individual level were observed for both methods, with an average standard deviation (s.d.) of 0.12 for PRS-16-CV and a much larger s.d. of 0.88 for PRS-Bayes. Using PRS-16-CV, only 25.0% of individuals with PRS point estimates in the lowest decile of PRS and 16.8% in the highest decile have their entire 95% CI fully contained in the lowest and highest decile, respectively, while PRS-Bayes was unable to find any eligible individuals. Only 19% of the individuals were concordantly identified as having high genetic risk (> 90th percentile) using the two PRS estimators. An increased relative risk of lung cancer comparing the highest PRS percentile to the lowest was observed when taking the CI into account (OR = 2.73, 95% CI: 2.12-3.50, P-value = 4.13 × 10-15) compared to using PRS-16-CV mean (OR = 2.23, 95% CI: 1.99-2.49, P-value = 5.70 × 10-46). Improved risk prediction performance with higher AUC was consistently observed in individuals identified by PRS-16-CV CI, and the best performance was achieved by incorporating age, gender, and detailed smoking pack-years (AUC: 0.73, 95% CI = 0.72-0.74). CONCLUSIONS Lung cancer PRS estimates using different methods have modest correlations at the individual level, highlighting the importance of considering individual-level uncertainty when evaluating the practical utility of PRS.
Collapse
Affiliation(s)
- Xinan Wang
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Harvard University, 667 Huntington Ave, Boston, MA, 02115, USA
| | - Ziwei Zhang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Yi Ding
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, USA
| | - Tony Chen
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Lorelei Mucci
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Demetrios Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Neil E Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Stephen Lam
- Department of Medicine, British Columbia Cancer Agency, University of British Columbia, Vancouver, Canada
| | - Adonina Tardon
- Faculty of Medicine, University of Oviedo and CIBERESP, Oviedo, Spain
| | - Chu Chen
- Department of Epidemiology, University of Washington School of Public Health, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Stig E Bojesen
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Copenhagen, Denmark
| | - Mattias Johansson
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Angela Risch
- Department of Biosciences and Medical Biology, Allergy-Cancer-BioNano Research Centre, University of Salzburg, and Cancer Cluster Salzburg, Salzburg, Austria
| | - Heike Bickeböller
- Department of Genetic Epidemiology, University Medical Center, Georg August University Göttingen, Göttingen, Germany
| | - H-Erich Wichmann
- Institute of Medical Informatics, Biometry and Epidemiology, Ludwig Maximilians University, Munich, Germany
| | - Gadi Rennert
- Clalit National Cancer Control Center, Carmel Medical Center and Technion Faculty of Medicine, Carmel, Haifa, Israel
| | - Susanne Arnold
- Markey Cancer Center, University of Kentucky, Lexington, KY, USA
| | - Paul Brennan
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - James D McKay
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - John K Field
- Department of Molecular and Clinical Cancer Medicine, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Sanjay S Shete
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Geoffrey Liu
- Princess Margaret Cancer Centre, Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
| | - Angeline S Andrew
- Department of Epidemiology, Department of Community and Family Medicine, Dartmouth Geisel School of Medicine, Hanover, NH, USA
| | - Lambertus A Kiemeney
- Department for Health Evidence, Department of Urology, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Annelie Behndig
- Department of Public Health and Clinical Medicine, Umeå University, Umeå, Sweden
| | | | - Angie Cox
- Department of Oncology and Metabolism, The Medical School, University of Sheffield, Sheffield, UK
| | - Philip Lazarus
- Department of Pharmaceutical Sciences, College of Pharmacy, Washington State University, Spokane, WA, USA
| | - Matthew B Schabath
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Melinda C Aldrich
- Department of Medicine, Department of Biomedical Informatics and Department of Thoracic Surgery, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Rayjean J Hung
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Christopher I Amos
- Institute for Clinical and Translational Research, Department of Medicine, Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Xihong Lin
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - David C Christiani
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Harvard University, 667 Huntington Ave, Boston, MA, 02115, USA.
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA.
| |
Collapse
|
5
|
Yarmolinsky J, Robinson JW, Mariosa D, Karhunen V, Huang J, Dimou N, Murphy N, Burrows K, Bouras E, Smith-Byrne K, Lewis SJ, Galesloot TE, Kiemeney LA, Vermeulen S, Martin P, Albanes D, Hou L, Newcomb PA, White E, Wolk A, Wu AH, Le Marchand L, Phipps AI, Buchanan DD, Zhao SS, Gill D, Chanock SJ, Purdue MP, Davey Smith G, Brennan P, Herzig KH, Järvelin MR, Amos CI, Hung RJ, Dehghan A, Johansson M, Gunter MJ, Tsilidis KK, Martin RM. Association between circulating inflammatory markers and adult cancer risk: a Mendelian randomization analysis. EBioMedicine 2024; 100:104991. [PMID: 38301482 PMCID: PMC10844944 DOI: 10.1016/j.ebiom.2024.104991] [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: 09/21/2023] [Revised: 01/15/2024] [Accepted: 01/17/2024] [Indexed: 02/03/2024] Open
Abstract
BACKGROUND Tumour-promoting inflammation is a "hallmark" of cancer and conventional epidemiological studies have reported links between various inflammatory markers and cancer risk. The causal nature of these relationships and, thus, the suitability of these markers as intervention targets for cancer prevention is unclear. METHODS We meta-analysed 6 genome-wide association studies of circulating inflammatory markers comprising 59,969 participants of European ancestry. We then used combined cis-Mendelian randomization and colocalisation analysis to evaluate the causal role of 66 circulating inflammatory markers in risk of 30 adult cancers in 338,294 cancer cases and up to 1,238,345 controls. Genetic instruments for inflammatory markers were constructed using genome-wide significant (P < 5.0 × 10-8) cis-acting SNPs (i.e., in or ±250 kb from the gene encoding the relevant protein) in weak linkage disequilibrium (LD, r2 < 0.10). Effect estimates were generated using inverse-variance weighted random-effects models and standard errors were inflated to account for weak LD between variants with reference to the 1000 Genomes Phase 3 CEU panel. A false discovery rate (FDR)-corrected P-value ("q-value") <0.05 was used as a threshold to define "strong evidence" to support associations and 0.05 ≤ q-value < 0.20 to define "suggestive evidence". A colocalisation posterior probability (PPH4) >70% was employed to indicate support for shared causal variants across inflammatory markers and cancer outcomes. Findings were replicated in the FinnGen study and then pooled using meta-analysis. FINDINGS We found strong evidence to support an association of genetically-proxied circulating pro-adrenomedullin concentrations with increased breast cancer risk (OR: 1.19, 95% CI: 1.10-1.29, q-value = 0.033, PPH4 = 84.3%) and suggestive evidence to support associations of interleukin-23 receptor concentrations with increased pancreatic cancer risk (OR: 1.42, 95% CI: 1.20-1.69, q-value = 0.055, PPH4 = 73.9%), prothrombin concentrations with decreased basal cell carcinoma risk (OR: 0.66, 95% CI: 0.53-0.81, q-value = 0.067, PPH4 = 81.8%), and interleukin-1 receptor-like 1 concentrations with decreased triple-negative breast cancer risk (OR: 0.92, 95% CI: 0.88-0.97, q-value = 0.15, PPH4 = 85.6%). These findings were replicated in pooled analyses with the FinnGen study. Though suggestive evidence was found to support an association of macrophage migration inhibitory factor concentrations with increased bladder cancer risk (OR: 2.46, 95% CI: 1.48-4.10, q-value = 0.072, PPH4 = 76.1%), this finding was not replicated when pooled with the FinnGen study. For 22 of 30 cancer outcomes examined, there was little evidence (q-value ≥0.20) that any of the 66 circulating inflammatory markers examined were associated with cancer risk. INTERPRETATION Our comprehensive joint Mendelian randomization and colocalisation analysis of the role of circulating inflammatory markers in cancer risk identified potential roles for 4 circulating inflammatory markers in risk of 4 site-specific cancers. Contrary to reports from some prior conventional epidemiological studies, we found little evidence of association of circulating inflammatory markers with the majority of site-specific cancers evaluated. FUNDING Cancer Research UK (C68933/A28534, C18281/A29019, PPRCPJT∖100005), World Cancer Research Fund (IIG_FULL_2020_022), National Institute for Health Research (NIHR202411, BRC-1215-20011), Medical Research Council (MC_UU_00011/1, MC_UU_00011/3, MC_UU_00011/6, and MC_UU_00011/4), Academy of Finland Project 326291, European Union's Horizon 2020 grant agreement no. 848158 (EarlyCause), French National Cancer Institute (INCa SHSESP20, 2020-076), Versus Arthritis (21173, 21754, 21755), National Institutes of Health (U19 CA203654), National Cancer Institute (U19CA203654).
Collapse
Affiliation(s)
- James Yarmolinsky
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK; Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK; Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, St Mary's Campus, London, UK.
| | - Jamie W Robinson
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK; Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Daniela Mariosa
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Ville Karhunen
- Research Unit of Population Health, Faculty of Medicine, University of Oulu, Oulu, Finland; Research Unit of Mathematical Sciences, University of Oulu, Oulu, Finland
| | - Jian Huang
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, St Mary's Campus, London, UK; Singapore Institute for Clinical Sciences (SICS), Agency for Science, Technology and Research (A∗STAR), Singapore, Singapore
| | - Niki Dimou
- Nutrition and Metabolism Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Neil Murphy
- Nutrition and Metabolism Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Kimberley Burrows
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK; Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Emmanouil Bouras
- Department of Hygiene and Epidemiology, University of Ioannina School of Medicine, Ioannina, Greece
| | - Karl Smith-Byrne
- The Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Sarah J Lewis
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK; Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | | | | | - Sita Vermeulen
- Department for Health Evidence, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Paul Martin
- School of Biochemistry, Biomedical Sciences Building, University of Bristol, University Walk, Bristol, UK
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lifang Hou
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Polly A Newcomb
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; School of Public Health, University of Washington, Seattle, WA, USA
| | - Emily White
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Department of Epidemiology, University of Washington School of Public Health, Seattle, WA, USA
| | - Alicja Wolk
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Anna H Wu
- University of Southern California, Preventative Medicine, Los Angeles, CA, USA
| | - Loïc Le Marchand
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI 96813, USA
| | - Amanda I Phipps
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Department of Epidemiology, University of Washington School of Public Health, Seattle, WA, USA
| | - Daniel D Buchanan
- Colorectal Oncogenomic Group, Department of Clinical Pathology, University of Melbourne, Parkville, Victoria, Australia; Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Parkville, Victoria, Australia; Genetic Medicine and Family Clinic, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Sizheng Steven Zhao
- Centre for Epidemiology Versus Arthritis, Faculty of Biological Medicine and Health, University of Manchester, Manchester, UK
| | - Dipender Gill
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, St Mary's Campus, London, UK
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Mark P Purdue
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - George Davey Smith
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK; Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Paul Brennan
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Karl-Heinz Herzig
- Institute of Biomedicine, Medical Research Center and Oulu University Hospital, University of Oulu, Oulu, Finland; Department of Pediatric Gastroenterology and Metabolic Diseases, Poznan University of Medical Sciences, Poznan, Poland
| | - Marjo-Riitta Järvelin
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France; Department of Epidemiology and Biostatistics, MRC Centre for Environment and Health, School of Public Health, Imperial College London, London, UK; Unit of Primary Health Care, Oulu University Hospital, OYS, Oulu, Finland; Department of Life Sciences, College of Health and Life Sciences, Brunel University London, London, UK
| | - Chris I Amos
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Rayjean J Hung
- Prosserman Centre for Population Health Research, Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Canada; Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
| | - Abbas Dehghan
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, St Mary's Campus, London, UK; Dementia Research Institute, Imperial College London, London, UK
| | - Mattias Johansson
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Marc J Gunter
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, St Mary's Campus, London, UK; Nutrition and Metabolism Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Kostas K Tsilidis
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, St Mary's Campus, London, UK; Department of Hygiene and Epidemiology, University of Ioannina School of Medicine, Ioannina, Greece
| | - Richard M Martin
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK; Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK; University Hospitals Bristol and Weston NHS Foundation Trust, National Institute for Health Research Bristol Biomedical Research Centre, University of Bristol, Bristol, UK
| |
Collapse
|
6
|
Wang Y, Pan L, He H, Li Z, Cui S, Yang A, Li W, Jia G, Han X, Wang X, Shan G. Prevalence, associated factors, and gene polymorphisms of obesity in Tibetan adults in Qinghai, China. BMC Public Health 2024; 24:305. [PMID: 38279121 PMCID: PMC10811834 DOI: 10.1186/s12889-023-17181-7] [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: 07/03/2023] [Accepted: 11/07/2023] [Indexed: 01/28/2024] Open
Abstract
OBJECTIVES To explore the prevalence and associated factors of obesity in Tibetan adults in Qinghai, China, and to determine the association between the FTO (rs1121980 and rs17817449) and MC4R gene (rs17782313 and rs12970134) polymorphisms with obesity. METHODS A cross-sectional survey was conducted in 2015 in Qinghai to selected Tibetan adults aged 20 to 80 years. Prevalence of obesity (BMI ≥ 28 kg/m2) and overweight (BMI 24 ~ 27.9 kg/m2) were evaluated. Multivariable logistic models were used to determine the associated factors. Pair-matched subjects of obesity cases and normal-weight controls were selected for the gene polymorphism analyses. Conditional logistic models were used to assess the association between gene polymorphisms with obesity. Additive and multiplicative gene-environment interactions were tested. RESULTS A total of 1741 Tibetan adults were enrolled. The age- and sex- standardized prevalence of obesity and overweight was 18.09% and 31.71%, respectively. Male sex, older age, heavy level of leisure-time exercise, current smoke, and heavy level of occupational physical activity were associated with both obesity and overweight. MC4R gene polymorphisms were associated with obesity in Tibetan adults. No significant gene-environment interaction was detected. CONCLUSION The prevalence of obesity and overweight in Tibetan adults was high. Both environmental and genetic factors contributed to the obesity prevalent.
Collapse
Affiliation(s)
- Ye Wang
- School of Population Medicine and Public Health, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Li Pan
- Department of Epidemiology and Statistics, Institute of Basic Medical Sciences, School of Basic Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, 5 Dong Dan San Tiao, Dong Cheng District, Beijing, 100005, China
| | - Huijing He
- Department of Epidemiology and Statistics, Institute of Basic Medical Sciences, School of Basic Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, 5 Dong Dan San Tiao, Dong Cheng District, Beijing, 100005, China
| | - Zhanquan Li
- Qinghai University Affiliated Hospital, Qinghai, China
| | - Sen Cui
- Qinghai University Affiliated Hospital, Qinghai, China
| | - Airong Yang
- Qinghai University Affiliated Hospital, Qinghai, China
| | - Wenfang Li
- Qinghai University Affiliated Hospital, Qinghai, China
| | - Guoqiang Jia
- Qinghai University Affiliated Hospital, Qinghai, China
| | - Ximing Han
- Qinghai University Affiliated Hospital, Qinghai, China
| | - Xianghua Wang
- Institute of Biomedical Engineering, Chinese Academy of Medical Sciences, Peking Union Medical College, 236 Baidi Road, Nankai District, Tianjin, 300192, China.
| | - Guangliang Shan
- School of Population Medicine and Public Health, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
- Department of Epidemiology and Statistics, Institute of Basic Medical Sciences, School of Basic Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, 5 Dong Dan San Tiao, Dong Cheng District, Beijing, 100005, China.
| |
Collapse
|
7
|
Paz V, Dashti HS, Burgess S, Garfield V. Selection of genetic instruments in Mendelian randomisation studies of sleep traits. Sleep Med 2023; 112:342-351. [PMID: 37956646 PMCID: PMC7615498 DOI: 10.1016/j.sleep.2023.10.036] [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: 05/17/2023] [Revised: 10/22/2023] [Accepted: 10/30/2023] [Indexed: 11/15/2023]
Abstract
This review explores the criteria used for the selection of genetic instruments of sleep traits in the context of Mendelian randomisation studies. This work was motivated by the fact that instrument selection is the most important decision when designing a Mendelian randomisation study. As far as we are aware, no review has sought to address this to date, even though the number of these studies is growing rapidly. The review is divided into the following sections which are essential for genetic instrument selection: 1) Single-gene region vs polygenic analysis; 2) Polygenic analysis: biologically-vs statistically-driven approaches; 3) P-value; 4) Linkage disequilibrium clumping; 5) Sample overlap; 6) Type of exposure; 7) Total (R2) and average strength (F-statistic) metrics; 8) Number of single-nucleotide polymorphisms; 9) Minor allele frequency and palindromic variants; 10) Confounding. Our main aim is to discuss how instrumental choice impacts analysis and compare the strategies that Mendelian randomisation studies of sleep traits have used. We hope that our review will enable more researchers to take a more considered approach when selecting genetic instruments for sleep exposures.
Collapse
Affiliation(s)
- Valentina Paz
- Instituto de Psicología Clínica, Facultad de Psicología, Universidad de la República, Tristán Narvaja, 1674, Montevideo, 11200, Uruguay; MRC Unit for Lifelong Health & Ageing, Institute of Cardiovascular Science, University College London, 1-19 Torrington Place, London, WC1E 7HB, UK.
| | - Hassan S Dashti
- Center for Genomic Medicine, Massachusetts General Hospital and Harvard Medical School, 185 Cambridge Street, Boston, MA, 02114, USA; Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA; Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital and Harvard Medical School, 55 Fruit Street, Edwards 4-410C, Boston, MA, 02114, USA
| | - Stephen Burgess
- MRC Biostatistics Unit, University of Cambridge, Forvie Site, Robinson Way, Cambridge, CB2 0SR, UK; Department of Public Health and Primary Care, University of Cambridge, Forvie Site, Robinson Way, Cambridge, CB2 0SR, UK
| | - Victoria Garfield
- MRC Unit for Lifelong Health & Ageing, Institute of Cardiovascular Science, University College London, 1-19 Torrington Place, London, WC1E 7HB, UK
| |
Collapse
|
8
|
Chen S, Guo Z, Yu Q. Genetic evidence for the causal association between type 1 diabetes and the risk of polycystic ovary syndrome. Hum Genomics 2023; 17:100. [PMID: 37957681 PMCID: PMC10641977 DOI: 10.1186/s40246-023-00550-z] [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: 09/19/2023] [Accepted: 11/07/2023] [Indexed: 11/15/2023] Open
Abstract
BACKGROUND Accumulating observational studies have identified associations between type 1 diabetes (T1D) and polycystic ovary syndrome (PCOS). Still, the evidence about the causal effect of this association is uncertain. METHODS We performed a two-sample Mendelian randomization (MR) analysis to test for the causal association between T1D and PCOS using data from a large-scale biopsy-confirmed genome-wide association study (GWAS) in European ancestries. We innovatively divided T1D into nine subgroups to be analyzed separately, including: type1 diabetes wide definition, type1 diabetes early onset, type 1 diabetes with coma, type 1 diabetes with ketoacidosis, type 1 diabetes with neurological complications, type 1 diabetes with ophthalmic complications, type 1 diabetes with peripheral circulatory complications, type 1 diabetes with renal complications, and type 1 diabetes with other specified/multiple/unspecified complications. GWAS data for PCOS were obtained from a large-scale GWAS (10,074 cases and 103,164 controls) for primary analysis and the IEU consortium for replication and meta-analysis. Sensitivity analyses were conducted to evaluate heterogeneity and pleiotropy. RESULTS Following rigorous instrument selection steps, the number of SNPs finally used for T1D nine subgroups varying from 6 to 36 was retained in MR estimation. However, we did not observe evidence of causal association between type 1 diabetes nine subgroups and PCOS using the IVW analysis, MR-Egger regression, and weighted median approaches, and all P values were > 0.05 with ORs near 1. Subsequent replicates and meta-analyses also yielded consistent results. A number of sensitivity analyses also did not reveal heterogeneity and pleiotropy, including Cochran's Q test, MR-Egger intercept test, MR-PRESSO global test, leave-one-out analysis, and funnel plot analysis. CONCLUSION This is the first MR study to investigate the causal relationship between type 1 diabetes and PCOS. Our findings failed to find substantial causal effect of type 1 diabetes on risk of PCOS. Further randomized controlled studies and MR studies are necessary.
Collapse
Affiliation(s)
- Shuwen Chen
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetric and Gynecologic Diseases, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Peking Union Medical College Hospital (Dongdan Campus), No.1 Shuaifuyuan Wangfujing Dongcheng District, Beijing, 100730, China
| | - Zaixin Guo
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetric and Gynecologic Diseases, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Peking Union Medical College Hospital (Dongdan Campus), No.1 Shuaifuyuan Wangfujing Dongcheng District, Beijing, 100730, China
| | - Qi Yu
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetric and Gynecologic Diseases, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Peking Union Medical College Hospital (Dongdan Campus), No.1 Shuaifuyuan Wangfujing Dongcheng District, Beijing, 100730, China.
| |
Collapse
|
9
|
Burgess S. Violation of the Constant Genetic Effect Assumption Can Result in Biased Estimates for Non-Linear Mendelian Randomization. Hum Hered 2023; 88:79-90. [PMID: 37651993 PMCID: PMC10614256 DOI: 10.1159/000531659] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [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: 12/12/2022] [Accepted: 06/12/2023] [Indexed: 09/02/2023] Open
Abstract
INTRODUCTION Non-linear Mendelian randomization is an extension of conventional Mendelian randomization that performs separate instrumental variable analyses in strata of the study population with different average levels of the exposure. The approach estimates a localized average causal effect function, representing the average causal effect of the exposure on the outcome at different levels of the exposure. The commonly used residual method for dividing the population into strata works under the assumption that the effect of the genetic instrument on the exposure is linear and constant in the study population. However, this assumption may not hold in practice. METHODS We use the recently developed doubly ranked method to re-analyse various datasets previously analysed using the residual method. In particular, we consider a genetic score for 25-hydroxyvitamin D (25[OH]D) used in a recent non-linear Mendelian randomization analysis to assess the potential effect of vitamin D supplementation on all-cause mortality. RESULTS The effect of the genetic score on 25(OH)D concentrations varies strongly, with a five-fold difference in the estimated genetic association with the exposure in the lowest and highest decile groups. Evidence for a protective causal effect of vitamin D supplementation on all-cause mortality in low vitamin D individuals is evident for the residual method but not for the doubly ranked method. We show that the constant genetic effect assumption is more reasonable for some exposures and less reasonable for others. If the doubly ranked method indicates that this assumption is violated, then estimates from both the residual and doubly ranked methods can be biased, although bias was smaller on average in the doubly ranked method. CONCLUSION Analysts wanting to perform non-linear Mendelian randomization should compare results from both the residual and doubly ranked methods, as well as consider transforming the exposure for the residual method to reduce heterogeneity in the genetic effect on the exposure.
Collapse
Affiliation(s)
- Stephen Burgess
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
- Department of Public Health and Primary Care, Cardiovascular Epidemiology Unit, University of Cambridge, Cambridge, UK
| |
Collapse
|
10
|
Middha P, Wang X, Behrens S, Bolla MK, Wang Q, Dennis J, Michailidou K, Ahearn TU, Andrulis IL, Anton-Culver H, Arndt V, Aronson KJ, Auer PL, Augustinsson A, Baert T, Freeman LEB, Becher H, Beckmann MW, Benitez J, Bojesen SE, Brauch H, Brenner H, Brooks-Wilson A, Campa D, Canzian F, Carracedo A, Castelao JE, Chanock SJ, Chenevix-Trench G, Cordina-Duverger E, Couch FJ, Cox A, Cross SS, Czene K, Dossus L, Dugué PA, Eliassen AH, Eriksson M, Evans DG, Fasching PA, Figueroa JD, Fletcher O, Flyger H, Gabrielson M, Gago-Dominguez M, Giles GG, González-Neira A, Grassmann F, Grundy A, Guénel P, Haiman CA, Håkansson N, Hall P, Hamann U, Hankinson SE, Harkness EF, Holleczek B, Hoppe R, Hopper JL, Houlston RS, Howell A, Hunter DJ, Ingvar C, Isaksson K, Jernström H, John EM, Jones ME, Kaaks R, Keeman R, Kitahara CM, Ko YD, Koutros S, Kurian AW, Lacey JV, Lambrechts D, Larson NL, Larsson S, Le Marchand L, Lejbkowicz F, Li S, Linet M, Lissowska J, Martinez ME, Maurer T, Mulligan AM, Mulot C, Murphy RA, Newman WG, Nielsen SF, Nordestgaard BG, Norman A, O'Brien KM, Olson JE, Patel AV, Prentice R, Rees-Punia E, Rennert G, Rhenius V, Ruddy KJ, Sandler DP, Scott CG, Shah M, Shu XO, Smeets A, Southey MC, Stone J, Tamimi RM, Taylor JA, Teras LR, Tomczyk K, Troester MA, Truong T, Vachon CM, Wang SS, Weinberg CR, Wildiers H, Willett W, Winham SJ, Wolk A, Yang XR, Zamora MP, Zheng W, Ziogas A, Dunning AM, Pharoah PDP, García-Closas M, Schmidt MK, Kraft P, Milne RL, Lindström S, Easton DF, Chang-Claude J. A genome-wide gene-environment interaction study of breast cancer risk for women of European ancestry. Breast Cancer Res 2023; 25:93. [PMID: 37559094 PMCID: PMC10411002 DOI: 10.1186/s13058-023-01691-8] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 07/27/2023] [Indexed: 08/11/2023] Open
Abstract
BACKGROUND Genome-wide studies of gene-environment interactions (G×E) may identify variants associated with disease risk in conjunction with lifestyle/environmental exposures. We conducted a genome-wide G×E analysis of ~ 7.6 million common variants and seven lifestyle/environmental risk factors for breast cancer risk overall and for estrogen receptor positive (ER +) breast cancer. METHODS Analyses were conducted using 72,285 breast cancer cases and 80,354 controls of European ancestry from the Breast Cancer Association Consortium. Gene-environment interactions were evaluated using standard unconditional logistic regression models and likelihood ratio tests for breast cancer risk overall and for ER + breast cancer. Bayesian False Discovery Probability was employed to assess the noteworthiness of each SNP-risk factor pairs. RESULTS Assuming a 1 × 10-5 prior probability of a true association for each SNP-risk factor pairs and a Bayesian False Discovery Probability < 15%, we identified two independent SNP-risk factor pairs: rs80018847(9p13)-LINGO2 and adult height in association with overall breast cancer risk (ORint = 0.94, 95% CI 0.92-0.96), and rs4770552(13q12)-SPATA13 and age at menarche for ER + breast cancer risk (ORint = 0.91, 95% CI 0.88-0.94). CONCLUSIONS Overall, the contribution of G×E interactions to the heritability of breast cancer is very small. At the population level, multiplicative G×E interactions do not make an important contribution to risk prediction in breast cancer.
Collapse
Affiliation(s)
- Pooja Middha
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - Xiaoliang Wang
- Department of Epidemiology, University of Washington School of Public Health, Seattle, WA, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Sabine Behrens
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Manjeet K Bolla
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Qin Wang
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Joe Dennis
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Kyriaki Michailidou
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
- Biostatistics Unit, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Thomas U Ahearn
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Irene L Andrulis
- Fred A. Litwin Center for Cancer Genetics, Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Hoda Anton-Culver
- Department of Medicine, Genetic Epidemiology Research Institute, University of California Irvine, Irvine, CA, USA
| | - Volker Arndt
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Kristan J Aronson
- Department of Public Health Sciences, and Cancer Research Institute, Queen's University, Kingston, ON, Canada
| | - Paul L Auer
- Division of Biostatistics, Institute for Health and Equity, and Cancer Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | | | - Thaïs Baert
- Department of Oncology, Leuven Multidisciplinary Breast Center, Leuven Cancer Institute, University Hospitals Leuven, Leuven, Belgium
| | - Laura E Beane Freeman
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Heiko Becher
- Institute of Medical Biometry and Epidemiology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Matthias W Beckmann
- Department of Gynecology and Obstetrics, Comprehensive Cancer Center Erlangen-EMN, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Javier Benitez
- Human Genetics Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Stig E Bojesen
- Copenhagen General Population Study, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Hiltrud Brauch
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany
- iFIT-Cluster of Excellence, University of Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Site Tübingen, Tübingen, Germany
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Daniele Campa
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Biology, University of Pisa, Pisa, Italy
| | - Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Angel Carracedo
- Genomic Medicine Group, International Cancer Genetics and Epidemiology Group, Fundación Pública Galega de Medicina Xenómica, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago, SERGAS, Santiago de Compostela, Spain
- Grupo de Medicina Xenómica, Centro de Investigación en Red de Enfermedades Raras (CIBERER) y Centro Nacional de Genotipado (CEGEN-PRB2), Universidad de Santiago de Compostela, Santiago de Compostela, Spain
| | - Jose E Castelao
- Oncology and Genetics Unit, Instituto de Investigación Sanitaria Galicia Sur (IISGS), Xerencia de Xestion Integrada de Vigo-SERGAS, Vigo, Spain
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Georgia Chenevix-Trench
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Emilie Cordina-Duverger
- Team 'Exposome and Heredity', CESP, Gustave Roussy, INSERM, University Paris-Saclay, UVSQ, Villejuif, France
| | - Fergus J Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Angela Cox
- Department of Oncology and Metabolism, Sheffield Institute for Nucleic Acids (SInFoNiA), University of Sheffield, Sheffield, UK
| | - Simon S Cross
- Academic Unit of Pathology, Department of Neuroscience, University of Sheffield, Sheffield, UK
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Laure Dossus
- Nutrition and Metabolism Section, International Agency for Research on Cancer (IARC-WHO), Lyon, France
| | - Pierre-Antoine Dugué
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia
| | - A Heather Eliassen
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Mikael Eriksson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - D Gareth Evans
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, School of Biological Sciences, University of Manchester, Manchester, UK
- North West Genomics Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester Academic Health Science Centre, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Peter A Fasching
- Department of Gynecology and Obstetrics, Comprehensive Cancer Center Erlangen-EMN, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Jonine D Figueroa
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Usher Institute of Population Health Sciences and Informatics, The University of Edinburgh, Edinburgh, UK
- Cancer Research UK Edinburgh Centre, The University of Edinburgh, Edinburgh, UK
| | - Olivia Fletcher
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Henrik Flyger
- Department of Breast Surgery, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
| | - Marike Gabrielson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Manuela Gago-Dominguez
- Genomic Medicine Group, International Cancer Genetics and Epidemiology Group, Fundación Pública Galega de Medicina Xenómica, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago, SERGAS, Santiago de Compostela, Spain
| | - Graham G Giles
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC, Australia
| | - Anna González-Neira
- Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Felix Grassmann
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Institute for Clinical Research and Systems Medicine, Health and Medical University, Potsdam, Germany
| | - Anne Grundy
- Department of Public Health Sciences, Queen's University, Kingston, ON, Canada
| | - Pascal Guénel
- Team 'Exposome and Heredity', CESP, Gustave Roussy, INSERM, University Paris-Saclay, UVSQ, Villejuif, France
| | - Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Niclas Håkansson
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Oncology, Södersjukhuset, Stockholm, Sweden
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Susan E Hankinson
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biostatistics and Epidemiology, University of Massachusetts, Amherst, Amherst, MA, USA
| | - Elaine F Harkness
- Division of Informatics, Imaging and Data Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
- Nightingale and Genesis Prevention Centre, Wythenshawe Hospital, Manchester University NHS Foundation Trust, Manchester, UK
- NIHR Manchester Biomedical Research Unit, Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust, Manchester, UK
| | | | - Reiner Hoppe
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany
- University of Tübingen, Tübingen, Germany
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC, Australia
| | - Richard S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Anthony Howell
- Division of Cancer Sciences, University of Manchester, Manchester, UK
| | - David J Hunter
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Christian Ingvar
- Surgery, Clinical Sciences in Lund, Lund University, Lund, Sweden
| | - Karolin Isaksson
- Department of Surgery, Kristianstad Hospital, Kristianstad, Sweden
| | - Helena Jernström
- Oncology, Clinical Sciences in Lund, Lund University, Lund, Sweden
| | - Esther M John
- Department of Epidemiology and Population Health, Stanford University School of Medicine, Stanford, CA, USA
- Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael E Jones
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Rudolf Kaaks
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Renske Keeman
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Cari M Kitahara
- Radiation Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Yon-Dschun Ko
- Department of Internal Medicine, Johanniter GmbH Bonn, Johanniter Krankenhaus, Bonn, Germany
| | - Stella Koutros
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Allison W Kurian
- Department of Epidemiology and Population Health, Stanford University School of Medicine, Stanford, CA, USA
- Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - James V Lacey
- Department of Computational and Quantitative Medicine, City of Hope, Duarte, CA, USA
- City of Hope Comprehensive Cancer Center, City of Hope, Duarte, CA, USA
| | - Diether Lambrechts
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
- VIB Center for Cancer Biology, VIB, Leuven, Belgium
| | - Nicole L Larson
- Department of Quantitative Health Sciences, Division of Epidemiology, Mayo Clinic, Rochester, MN, USA
| | - Susanna Larsson
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Flavio Lejbkowicz
- Clalit National Cancer Control Center, Carmel Medical Center and Technion Faculty of Medicine, Haifa, Israel
| | - Shuai Li
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC, Australia
| | - Martha Linet
- Radiation Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Jolanta Lissowska
- Department of Cancer Epidemiology and Prevention, M. Sklodowska-Curie National Research Oncology Institute, Warsaw, Poland
| | - Maria Elena Martinez
- Moores Cancer Center and Herbert Wertheim School of Public Health and Human Longevity Science, University of California, San Diego, La Jolla, CA, USA
| | - Tabea Maurer
- Cancer Epidemiology Group, University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Anna Marie Mulligan
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Laboratory Medicine Program, University Health Network, Toronto, ON, Canada
| | - Claire Mulot
- INSERM UMR-S1138. CRB EPIGENETEC, Université Paris Cité, Paris, France
| | - Rachel A Murphy
- School of Population and Public Health, University of British Columbia, Vancouver, BC, Canada
- Cancer Control Research, BC Cancer, Vancouver, BC, Canada
| | - William G Newman
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, School of Biological Sciences, University of Manchester, Manchester, UK
- North West Genomics Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester Academic Health Science Centre, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Sune F Nielsen
- Copenhagen General Population Study, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
| | - Børge G Nordestgaard
- Copenhagen General Population Study, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Aaron Norman
- Department of Quantitative Health Sciences, Division of Epidemiology, Mayo Clinic, Rochester, MN, USA
| | - Katie M O'Brien
- Epidemiology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Janet E Olson
- Department of Quantitative Health Sciences, Division of Epidemiology, Mayo Clinic, Rochester, MN, USA
| | - Alpa V Patel
- Department of Population Science, American Cancer Society, Atlanta, GA, USA
| | - Ross Prentice
- Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Erika Rees-Punia
- Department of Population Science, American Cancer Society, Atlanta, GA, USA
| | - Gad Rennert
- Clalit National Cancer Control Center, Carmel Medical Center and Technion Faculty of Medicine, Haifa, Israel
| | - Valerie Rhenius
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | | | - Dale P Sandler
- Epidemiology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Christopher G Scott
- Department of Quantitative Health Sciences, Division of Clinical Trials and Biostatistics, Mayo Clinic, Rochester, MN, USA
| | - Mitul Shah
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Ann Smeets
- Department of Surgical Oncology, University Hospitals Leuven, Leuven, Belgium
| | - Melissa C Southey
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia
- Department of Clinical Pathology, The University of Melbourne, Melbourne, VIC, Australia
| | - Jennifer Stone
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC, Australia
- Genetic Epidemiology Group, School of Population and Global Health, University of Western Australia, Perth, WA, Australia
| | - Rulla M Tamimi
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Population Health Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Jack A Taylor
- Epidemiology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
- Epigenetic and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Lauren R Teras
- Department of Population Science, American Cancer Society, Atlanta, GA, USA
| | - Katarzyna Tomczyk
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Melissa A Troester
- Department of Epidemiology, Gillings School of Global Public Health and UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Thérèse Truong
- Team 'Exposome and Heredity', CESP, Gustave Roussy, INSERM, University Paris-Saclay, UVSQ, Villejuif, France
| | - Celine M Vachon
- Department of Quantitative Health Sciences, Division of Epidemiology, Mayo Clinic, Rochester, MN, USA
| | - Sophia S Wang
- Department of Computational and Quantitative Medicine, City of Hope, Duarte, CA, USA
- City of Hope Comprehensive Cancer Center, City of Hope, Duarte, CA, USA
| | - Clarice R Weinberg
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Hans Wildiers
- Department of Oncology, Leuven Multidisciplinary Breast Center, Leuven Cancer Institute, University Hospitals Leuven, Leuven, Belgium
| | - Walter Willett
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Stacey J Winham
- Division of Computational Biology, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Alicja Wolk
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Xiaohong R Yang
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - M Pilar Zamora
- Servicio de Oncología Médica, Hospital Universitario La Paz, Madrid, Spain
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Argyrios Ziogas
- Department of Medicine, Genetic Epidemiology Research Institute, University of California Irvine, Irvine, CA, USA
| | - Alison M Dunning
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Paul D P Pharoah
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Montserrat García-Closas
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Marjanka K Schmidt
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Division of Psychosocial Research and Epidemiology, The Netherlands Cancer Institute - Antoni Van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Peter Kraft
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Roger L Milne
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC, Australia
| | - Sara Lindström
- Department of Epidemiology, University of Washington School of Public Health, Seattle, WA, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Douglas F Easton
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Cancer Epidemiology Group, University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| |
Collapse
|
11
|
Hu C, Zhou Y, Wu X, Jia X, Zhu Y, Zheng R, Wang S, Lin L, Qi H, Lin H, Li M, Wang T, Zhao Z, Xu M, Xu Y, Chen Y, Ning G, Borges MC, Wang W, Zheng J, Bi Y, Lu J. Evaluating the distinct pleiotropic effects of omega-3 fatty acids on type 2 diabetes mellitus: a mendelian randomization study. J Transl Med 2023; 21:370. [PMID: 37286992 DOI: 10.1186/s12967-023-04202-7] [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: 03/16/2023] [Accepted: 05/14/2023] [Indexed: 06/09/2023] Open
Abstract
BACKGROUND Observational studies and conventional Mendelian randomization (MR) studies showed inconclusive evidence to support the association between omega-3 fatty acids and type 2 diabetes. We aim to evaluate the causal effect of omega-3 fatty acids on type 2 diabetes mellitus (T2DM), and the distinct intermediate phenotypes linking the two. METHODS Two-sample MR was performed using genetic instruments derived from a recent genome-wide association study (GWAS) of omega-3 fatty acids (N = 114,999) from UK Biobank and outcome data obtained from a large-scale T2DM GWAS (62,892 cases and 596,424 controls) in European ancestry. MR-Clust was applied to determine clustered genetic instruments of omega-3 fatty acids that influences T2DM. Two-step MR analysis was used to identify potential intermediate phenotypes (e.g. glycemic traits) that linking omega-3 fatty acids with T2DM. RESULTS Univariate MR showed heterogenous effect of omega-3 fatty acids on T2DM. At least two pleiotropic effects between omega-3 fatty acids and T2DM were identified using MR-Clust. For cluster 1 with seven instruments, increasing omega-3 fatty acids reduced T2DM risk (OR: 0.52, 95%CI 0.45-0.59), and decreased HOMA-IR (β = - 0.13, SE = 0.05, P = 0.02). On the contrary, MR analysis using 10 instruments in cluster 2 showed that increasing omega-3 fatty acids increased T2DM risk (OR:1.10; 95%CI 1.06-1.15), and decreased HOMA-B (β = - 0.04, SE = 0.01, P = 4.52 × 10-5). Two-step MR indicated that increasing omega-3 fatty acid levels decreased T2DM risk via decreasing HOMA-IR in cluster 1, while increased T2DM risk via decreasing HOMA-B in cluster 2. CONCLUSIONS This study provides evidence to support two distinct pleiotropic effects of omega-3 fatty acids on T2DM risk influenced by different gene clusters, which could be partially explained by distinct effects of omega-3 fatty acids on insulin resistance and beta cell dysfunction. The pleiotropic feature of omega-3 fatty acids variants and its complex relationships with T2DM need to be carefully considered in future genetic and clinical studies.
Collapse
Affiliation(s)
- Chunyan Hu
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Rui Jin 2nd Road, Shanghai, 200025, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yulin Zhou
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Rui Jin 2nd Road, Shanghai, 200025, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xueyan Wu
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Rui Jin 2nd Road, Shanghai, 200025, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaojing Jia
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Rui Jin 2nd Road, Shanghai, 200025, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuanyue Zhu
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Rui Jin 2nd Road, Shanghai, 200025, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ruizhi Zheng
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Rui Jin 2nd Road, Shanghai, 200025, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shuangyuan Wang
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Rui Jin 2nd Road, Shanghai, 200025, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lin Lin
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Rui Jin 2nd Road, Shanghai, 200025, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hongyan Qi
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Rui Jin 2nd Road, Shanghai, 200025, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hong Lin
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Rui Jin 2nd Road, Shanghai, 200025, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Mian Li
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Rui Jin 2nd Road, Shanghai, 200025, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Tiange Wang
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Rui Jin 2nd Road, Shanghai, 200025, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhiyun Zhao
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Rui Jin 2nd Road, Shanghai, 200025, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Min Xu
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Rui Jin 2nd Road, Shanghai, 200025, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yu Xu
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Rui Jin 2nd Road, Shanghai, 200025, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuhong Chen
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Rui Jin 2nd Road, Shanghai, 200025, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Guang Ning
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Rui Jin 2nd Road, Shanghai, 200025, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Maria-Carolina Borges
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Weiqing Wang
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Rui Jin 2nd Road, Shanghai, 200025, China.
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Jie Zheng
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Rui Jin 2nd Road, Shanghai, 200025, China.
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK.
| | - Yufang Bi
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Rui Jin 2nd Road, Shanghai, 200025, China.
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Jieli Lu
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Rui Jin 2nd Road, Shanghai, 200025, China.
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| |
Collapse
|
12
|
Campa D, Gentiluomo M, Stein A, Aoki MN, Oliverius M, Vodičková L, Jamroziak K, Theodoropoulos G, Pasquali C, Greenhalf W, Arcidiacono PG, Uzunoglu F, Pezzilli R, Luchini C, Puzzono M, Loos M, Giaccherini M, Katzke V, Mambrini A, Kiudeliene E, Federico KE, Johansen J, Hussein T, Mohelnikova-Duchonova B, van Eijck CHJ, Brenner H, Farinella R, Pérez JS, Lovecek M, Büchler MW, Hlavac V, Izbicki JR, Hackert T, Chammas R, Zerbi A, Lawlor R, Felici A, Götz M, Capurso G, Ginocchi L, Gazouli M, Kupcinskas J, Cavestro GM, Vodicka P, Moz S, Neoptolemos JP, Kunovsky L, Bojesen SE, Carrara S, Gioffreda D, Morkunas E, Abian O, Bunduc S, Basso D, Boggi U, Wlodarczyk B, Szentesi A, Vanella G, Chen I, Bijlsma MF, Kiudelis V, Landi S, Schöttker B, Corradi C, Giese N, Kaaks R, Peduzzi G, Hegyi P, Morelli L, Furbetta N, Soucek P, Latiano A, Talar-Wojnarowska R, Lindgaard SC, Dijk F, Milanetto AC, Tavano F, Cervena K, Erőss B, Testoni SG, Verhagen-Oldenampsen JHE, Małecka-Wojciesko E, Costello E, Salvia R, Maiello E, Ermini S, Sperti C, Holleczek B, Perri F, Skieceviciene J, Archibugi L, Lucchesi M, Rizzato C, Canzian F. The PANcreatic Disease ReseArch (PANDoRA) consortium: Ten years' experience of association studies to understand the genetic architecture of pancreatic cancer. Crit Rev Oncol Hematol 2023; 186:104020. [PMID: 37164172 DOI: 10.1016/j.critrevonc.2023.104020] [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: 03/06/2023] [Revised: 05/05/2023] [Accepted: 05/07/2023] [Indexed: 05/12/2023] Open
Abstract
Pancreatic cancer has an incidence that almost matches its mortality. Only a small number of risk factors and 33 susceptibility loci have been identified. so Moreover, the relative rarity of pancreatic cancer poses significant hurdles for research aimed at increasing our knowledge of the genetic mechanisms contributing to the disease. Additionally, the inability to adequately power research questions prevents small monocentric studies from being successful. Several consortia have been established to pursue a better understanding of the genetic architecture of pancreatic cancers. The Pancreatic disease research (PANDoRA) consortium is the largest in Europe. PANDoRA is spread across 12 European countries, Brazil and Japan, bringing together 29 basic and clinical research groups. In the last ten years, PANDoRA has contributed to the discovery of 25 susceptibility loci, a feat that will be instrumental in stratifying the population by risk and optimizing preventive strategies.
Collapse
Affiliation(s)
- Daniele Campa
- Unit of Genetic, Department of Biology, University of Pisa, Pisa, Italy.
| | - Manuel Gentiluomo
- Unit of Genetic, Department of Biology, University of Pisa, Pisa, Italy
| | - Angelika Stein
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Mateus Nóbrega Aoki
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Curitiba, Brazil
| | - Martin Oliverius
- Department of Surgery, University Hospital Kralovske Vinohrady, Third Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Ludmila Vodičková
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic; Institute of Biology and Medical Genetics, 1st Faculty of Medicine Charles University and General University Hospital in Prague, Prague, Czech Republic; Biomedical Centre, Faculty of Medicine in Pilsen Charles University, Pilsen, Czech Republic
| | - Krzysztof Jamroziak
- Department of Hematology, Transplantation and Internal Medicine, Medical University of Warsaw, Warsaw, Poland
| | - George Theodoropoulos
- First Department of Propaedeutic Surgery, Hippocration General Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Claudio Pasquali
- Dept. of Surgery, Oncology and Gastroenterology, University of Padova Chirurgia Generale 3, Padova, Italy
| | - William Greenhalf
- Liverpool Experimental Cancer Medicine Centre, University of Liverpool, Liverpool, United Kingdom
| | - Paolo Giorgio Arcidiacono
- Pancreato-Biliary Endoscopy and Endosonography Division, Pancreas Translational and Clinical Research Center, IRCCS San Raffaele Scientic Institute, Milan, Italy
| | - Faik Uzunoglu
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Claudio Luchini
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - Marta Puzzono
- Gastroenterology and Gastrointestinal Endoscopy Unit, Vita-Salute San Raffaele University, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Martin Loos
- Department of General, Visceral and Transplantation Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | | | - Verena Katzke
- Division of Cancer Epidemiology C020, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Andrea Mambrini
- Oncological Department Massa Carrara, Azienda USL Toscana Nord Ovest, Carrara, Italy
| | - Edita Kiudeliene
- Institute for Digestive Research and Gastroenterology Department, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | | | - Julia Johansen
- Departments of Oncology and Medicine, Copenhagen University Hospital, Herlev, Denmark
| | - Tamás Hussein
- Institute of Pancreatic Diseases, Semmelweis University, Budapest, Hungary; Center for Translational Medicine, Semmelweis University, Budapest, Hungary
| | | | - Casper H J van Eijck
- Department of Surgery, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany; Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany; German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Juan Sainz Pérez
- Genomic Oncology Area, GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, Granada, Spain; Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Complejo Hospitales Universitarios de Granada, Universidad de Granada, Granada, Spain; Department of Immunology, University of Granada, Granada, Spain
| | - Martin Lovecek
- Department of Surgery I, University Hospital Olomouc, Olomouc, Czech Republic
| | - Markus W Büchler
- Department of General, Visceral and Transplantation Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Viktor Hlavac
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Jakob R Izbicki
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Thilo Hackert
- Department of General, Visceral and Transplantation Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Roger Chammas
- Center for Translational Research in Oncology (LIM24), Departamento de Radiologia e Oncologia, Instituto Do Câncer Do Estado de São Paulo (ICESP), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo (HCFMUSP), São Paulo, Brazil
| | - Alessandro Zerbi
- Pancreatic Unit, IRCCS Humanitas Research Hospital, Milan, Italy; Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Rita Lawlor
- ARC-Net Research Center, Department of Diagnostics and Public Health, University and Hospital Trust of Verona, Verona, Italy
| | - Alessio Felici
- Unit of Genetic, Department of Biology, University of Pisa, Pisa, Italy
| | - Mara Götz
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Gabriele Capurso
- Pancreato-Biliary Endoscopy and Endosonography Division, Pancreas Translational and Clinical Research Center, San Raffaele Scientific Institute, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan, Italy; Digestive and Liver Disease Unit, Sant' Andrea Hospital, Rome, Italy
| | - Laura Ginocchi
- Oncological Department Massa Carrara, Azienda USL Toscana Nord Ovest, Carrara, Italy
| | - Maria Gazouli
- Laboratory of Biology, Department of Basic Medical Sciences, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Juozas Kupcinskas
- Institute for Digestive Research and Gastroenterology Department, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Giulia Martina Cavestro
- Gastroenterology and Gastrointestinal Endoscopy Unit, Vita-Salute San Raffaele University, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Pavel Vodicka
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic; Institute of Biology and Medical Genetics, 1st Faculty of Medicine Charles University and General University Hospital in Prague, Prague, Czech Republic; Biomedical Centre, Faculty of Medicine in Pilsen Charles University, Pilsen, Czech Republic
| | - Stefania Moz
- Azienda Ospedale-Università di Padova Medicina di Laboratorio, Padova, Italy
| | - John P Neoptolemos
- Department of General, Visceral and Transplantation Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Lumir Kunovsky
- Department of Surgery, University Hospital Brno, Faculty of Medicine, Masaryk University, Brno, Czech Republic; Department of Gastroenterology and Digestive Endoscopy, Masaryk Memorial Cancer Institute, Brno, Czech Republic; 2nd Department of Internal Medicine - Gastroenterology and Geriatrics, University Hospital Olomouc, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
| | - Stig E Bojesen
- Departments of Oncology and Medicine, Copenhagen University Hospital, Herlev, Denmark
| | - Silvia Carrara
- Endoscopic Unit, Department of Gastroenterology, IRCCS Humanitas Research Hospital, Milan, Italy
| | - Domenica Gioffreda
- Division of Gastroenterology and Research Laboratory, Fondazione IRCCS "Casa Sollievo della Sofferenza" Hospital, San Giovanni Rotondo, Italy
| | - Egidijus Morkunas
- Institute for Digestive Research and Gastroenterology Department, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Olga Abian
- Instituto BIFI-Universidad de Zaragoza, Zaragoza, Spain
| | - Stefania Bunduc
- Center for Translational Medicine, Semmelweis University, Budapest, Hungary; Carol Davila University of Medicine and Pharmacy, Bucharest, Romania; Center for Digestive Diseases and Liver Transplant, Fundeni Clinical Insitute, Bucharest, Romania
| | - Daniela Basso
- Dept. of Medicine, University of Padova Medicina di Laboratorio, Padova, Italy
| | - Ugo Boggi
- Division of General and Transplant Surgery, Pisa University Hospital, Pisa, Italy
| | - Barbara Wlodarczyk
- Dept of Digestive Tract Diseases, Medical University of Lodz, Lodz, Poland
| | - Andrea Szentesi
- Institute for Translational Medicine, Medical School, University of Pécs, Pécs, Hungary
| | - Giuseppe Vanella
- Pancreato-Biliary Endoscopy and Endosonography Division, Pancreas Translational and Clinical Research Center, San Raffaele Scientific Institute, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan, Italy; Digestive and Liver Disease Unit, Sant' Andrea Hospital, Rome, Italy
| | - Inna Chen
- Departments of Oncology and Medicine, Copenhagen University Hospital, Herlev, Denmark
| | - Maarten F Bijlsma
- Center for Experimental and Molecular Medicine, Laboratory of Experimental Oncology and Radiobiology, Amsterdam UMC location University of Amsterdam, Amsterdam, the Netherlands; Oncode Institute, Amsterdam, the Netherlands; Imaging and Biomarkers, Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Vytautas Kiudelis
- Institute for Digestive Research and Gastroenterology Department, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Stefano Landi
- Unit of Genetic, Department of Biology, University of Pisa, Pisa, Italy
| | - Ben Schöttker
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Chiara Corradi
- Unit of Genetic, Department of Biology, University of Pisa, Pisa, Italy
| | - Nathalia Giese
- Department of General, Visceral and Transplantation Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Rudolf Kaaks
- Division of Cancer Epidemiology C020, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Giulia Peduzzi
- Unit of Genetic, Department of Biology, University of Pisa, Pisa, Italy
| | - Péter Hegyi
- Institute of Pancreatic Diseases, Semmelweis University, Budapest, Hungary; Center for Translational Medicine, Semmelweis University, Budapest, Hungary; Institute for Translational Medicine, Medical School, University of Pécs, Pécs, Hungary; Translational Pancreatology Research Group, Interdisciplinary Centre of Excellence for Research Development and Innovation University of Szeged, Szeged, Hungary
| | - Luca Morelli
- General Surgery Unit, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Niccolò Furbetta
- General Surgery Unit, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Pavel Soucek
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Anna Latiano
- Division of Gastroenterology and Research Laboratory, Fondazione IRCCS "Casa Sollievo della Sofferenza" Hospital, San Giovanni Rotondo, Italy
| | | | - Sidsel C Lindgaard
- Departments of Oncology and Medicine, Copenhagen University Hospital, Herlev, Denmark
| | - Frederike Dijk
- Imaging and Biomarkers, Cancer Center Amsterdam, Amsterdam, the Netherlands; Department of Pathology, Amsterdam UMC location University of Amsterdam, Amsterdam, the Netherlands
| | - Anna Caterina Milanetto
- Dept. of Surgery, Oncology and Gastroenterology, University of Padova Chirurgia Generale 3, Padova, Italy
| | - Francesca Tavano
- Division of Gastroenterology and Research Laboratory, Fondazione IRCCS "Casa Sollievo della Sofferenza" Hospital, San Giovanni Rotondo, Italy
| | - Klara Cervena
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic; Institute of Biology and Medical Genetics, 1st Faculty of Medicine Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Bálint Erőss
- Institute of Pancreatic Diseases, Semmelweis University, Budapest, Hungary; Center for Translational Medicine, Semmelweis University, Budapest, Hungary; Institute for Translational Medicine, Medical School, University of Pécs, Pécs, Hungary
| | - Sabrina G Testoni
- Pancreato-Biliary Endoscopy and Endosonography Division, Pancreas Translational and Clinical Research Center, IRCCS San Raffaele Scientic Institute, Milan, Italy
| | | | | | - Eithne Costello
- Liverpool Experimental Cancer Medicine Centre, University of Liverpool, Liverpool, United Kingdom
| | - Roberto Salvia
- Department of Surgery, The Pancreas Institute, University and Hospital Trust of Verona, Verona, Italy
| | - Evaristo Maiello
- Department of Oncology, Fondazione IRCCS "Casa Sollievo della Sofferenza" Hospital, San Giovanni Rotondo, Italy
| | | | - Cosimo Sperti
- Dept. of Surgery, Oncology and Gastroenterology, University of Padova Chirurgia Generale 1, Padova, Italy
| | - Bernd Holleczek
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany; Saarland Cancer Registry, Saarbrücken, Germany
| | - Francesco Perri
- Division of Gastroenterology and Research Laboratory, Fondazione IRCCS "Casa Sollievo della Sofferenza" Hospital, San Giovanni Rotondo, Italy
| | - Jurgita Skieceviciene
- Institute for Digestive Research and Gastroenterology Department, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Livia Archibugi
- Pancreato-Biliary Endoscopy and Endosonography Division, Pancreas Translational and Clinical Research Center, San Raffaele Scientific Institute, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan, Italy; Digestive and Liver Disease Unit, Sant' Andrea Hospital, Rome, Italy
| | - Maurizio Lucchesi
- Oncological Department Massa Carrara, Azienda USL Toscana Nord Ovest, Carrara, Italy
| | - Cosmeri Rizzato
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany.
| |
Collapse
|
13
|
Cronjé HT, Karhunen V, Hovingh GK, Coppieters K, Lagerstedt JO, Nyberg M, Gill D. Genetic evidence implicating natriuretic peptide receptor-3 in cardiovascular disease risk: a Mendelian randomization study. BMC Med 2023; 21:158. [PMID: 37101178 PMCID: PMC10134514 DOI: 10.1186/s12916-023-02867-x] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 04/17/2023] [Indexed: 04/28/2023] Open
Abstract
BACKGROUND C-type natriuretic peptide (CNP) is a known target for promoting growth and has been implicated as a therapeutic opportunity for the prevention and treatment of cardiovascular disease (CVD). This study aimed to explore the effect of CNP on CVD risk using the Mendelian randomization (MR) framework. METHODS Instrumental variables mimicking the effects of pharmacological intervention on CNP were identified as uncorrelated genetic variants located in the genes coding for its primary receptors, natriuretic peptide receptors-2 and 3 (NPR2 and NPR3), that associated with height. We performed MR and colocalization analyses to investigate the effects of NPR2 signalling and NPR3 function on CVD outcomes and risk factors. MR estimates were compared to those obtained when considering height variants from throughout the genome. RESULTS Genetically-proxied reduced NPR3 function was associated with a lower risk of CVD, with odds ratio (OR) 0.74 per standard deviation (SD) higher NPR3-predicted height, and 95% confidence interval (95% CI) 0.64-0.86. This effect was greater in magnitude than observed when considering height variants from throughout the genome. For CVD subtypes, similar MR associations for NPR3-predicted height were observed when considering the outcomes of coronary artery disease (0.75, 95% CI 0.60-0.92), stroke (0.69, 95% CI 0.50-0.95) and heart failure (0.77, 95% CI 0.58-1.02). Consideration of CVD risk factors identified systolic blood pressure (SBP) as a potential mediator of the NPR3-related CVD risk lowering. For stroke, we found that the MR estimate for NPR3 was greater in magnitude than could be explained by a genetically predicted SBP effect alone. Colocalization results largely supported the MR findings, with no evidence of results being driven by effects due to variants in linkage disequilibrium. There was no MR evidence supporting effects of NPR2 on CVD risk, although this null finding could be attributable to fewer genetic variants being identified to instrument this target. CONCLUSIONS This genetic analysis supports the cardioprotective effects of pharmacologically inhibiting NPR3 receptor function, which is only partly mediated by an effect on blood pressure. There was unlikely sufficient statistical power to investigate the cardioprotective effects of NPR2 signalling.
Collapse
Affiliation(s)
- Héléne T Cronjé
- Department of Public Health, Section of Epidemiology, University of Copenhagen, Copenhagen, Denmark.
| | - Ville Karhunen
- Faculty of Science, Research Unit of Mathematical Sciences, University of Oulu, Oulu, Finland
- Research Unit of Population Health, Faculty of Medicine, University of Oulu, Oulu, Finland
| | - G Kees Hovingh
- Department of Vascular Medicine, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
- Global Chief Medical Office, Novo Nordisk, Copenhagen, Denmark
| | - Ken Coppieters
- Global Project Management, Global Drug Discovery, Novo Nordisk, Copenhagen, Denmark
| | - Jens O Lagerstedt
- Rare Endocrine Disorders, Research and Early Development, Novo Nordisk, Copenhagen, Denmark
- Department of Experimental Medical Science, Lund University, 221 84, Lund, Sweden
| | - Michael Nyberg
- Vascular Biology, Research and Early Development, Novo Nordisk, Maaloev, Denmark
| | - Dipender Gill
- Chief Scientific Advisor Office, Research and Early Development, Novo Nordisk, Copenhagen, Denmark.
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK.
| |
Collapse
|
14
|
Asghar F, Bano A, Waheed F, Ahmed Anjum A, Ejaz H, Javed N. Association of exogenous factors with molecular epidemiology of Staphylococcus aureus in human oral cavity. Saudi J Biol Sci 2023; 30:103613. [PMID: 36936700 PMCID: PMC10018566 DOI: 10.1016/j.sjbs.2023.103613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 02/11/2023] [Accepted: 02/23/2023] [Indexed: 03/05/2023] Open
Abstract
The frequency of Staphylococcus aureus strains associated with oral cavity microbiota has prodigious consideration. Although S. aureus has been reflected as an ephemeral member of the human oral cavity microbiota, the isolation, identification, and characterization of S. aureus is important. The present study aimed to characterize S. aureus strains from the oral cavity microflora, isolation of S. aureus from the human oral cavity microbiota, and demographic information of the participants to evaluate exogenous factors associated with the presence of S. aureus and their genetic analysis linkage with different factors. The method used in this study is the isolation of oral cavity microbiomes using sheep blood agar and Mannitol salt agar. We performed antibiotic profiling with various antibiotics and genetic analysis utilizing gene-specific primers for specific genes, including nuc, mecA, pvl, agr, and coa. A significant number of S. aureus isolates were found in the oral cavity of humans 18/84 (21.42%), and all 18 strains tested positive for the confirmatory nuc gene. Antibiotic resistance-conferring gene mecA was positive in 10 (55.6%) isolates. It was found that the occurrence of pvl, agr, and coagulase (coa) genes was 9 (50%), 6 (33.33%), and 10 (55.6%), respectively. The genetic analysis reported that significant associations were present between male and mecA gene (P = 0.03) and coa (P = 0.03), smokers with the occurrence of mecA (P = 0.02), agr (P = 0.048) and coa (P = 0.02) genes. Likewise, the association of antibiotic usage was significantly found with mecA (P = 0.02), coa (P = 0.02); however, the individuals who have taken orthodontic treatment recently have a significant association with agr (P = 0.017). The use of mouth rinse was significantly associated with the prevalence of the pvl gene (P = 0.01), and tooth brushing frequency and inflammation of the buccal cavity were also statistically significant in relation to pvl gene prevalence (P = 0.02, 0.00, respectively). Moreover, calories and weight-controlled diet were significantly associated with mecA, agr, and highly significant with coa (P = 0.02, 0.048, 0.000), so all P < 0.05, and no significant association was found between the socioeconomic status of individuals with aforementioned analyzed genes.
Collapse
Affiliation(s)
- Farah Asghar
- Institute of Microbiology and Molecular Genetics, University of the Punjab, Lahore, Pakistan
| | - Abida Bano
- Institute of Microbiology and Molecular Genetics, University of the Punjab, Lahore, Pakistan
| | - Fadia Waheed
- Institute of Microbiology and Molecular Genetics, University of the Punjab, Lahore, Pakistan
| | - Aftab Ahmed Anjum
- Quality Operations Laboratory, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Hasan Ejaz
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Sakaka 72388, Saudi Arabia
| | - Numan Javed
- Institute of Microbiology and Molecular Genetics, University of the Punjab, Lahore, Pakistan
| |
Collapse
|
15
|
Salerno J, Coughlin SS, Goodman KW, Hlaing WM. Current ethical and social issues in epidemiology. Ann Epidemiol 2023; 80:37-42. [PMID: 36758845 DOI: 10.1016/j.annepidem.2023.02.001] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 02/01/2023] [Accepted: 02/01/2023] [Indexed: 02/10/2023]
Abstract
PURPOSE The American College of Epidemiology held its 2021 Annual Meeting virtually, September 8-10, with a conference theme of 'From Womb to Tomb: Insights from Health Emergencies'. The American College of Epidemiology Ethics Committee hosted a symposium session in recognition of the ethical and social challenges brought to light by the coronavirus disease 2019 pandemic and on the occasion of the publication of the third edition of the classic text, Ethics and Epidemiology. The American College of Epidemiology Ethics Committee invited the book editor and contributing authors to present at the symposium session titled 'Current Ethical and Social Issues in Epidemiology.' The purpose of this paper is to further highlight the ethical challenges and presentations. METHODS Three speakers with expertise in ethics, health law, health policy, global health, health information technology, and translational research in epidemiology and public health were selected to present on the social and ethical issues in the current landscape. Dr. S Coughlin presented on the 'Ethical and Social Issues in Epidemiology', Dr. L Beskow presented on 'Ethical Challenges in Genetic Epidemiology', and Dr. K Goodman presented on the 'Ethics of Health Informatics'. RESULTS New digital sources of data and technologies are driving the ethical challenges and opportunities in epidemiology and public health as it relates to the three emerging topic areas identified: (1) digital epidemiology, (2) genetic epidemiology, and (3) health informatics. New complexities such as the reliance on social media to control infectious disease outbreaks and the introduction of computing advancements are requiring re-evaluation of traditional bioethical frameworks for epidemiology research and public health practice. We identified several cross-cutting ethical and social issues related to informed consent, benefits, risks and harms, and privacy and confidentiality and summarized these alongside more nuanced ethical considerations such as algorithmic bias, group harms related to data (mis)representation, risks of misinformation, return of genomic research results, maintaining data security, and data sharing. We offered an integrated synthesis of the stages of epidemiology research planning and conduct with the ethical issues that are most relevant in these emerging topic areas. CONCLUSIONS New realities exist for epidemiology and public health as professional groups who are faced with addressing population health, and especially given the recent pandemic and the widespread use of digital tools and technologies. Many ethical issues can be understood in the context of existing ethical frameworks; however, they have yet to be clearly identified or connected with the new technical and methodological applications of digital tools and technologies currently in use for epidemiology research and public health practice. To address current ethical challenges, we offered a synthesis of traditional ethical principles in public health science alongside more nuanced ethical considerations for emerging technologies and aligned these with lifecycle stages of epidemiology research. By critically reflecting on the impact of new digital sources of data and technologies on epidemiology research and public health practice, specifically in the control of infectious outbreaks, we offered insights on cultivating these new areas of professional growth while striving to improve population health.
Collapse
Affiliation(s)
- Jennifer Salerno
- Department of Family Medicine, Faculty of Health Sciences, McMaster University, Hamilton, ON, Canada; Department of Health Research Methods, Evidence, and Impact, Faculty of Health Sciences, McMaster University, Hamilton, ON, Canada.
| | - Steven S Coughlin
- Department of Population Health Sciences, Medical College of Georgia, Augusta University, Augusta, GA; Institute of Public and Preventive Health, Augusta University, Augusta, GA
| | - Kenneth W Goodman
- Institute for Bioethics and Health Policy, University of Miami Miller School of Medicine, Miami, FL
| | - WayWay M Hlaing
- Division of Epidemiology and Population Sciences, Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL
| |
Collapse
|
16
|
Abstract
Waldenström macroglobulinemia (WM) is a rare subtype of non-Hodgkin lymphoma characterized by the presence of lymphoplasmacytic lymphoma (LPL) in the bone marrow accompanied by a monoclonal immunoglobulin type M (IgM) in the serum. WM was first described only 80 years ago and became reportable in the US as a malignancy in 1988. Very little systematic research was conducted prior to 2000 to characterize incidence, clinical characteristics, risk factors or diagnostic and prognostic criteria, and there were essentially no WM-specific clinical interventional trials. Since the inaugural meeting of the International Workshop in Waldenström's Macroglobulinemia (IWWM) in 2000, WM has become the focus of a steadily increasing and productive body of research, engaging a growing number of investigators throughout the world. This introductory overview provides summary of the current understanding of the epidemiology of WM/LPL as a backdrop for a series of consensus panel recommendations arising from research presented at the 11th IWWM.
Collapse
Affiliation(s)
- Mary L McMaster
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, MD; Department of Health and Human Services, Commissioned Corps of the United States Public Health Service, Washington, DC.
| |
Collapse
|
17
|
Khaire AS, Wimberly CE, Semmes EC, Hurst JH, Walsh KM. An integrated genome and phenome-wide association study approach to understanding Alzheimer's disease predisposition. Neurobiol Aging 2022; 118:117-123. [PMID: 35715361 PMCID: PMC9787699 DOI: 10.1016/j.neurobiolaging.2022.05.011] [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: 01/03/2022] [Revised: 05/13/2022] [Accepted: 05/23/2022] [Indexed: 12/25/2022]
Abstract
Genome-wide association studies (GWAS) have identified common single nucleotide polymorphisms (SNPs) that increase late-onset Alzheimer's disease (LOAD) risk. To identify additional LOAD-associated variants and provide insight into underlying disease biology, we performed a phenome-wide association study on 23 known LOAD-associated SNPs and 4:1 matched control SNPs using UK Biobank data. LOAD-associated SNPs were significantly enriched for associations with 8/778 queried traits, including 3 platelet traits. The strongest enrichment was for platelet distribution width (PDW) (p = 1.2 × 10-5), but increased PDW was not associated with LOAD susceptibility in Mendelian randomization analysis. Of 384 PDW-associated SNPs identified by prior GWAS, 36 were nominally associated with LOAD risk (17,008 cases; 37,154 controls) and 5 survived false-discovery rate correction. Associations confirmed known LOAD risk loci near PICALM, CD2AP, SPI1, and NDUFAF6, and identified a novel risk locus in epidermal growth factor receptor. Integrating GWAS and phenome-wide association study data reveals substantial pleiotropy between genetic determinants of LOAD and of platelet morphology, and for the first time implicates epidermal growth factor receptor - a mediator of β-amyloid toxicity - in Alzheimer's disease susceptibility.
Collapse
Affiliation(s)
- Archita S Khaire
- Division of Neuro-epidemiology, Department of Neurosurgery, Duke University, Durham, NC, USA
| | - Courtney E Wimberly
- Division of Neuro-epidemiology, Department of Neurosurgery, Duke University, Durham, NC, USA
| | - Eleanor C Semmes
- Medical Scientist Training Program, Duke University, Durham, NC, USA; Children's Health and Discovery Initiative, Department of Pediatrics, Duke University, Durham, NC, USA
| | - Jillian H Hurst
- Children's Health and Discovery Initiative, Department of Pediatrics, Duke University, Durham, NC, USA
| | - Kyle M Walsh
- Division of Neuro-epidemiology, Department of Neurosurgery, Duke University, Durham, NC, USA; Children's Health and Discovery Initiative, Department of Pediatrics, Duke University, Durham, NC, USA; Center for the Study of Aging and Human Development, Duke University, Durham, NC, USA.
| |
Collapse
|
18
|
Berry DS, Hernandez N, Clark LN, Louis ED. Lack of Familial Aggregation of the "Essential Tremor-Plus" Phenotype in Familial Essential Tremor. Neuroepidemiology 2022; 56:373-379. [PMID: 35940165 PMCID: PMC9633447 DOI: 10.1159/000526278] [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: 06/15/2022] [Accepted: 07/20/2022] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Essential tremor (ET) is a highly prevalent neurological disease that frequently runs in families. A recent and controversial proposal is to separate ET patients into two distinct groups - ET versus ET-plus. If this were a valid construct, one would expect in familial aggregation studies to observe that ET-plus would cluster in some families yet be absent in others, rather than being randomly distributed across families. We examined whether there is evidence of familial aggregation of ET-plus. METHODS Probands (n = 84 [56 ET-plus and 28 ET]) and their first- and second-degree relatives (n = 182 and 48) enrolled in a genetics study. χ2 and generalized estimating equations (GEE) tested associations between probands' ET-plus status and the ET-plus status of their relatives. RESULTS χ2 analyses revealed that ET-plus was no more prevalent in relatives of probands diagnosed with ET-plus than in relatives of probands diagnosed with ET, p > 0.05. Restricting relatives to first-degree relatives similarly did not detect a significant association (p = 0.88). GEE yielded similar results (respective p's = 0.39 and 0.81). CONCLUSION The data demonstrate that ET-plus does not seem to aggregate in families. As such, they do not lend support to the notion that ET-plus is a valid biological construct.
Collapse
Affiliation(s)
- Diane S Berry
- Department of Neurology, University of Texas Southwestern Medical Center, Dallas, Texas, USA,
| | - Nora Hernandez
- Department of Neurology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Lorraine N Clark
- The Taub Institute for Research on Alzheimer's Disease and The Aging Brain, Columbia University Irving Medical Center, New York, New York, USA
- Department of Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York, USA
| | - Elan D Louis
- Department of Neurology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| |
Collapse
|
19
|
Chen VL, Burkholder DA, Moran IJ, DiBattista JV, Miller MJ, Chen Y, Du X, Oliveri A, Cushing KC, Lok AS, Speliotes EK. Hepatic decompensation is accelerated in patients with cirrhosis and alpha-1 antitrypsin Pi∗MZ genotype. JHEP Rep 2022; 4:100483. [PMID: 35571533 PMCID: PMC9097455 DOI: 10.1016/j.jhepr.2022.100483] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 03/01/2022] [Accepted: 03/22/2022] [Indexed: 02/03/2023] Open
Abstract
Background & Aims Alpha-1 antitrypsin deficiency is caused by mutations in SERPINA1, most commonly homozygosity for the Pi∗Z variant, and can present as liver disease. While heterozygosity for Pi∗Z (Pi∗MZ) is linked to increased risk of cirrhosis, whether the Pi∗MZ genotype is associated with an increased rate of decompensation among patients who already have compensated cirrhosis is not known. Methods This was a retrospective study of Michigan Genomics Initiative participants with baseline compensated cirrhosis. The primary predictors were Pi∗MZ or Pi∗MS genotype (vs. Pi∗MM). The primary outcomes were hepatic decompensation with ascites, hepatic encephalopathy, or variceal bleeding, or the combined endpoint of liver-related death or liver transplant, both modeled with Fine-Gray competing risk models. Results We included 576 patients with baseline compensated cirrhosis who had undergone genotyping, of whom 474 had Pi∗MM, 49 had Pi∗MZ, and 52 had Pi∗MS genotypes. Compared to Pi∗MM genotype, Pi∗MZ was associated with increased rates of hepatic decompensation (hazard ratio 1.81; 95% CI 1.22-2.69; p = 0.003) and liver transplant or liver-related death (hazard ratio 2.07; 95% CI 1.21-3.52; p = 0.078). These associations remained significant after adjustment for severity of underlying liver disease, and were robust across subgroup analyses based on etiology, sex, obesity, and diabetes status. Pi∗MS was not associated with decompensation or death/transplantation. Conclusions The SERPINA1 Pi∗MZ genotype is associated with an increased rate of hepatic decompensation and decreased transplant-free survival among patients with baseline compensated cirrhosis. Lay summary There is a mutation in the gene SERPINA1 called Pi∗MZ which increases risk of liver scarring (cirrhosis); however, it is not known what effect Pi∗MZ has if someone already has cirrhosis. In this study, we found that people who had cirrhosis and Pi∗MZ developed complications from cirrhosis faster than those who did not have the mutation.
Collapse
Affiliation(s)
- Vincent L. Chen
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan Ann Arbor, MI, USA
| | | | - Isabel J. Moran
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan Ann Arbor, MI, USA
| | | | - Matthew J. Miller
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Yanhua Chen
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan Ann Arbor, MI, USA
| | - Xiaomeng Du
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan Ann Arbor, MI, USA
| | - Antonino Oliveri
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan Ann Arbor, MI, USA
| | - Kelly C. Cushing
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan Ann Arbor, MI, USA
| | - Anna S. Lok
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan Ann Arbor, MI, USA
| | - Elizabeth K. Speliotes
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan Ann Arbor, MI, USA
| |
Collapse
|
20
|
Dorling L, Carvalho S, Allen J, Parsons MT, Fortuno C, González-Neira A, Heijl SM, Adank MA, Ahearn TU, Andrulis IL, Auvinen P, Becher H, Beckmann MW, Behrens S, Bermisheva M, Bogdanova NV, Bojesen SE, Bolla MK, Bremer M, Briceno I, Camp NJ, Campbell A, Castelao JE, Chang-Claude J, Chanock SJ, Chenevix-Trench G, Collée JM, Czene K, Dennis J, Dörk T, Eriksson M, Evans DG, Fasching PA, Figueroa J, Flyger H, Gabrielson M, Gago-Dominguez M, García-Closas M, Giles GG, Glendon G, Guénel P, Gündert M, Hadjisavvas A, Hahnen E, Hall P, Hamann U, Harkness EF, Hartman M, Hogervorst FBL, Hollestelle A, Hoppe R, Howell A, Jakubowska A, Jung A, Khusnutdinova E, Kim SW, Ko YD, Kristensen VN, Lakeman IMM, Li J, Lindblom A, Loizidou MA, Lophatananon A, Lubiński J, Luccarini C, Madsen MJ, Mannermaa A, Manoochehri M, Margolin S, Mavroudis D, Milne RL, Mohd Taib NA, Muir K, Nevanlinna H, Newman WG, Oosterwijk JC, Park SK, Peterlongo P, Radice P, Saloustros E, Sawyer EJ, Schmutzler RK, Shah M, Sim X, Southey MC, Surowy H, Suvanto M, Tomlinson I, Torres D, Truong T, van Asperen CJ, Waltes R, Wang Q, Yang XR, Pharoah PDP, Schmidt MK, Benitez J, Vroling B, Dunning AM, Teo SH, Kvist A, de la Hoya M, Devilee P, Spurdle AB, Vreeswijk MPG, Easton DF. Breast cancer risks associated with missense variants in breast cancer susceptibility genes. Genome Med 2022; 14:51. [PMID: 35585550 PMCID: PMC9116026 DOI: 10.1186/s13073-022-01052-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [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: 08/20/2021] [Accepted: 05/04/2022] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Protein truncating variants in ATM, BRCA1, BRCA2, CHEK2, and PALB2 are associated with increased breast cancer risk, but risks associated with missense variants in these genes are uncertain. METHODS We analyzed data on 59,639 breast cancer cases and 53,165 controls from studies participating in the Breast Cancer Association Consortium BRIDGES project. We sampled training (80%) and validation (20%) sets to analyze rare missense variants in ATM (1146 training variants), BRCA1 (644), BRCA2 (1425), CHEK2 (325), and PALB2 (472). We evaluated breast cancer risks according to five in silico prediction-of-deleteriousness algorithms, functional protein domain, and frequency, using logistic regression models and also mixture models in which a subset of variants was assumed to be risk-associated. RESULTS The most predictive in silico algorithms were Helix (BRCA1, BRCA2 and CHEK2) and CADD (ATM). Increased risks appeared restricted to functional protein domains for ATM (FAT and PIK domains) and BRCA1 (RING and BRCT domains). For ATM, BRCA1, and BRCA2, data were compatible with small subsets (approximately 7%, 2%, and 0.6%, respectively) of rare missense variants giving similar risk to those of protein truncating variants in the same gene. For CHEK2, data were more consistent with a large fraction (approximately 60%) of rare missense variants giving a lower risk (OR 1.75, 95% CI (1.47-2.08)) than CHEK2 protein truncating variants. There was little evidence for an association with risk for missense variants in PALB2. The best fitting models were well calibrated in the validation set. CONCLUSIONS These results will inform risk prediction models and the selection of candidate variants for functional assays and could contribute to the clinical reporting of gene panel testing for breast cancer susceptibility.
Collapse
Affiliation(s)
- Leila Dorling
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Sara Carvalho
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Jamie Allen
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Michael T Parsons
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Cristina Fortuno
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Anna González-Neira
- Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), 28029, Madrid, Spain
| | | | - Muriel A Adank
- Family Cancer Clinic, The Netherlands Cancer Institute - Antoni Van Leeuwenhoek Hospital, Amsterdam, 1066 CX, The Netherlands
| | - Thomas U Ahearn
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20850, USA
| | - Irene L Andrulis
- Fred A. Litwin Center for Cancer Genetics, Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Päivi Auvinen
- Translational Cancer Research Area, University of Eastern Finland, 70210, Kuopio, Finland
- Institute of Clinical Medicine, Oncology, University of Eastern Finland, 70210, Kuopio, Finland
- Department of Oncology, Cancer Center, Kuopio University Hospital, 70210, Kuopio, Finland
| | - Heiko Becher
- Institute of Medical Biometry and Epidemiology, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Matthias W Beckmann
- Department of Gynecology and Obstetrics, Comprehensive Cancer Center Erlangen-EMN, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg (FAU), 91054, Erlangen, Germany
| | - Sabine Behrens
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Marina Bermisheva
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa, 450054, Russia
| | - Natalia V Bogdanova
- Department of Radiation Oncology, Hannover Medical School, 30625, Hannover, Germany
- Gynaecology Research Unit, Hannover Medical School, 30625, Hannover, Germany
- N.N. Alexandrov Research Institute of Oncology and Medical Radiology, 223040, Minsk, Belarus
| | - Stig E Bojesen
- Copenhagen General Population Study, Herlev and Gentofte Hospital, Copenhagen University Hospital, 2730, Herlev, Denmark
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, 2730, Herlev, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Manjeet K Bolla
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Michael Bremer
- Department of Radiation Oncology, Hannover Medical School, 30625, Hannover, Germany
| | - Ignacio Briceno
- Medical Faculty, Universidad de La Sabana, 140013, Bogota, Colombia
| | - Nicola J Camp
- Department of Internal Medicine and Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, 84112, USA
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, Institute of Genetics & Cancer, The University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, UK
- Usher Institute of Population Health Sciences and Informatics, The University of Edinburgh, Edinburgh, EH16 4UX, UK
| | - Jose E Castelao
- Oncology and Genetics Unit, Instituto de Investigacion Sanitaria Galicia Sur (IISGS), Xerencia de Xestion Integrada de Vigo-SERGAS, 36312, Vigo, Spain
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Cancer Epidemiology Group, University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20850, USA
| | - Georgia Chenevix-Trench
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - J Margriet Collée
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, 3015 CN, The Netherlands
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 65, Stockholm, Sweden
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Thilo Dörk
- Gynaecology Research Unit, Hannover Medical School, 30625, Hannover, Germany
| | - Mikael Eriksson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 65, Stockholm, Sweden
| | - D Gareth Evans
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M13 9WL, UK
- North West Genomics Laboratory Hub, Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, M13 9WL, UK
- Nightingale & Genesis Prevention Centre, Wythenshawe Hospital, Manchester University NHS Foundation Trust, Manchester, M23 9LT, UK
- NIHR Manchester Biomedical Research Centre, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, M13 9WL, UK
| | - Peter A Fasching
- Department of Gynecology and Obstetrics, Comprehensive Cancer Center Erlangen-EMN, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg (FAU), 91054, Erlangen, Germany
- David Geffen School of Medicine, Department of Medicine Division of Hematology and Oncology, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Jonine Figueroa
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20850, USA
- Usher Institute of Population Health Sciences and Informatics, The University of Edinburgh, Edinburgh, EH16 4UX, UK
- Cancer Research UK Edinburgh Centre, The University of Edinburgh, Edinburgh, EH4 2XR, UK
| | - Henrik Flyger
- Department of Breast Surgery, Herlev and Gentofte Hospital, Copenhagen University Hospital, 2730, Herlev, Denmark
| | - Marike Gabrielson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 65, Stockholm, Sweden
| | - Manuela Gago-Dominguez
- Fundación Pública Galega de Medicina Xenómica, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago, SERGAS, , 15706, Santiago de Compostela, Spain
- Moores Cancer Center, University of California San Diego, La Jolla, CA, 92037, USA
| | - Montserrat García-Closas
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20850, USA
| | - Graham G Giles
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, 3004, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC, 3010, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, 3168, Australia
| | - Gord Glendon
- Fred A. Litwin Center for Cancer Genetics, Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
| | - Pascal Guénel
- Team "Exposome and Heredity", CESP, Inserm, Gustave Roussy, University Paris-Saclay, UVSQ, Villejuif, France
| | - Melanie Gündert
- Molecular Epidemiology Group, C080, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Molecular Biology of Breast Cancer, University Womens Clinic Heidelberg, University of Heidelberg, 69120, Heidelberg, Germany
- Institute of Diabetes Research, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Germany
| | - Andreas Hadjisavvas
- Cancer Genetics, Therapeutics and Ultrastructural Pathology, The Cyprus Institute of Neurology & Genetics, 2371, Nicosia, Cyprus
- Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology & Genetics, 2371, Nicosia, Cyprus
| | - Eric Hahnen
- Center for Familial Breast and Ovarian Cancer, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937, Cologne, Germany
- Center for Integrated Oncology (CIO), Faculty of Medicine, University Hospital Cologne, University of Cologne, 50937, Cologne, Germany
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 65, Stockholm, Sweden
- Department of Oncology, 118 83, Södersjukhuset, Stockholm, Sweden
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Elaine F Harkness
- Nightingale & Genesis Prevention Centre, Wythenshawe Hospital, Manchester University NHS Foundation Trust, Manchester, M23 9LT, UK
- NIHR Manchester Biomedical Research Centre, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, M13 9WL, UK
- Division of Informatics, Imaging and Data Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M13 9PT, UK
| | - Mikael Hartman
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, 117549, Singapore
- Department of Surgery, National University Health System, Singapore, 119228, Singapore
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, 119228, Singapore
| | - Frans B L Hogervorst
- Family Cancer Clinic, The Netherlands Cancer Institute - Antoni Van Leeuwenhoek Hospital, Amsterdam, 1066 CX, The Netherlands
| | - Antoinette Hollestelle
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, 3015 GD, The Netherlands
| | - Reiner Hoppe
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, 70376, Stuttgart, Germany
- University of Tübingen, 72074, Tübingen, Germany
| | - Anthony Howell
- NIHR Manchester Biomedical Research Centre, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, M13 9WL, UK
- Division of Cancer Sciences, University of Manchester, Manchester, M13 9PL, UK
| | - Anna Jakubowska
- Department of Genetics and Pathology, Pomeranian Medical University, 71-252, Szczecin, Poland
- Independent Laboratory of Molecular Biology and Genetic Diagnostics, Pomeranian Medical University, 71-252, Szczecin, Poland
| | - Audrey Jung
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Elza Khusnutdinova
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa, 450054, Russia
- Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, 450000, Russia
| | - Sung-Won Kim
- Department of Surgery, Daerim Saint Mary's Hospital, Seoul, 07442, Korea
| | - Yon-Dschun Ko
- Department of Internal Medicine, Johanniter GmbH Bonn, Johanniter Krankenhaus, 53113, Bonn, Germany
| | - Vessela N Kristensen
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, 0450, Oslo, Norway
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, 0379, Oslo, Norway
| | - Inge M M Lakeman
- Department of Human Genetics, Leiden University Medical Center, Leiden, 2333 ZA, The Netherlands
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, 2333 ZA, The Netherlands
| | - Jingmei Li
- Department of Surgery, National University Health System, Singapore, 119228, Singapore
- Human Genetics Division, Genome Institute of Singapore, Singapore, 138672, Singapore
| | - Annika Lindblom
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, 171 76, Stockholm, Sweden
| | - Maria A Loizidou
- Cancer Genetics, Therapeutics and Ultrastructural Pathology, The Cyprus Institute of Neurology & Genetics, 2371, Nicosia, Cyprus
- Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology & Genetics, 2371, Nicosia, Cyprus
| | - Artitaya Lophatananon
- Division of Population Health, Health Services Research and Primary Care, School of Health Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, M13 9PL, UK
| | - Jan Lubiński
- Department of Genetics and Pathology, Pomeranian Medical University, 71-252, Szczecin, Poland
| | - Craig Luccarini
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Michael J Madsen
- Department of Internal Medicine and Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, 84112, USA
| | - Arto Mannermaa
- Translational Cancer Research Area, University of Eastern Finland, 70210, Kuopio, Finland
- Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, 70210, Kuopio, Finland
- Biobank of Eastern Finland, Kuopio University Hospital, Kuopio, Finland
| | - Mehdi Manoochehri
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Sara Margolin
- Department of Oncology, 118 83, Södersjukhuset, Stockholm, Sweden
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, 118 83, Stockholm, Sweden
| | - Dimitrios Mavroudis
- Department of Medical Oncology, University Hospital of Heraklion, 711 10, Heraklion, Greece
| | - Roger L Milne
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, 3004, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC, 3010, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, 3168, Australia
| | - Nur Aishah Mohd Taib
- Breast Cancer Research Unit, Faculty of Medicine, University Malaya Cancer Research Institute, University of Malaya, 50603, Kuala Lumpur, Malaysia
- Department of Surgery, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Kenneth Muir
- Division of Population Health, Health Services Research and Primary Care, School of Health Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, M13 9PL, UK
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, Helsinki University Hospital, University of Helsinki, 00290, Helsinki, Finland
| | - William G Newman
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M13 9WL, UK
- North West Genomics Laboratory Hub, Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, M13 9WL, UK
- NIHR Manchester Biomedical Research Centre, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, M13 9WL, UK
| | - Jan C Oosterwijk
- Department of Genetics, University Medical Center Groningen, University Groningen, Groningen, 9713 GZ, The Netherlands
| | - Sue K Park
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, 03080, Korea
- Convergence Graduate Program in Innovative Medical Science, Seoul National University College of Medicine, Seoul, 03080, South Korea
- Cancer Research Institute, Seoul National University, Seoul, 03080, Korea
| | - Paolo Peterlongo
- Genome Diagnostics Program, IFOM - the FIRC Institute of Molecular Oncology, 20139, Milan, Italy
| | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Research, Fondazione IRCCS Istituto Nazionale Dei Tumori (INT), 20133, Milan, Italy
| | | | - Elinor J Sawyer
- School of Cancer & Pharmaceutical Sciences, Comprehensive Cancer Centre, Guy's Campus, King's College London, London, UK
| | - Rita K Schmutzler
- Center for Familial Breast and Ovarian Cancer, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937, Cologne, Germany
- Center for Integrated Oncology (CIO), Faculty of Medicine, University Hospital Cologne, University of Cologne, 50937, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
| | - Mitul Shah
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Xueling Sim
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, 117549, Singapore
| | - Melissa C Southey
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, 3004, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, 3168, Australia
- Department of Clinical Pathology, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Harald Surowy
- Molecular Epidemiology Group, C080, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Molecular Biology of Breast Cancer, University Womens Clinic Heidelberg, University of Heidelberg, 69120, Heidelberg, Germany
| | - Maija Suvanto
- Department of Obstetrics and Gynecology, Helsinki University Hospital, University of Helsinki, 00290, Helsinki, Finland
| | - Ian Tomlinson
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, B15 2TT, UK
- Wellcome Trust Centre for Human Genetics and Oxford NIHR Biomedical Research Centre, University of Oxford, Oxford, OX3 7BN, UK
| | - Diana Torres
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Institute of Human Genetics, Pontificia Universidad Javeriana, 110231, Bogota, Colombia
| | - Thérèse Truong
- Team "Exposome and Heredity", CESP, Inserm, Gustave Roussy, University Paris-Saclay, UVSQ, Villejuif, France
| | - Christi J van Asperen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, 2333 ZA, The Netherlands
| | - Regina Waltes
- Gynaecology Research Unit, Hannover Medical School, 30625, Hannover, Germany
| | - Qin Wang
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Xiaohong R Yang
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20850, USA
| | - Paul D P Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Marjanka K Schmidt
- Division of Molecular Pathology, The Netherlands Cancer Institute - Antoni Van Leeuwenhoek Hospital, Amsterdam, 1066 CX, The Netherlands
- Division of Psychosocial Research and Epidemiology, The Netherlands Cancer Institute - Antoni Van Leeuwenhoek Hospital, Amsterdam, 1066 CX, The Netherlands
| | - Javier Benitez
- Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), 28029, Madrid, Spain
- Biomedical Network On Rare Diseases (CIBERER), 28029, Madrid, Spain
| | - Bas Vroling
- Bio-Prodict, Nijmegen, The Netherlands
- Centre for Molecular and Biomolecular Informatics (CMBI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Alison M Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Soo Hwang Teo
- Breast Cancer Research Unit, Faculty of Medicine, University Malaya Cancer Research Institute, University of Malaya, 50603, Kuala Lumpur, Malaysia
- Breast Cancer Research Programme, Cancer Research Malaysia, Subang Jaya, 47500, Selangor, Malaysia
| | - Anders Kvist
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 22381, Lund, Sweden
| | - Miguel de la Hoya
- Molecular Oncology Laboratory, Hospital Clinico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), 28040, Madrid, Spain
| | - Peter Devilee
- Department of Human Genetics, Leiden University Medical Center, Leiden, 2333 ZA, The Netherlands
- Department of Pathology, Leiden University Medical Center, Leiden, 2333 ZA, The Netherlands
| | - Amanda B Spurdle
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Maaike P G Vreeswijk
- Department of Human Genetics, Leiden University Medical Center, Leiden, 2333 ZA, The Netherlands
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK.
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, CB1 8RN, UK.
| |
Collapse
|
21
|
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.
Collapse
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.
| |
Collapse
|
22
|
Okekunle A, Asowata O, Akinpeloye O, Olahan R, Ayodele A, Olaleye B, Akanni O, Akpa O. Community-based Investigation of the Risk Factors for Cardiovascular Diseases in Ibadan and suburbs (COMBAT-CVDs): Design and Methods. Afr J Biomed Res 2022; 25:265-271. [PMID: 35812130 PMCID: PMC9265233] [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] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Africa is gradually becoming the epicentre for the burden of cardiovascular diseases (CVDs) worldwide, and community-based data alluding to the pattern and dynamics of escalating epidemiological thresholds of CVDs among indigenous Africans are limited. This manuscript focuses on the design and methods of Community-based Investigation of the Risk Factors for Cardiovascular Diseases in Ibadan and suburbs (COMBAT-CVDs), an ongoing community-based door-to-door study assessing the profile, burden and dynamics of CVDs risk factors among residents of Ibadan and suburbs. COMBAT-CVDs is a cohort of community-dwelling indigenous Africans, males and females, ≥18years from ten communities in Ibadan, Nigeria. The recruitment of participants for the first wave (W0) started in 2020, covering; questionnaire administration and physical examination. The World Health Organization's STEPS Instrument for Chronic Disease Risk Factor Surveillance was used for data collection. Data were collected on sociodemographic, socioeconomic and lifestyle-related characteristics, history of CVDs, stress, depression and sleep quality. Also, anthropometric and blood pressure measures were conducted by trained personnel using standard operating procedures and instruments. Data collection for the second wave is underway, and the collection of blood and other biological samples for genetic epidemiology is planned, subject to availability of funds. For the W0 recruitment, a total of 3638 community-dwelling adults (males - 54.6% and females - 45.4%) participated with a ≥99.7% response rate. The COMBAT-CVDs will likely provide novel data, insightful characterization of CVDs risk factors and evidence for context-specific and culturally relevant interventions for the community-based prevention and management of CVDs among Africans in this setting.
Collapse
Affiliation(s)
- A.P. Okekunle
- Department of Epidemiology and Medical Statistics, College of Medicine, University of Ibadan, Ibadan, Nigeria
- The Postgraduate College, University of Ibadan, Ibadan, 200284, Nigeria
| | - O.J. Asowata
- Department of Epidemiology and Medical Statistics, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - O.J. Akinpeloye
- Department of Epidemiology and Medical Statistics, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - R. Olahan
- Department of Epidemiology and Medical Statistics, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - A.E. Ayodele
- Department of Epidemiology and Medical Statistics, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - B.J. Olaleye
- Department of Epidemiology and Medical Statistics, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - O.O. Akanni
- Department of Epidemiology and Medical Statistics, College of Medicine, University of Ibadan, Ibadan, Nigeria
- Department of Public Health, Lead City University, Ibadan, Nigeria
| | - O.M. Akpa
- Department of Epidemiology and Medical Statistics, College of Medicine, University of Ibadan, Ibadan, Nigeria
- The Postgraduate College, University of Ibadan, Ibadan, 200284, Nigeria
- Institute of Cardiovascular Diseases, College of Medicine, University of Ibadan, 200284 Ibadan, Nigeria
| |
Collapse
|
23
|
Breetvelt EJ, Smit KC, van Setten J, Merico D, Wang X, Vaartjes I, Bassett AS, Boks MPM, Szatmari P, Scherer SW, Kahn RS, Vorstman JAS. A Regional Burden of Sequence-Level Variation in the 22q11.2 Region Influences Schizophrenia Risk and Educational Attainment. Biol Psychiatry 2022; 91:718-726. [PMID: 35063188 DOI: 10.1016/j.biopsych.2021.11.019] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 10/25/2021] [Accepted: 11/12/2021] [Indexed: 12/12/2022]
Abstract
BACKGROUND Genomic loci where recurrent pathogenic copy number variants are associated with psychiatric phenotypes in the population may also be sensitive to the collective impact of multiple functional low-frequency single nucleotide variants (SNVs). METHODS We examined the cumulative impact of low-frequency, functional SNVs within the 22q11.2 region on schizophrenia risk in a discovery cohort and an independent replication cohort (N = 1933 and N = 11,128, respectively), as well as the impact on educational attainment (EA) in a third, independent, general population cohort (N = 2081). In the discovery and EA cohorts, SNVs were identified using genotyping arrays; in the replication cohort, whole-exome sequencing was available. For verification, we compared the regional SNV count for schizophrenia cases in the discovery cohort with a normative count distribution derived from a large population dataset (N = 26,500) using bootstrap procedures. RESULTS In both schizophrenia cohorts, an increased regional SNV burden (≥4 low-frequency SNVs) in the 22q11.2 region was associated with schizophrenia (discovery cohort: odds ratio = 7.48, p = .039; replication cohort: odds ratio = 1.92, p = .004). In the EA cohort, an increased regional SNV burden at 22q11.2 was associated with decreased EA (odds ratio = 4.65, p = .049). Comparing the SNV count for schizophrenia cases with a normative distribution confirmed the unique nature of the distribution for schizophrenia cases (p = .002). CONCLUSIONS In the general population, an increased burden of low-frequency, functional SNVs in the 22q11.2 region is associated with schizophrenia risk and a decrease in EA. These findings suggest that in addition to structural variation, a cumulative regional burden of low-frequency, functional SNVs in the 22q11.2 region can also have a relevant phenotypic impact.
Collapse
Affiliation(s)
- Elemi J Breetvelt
- Department of Psychiatry, The Hospital for Sick Children, Toronto, Ontario, Canada; Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada.
| | - Karel C Smit
- Department of Psychiatry, University Medical Center Utrecht Brain Center, Utrecht, The Netherlands; Department of Medical Oncology, University Medical Center Utrecht, University of Utrecht, Utrecht, The Netherlands; Department of Epidemiology, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, University of Utrecht, Utrecht, The Netherlands
| | - Jessica van Setten
- Department of Cardiology, University Medical Center Utrecht, University of Utrecht, Utrecht, The Netherlands
| | - Daniele Merico
- Center for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada; Deep Genomics Inc., Toronto, Ontario, Canada
| | - Xiao Wang
- Center for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Ilonca Vaartjes
- Department of Epidemiology, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, University of Utrecht, Utrecht, The Netherlands
| | - Anne S Bassett
- Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada; Dalglish Family 22q Clinic for Adults with 22q11.2 Deletion Syndrome, Toronto General Hospital, University Health Network, Toronto, Ontario, Canada; Clinical Genetics Research Program, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada; Medical Genetics and Genomics Residency Training Program, University of Toronto, Toronto, Ontario, Canada; Toronto General Research Institute, Toronto, Ontario, Canada; Campbell Family Mental Health Research Institute, Toronto, Ontario, Canada
| | - Marco P M Boks
- Department of Psychiatry, University Medical Center Utrecht Brain Center, Utrecht, The Netherlands
| | - Peter Szatmari
- Department of Psychiatry, The Hospital for Sick Children, Toronto, Ontario, Canada; Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada
| | - Stephen W Scherer
- Center for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada; McLaughlin Centre and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - René S Kahn
- Department of Psychiatry, University Medical Center Utrecht Brain Center, Utrecht, The Netherlands; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, NewYork, New York
| | - Jacob A S Vorstman
- Department of Psychiatry, The Hospital for Sick Children, Toronto, Ontario, Canada; Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada; Program in Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada; Department of Psychiatry, University Medical Center Utrecht Brain Center, Utrecht, The Netherlands
| |
Collapse
|
24
|
Sutton M, Sugier PE, Truong T, Liquet B. Leveraging pleiotropic association using sparse group variable selection in genomics data. BMC Med Res Methodol 2022; 22:9. [PMID: 34996381 PMCID: PMC8742466 DOI: 10.1186/s12874-021-01491-8] [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: 05/26/2021] [Accepted: 12/03/2021] [Indexed: 12/04/2022] Open
Abstract
Background Genome-wide association studies (GWAS) have identified genetic variants associated with multiple complex diseases. We can leverage this phenomenon, known as pleiotropy, to integrate multiple data sources in a joint analysis. Often integrating additional information such as gene pathway knowledge can improve statistical efficiency and biological interpretation. In this article, we propose statistical methods which incorporate both gene pathway and pleiotropy knowledge to increase statistical power and identify important risk variants affecting multiple traits. Methods We propose novel feature selection methods for the group variable selection in multi-task regression problem. We develop penalised likelihood methods exploiting different penalties to induce structured sparsity at a gene (or pathway) and SNP level across all studies. We implement an alternating direction method of multipliers (ADMM) algorithm for our penalised regression methods. The performance of our approaches are compared to a subset based meta analysis approach on simulated data sets. A bootstrap sampling strategy is provided to explore the stability of the penalised methods. Results Our methods are applied to identify potential pleiotropy in an application considering the joint analysis of thyroid and breast cancers. The methods were able to detect eleven potential pleiotropic SNPs and six pathways. A simulation study found that our method was able to detect more true signals than a popular competing method while retaining a similar false discovery rate. Conclusion We developed feature selection methods for jointly analysing multiple logistic regression tasks where prior grouping knowledge is available. Our method performed well on both simulation studies and when applied to a real data analysis of multiple cancers.
Collapse
Affiliation(s)
- Matthew Sutton
- Queensland University of Technology Centre for Data Science, Brisbane, Australia.
| | - Pierre-Emmanuel Sugier
- Laboratoire De Mathématiques et de leurs Applications de PAU E2S UPPA, CNRS, Pau, France.,University Paris-Saclay, UVSQ, Inserm, Gustave Roussy, CESP, Team "Exposome and Heredity", Villejuif, France
| | - Therese Truong
- University Paris-Saclay, UVSQ, Inserm, Gustave Roussy, CESP, Team "Exposome and Heredity", Villejuif, France
| | - Benoit Liquet
- Laboratoire De Mathématiques et de leurs Applications de PAU E2S UPPA, CNRS, Pau, France.,Department of Mathematics and Statistics, Macquarie University, Sydney, Australia
| |
Collapse
|
25
|
Moe JS, Bolstad I, Mørland JG, Bramness JG. GABA A subunit single nucleotide polymorphisms show sex-specific association to alcohol consumption and mental distress in a Norwegian population-based sample. Psychiatry Res 2022; 307:114257. [PMID: 34852975 DOI: 10.1016/j.psychres.2021.114257] [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] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 10/11/2021] [Accepted: 10/29/2021] [Indexed: 10/19/2022]
Abstract
Little is known about genetic influences on the relationship between alcohol consumption and mental distress in the general population, where the majority report consumption and distress far below diagnostic thresholds. This study investigated single nucleotide polymorphisms (SNPs) from candidate gene studies on alcohol use disorder and depressive disorders, for association with alcohol consumption and with mental distress in a population-based sample from the Cohort of Norway (n = 1978, 49% women). The relationship between alcohol consumption and mental distress was further examined for genotype modification. There was a positive correlation between mental distress and alcohol consumption in men, as well as an association between SNPs and mental distress in men (GABRG1, GABRA2, DRD2, ANKK1, MTHFR) and women (CHRM2, MTHFR) and between SNPs and alcohol consumption in women (GABRA2, MTHFR). No modification by SNP genotype was found on the relationship between alcohol consumption and mental distress. The association between mental distress and GABRG1 in men remained significant after correcting for multiple comparisons. The results indicate that alcohol consumption and mental distress are associated in the general population even at levels below clinical thresholds and point to SNPs in genes related to GABAergic signalling for level of mental distress in men.
Collapse
Affiliation(s)
- Jenny Skumsnes Moe
- Norwegian National Advisory Unit on Concurrent Substance Abuse and Mental Disorders, Innlandet Hospital Trust, Brumunddal, Norway; Institute of Clinical Medicine, UiT - The Arctic University of Norway, Tromsø, Norway.
| | - Ingeborg Bolstad
- Norwegian National Advisory Unit on Concurrent Substance Abuse and Mental Disorders, Innlandet Hospital Trust, Brumunddal, Norway; Blue Cross East, Norway
| | - Jørg Gustav Mørland
- Division of Health Data and Organization, Norwegian Institute of Public Health, Oslo, Norway; Institute of Clinical Medicine, University of Oslo, Norway
| | - Jørgen Gustav Bramness
- Norwegian National Advisory Unit on Concurrent Substance Abuse and Mental Disorders, Innlandet Hospital Trust, Brumunddal, Norway; Institute of Clinical Medicine, UiT - The Arctic University of Norway, Tromsø, Norway; Department of Alcohol, Tobacco and Drugs, Norwegian Institute of Public Health, Oslo, Norway
| |
Collapse
|
26
|
Jain A, Bhoyar RC, Pandhare K, Mishra A, Sharma D, Imran M, Senthivel V, Divakar MK, Rophina M, Jolly B, Batra A, Sharma S, Siwach S, Jadhao AG, Palande NV, Jha GN, Ashrafi N, Mishra PK, A K V, Jain S, Dash D, Kumar NS, Vanlallawma A, Sarma RJ, Chhakchhuak L, Kalyanaraman S, Mahadevan R, Kandasamy S, B M P, Rajagopal RE, Ramya J E, Devi P N, Bajaj A, Gupta V, Mathew S, Goswami S, Mangla M, Prakash S, Joshi K, Meyakumla, S S, Gajjar D, Soraisham R, Yadav R, Devi YS, Gupta A, Mukerji M, Ramalingam S, B K B, Scaria V, Sivasubbu S. Genetic epidemiology of autoinflammatory disease variants in Indian population from 1029 whole genomes. J Genet Eng Biotechnol 2021; 19:183. [PMID: 34905135 PMCID: PMC8671593 DOI: 10.1186/s43141-021-00268-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 10/13/2021] [Indexed: 11/16/2022]
Abstract
Background Autoinflammatory disorders are the group of inherited inflammatory disorders caused due to the genetic defect in the genes that regulates innate immune systems. These have been clinically characterized based on the duration and occurrence of unprovoked fever, skin rash, and patient’s ancestry. There are several autoinflammatory disorders that are found to be prevalent in a specific population and whose disease genetic epidemiology within the population has been well understood. However, India has a limited number of genetic studies reported for autoinflammatory disorders till date. The whole genome sequencing and analysis of 1029 Indian individuals performed under the IndiGen project persuaded us to perform the genetic epidemiology of the autoinflammatory disorders in India. Results We have systematically annotated the genetic variants of 56 genes implicated in autoinflammatory disorder. These genetic variants were reclassified into five categories (i.e., pathogenic, likely pathogenic, benign, likely benign, and variant of uncertain significance (VUS)) according to the American College of Medical Genetics and Association of Molecular pathology (ACMG-AMP) guidelines. Our analysis revealed 20 pathogenic and likely pathogenic variants with significant differences in the allele frequency compared with the global population. We also found six causal founder variants in the IndiGen dataset belonging to different ancestry. We have performed haplotype prediction analysis for founder mutations haplotype that reveals the admixture of the South Asian population with other populations. The cumulative carrier frequency of the autoinflammatory disorder in India was found to be 3.5% which is much higher than reported. Conclusion With such frequency in the Indian population, there is a great need for awareness among clinicians as well as the general public regarding the autoinflammatory disorder. To the best of our knowledge, this is the first and most comprehensive population scale genetic epidemiological study being reported from India. Supplementary Information The online version contains supplementary material available at 10.1186/s43141-021-00268-2.
Collapse
Affiliation(s)
- Abhinav Jain
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Rahul C Bhoyar
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India
| | - Kavita Pandhare
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India
| | - Anushree Mishra
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India
| | - Disha Sharma
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India
| | - Mohamed Imran
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Vigneshwar Senthivel
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Mohit Kumar Divakar
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Mercy Rophina
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Bani Jolly
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Arushi Batra
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Sumit Sharma
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India
| | - Sanjay Siwach
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India
| | - Arun G Jadhao
- Department of Zoology, RTM Nagpur University, Nagpur, Maharashtra, 440033, India
| | - Nikhil V Palande
- Department of Zoology, Shri Mathuradas Mohota College of Science, Nagpur, Maharashtra, 440009, India
| | - Ganga Nath Jha
- Department of Anthropology, Vinoba Bhave University, Hazaribag, Jharkhand, 825301, India
| | - Nishat Ashrafi
- Department of Anthropology, Vinoba Bhave University, Hazaribag, Jharkhand, 825301, India
| | - Prashant Kumar Mishra
- Department of Biotechnology, Vinoba Bhave University, Hazaribag, Jharkhand, 825301, India
| | - Vidhya A K
- Department of Biochemistry, Dr. Kongu Science and Art College, Erode, Tamil Nadu, 638107, India
| | - Suman Jain
- Thalassemia and Sickle Cell Society, Hyderabad, Telangana, 500052, India
| | - Debasis Dash
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | | | - Andrew Vanlallawma
- Department of Biotechnology, Mizoram University, Aizawl, Mizoram, 796004, India
| | - Ranjan Jyoti Sarma
- Department of Biotechnology, Mizoram University, Aizawl, Mizoram, 796004, India
| | | | | | - Radha Mahadevan
- TVMC, Tirunelveli Medical College, Tirunelveli, Tamil Nadu, 627011, India
| | - Sunitha Kandasamy
- TVMC, Tirunelveli Medical College, Tirunelveli, Tamil Nadu, 627011, India
| | - Pabitha B M
- TVMC, Tirunelveli Medical College, Tirunelveli, Tamil Nadu, 627011, India
| | | | - Ezhil Ramya J
- TVMC, Tirunelveli Medical College, Tirunelveli, Tamil Nadu, 627011, India
| | - Nirmala Devi P
- TVMC, Tirunelveli Medical College, Tirunelveli, Tamil Nadu, 627011, India
| | - Anjali Bajaj
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Vishu Gupta
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Samatha Mathew
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Sangam Goswami
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Mohit Mangla
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Savinitha Prakash
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India
| | - Kandarp Joshi
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India
| | - Meyakumla
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India
| | - Sreedevi S
- Department of Microbiology, St.Pious X Degree & PG College for Women, Hyderabad, Telangana, 500076, India
| | - Devarshi Gajjar
- Department of Microbiology, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat, 390002, India
| | - Ronibala Soraisham
- Department of Dermatology, Venereology and Leprology, Regional Institute of Medical Sciences, Imphal, Manipur, 795004, India
| | - Rohit Yadav
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Yumnam Silla Devi
- CSIR- North East Institute of Science and Technology, Jorhat, Assam, 785006, India
| | - Aayush Gupta
- Department of Dermatology, Dr. D.Y. Patil Medical College, Pune, Maharashtra, 411018, India
| | - Mitali Mukerji
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Sivaprakash Ramalingam
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Binukumar B K
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Vinod Scaria
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India. .,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India.
| | - Sridhar Sivasubbu
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India. .,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India.
| |
Collapse
|
27
|
Morgenstern-Kaplan D, Raijman-Policar J, Majzner-Aronovich S, Aradhya S, Pineda-Alvarez DE, Aguinaga M, García-Vences EE. Carrier screening in the Mexican Jewish community using a pan-ethnic expanded carrier screening NGS panel. Genet Med 2021; 24:821-830. [PMID: 34961661 DOI: 10.1016/j.gim.2021.11.019] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 11/20/2021] [Accepted: 11/22/2021] [Indexed: 10/19/2022] Open
Abstract
PURPOSE The Mexican Jewish community (MJC) is a previously uncharacterized, genetically isolated group composed of Ashkenazi and Sephardi-Mizrahi Jews who migrated in the early 1900s. We aimed to determine the heterozygote frequency of disease-causing variants in 302 genes in this population. METHODS We conducted a cross-sectional study of the MJC involving individuals representing Ashkenazi Jews, Sephardi-Mizrahi Jews, or mixed-ancestry Jews. We offered saliva-based preconception pan-ethnic expanded carrier screening, which examined 302 genes. We analyzed heterozygote frequencies of pathogenic/likely pathogenic variants and compared them with those in the Genome Aggregation Database (gnomAD). RESULTS We recruited 208 participants. The carrier screening results showed that 72.1% were heterozygous for at least 1 severe disease-causing variant in 1 of the genes analyzed. The most common genes with severe disease-causing variants were CFTR (16.8% of participants), MEFV (11.5%), WNT10A (6.7%), and GBA (6.7%). The allele frequencies were compared with those in the gnomAD; 85% of variant frequencies were statistically different from those found in gnomAD (P <.05). Finally, 6% of couples were at risk of having a child with a severe disorder. CONCLUSION The heterozygote frequency of at least 1 severe disease-causing variant in the MJC was 72.1%. The use of carrier screening in the MJC and other understudied populations could help parents make more informed decisions.
Collapse
Affiliation(s)
- Dan Morgenstern-Kaplan
- Centro de Investigación en Ciencias de la Salud (CICSA), Health Sciences Faculty, Anahuac University, Mexico City, Mexico.
| | - Jaime Raijman-Policar
- Centro de Investigación en Ciencias de la Salud (CICSA), Health Sciences Faculty, Anahuac University, Mexico City, Mexico
| | - Sore Majzner-Aronovich
- Centro de Investigación en Ciencias de la Salud (CICSA), Health Sciences Faculty, Anahuac University, Mexico City, Mexico
| | | | | | - Mónica Aguinaga
- Centro de Investigación en Ciencias de la Salud (CICSA), Health Sciences Faculty, Anahuac University, Mexico City, Mexico; Sexual and Reproductive Health Department, National Institute of Perinatology, Mexico City, Mexico
| | - Edna Elisa García-Vences
- Centro de Investigación en Ciencias de la Salud (CICSA), Health Sciences Faculty, Anahuac University, Mexico City, Mexico
| |
Collapse
|
28
|
Wang MH, Lou J, Cao L, Zhao S, Chan RW, Chan PK, Chan MCW, Chong MK, Wu WK, Wei Y, Zhang H, Zee BC, Yeoh EK. Characterization of key amino acid substitutions and dynamics of the influenza virus H3N2 hemagglutinin. J Infect 2021; 83:671-677. [PMID: 34627840 DOI: 10.1016/j.jinf.2021.09.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 06/10/2021] [Accepted: 09/30/2021] [Indexed: 10/20/2022]
Abstract
The annual epidemics of seasonal influenza is partly attributed to the continued virus evolution. It is challenging to evaluate the effect of influenza virus mutations on evading population immunity. In this study, we introduce a novel statistical and computational approach to measure the dynamic molecular determinants underlying epidemics using effective mutations (EMs), and account for the time of waning mutation advantage against herd immunity by measuring the effective mutation periods (EMPs). Extensive analysis is performed on the sequencing and epidemiology data of H3N2 epidemics in ten regions from season to season. We systematically identified 46 EMs in the hemagglutinin (HA) gene, in which the majority were antigenic sites. Eight EMs were located in immunosubdominant stalk domain, an important target for developing broadly reactive antibodies. The EMs might provide timely information on key substitutions for influenza vaccines antigen design. The EMP suggested that major genetic variants of H3N2 circulated in Southeast Asia for an average duration of 4.5 years (SD 2.4) compared to a significantly shorter 2.0 years (SD 1.0) in temperate regions. The proposed method bridges population epidemics and molecular characteristics of infectious diseases, and would find broad applications in various pathogens mutation estimations.
Collapse
Affiliation(s)
- Maggie Haitian Wang
- JC School of Public Health and Primary Care, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China; CUHK Shenzhen Research Institute, Shenzhen, China.
| | - Jingzhi Lou
- JC School of Public Health and Primary Care, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China; CUHK Shenzhen Research Institute, Shenzhen, China
| | - Lirong Cao
- JC School of Public Health and Primary Care, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China; CUHK Shenzhen Research Institute, Shenzhen, China
| | - Shi Zhao
- JC School of Public Health and Primary Care, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China; CUHK Shenzhen Research Institute, Shenzhen, China
| | - Renee Wy Chan
- CUHK-UMCU Joint Research Laboratory of Respiratory Virus & Immunobiology, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China; Department of Paediatrics, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
| | - Paul Ks Chan
- Department of Microbiology, Stanley Ho Center for Emerging Infectious Diseases, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
| | - Martin Chi-Wai Chan
- Department of Microbiology, Stanley Ho Center for Emerging Infectious Diseases, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
| | - Marc Kc Chong
- JC School of Public Health and Primary Care, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China; CUHK Shenzhen Research Institute, Shenzhen, China
| | - William Kk Wu
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
| | - Yuchen Wei
- Department of Microbiology, Stanley Ho Center for Emerging Infectious Diseases, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
| | - Haoyang Zhang
- JC School of Public Health and Primary Care, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
| | - Benny Cy Zee
- JC School of Public Health and Primary Care, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China; CUHK Shenzhen Research Institute, Shenzhen, China
| | - Eng-Kiong Yeoh
- JC School of Public Health and Primary Care, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China.
| |
Collapse
|
29
|
Knowles EEM, Peralta JM, Almasy L, Nimgaonkar V, McMahon FJ, McIntosh AM, Thomson P, Mathias SR, Gur RC, Curran JE, Raventós H, Contreras J, Jablensky A, Badcock J, Blangero J, Gur RE, Glahn DC. Genetic Overlap Profiles of Cognitive Ability in Psychotic and Affective Illnesses: A Multisite Study of Multiplex Pedigrees. Biol Psychiatry 2021; 90:373-84. [PMID: 33975707 DOI: 10.1016/j.biopsych.2021.03.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 01/08/2021] [Accepted: 03/10/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND Cognitive impairment is a key feature of psychiatric illness, making cognition an important tool for exploring of the genetics of illness risk. It remains unclear which measures should be prioritized in pleiotropy-guided research. Here, we generate profiles of genetic overlap between psychotic and affective disorders and cognitive measures in Caucasian and Hispanic groups. METHODS Data were from 4 samples of extended pedigrees (N = 3046). Coefficient of relationship analyses were used to estimate genetic overlap between illness risk and cognitive ability. Results were meta-analyzed. RESULTS Psychosis was characterized by cognitive impairments on all measures with a generalized profile of genetic overlap. General cognitive ability shared greatest genetic overlap with psychosis risk (average endophenotype ranking value [ERV] across samples from a random-effects meta-analysis = 0.32), followed by verbal memory (ERV = 0.24), executive function (ERV = 0.22), and working memory (ERV = 0.21). For bipolar disorder, there was genetic overlap with processing speed (ERV = 0.05) and verbal memory (ERV = 0.11), but these were confined to select samples. Major depressive disorder was characterized by enhanced working and face memory performance, as reflected in significant genetic overlap in 2 samples. CONCLUSIONS There is substantial genetic overlap between risk for psychosis and a range of cognitive abilities (including general intelligence). Most of these effects are largely stable across of ascertainment strategy and ethnicity. Genetic overlap between affective disorders and cognition, on the other hand, tends to be specific to ascertainment strategy, ethnicity, and cognitive test battery.
Collapse
|
30
|
Wu PF, Lu H, Zhou X, Liang X, Li R, Zhang W, Li D, Xia K. Assessment of causal effects of physical activity on neurodegenerative diseases: A Mendelian randomization study. J Sport Health Sci 2021; 10:454-461. [PMID: 33515719 PMCID: PMC8343066 DOI: 10.1016/j.jshs.2021.01.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 10/13/2020] [Accepted: 12/17/2020] [Indexed: 05/14/2023]
Abstract
BACKGROUND Physical activity has been hypothesized to play a protective role in neurodegenerative diseases. However, effect estimates previously derived from observational studies were prone to confounding or reverse causation. METHODS We performed a two-sample Mendelian randomization (MR) analysis to explore the causal association of accelerometer-measured physical activity with 3 common neurodegenerative diseases: Alzheimer's disease (AD), Parkinson's disease (PD), and amyotrophic lateral sclerosis (ALS). We selected genetic instrumental variants reaching genome-wide significance (p < 5 × 10-8) from 2 largest meta-analyses of about 91,100 UK Biobank participants. Summary statistics for AD, PD, and ALS were retrieved from the up-to-date studies in European ancestry led by the international consortia. The random-effect, inverse-variance weighted MR was employed as the primary method, while MR pleiotropy residual sum and outlier (MR-PRESSO), weighted median, and MR-Egger were implemented as sensitivity tests. All statistical analyses were performed using the R programming language (Version 3.6.1; R Foundation for Statistical Computing, Vienna, Austria). RESULTS Primary MR analysis and replication analysis utilized 5 and 8 instrumental variables, which explained 0.2% and 0.4% variance in physical activity, respectively. In each set, one variant at 17q21 was significantly associated with PD, and MR sensitivity analyses indicated them it as an outlier and source of heterogeneity and pleiotropy. Primary results with the removal of outlier variants suggested odds ratios (ORs) of neurodegenerative diseases per unit increase in objectively measured physical activity were 1.52 for AD (95% confidence interval (95%CI): 0.88-2.63, p = 0.13) and 3.35 for PD (95%CI: 1.32-8.48, p = 0.01), while inconsistent results were shown in the replication set for AD (OR = 1.06, 95%CI: 1.01-1.12, p = 0.02) and PD (OR = 0.99, 95%CI: 0.88-0.12, p = 0.97). Similarly, the beneficial effect of physical activity on ALS (OR = 0.51, 95%CI: 0.29-0.91, p = 0.02) was not confirmed in the replication analysis (OR = 0.96, 95%CI: 0.91-1.02, p = 0.22). CONCLUSION Genetically predicted physical activity was not robustly associated with risk of neurodegenerative disorders. Triangulating evidence across other studies is necessary in order to elucidate whether enhancing physical activity is an effective approach in preventing the onset of AD, PD, or ALS.
Collapse
Affiliation(s)
- Peng-Fei Wu
- Center for Medical Genetics & Hunan Provincial Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410008, China; Department of Neurology, Beth Israel Deaconess Medical Center & Harvard Medical School, Boston, MA 02115, USA
| | - Hui Lu
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing 100053, China.
| | - Xiaoting Zhou
- Department of Neurology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Xuchen Liang
- School of Physical Education, Henan University, Kaifeng 475001, China
| | - Ruizhuo Li
- School of Medicine, South China University of Technology, Guangzhou 510006, China
| | - Wan Zhang
- Department of Neurology, Beth Israel Deaconess Medical Center & Harvard Medical School, Boston, MA 02115, USA; Department of Biology, College of Arts & Sciences, Boston University, Boston, MA 02215, USA
| | - Danyang Li
- Department of Biology, College of Arts & Sciences, Boston University, Boston, MA 02215, USA
| | - Kun Xia
- Center for Medical Genetics & Hunan Provincial Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410008, China; CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai 200031, China.
| |
Collapse
|
31
|
Wan JY, Goodman DL, Willems EL, Freedland AR, Norden-Krichmar TM, Santorico SA, Edwards KL. Genome-wide association analysis of metabolic syndrome quantitative traits in the GENNID multiethnic family study. Diabetol Metab Syndr 2021; 13:59. [PMID: 34074324 PMCID: PMC8170963 DOI: 10.1186/s13098-021-00670-3] [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] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 04/28/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND To identify genetic associations of quantitative metabolic syndrome (MetS) traits and characterize heterogeneity across ethnic groups. METHODS Data was collected from GENetics of Noninsulin dependent Diabetes Mellitus (GENNID), a multiethnic resource of Type 2 diabetic families and included 1520 subjects in 259 African-American, European-American, Japanese-Americans, and Mexican-American families. We focused on eight MetS traits: weight, waist circumference, systolic and diastolic blood pressure, high-density lipoprotein, triglycerides, fasting glucose, and insulin. Using genotyped and imputed data from Illumina's Multiethnic array, we conducted genome-wide association analyses with linear mixed models for all ethnicities, except for the smaller Japanese-American group, where we used additive genetic models with gene-dropping. RESULTS Findings included ethnic-specific genetic associations and heterogeneity across ethnicities. Most significant associations were outside our candidate linkage regions and were coincident within a gene or intergenic region, with two exceptions in European-American families: (a) within previously identified linkage region on chromosome 2, two significant GLI2-TFCP2L1 associations with weight, and (b) one chromosome 11 variant near CADM1-LINC00900 with pleiotropic blood pressure effects. CONCLUSIONS This multiethnic family study found genetic heterogeneity and coincident associations (with one case of pleiotropy), highlighting the importance of including diverse populations in genetic research and illustrating the complex genetic architecture underlying MetS.
Collapse
Affiliation(s)
- Jia Y Wan
- Department of Epidemiology and Biostatistics, Program in Public Health, University of California, 635 E. Peltason Dr, Mail Code: 7550, Irvine, CA, 92697, USA
| | - Deborah L Goodman
- Department of Epidemiology and Biostatistics, Program in Public Health, University of California, 635 E. Peltason Dr, Mail Code: 7550, Irvine, CA, 92697, USA
| | - Emileigh L Willems
- Department of Mathematical and Statistical Sciences, University of Colorado, Denver, CO, USA
| | - Alexis R Freedland
- Department of Epidemiology and Biostatistics, Program in Public Health, University of California, 635 E. Peltason Dr, Mail Code: 7550, Irvine, CA, 92697, USA
| | - Trina M Norden-Krichmar
- Department of Epidemiology and Biostatistics, Program in Public Health, University of California, 635 E. Peltason Dr, Mail Code: 7550, Irvine, CA, 92697, USA
| | - Stephanie A Santorico
- Department of Mathematical and Statistical Sciences, University of Colorado, Denver, CO, USA
- Human Medical Genetics and Genomics Program, University of Colorado, Denver, CO, USA
- Department of Biostatistics & Informatics, University of Colorado, Denver, CO, USA
- Division of Biomedical Informatics & Personalized Medicine, University of Colorado School of Medicine, Aurora, CO, USA
| | - Karen L Edwards
- Department of Epidemiology and Biostatistics, Program in Public Health, University of California, 635 E. Peltason Dr, Mail Code: 7550, Irvine, CA, 92697, USA.
| |
Collapse
|
32
|
Russell AE, Hemani G, Jones HJ, Ford T, Gunnell D, Heron J, Joinson C, Moran P, Relton C, Suderman M, Watkins S, Mars B. An exploration of the genetic epidemiology of non-suicidal self-harm and suicide attempt. BMC Psychiatry 2021; 21:207. [PMID: 33892675 PMCID: PMC8066869 DOI: 10.1186/s12888-021-03216-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 04/14/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Empirical evidence supporting the distinction between suicide attempt (SA) and non-suicidal self-harm (NSSH) is lacking. Although NSSH is a risk factor for SA, we do not currently know whether these behaviours lie on a continuum of severity, or whether they are discrete outcomes with different aetiologies. We conducted this exploratory genetic epidemiology study to investigate this issue further. METHODS We explored the extent of genetic overlap between NSSH and SA in a large, richly-phenotyped cohort (the Avon Longitudinal Study of Parents and Children; N = 4959), utilising individual-level genetic and phenotypic data to conduct analyses of genome-wide complex traits and polygenic risk scores (PRS). RESULTS The single nucleotide polymorphism heritability of NSSH was estimated to be 13% (SE 0.07) and that of SA to be 0% (SE 0.07). Of the traits investigated, NSSH was most strongly correlated with higher IQ (rG = 0.31, SE = 0.22), there was little evidence of high genetic correlation between NSSH and SA (rG = - 0.1, SE = 0.54), likely due to the low heritability estimate for SA. The PRS for depression differentiated between those with NSSH and SA in multinomial regression. The optimal PRS prediction model for SA (Nagelkerke R2 0.022, p < 0.001) included ADHD, depression, income, anorexia and neuroticism and explained more variance than the optimal prediction model for NSSH (Nagelkerke R2 0.010, p < 0.001) which included ADHD, alcohol consumption, autism spectrum conditions, depression, IQ, neuroticism and suicide attempt. CONCLUSIONS Our findings suggest that SA does not have a large genetic component, and that although NSSH and SA are not discrete outcomes there appears to be little genetic overlap between the two. The relatively small sample size and resulting low heritability estimate for SA was a limitation of the study. Combined with low heritability estimates, this implies that family or population structures in SA GWASs may contribute to signals detected.
Collapse
Affiliation(s)
- Abigail Emma Russell
- Children and Young People's Mental Health Research Collaboration (ChYMe), University of Exeter College of Medicine and Health, Exeter, UK.
| | - Gibran Hemani
- MRC Integrative Epidemiology Unit, University of Bristol Medical School, Bristol, UK
- Population Health Sciences, University of Bristol Medical School, Bristol, UK
| | - Hannah J Jones
- Centre for Academic Mental Health, Population Health Sciences, University of Bristol Medical School, Bristol, UK
| | - Tamsin Ford
- University of Cambridge Department of Psychiatry, Cambridge, UK
| | - David Gunnell
- Centre for Academic Mental Health, Population Health Sciences, University of Bristol Medical School, Bristol, UK
- NIHR Biomedical Research Centre at the University Hospitals Bristol NHS Foundation Trust and the University of Bristol, Bristol, UK
| | - Jon Heron
- Centre for Academic Mental Health, Population Health Sciences, University of Bristol Medical School, Bristol, UK
| | - Carol Joinson
- Centre for Academic Mental Health, Population Health Sciences, University of Bristol Medical School, Bristol, UK
| | - Paul Moran
- Centre for Academic Mental Health, Population Health Sciences, University of Bristol Medical School, Bristol, UK
- NIHR Biomedical Research Centre at the University Hospitals Bristol NHS Foundation Trust and the University of Bristol, Bristol, UK
| | - Caroline Relton
- MRC Integrative Epidemiology Unit, University of Bristol Medical School, Bristol, UK
- Population Health Sciences, University of Bristol Medical School, Bristol, UK
| | - Matthew Suderman
- MRC Integrative Epidemiology Unit, University of Bristol Medical School, Bristol, UK
- Population Health Sciences, University of Bristol Medical School, Bristol, UK
| | - Sarah Watkins
- Centre for Academic Mental Health, Population Health Sciences, University of Bristol Medical School, Bristol, UK
| | - Becky Mars
- Centre for Academic Mental Health, Population Health Sciences, University of Bristol Medical School, Bristol, UK
- NIHR Biomedical Research Centre at the University Hospitals Bristol NHS Foundation Trust and the University of Bristol, Bristol, UK
| |
Collapse
|
33
|
Al-Soufi L, Costas J. Colocalization of association signals at nicotinic acetylcholine receptor genes between schizophrenia and smoking traits. Drug Alcohol Depend 2021; 220:108517. [PMID: 33454625 DOI: 10.1016/j.drugalcdep.2021.108517] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 12/16/2020] [Accepted: 12/17/2020] [Indexed: 11/20/2022]
Abstract
BACKGROUND Epidemiological data suggest that smoking may be a risk factor for schizophrenia (SCZ), but more evidence is needed. Two regions coding nicotinic acetylcholine receptor (nAchR) subunits, atCHRNA2 and the CHRNA5/A3/B4 cluster, were associated with SCZ in genome-wide association studies (GWAS). Additionally, a signal at CHRNA4 is near significance. CHRNA2 was also associated with cannabis use disorder (CUD). These regions were also associated with smoking behaviors. If tobacco is a risk factor, the GWAS signals at smoking behaviors and SCZ have to be due to the same causal variants, i.e. they have to colocalize, although colocalization does not necessarily imply causality. Here, we present colocalization analysis at these loci between SCZ and smoking behaviors. METHODS The Bayesian approach implemented in coloc was used to check for posterior probability of colocalization versus independent signals at the three loci with some evidence of association with SCZ and smoking behaviors, using GWAS summary statistics. Colocalization was also assessed for positive control traits and CUD. Three different sensibility analyses were used to confirm the results. A visualization tool, LocusCompare, was used to facilitate interpretation of the coloc results. RESULTS Evidence for colocalization of GWAS signals between SCZ and smoking behaviors was found for CHRNA2. Evidence for independent causal variants was found for the other two loci. CUD GWAS signal at CHRNA2 colocalizes with SCZ and smoking behaviors. CONCLUSIONS Overall, the results indicate that the association between some nAchR subunit genes and SCZ cannot be solely explained by their effect on smoking behaviors.
Collapse
|
34
|
Go TH, Kwak KI, Jang JY, Yu M, Kim HS, Kim JY, Koh SB, Kang DR. Inference of a causal relation between low-density lipoprotein cholesterol and hypertension using mendelian randomization analysis. Clin Hypertens 2021; 27:7. [PMID: 33637130 DOI: 10.1186/s40885-021-00162-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 01/08/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND It is known in some studies that higher the LDL-C, the greater the risk of developing cardiovascular disease. However, studies of the causal effects between LDL-C and hypertension are limited by their observational study design, and genetic epidemiology studies of associations between LDL-C and hypertension are lacking, as are studies using data for Koreans. In this study, we confirmed the causal effect of LDL-C on hypertension using Korean chip data. METHOD The epidemiology and genotype data were collected from the Korean Genome and Epidemiology Study conducted by the Korea National Institute of Health and covered 20,701 subjects. Single-nucleotide polymorphisms associated with LDL-C were selected (p-value < 5 × 10- 8) from the Global Lipids Genetics Consortium database, and Mendelian randomization analysis (MRA) was performed with counted genetic risk scores and weighted genetic risk scores (WGRSs) for 24 single-nucleotide polymorphisms. RESULT The assumptions for MRA were statistically confirmed, and WGRSs showed a strong association with LDL-C. Interestingly, while the relationship between LDL-C and hypertension was not statistically significant in the observational study, MRA study demonstrated that the risk of hypertension increased as LDL-C increased in both men and women. CONCLUSIONS The results of this study confirmed that the relationship between LDL-C and hypertension is greatly influenced by genetic information.
Collapse
|
35
|
Abstract
BACKGROUND The increasing number of genome-wide association studies (GWAS) has revealed several loci that are associated to multiple distinct phenotypes, suggesting the existence of pleiotropic effects. Highlighting these cross-phenotype genetic associations could help to identify and understand common biological mechanisms underlying some diseases. Common approaches test the association between genetic variants and multiple traits at the SNP level. In this paper, we propose a novel gene- and a pathway-level approach in the case where several independent GWAS on independent traits are available. The method is based on a generalization of the sparse group Partial Least Squares (sgPLS) to take into account groups of variables, and a Lasso penalization that links all independent data sets. This method, called joint-sgPLS, is able to convincingly detect signal at the variable level and at the group level. RESULTS Our method has the advantage to propose a global readable model while coping with the architecture of data. It can outperform traditional methods and provides a wider insight in terms of a priori information. We compared the performance of the proposed method to other benchmark methods on simulated data and gave an example of application on real data with the aim to highlight common susceptibility variants to breast and thyroid cancers. CONCLUSION The joint-sgPLS shows interesting properties for detecting a signal. As an extension of the PLS, the method is suited for data with a large number of variables. The choice of Lasso penalization copes with architectures of groups of variables and observations sets. Furthermore, although the method has been applied to a genetic study, its formulation is adapted to any data with high number of variables and an exposed a priori architecture in other application fields.
Collapse
Affiliation(s)
- Camilo Broc
- LIST, CEA, Laboratory for Data Sciences and Decision (Digiteo), Gif-sur-Yvette, France
- CNRS, Laboratoire de Mathématiques et de leurs Applications de PAU E2S UPPA, Pau, France
| | - Therese Truong
- UVSQ, Inserm, CESP, Université Paris-Saclay, 94807 Villejuif, France
- Institut Gustave Roussy, 94805 Villejuif, France
| | - Benoit Liquet
- CNRS, Laboratoire de Mathématiques et de leurs Applications de PAU E2S UPPA, Pau, France
- Department of Mathematics and Statistics, Macquarie University, Sydney, Australia
| |
Collapse
|
36
|
Dennis JK, Sealock JM, Straub P, Lee YH, Hucks D, Actkins K, Faucon A, Feng YCA, Ge T, Goleva SB, Niarchou M, Singh K, Morley T, Smoller JW, Ruderfer DM, Mosley JD, Chen G, Davis LK. Clinical laboratory test-wide association scan of polygenic scores identifies biomarkers of complex disease. Genome Med 2021; 13:6. [PMID: 33441150 PMCID: PMC7807864 DOI: 10.1186/s13073-020-00820-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [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: 02/25/2020] [Accepted: 12/08/2020] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Clinical laboratory (lab) tests are used in clinical practice to diagnose, treat, and monitor disease conditions. Test results are stored in electronic health records (EHRs), and a growing number of EHRs are linked to patient DNA, offering unprecedented opportunities to query relationships between genetic risk for complex disease and quantitative physiological measurements collected on large populations. METHODS A total of 3075 quantitative lab tests were extracted from Vanderbilt University Medical Center's (VUMC) EHR system and cleaned for population-level analysis according to our QualityLab protocol. Lab values extracted from BioVU were compared with previous population studies using heritability and genetic correlation analyses. We then tested the hypothesis that polygenic risk scores for biomarkers and complex disease are associated with biomarkers of disease extracted from the EHR. In a proof of concept analyses, we focused on lipids and coronary artery disease (CAD). We cleaned lab traits extracted from the EHR performed lab-wide association scans (LabWAS) of the lipids and CAD polygenic risk scores across 315 heritable lab tests then replicated the pipeline and analyses in the Massachusetts General Brigham Biobank. RESULTS Heritability estimates of lipid values (after cleaning with QualityLab) were comparable to previous reports and polygenic scores for lipids were strongly associated with their referent lipid in a LabWAS. LabWAS of the polygenic score for CAD recapitulated canonical heart disease biomarker profiles including decreased HDL, increased pre-medication LDL, triglycerides, blood glucose, and glycated hemoglobin (HgbA1C) in European and African descent populations. Notably, many of these associations remained even after adjusting for the presence of cardiovascular disease and were replicated in the MGBB. CONCLUSIONS Polygenic risk scores can be used to identify biomarkers of complex disease in large-scale EHR-based genomic analyses, providing new avenues for discovery of novel biomarkers and deeper understanding of disease trajectories in pre-symptomatic individuals. We present two methods and associated software, QualityLab and LabWAS, to clean and analyze EHR labs at scale and perform a Lab-Wide Association Scan.
Collapse
Affiliation(s)
- Jessica K Dennis
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V5Z 4H4, Canada
| | - Julia M Sealock
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Peter Straub
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Younga H Lee
- Psychiatric & Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Psychiatry, Harvard Medical School, Boston, MA, 02115, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Donald Hucks
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Ky'Era Actkins
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Department of Microbiology, Immunology, and Physiology, Meharry Medical College, Nashville, TN, 37232, USA
| | - Annika Faucon
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Yen-Chen Anne Feng
- Psychiatric & Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Tian Ge
- Psychiatric & Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Psychiatry, Harvard Medical School, Boston, MA, 02115, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Slavina B Goleva
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Maria Niarchou
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Kritika Singh
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Theodore Morley
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Jordan W Smoller
- Psychiatric & Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Psychiatry, Harvard Medical School, Boston, MA, 02115, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Douglas M Ruderfer
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Department of Psychiatry and Behavioral Sciences, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Departments of Medicine and Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Jonathan D Mosley
- Departments of Medicine and Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Guanhua Chen
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Lea K Davis
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA.
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, 37232, USA.
- Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, TN, 37232, USA.
- Department of Psychiatry and Behavioral Sciences, Vanderbilt University Medical Center, Nashville, TN, 37232, USA.
- Departments of Medicine and Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, 37232, USA.
- Division of Genetic Medicine, Department of Medicine, Vanderbilt Genetics Institute, Vanderbilt University, 511-A Light Hall, 2215 Garland Ave, Nashville, TN, 37232, USA.
| |
Collapse
|
37
|
Lin YC, Brooks JD, Bull SB, Gagnon F, Greenwood CMT, Hung RJ, Lawless J, Paterson AD, Sun L, Strug LJ. Statistical power in COVID-19 case-control host genomic study design. Genome Med 2020; 12:115. [PMID: 33371892 PMCID: PMC7768597 DOI: 10.1186/s13073-020-00818-2] [Citation(s) in RCA: 4] [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: 09/01/2020] [Accepted: 12/07/2020] [Indexed: 12/21/2022] Open
Abstract
The identification of genetic variation that directly impacts infection susceptibility to SARS-CoV-2 and disease severity of COVID-19 is an important step towards risk stratification, personalized treatment plans, therapeutic, and vaccine development and deployment. Given the importance of study design in infectious disease genetic epidemiology, we use simulation and draw on current estimates of exposure, infectivity, and test accuracy of COVID-19 to demonstrate the feasibility of detecting host genetic factors associated with susceptibility and severity in published COVID-19 study designs. We demonstrate that limited phenotypic data and exposure/infection information in the early stages of the pandemic significantly impact the ability to detect most genetic variants with moderate effect sizes, especially when studying susceptibility to SARS-CoV-2 infection. Our insights can aid in the interpretation of genetic findings emerging in the literature and guide the design of future host genetic studies.
Collapse
Affiliation(s)
- Yu-Chung Lin
- Dalla Lana School of Public Health, University of Toronto, Room 500, 155 College St, Toronto, ON, M5T3M7, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Room 12.9801, 686 Bay Street, Toronto, ON, M5G0A4, Canada
| | - Jennifer D Brooks
- Dalla Lana School of Public Health, University of Toronto, Room 500, 155 College St, Toronto, ON, M5T3M7, Canada
| | - Shelley B Bull
- Dalla Lana School of Public Health, University of Toronto, Room 500, 155 College St, Toronto, ON, M5T3M7, Canada
- Prosserman Centre for Population Health Research, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
| | - France Gagnon
- Dalla Lana School of Public Health, University of Toronto, Room 500, 155 College St, Toronto, ON, M5T3M7, Canada
| | - Celia M T Greenwood
- Gerald Bronfman Department of Oncology, Department of Epidemiology, Biostatistics & Occupational Health, Department of Human Genetics, McGill University, Montreal, QC, Canada
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada
| | - Rayjean J Hung
- Dalla Lana School of Public Health, University of Toronto, Room 500, 155 College St, Toronto, ON, M5T3M7, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Room 12.9801, 686 Bay Street, Toronto, ON, M5G0A4, Canada
| | - Jerald Lawless
- Department of Statistics and Actuarial Science, University of Waterloo, Waterloo, ON, Canada
| | - Andrew D Paterson
- Dalla Lana School of Public Health, University of Toronto, Room 500, 155 College St, Toronto, ON, M5T3M7, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Room 12.9801, 686 Bay Street, Toronto, ON, M5G0A4, Canada
| | - Lei Sun
- Dalla Lana School of Public Health, University of Toronto, Room 500, 155 College St, Toronto, ON, M5T3M7, Canada
- Department of Statistical Sciences, University of Toronto, 9th Floor, Ontario Power Building 700 University Ave, Toronto, ON, M5G 1Z5, Canada
| | - Lisa J Strug
- Dalla Lana School of Public Health, University of Toronto, Room 500, 155 College St, Toronto, ON, M5T3M7, Canada.
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Room 12.9801, 686 Bay Street, Toronto, ON, M5G0A4, Canada.
- Department of Statistical Sciences, University of Toronto, 9th Floor, Ontario Power Building 700 University Ave, Toronto, ON, M5G 1Z5, Canada.
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada.
| |
Collapse
|
38
|
Beghi S, Cavaliere F, Buschini A. Gene polymorphisms in calcium-calmodulin pathway: Focus on cardiovascular disease. Mutat Res Rev Mutat Res 2020; 786:108325. [PMID: 33339582 DOI: 10.1016/j.mrrev.2020.108325] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 07/22/2020] [Accepted: 07/24/2020] [Indexed: 12/30/2022]
Abstract
Cardiovascular disease is the leading cause of death in industrialized countries and affects an increasing number of people. Several risk factors play an important role in the etiology of this disease, such as an unhealthy lifestyle. It is increasingly clear that genetic factors influencing the molecular basis of excitation-contraction mechanisms in the heart could contribute to modify the individual's risk. Thanks to the progress that has been made in understanding calcium signaling in the heart, it is assumed that calmodulin can play a crucial role in the excitation-contraction coupling. In fact, calmodulin (CaM) binds calcium and consequently regulates calcium channels. Several works show how some polymorphic variants can be considered predisposing factors to complex pathologies. Therefore, we hypothesize that the identification of polymorphic variants of proteins involved in the CaM pathway could be important for understanding how genetic traits can influence predisposition to myocardial infarction. This review considers each pathway of the three different isoforms of calmodulin (CaM1; CaM2; CaM3) and focuses on some common proteins involved in the three pathways, with the aim of analyzing the polymorphisms studied in the literature and understanding if they are associated with cardiovascular disease.
Collapse
Affiliation(s)
- Sofia Beghi
- University of Parma, Department of Chemistry, Life Sciences and Environmental Sustainability, Parco Area Delle Scienze 11A, 43124, Parma, Italy
| | - Francesca Cavaliere
- University of Parma, Department of Food and Drug, Parco Area Delle Scienze 17A, 43124, Parma, Italy
| | - Annamaria Buschini
- University of Parma, Department of Chemistry, Life Sciences and Environmental Sustainability, Parco Area Delle Scienze 11A, 43124, Parma, Italy.
| |
Collapse
|
39
|
Sigurdson MK, Khoury MJ, Ioannidis JPA. Redundant meta-analyses are common in genetic epidemiology. J Clin Epidemiol 2020; 127:40-48. [PMID: 32540390 DOI: 10.1016/j.jclinepi.2020.05.035] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 05/02/2020] [Accepted: 05/13/2020] [Indexed: 11/18/2022]
Abstract
OBJECTIVES The massive growth in the publication of meta-analyses may cause redundancy and wasted efforts. We performed a metaepidemiologic study to evaluate the extent of potential redundancy in published meta-analyses in genetic epidemiology. STUDY DESIGN AND SETTING Using a sample of 38 index meta-analyses of genetic associations published in 2010, we retrieved additional meta-analyses that evaluated identical associations (same genetic variant and phenotype) using the Human Genome Epidemiology (HuGE) Navigator and PubMed databases. We analyzed the frequency of potential duplication and examined whether subsequent meta-analyses cited previous meta-analyses on the exact same association. RESULTS Based on 38 index meta-analyses, we retrieved a total of 99 duplicate meta-analyses. Only 12 (32%) of the index meta-analyses were unambiguously unique. We found a mean of 2.6 duplicates and a median of 2 duplicates per meta-analysis. In case studies, only 29-54% of previously published meta-analyses were cited by subsequent ones. CONCLUSION These results suggest that duplication is common in meta-analyses of genetic associations.
Collapse
Affiliation(s)
- Matthew K Sigurdson
- Department of Health Research and Policy, Stanford University School of Medicine, Stanford University, Stanford, CA, USA; Meta-Research Innovation Center at Stanford (METRICS), Stanford University, Stanford, CA, USA.
| | - Muin J Khoury
- Office of Public Health Genomics, Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA
| | - John P A Ioannidis
- Department of Health Research and Policy, Stanford University School of Medicine, Stanford University, Stanford, CA, USA; Meta-Research Innovation Center at Stanford (METRICS), Stanford University, Stanford, CA, USA; Department of Statistics, Stanford University School of Humanities and Science, Stanford University, Stanford, CA, USA; Department of Biomedical Data Science, Stanford University School of Medicine, Stanford University, Stanford, CA, USA; Stanford Prevention Research Center, Department of Medicine, Stanford University, Stanford, CA, USA
| |
Collapse
|
40
|
Gerring ZF, Lupton MK, Edey D, Gamazon ER, Derks EM. An analysis of genetically regulated gene expression across multiple tissues implicates novel gene candidates in Alzheimer's disease. Alzheimers Res Ther 2020; 12:43. [PMID: 32299494 PMCID: PMC7164172 DOI: 10.1186/s13195-020-00611-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 04/01/2020] [Indexed: 12/19/2022]
Abstract
Introduction Genome-wide association studies (GWAS) have successfully identified multiple independent genetic loci that harbour variants associated with Alzheimer’s disease, but the exact causal genes and biological pathways are largely unknown. Methods To prioritise likely causal genes associated with Alzheimer’s disease, we used S-PrediXcan to integrate expression quantitative trait loci (eQTL) from the Genotype-Tissue Expression (GTEx) study and CommonMind Consortium (CMC) with Alzheimer’s disease GWAS summary statistics. We meta-analysed the GTEx results using S-MultiXcan, prioritised disease-implicated loci using a computational fine-mapping approach, and performed a biological pathway analysis on the gene-based results. Results We identified 126 tissue-specific gene-based associations across 48 GTEx tissues, targeting 50 unique genes. Meta-analysis of the tissue-specific associations identified 73 genes whose expression was associated with Alzheimer’s disease. Additional analyses in the dorsolateral prefrontal cortex from the CMC identified 12 significant associations, 8 of which also had a significant association in GTEx tissues. Fine-mapping of causal gene sets prioritised gene candidates in 10 Alzheimer’s disease loci with strong evidence for causality. Biological pathway analyses of the meta-analysed GTEx data and CMC data identified a significant enrichment of Alzheimer’s disease association signals in plasma lipoprotein clearance, in addition to multiple immune-related pathways. Conclusions Gene expression data from brain and peripheral tissues can improve power to detect regulatory variation underlying Alzheimer’s disease. However, the associations in peripheral tissues may reflect tissue-shared regulatory variation for a gene. Therefore, future functional studies should be performed to validate the biological meaning of these associations and whether they represent new pathogenic tissues.
Collapse
Affiliation(s)
- Zachary F Gerring
- Translational Neurogenomics Laboratory, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, QLD, 4006, Australia.
| | - Michelle K Lupton
- Genetic Epidemiology Laboratory, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, QLD, 4006, Australia
| | - Daniel Edey
- Translational Neurogenomics Laboratory, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, QLD, 4006, Australia
| | - Eric R Gamazon
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University, 1211 21st Ave S, Nashville, TN, 37212, USA
| | - Eske M Derks
- Translational Neurogenomics Laboratory, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, QLD, 4006, Australia
| |
Collapse
|
41
|
Rivera MA, Fahey TD, López-Taylor JR, Martínez JL. The Association of Aquaporin-1 Gene with Marathon Running Performance Level: a Confirmatory Study Conducted in Male Hispanic Marathon Runners. Sports Med Open 2020; 6:16. [PMID: 32198675 PMCID: PMC7083975 DOI: 10.1186/s40798-020-00243-0] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 02/19/2020] [Indexed: 01/10/2023]
Abstract
Background Replication studies are essential for identifying credible associations between alleles and phenotypes. Validation of genotype-phenotype associations in the sports and exercise field is rare. An initial genetic association study suggested that rs1049305 (C > G) in the 3′ untranslated region (3′UTR) of the aquaporin-1 (AQP1) gene was associated with marathon running (MR) performance level in Hispanic males. To validate this finding, we conducted a replication analysis in an independent case-control sample of Hispanic male marathon runners (n = 1430; cases n = 713 and controls n = 717). A meta-analysis was utilized to test the extent of the association between the initial results and the present report. It also provided to test the heterogeneity (variation) between the two studies. Results The replication study showed a statistically significant (p ≤ 0.05) association between rs1049305 (C > G) of the AQP1 gene and MR performance level. Association test results using a fixed effect model for the combined, original study and the present report, yielded an odds ratio = 1.28, 95% confidence interval = 1.13–1.45, p = 0.0001. The extent of the measures of heterogeneity was Tau-squared = 0, H statistic = 1, I2 statistic = 0, and Cochran’s Q test (Q = 0.29; p value 0.59), indicated the variation between studies were due to chance and not to differences in heterogeneity between the two studies. Within the limitations of the present replication, contrast of two studies and its effects on meta-analysis, the findings were robust. Conclusion This study successfully replicated the results of Martínez et al. (Med Sportiva 13:251-5, 2009). The meta-analysis provided further epidemiological credibility for the hypothesis of association between the DNA rs1049305 (C > G) variation in the 3′UTR of the AQP1 gene and MR running performance level in Hispanics male marathon runners. It is not precluded that a linked DNA structure in the surrounding molecular neighborhood could be of influence by been part of the overly complex phenotype of MR performance level.
Collapse
Affiliation(s)
- Miguel A Rivera
- Department of Physical Medicine, Rehabilitation & Sports Medicine, School of Medicine, University of Puerto Rico, Main Building Office A204, San Juan, PR, 00936, USA.
| | - Thomas D Fahey
- Department of Kinesiology, California State University, Chico, CA, USA
| | - Juan R López-Taylor
- Physical Activity and Applied Sport Sciences Institute, Universidad de Guadalajara, Guadalajara, Jalisco, México
| | | |
Collapse
|
42
|
Arbeeva L, Yau M, Mitchell BD, Jackson RD, Ryan K, Golightly YM, Hannan MT, Nelson A, Jordan JM, Hochberg MC. Genome-wide meta-analysis identified novel variant associated with hallux valgus in Caucasians. J Foot Ankle Res 2020; 13:11. [PMID: 32131869 PMCID: PMC7057609 DOI: 10.1186/s13047-020-0379-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 02/20/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Hallux valgus, one of the most common structural foot deformities, is highly heritable. However, previous efforts to elucidate the genetic underpinnings of hallux valgus through a genome-wide association study (GWAS) conducted in 4409 Caucasians did not identify genome-wide significant associations with hallux valgus in both gender-specific and sex-combined GWAS meta-analyses. In this analysis, we add newly available data and more densely imputed genotypes to identify novel genetic variants associated with hallux valgus. METHODS A total of 5925 individuals of European Ancestry were categorized into two groups: 'hallux valgus present' (n = 2314) or 'no deformity' (n = 3611) as determined by trained examiners or using the Manchester grading scale. Genotyping was performed using commercially available arrays followed by imputation to the Haplotype Reference Consortium (HRC) reference panel version 1.1. We conducted both sex-specific and sex-combined association analyses using logistic regression and generalized estimating equations as appropriate in each cohort. Results were then combined in a fixed-effects inverse-variance meta-analyses. Functional Mapping and Annotation web-based platform (FUMA) was used for positional mapping, gene and gene-set analyses. RESULTS We identified a novel locus in the intronic region of CLCA2 on chromosome 1, rs55807512 (OR = 0.48, p = 2.96E-09), an expression quantitative trait locus for COL24A1, a member of the collagen gene family. CONCLUSION In this report of the largest GWAS of hallux valgus to date, we identified a novel genome-wide significant locus for hallux valgus. Additional replication and functional follow-up will be needed to determine the functional role of this locus in hallux valgus biology.
Collapse
Affiliation(s)
- Liubov Arbeeva
- Thurston Arthritis Research Center, University of North Carolina, Thurston Arthritis Research Center, 3300 Thurston Building, Campus Box #7280, Chapel Hill, NC, 27599-7280, USA.
| | - Michelle Yau
- Hebrew SeniorLife Marcus Institute for Aging Research and Harvard Medical School, Boston, MA, USA
| | - Braxton D Mitchell
- University of Maryland School of Medicine, Baltimore, MD, USA
- Geriatrics Research and Education Clinical Center, Baltimore Veterans Administration Medical Center, Baltimore, MD, USA
| | - Rebecca D Jackson
- Department of Internal Medicine, Division of Endocrinology, Diabetes and Metabolism, The Ohio State University, Columbus, OH, USA
| | - Kathleen Ryan
- University of Maryland School of Medicine, Baltimore, MD, USA
| | - Yvonne M Golightly
- Thurston Arthritis Research Center, University of North Carolina, Thurston Arthritis Research Center, 3300 Thurston Building, Campus Box #7280, Chapel Hill, NC, 27599-7280, USA
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
- Injury Prevention Research Center, University of North Carolina, Chapel Hill, North Carolina, USA
- Division of Physical Therapy, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Marian T Hannan
- Hebrew SeniorLife Marcus Institute for Aging Research and Harvard Medical School, Boston, MA, USA
| | - Amanda Nelson
- Thurston Arthritis Research Center, University of North Carolina, Thurston Arthritis Research Center, 3300 Thurston Building, Campus Box #7280, Chapel Hill, NC, 27599-7280, USA
- Department of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Joanne M Jordan
- Thurston Arthritis Research Center, University of North Carolina, Thurston Arthritis Research Center, 3300 Thurston Building, Campus Box #7280, Chapel Hill, NC, 27599-7280, USA
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
- Department of Medicine, University of North Carolina, Chapel Hill, NC, USA
- Department of Orthopedics, University of North Carolina, Chapel Hill, NC, USA
| | - Marc C Hochberg
- University of Maryland School of Medicine, Baltimore, MD, USA
| |
Collapse
|
43
|
Davey Smith G, Holmes MV, Davies NM, Ebrahim S. Mendel's laws, Mendelian randomization and causal inference in observational data: substantive and nomenclatural issues. Eur J Epidemiol 2020; 35:99-111. [PMID: 32207040 PMCID: PMC7125255 DOI: 10.1007/s10654-020-00622-7] [Citation(s) in RCA: 98] [Impact Index Per Article: 24.5] [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: 02/19/2020] [Accepted: 03/09/2020] [Indexed: 12/16/2022]
Abstract
We respond to criticisms of Mendelian randomization (MR) by Mukamal, Stampfer and Rimm (MSR). MSR consider that MR is receiving too much attention and should be renamed. We explain how MR links to Mendel's laws, the origin of the name and our lack of concern regarding nomenclature. We address MSR's substantive points regarding MR of alcohol and cardiovascular disease, an issue on which they dispute the MR findings. We demonstrate that their strictures with respect to population stratification, confounding, weak instrument bias, pleiotropy and confounding have been addressed, and summarise how the field has advanced in relation to the issues they raise. We agree with MSR that "the hard problem of conducting high-quality, reproducible epidemiology" should be addressed by epidemiologists. However we see more evidence of confrontation of this issue within MR, as opposed to conventional observational epidemiology, within which the same methods that have demonstrably failed in the past are simply rolled out into new areas, leaving their previous failures unexamined.
Collapse
Affiliation(s)
- George Davey Smith
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK.
| | - Michael V Holmes
- Medical Research Council Population Health Research Unit (MRC PHRU), Department of Population Health, University of Oxford, Nuffield, Oxford, UK
- Clinical Trial Service Unit and Epidemiological Studies Unit (CTSU), Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Neil M Davies
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
| | - Shah Ebrahim
- London School of Hygiene and Tropical Medicine, London, UK
| |
Collapse
|
44
|
Kjaergaard AD, Helby J, Johansen JS, Nordestgaard BG, Bojesen SE. Elevated plasma YKL-40 and risk of infectious disease: a prospective study of 94665 individuals from the general population. Clin Microbiol Infect 2020; 26:1411.e1-1411.e9. [PMID: 31972315 DOI: 10.1016/j.cmi.2020.01.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 01/06/2020] [Accepted: 01/11/2020] [Indexed: 01/08/2023]
Abstract
OBJECTIVES YKL-40 is an acute phase protein elevated in patients with infectious and inflammatory diseases. We tested the hypothesis that baseline elevated YKL-40 is associated with increased risk of future infectious disease in healthy individuals in the general population. METHODS We prospectively followed 94 665 individuals from the Danish general population for up to 23 years and analysed for plasma YKL-40 levels (n = 21 584) and CHI3L1 rs4950928 genotype (n = 94 184). Endpoints were any infection, bacterial pneumonia, urinary tract infection, skin infection, sepsis, diarrhoeal disease, and other infections. RESULTS For YKL-40 percentile category 91-100% versus 0-33%, the multifactorially and C-reactive protein (CRP) adjusted hazard ratios were 1.71 (95% confidence interval 1.50-1.96; p 4 × 10-14) for any infection, 1.97 (1.64-2.37; p 4 × 10-13) for bacterial pneumonia, 1.62 (1.24-2.11; p 0.002) for urinary tract infection, 1.74 (1.31-2.32; p 2 × 10-4) for skin infection, 1.76 (1.25-2.46; p 0.004) for sepsis, 1.90 (1.29-2.78; p 0.002) for diarrhoeal disease and 2.71 (1.38-5.35; p 0.01) for other infections. In multifactorially and CRP-adjusted models, a twofold increase in YKL-40 was associated with increased risk of all infectious disease endpoints. Mendelian randomization did not support causality, as CHI3L1 rs4950928 was associated with 94% and 190% higher YKL-40 levels (for CG and CC versus GG genotype), but not with increased risk of any infectious disease endpoint. DISCUSSION Baseline elevated plasma YKL-40 was not a cause but a strong marker of increased risk of future infectious diseases in individuals in the general population.
Collapse
Affiliation(s)
- A D Kjaergaard
- Department of Clinical Epidemiology and Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus, Denmark.
| | - J Helby
- Department of Clinical Biochemistry, Department of Internal Medicine, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
| | - J S Johansen
- Department of Oncology and Medicine, Herlev and Gentofte Hospital, Copenhagen University Hospital, Denmark and Faculty of Health and Medical Sciences, University of Copenhagen, Herlev, Denmark
| | - B G Nordestgaard
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Faculty of Health and Medical Sciences, University of Copenhagen, Herlev, Denmark
| | - S E Bojesen
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Faculty of Health and Medical Sciences, University of Copenhagen, Herlev, Denmark
| |
Collapse
|
45
|
Ruiz-Arenas C, Cáceres A, Moreno V, González JR. Common polymorphic inversions at 17q21.31 and 8p23.1 associate with cancer prognosis. Hum Genomics 2019; 13:57. [PMID: 31753042 PMCID: PMC6873427 DOI: 10.1186/s40246-019-0242-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [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: 01/01/2019] [Accepted: 10/09/2019] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Chromosomal inversions are structural genetic variants where a chromosome segment changes its orientation. While sporadic de novo inversions are known genetic risk factors for cancer susceptibility, it is unknown if common polymorphic inversions are also associated with the prognosis of common tumors, as they have been linked to other complex diseases. We studied the association of two well-characterized human inversions at 17q21.31 and 8p23.1 with the prognosis of lung, liver, breast, colorectal, and stomach cancers. RESULTS Using data from The Cancer Genome Atlas (TCGA), we observed that inv8p23.1 was associated with overall survival in breast cancer and that inv17q21.31 was associated with overall survival in stomach cancer. In the meta-analysis of two independent studies, inv17q21.31 heterozygosity was significantly associated with colorectal disease-free survival. We found that the association was mediated by the de-methylation of cg08283464 and cg03999934, also linked to lower disease-free survival. CONCLUSIONS Our results suggest that chromosomal inversions are important genetic factors of tumor prognosis, likely affecting changes in methylation patterns.
Collapse
Affiliation(s)
- Carlos Ruiz-Arenas
- Barcelona Institute for Global Health, ISGlobal, Doctor Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Alejandro Cáceres
- Barcelona Institute for Global Health, ISGlobal, Doctor Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Victor Moreno
- Programa de Prevención y Control del Cáncer, Instituto Catalán de Oncología, L'Hospitalet, Barcelona, Spain
| | - Juan R González
- Barcelona Institute for Global Health, ISGlobal, Doctor Aiguader 88, 08003, Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain.
| |
Collapse
|
46
|
Affiliation(s)
- Ping An
- Basic Research Laboratory, Molecular Genetic Epidemiology Section, Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Ju-Tao Guo
- Baruch S. Blumberg Institute, Hepatitis B Foundation, Doylestown, PA, United States
| | - Cheryl A Winkler
- Basic Research Laboratory, Molecular Genetic Epidemiology Section, Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| |
Collapse
|
47
|
Yao S, Kuja-Halkola R, Martin J, Lu Y, Lichtenstein P, Norring C, Birgegård A, Yilmaz Z, Hübel C, Watson H, Baker J, Almqvist C, Thornton LM, Magnusson PK, Bulik CM, Larsson H. Associations Between Attention-Deficit/Hyperactivity Disorder and Various Eating Disorders: A Swedish Nationwide Population Study Using Multiple Genetically Informative Approaches. Biol Psychiatry 2019; 86:577-586. [PMID: 31301758 PMCID: PMC6776821 DOI: 10.1016/j.biopsych.2019.04.036] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [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: 01/30/2019] [Revised: 04/15/2019] [Accepted: 04/22/2019] [Indexed: 12/21/2022]
Abstract
BACKGROUND Although attention-deficit/hyperactivity disorder (ADHD) and eating disorders (EDs) frequently co-occur, little is known about the shared etiology. In this study, we comprehensively investigated the genetic association between ADHD and various EDs, including anorexia nervosa (AN) and other EDs such as bulimia nervosa. METHODS We applied different genetically informative designs to register-based information of a Swedish nationwide population (N = 3,550,118). We first examined the familial coaggregation of clinically diagnosed ADHD and EDs across multiple types of relatives. We then applied quantitative genetic modeling in full-sisters and maternal half-sisters to estimate the genetic correlations between ADHD and EDs. We further tested the associations between ADHD polygenic risk scores and ED symptoms, and between AN polygenic risk scores and ADHD symptoms, in a genotyped population-based sample (N = 13,472). RESULTS Increased risk of all types of EDs was found in individuals with ADHD (any ED: odds ratio [OR] = 3.97, 95% confidence interval [CI] = 3.81, 4.14; AN: OR = 2.68, 95% CI = 2.15, 2.86; other EDs: OR = 4.66, 95% CI = 4.47, 4.87; bulimia nervosa: OR = 5.01, 95% CI = 4.63, 5.41) and their relatives compared with individuals without ADHD and their relatives. The magnitude of the associations decreased as the degree of relatedness decreased, suggesting shared familial liability between ADHD and EDs. Quantitative genetic models revealed stronger genetic correlation of ADHD with other EDs (.37, 95% CI = .31, .42) than with AN (.14, 95% CI = .05, .22). ADHD polygenic risk scores correlated positively with ED symptom measures overall and with the subscales Drive for Thinness and Body Dissatisfaction despite small effect sizes. CONCLUSIONS We observed stronger genetic association with ADHD for non-AN EDs than for AN, highlighting specific genetic correlation beyond a general genetic factor across psychiatric disorders.
Collapse
Affiliation(s)
- Shuyang Yao
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.
| | - Ralf Kuja-Halkola
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Joanna Martin
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden,MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
| | - Yi Lu
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Paul Lichtenstein
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Claes Norring
- Department of Clinical Neuroscience, Centre for Psychiatry Research, Karolinska Institutet, Stockholm, Sweden,Stockholm Health Care Services, Stockholm County Council, Stockholm, Sweden
| | - Andreas Birgegård
- Department of Clinical Neuroscience, Centre for Psychiatry Research, Karolinska Institutet, Stockholm, Sweden,Stockholm Health Care Services, Stockholm County Council, Stockholm, Sweden
| | - Zeynep Yilmaz
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Christopher Hübel
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden,Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, UK
| | - Hunna Watson
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Jessica Baker
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Catarina Almqvist
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden,Astrid Lindgren Children’s Hospital, Karolinska University Hospital, Stockholm, Sweden
| | | | - Laura M. Thornton
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Patrik K. Magnusson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Cynthia M. Bulik
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden,Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina,Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Henrik Larsson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden,School of Medical Sciences, Örebro University, Örebro, Sweden
| |
Collapse
|
48
|
Abstract
Mendelian randomization (MR) in epidemiology is the use of genetic variants as instrumental variables (IVs) in non-experimental design to make causality of a modifiable exposure on an outcome or disease. It assesses the causal effect between risk factor and a clinical outcome. The main reason to approach MR is to avoid the problem of residual confounding. There is no association between the genotype of early pregnancy and the disease, and the genotype of an individual cannot be changed. For this reason, it results with randomly assigned case-control studies can be set by regressing the measurements. IVs in MR are used genetic variants for estimating the causality. Usually an outcome is a disease and an exposure is risk factor, intermediate phenotype which may be a biomarker. The choice of the genetic variable as IV (Z) is essential to a successful in MR analysis. MR is named 'Mendelian deconfounding' as it gives to estimate of the causality free from biases due to confounding (C). To estimate unbiased estimation of the causality of the exposure (X) on the clinically relevant outcome (Y), Z has the 3 core assumptions (A1-A3). A1) Z is independent of C; A2) Z is associated with X; and A3) Z is independent of Y given X and C; The purpose of this review provides an overview of the MR analysis and is to explain that using an IV is proposed as an alternative statistical method to estimate causal effect of exposure and outcome under controlling for a confounder.
Collapse
Affiliation(s)
- Kwan Lee
- Department of Preventive Medicine, Dongguk University College of Medicine, Goyang, Korea
| | - Chi-Yeon Lim
- Department of Biostatistics, Dongguk University College of Medicine, Goyang, Korea
| |
Collapse
|
49
|
Chen N, Caruso C, Alonso A, Derebail VK, Kshirsagar AV, Sharrett AR, Key NS, Gottesman RF, Grove ML, Bressler J, Boerwinkle E, Windham BG, Mosley TH, Hyacinth HI. Association of sickle cell trait with measures of cognitive function and dementia in African Americans. eNeurologicalSci 2019; 16:100201. [PMID: 31384675 PMCID: PMC6661502 DOI: 10.1016/j.ensci.2019.100201] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [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: 07/16/2019] [Accepted: 07/21/2019] [Indexed: 12/22/2022] Open
Abstract
OBJECTIVE The incidence and prevalence of cognitive decline and dementia are significantly higher among African Americans compared with non-Hispanic Whites. The aim of this study was to determine whether inheritance of the sickle cell trait (SCT) i.e. heterozygosity for the sickle cell mutation increases the risk of cognitive decline or dementia Among African Americans. METHODS We studied African American participants enrolled in the Atherosclerosis Risk in Communities study. SCT genotype at baseline and outcome data from cognitive assessments at visits 2, 4 and 5, and an MRI performed at visit 5 were analyzed for the association between SCT and risk of cognitive impairment and/or dementia. RESULTS There was no significant difference in risk factors profile between participants with SCT (N = 176) and those without SCT (N = 2532). SCT was not independently associated with a higher prevalence of global or domain-specific cognitive impairment at baseline or with more rapid cognitive decline. Participants with SCT had slightly lower incidence of dementia (HR = 0.63 [0.38, 1.05]). On the other hand, SCT seems to interact with the apolipoprotein E ε4 risk allele resulting in poor performance on digit symbol substitution test at baseline (z-score = -0.08, Pinteraction = 0.05) and over time (z-score = -0.12, Pinteraction = 0.04); and with diabetes mellitus leading to a moderately increased risk of dementia (HR = 2.06 [0.89, 4.78], Pinteraction = 0.01). CONCLUSIONS SCT was not an independent risk factor for prevalence or incidence of cognitive decline or dementia, although it may interact with and modify other putative risk factors for cognitive decline and dementia.
Collapse
Affiliation(s)
- Nemin Chen
- Department of Epidemiology, University of Pittsburg, Pittsburg, PA, United States of America
| | - Christina Caruso
- Aflac Cancer and Blood Disorder Center of Children's Healthcare of Atlanta, Emory Department of Pediatrics, Atlanta, GA, United States of America
| | - Alvaro Alonso
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, United States of America
| | - Vimal K. Derebail
- UNC Kidney Center, Division of Nephrology and Hypertension, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Abhijit V. Kshirsagar
- UNC Kidney Center, Division of Nephrology and Hypertension, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - A. Richey Sharrett
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States of America
| | - Nigel S. Key
- University of North Carolina, Department of Medicine, Chapel Hill, NC, United States of America
| | - Rebecca F. Gottesman
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States of America
- Department of Neurology, Johns Hopkins University, Baltimore, MD, United States of America
| | - Megan L. Grove
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, United States of America
| | - Jan Bressler
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, United States of America
| | - Eric Boerwinkle
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, United States of America
- Human Genome Sequencing Center at Baylor College of Medicine, Houston, TX, United States of America
| | - B. Gwen Windham
- University of Mississippi Medical Center, Department of Medicine/Geriatrics, Jackson, MS, United States of America
| | - Thomas H. Mosley
- MIND Center, University of Mississippi Medical Center, Jackson, MS, United States of America
| | - Hyacinth I. Hyacinth
- Aflac Cancer and Blood Disorder Center of Children's Healthcare of Atlanta, Emory Department of Pediatrics, Atlanta, GA, United States of America
| |
Collapse
|
50
|
Tridente A, Holloway PAH, Hutton P, Gordon AC, Mills GH, Clarke GM, Chiche JD, Stuber F, Garrard C, Hinds C, Bion J. Methodological challenges in European ethics approvals for a genetic epidemiology study in critically ill patients: the GenOSept experience. BMC Med Ethics 2019; 20:30. [PMID: 31064358 PMCID: PMC6503539 DOI: 10.1186/s12910-019-0370-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 04/22/2019] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND During the set-up phase of an international study of genetic influences on outcomes from sepsis, we aimed to characterise potential differences in ethics approval processes and outcomes in participating European countries. METHODS Between 2005 and 2007 of the FP6-funded international Genetics Of Sepsis and Septic Shock (GenOSept) project, we asked national coordinators to complete a structured survey of research ethic committee (REC) approval structures and processes in their countries, and linked these data to outcomes. Survey findings were reconfirmed or modified in 2017. RESULTS Eighteen countries participated in the study, recruiting 2257 patients from 160 ICUs. National practices differed widely in terms of composition of RECs, procedures and duration of the ethics approval process. Eight (44.4%) countries used a single centralised process for approval, seven (38.9%) required approval by an ethics committee in each participating hospital, and three (16.7%) required both. Outcomes of the application process differed widely between countries because of differences in national legislation, and differed within countries because of interpretation of the ethics of conducting research in patients lacking capacity. The RECs in four countries had no lay representation. The median time from submission to final decision was 1.5 (interquartile range 1-7) months; in nine (50%) approval was received within 1 month; six took over 6 months, and in one 24 months; had all countries been able to match the most efficient approvals processes, an additional 74 months of country or institution-level recruitment would have been available. In three countries, rejection of the application by some local RECs resulted in loss of centres; and one country rejected the application outright. CONCLUSIONS The potential benefits of the single application portal offered by the European Clinical Trials Regulation will not be realised without harmonisation of research ethics committee practices as well as national legislation.
Collapse
Affiliation(s)
- Ascanio Tridente
- Whiston Hospital, Prescot, Merseyside and Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool, UK
| | | | - Paula Hutton
- Intensive Care Unit, John Radcliffe Hospital, Oxford, UK
| | | | | | | | | | - Frank Stuber
- Department of Anaesthesiology and Pain Medicine, Bern University Hospital and University of Bern, Bern, Switzerland
| | | | - Charles Hinds
- Barts and the London Queen Mary School of Medicine, London, UK
| | - Julian Bion
- Institute of Clinical Sciences, University of Birmingham, Birmingham, UK
| |
Collapse
|