1
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Antó JM, Pearce N, Douwes J, Garcia-Aymerich J, Pembrey L, Richiardi L, Sunyer J. Why has epidemiology not (yet) succeeded in identifying the origin of the asthma epidemic? Int J Epidemiol 2023; 52:974-983. [PMID: 37004248 PMCID: PMC10396414 DOI: 10.1093/ije/dyad035] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 03/15/2023] [Indexed: 04/04/2023] Open
Affiliation(s)
- Josep M Antó
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain
- Hospital del Mar Medical Research Institute, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Neil Pearce
- Department of Non-communicable Disease Epidemiology and Medical Statistics, London School of Hygiene and Tropical Medicine, London, UK
| | - Jeroen Douwes
- Research Centre for Hauora and Health, Massey University, Wellington, New Zealand
| | - Judith Garcia-Aymerich
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Lucy Pembrey
- Department of Medical Statistics, London School of Hygiene and Tropical Medicine, London, UK
| | - Lorenzo Richiardi
- Cancer Epidemiology Unit, Department of Medical Sciences, University of Turin, and CPO-Piemonte, Torino, Italy
| | - Jordi Sunyer
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain
- Hospital del Mar Medical Research Institute, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
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2
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Li R, Ugai T, Xu L, Zucker D, Ogino S, Wang M. Utility of Continuous Disease Subtyping Systems for Improved Evaluation of Etiologic Heterogeneity. Cancers (Basel) 2022; 14:1811. [PMID: 35406583 PMCID: PMC8997600 DOI: 10.3390/cancers14071811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/26/2022] [Accepted: 03/31/2022] [Indexed: 12/04/2022] Open
Abstract
Molecular pathologic diagnosis is important in clinical (oncology) practice. Integration of molecular pathology into epidemiological methods (i.e., molecular pathological epidemiology) allows for investigating the distinct etiology of disease subtypes based on biomarker analyses, thereby contributing to precision medicine and prevention. However, existing approaches for investigating etiological heterogeneity deal with categorical subtypes. We aimed to fully leverage continuous measures available in most biomarker readouts (gene/protein expression levels, signaling pathway activation, immune cell counts, microbiome/microbial abundance in tumor microenvironment, etc.). We present a cause-specific Cox proportional hazards regression model for evaluating how the exposure-disease subtype association changes across continuous subtyping biomarker levels. Utilizing two longitudinal observational prospective cohort studies, we investigated how the association of alcohol intake (a risk factor) with colorectal cancer incidence differed across the continuous values of tumor epigenetic DNA methylation at long interspersed nucleotide element-1 (LINE-1). The heterogeneous alcohol effect was modeled using different functions of the LINE-1 marker to demonstrate the method's flexibility. This real-world proof-of-principle computational application demonstrates how the new method enables visualizing the trend of the exposure effect over continuous marker levels. The utilization of continuous biomarker data without categorization for investigating etiological heterogeneity can advance our understanding of biological and pathogenic mechanisms.
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Affiliation(s)
- Ruitong Li
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; (R.L.); (S.O.)
| | - Tomotaka Ugai
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA;
- Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Lantian Xu
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA;
| | - David Zucker
- Department of Statistics and Data Science, Hebrew University, Jerusalem 91905, Israel;
| | - Shuji Ogino
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; (R.L.); (S.O.)
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA;
- Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Cancer Immunology and Cancer Epidemiology Programs, Dana-Farber Harvard Cancer Center, Boston, MA 02115, USA
| | - Molin Wang
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA;
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA;
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
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3
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Carr PR, Alwers E, Bienert S, Weberpals J, Kloor M, Brenner H, Hoffmeister M. Lifestyle factors and risk of sporadic colorectal cancer by microsatellite instability status: a systematic review and meta-analyses. Ann Oncol 2019; 29:825-834. [PMID: 29438474 DOI: 10.1093/annonc/mdy059] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Introduction The association of lifestyle factors with molecular pathological subtypes of colorectal cancer (CRC), such as microsatellite instability (MSI), could provide further knowledge about the colorectal carcinogenic process. The aim of this review was to evaluate possible associations between lifestyle factors and risk of sporadic CRC by MSI status. Methods PubMed and Web of Science were searched for studies investigating the association between alcohol, body mass index, dietary fiber, hormone replacement therapy (HRT), non-steroidal anti-inflammatory drugs, physical activity, red meat, smoking, or statin use, with MSI-high (MSI-H) and microsatellite stable (MSS) CRC. Meta-analyses were carried out to calculate summary relative risks (sRR). Results Overall, 31 studies reporting on the association between lifestyle factors and CRC according to MSI status were included in this review. Ever smoking was associated with MSI-H (sRR = 1.62; 95% CI: 1.40-1.88) and MSS/MSI-low CRC (sRR = 1.10; 95% CI: 1.01-1.20), but the association was significantly stronger for MSI-H CRC. The use of HRT was associated with a 20% decrease (sRR = 0.80; 95% CI: 0.73-0.89) in the risk of MSS CRC, but was not associated with MSI-H CRC. An increase in body mass index per 5 kg/m2 was equally associated with MSS and MSI-H CRC (sRR = 1.22, in both cases), but was statistically significant for MSS CRC only (95% CI: 1.11-1.34 and 0.94-1.58, respectively). Limited evidence for associations between other lifestyle factors and CRC by MSI status exists. Conclusions Lifestyle factors, such as HRT and smoking are differentially associated with the risk of MSI-H and MSS CRC. Further research on associations of lifestyle factors and CRC subtypes is necessary to provide a better understanding of the CRC disease pathway.
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Affiliation(s)
- P R Carr
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - E Alwers
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - S Bienert
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - J Weberpals
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - M Kloor
- Department of Applied Tumor Biology, Institute of Pathology, University of Heidelberg, Heidelberg, Germany
| | - H 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
| | - M Hoffmeister
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
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4
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Peng C, Wang J, Asante I, Louie S, Jin R, Chatzi L, Casey G, Thomas DC, Conti DV. A latent unknown clustering integrating multi-omics data (LUCID) with phenotypic traits. Bioinformatics 2019; 36:842-850. [PMID: 31504184 PMCID: PMC7986585 DOI: 10.1093/bioinformatics/btz667] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 08/04/2019] [Accepted: 08/21/2019] [Indexed: 01/31/2023] Open
Abstract
MOTIVATION Epidemiologic, clinical and translational studies are increasingly generating multiplatform omics data. Methods that can integrate across multiple high-dimensional data types while accounting for differential patterns are critical for uncovering novel associations and underlying relevant subgroups. RESULTS We propose an integrative model to estimate latent unknown clusters (LUCID) aiming to both distinguish unique genomic, exposure and informative biomarkers/omic effects while jointly estimating subgroups relevant to the outcome of interest. Simulation studies indicate that we can obtain consistent estimates reflective of the true simulated values, accurately estimate subgroups and recapitulate subgroup-specific effects. We also demonstrate the use of the integrated model for future prediction of risk subgroups and phenotypes. We apply this approach to two real data applications to highlight the integration of genomic, exposure and metabolomic data. AVAILABILITY AND IMPLEMENTATION The LUCID method is implemented through the LUCIDus R package available on CRAN (https://CRAN.R-project.org/package=LUCIDus). SUPPLEMENTARY INFORMATION Supplementary materials are available at Bioinformatics online.
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Affiliation(s)
- Cheng Peng
- Department of Preventive Medicine, Keck School of Medicine, Los Angeles, CA 90089, USA
| | - Jun Wang
- Department of Preventive Medicine, Keck School of Medicine, Los Angeles, CA 90089, USA
| | - Isaac Asante
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, CA 90089, USA
| | - Stan Louie
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, CA 90089, USA
| | - Ran Jin
- Department of Preventive Medicine, Keck School of Medicine, Los Angeles, CA 90089, USA
| | - Lida Chatzi
- Department of Preventive Medicine, Keck School of Medicine, Los Angeles, CA 90089, USA
| | - Graham Casey
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, VA 22908, USA
| | - Duncan C Thomas
- Department of Preventive Medicine, Keck School of Medicine, Los Angeles, CA 90089, USA
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5
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Marlow R, Finn A, Henderson J. Assessing the association between bronchiolitis in infancy and recurrent wheeze: a whole English birth cohort case-control study. Thorax 2019; 74:503-505. [PMID: 30948437 DOI: 10.1136/thoraxjnl-2018-212203] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 11/08/2018] [Accepted: 11/26/2018] [Indexed: 11/04/2022]
Abstract
The precise association between bronchiolitis and predisposition to childhood wheeze is unclear. We assessed bronchiolitis aetiology and later wheeze phenotypes in the entire 2007 English birth cohort. All infants admitted to hospital in England during their first year of life with bronchiolitis or urinary tract infection (UTI) were followed using Hospital Episode Statistics to determine risk and characteristics of wheeze admission over the subsequent 8 years. In our cohort of 21 272 children compared with UTI, the risk of wheeze admission was higher with previous bronchiolitis (risk ratio (RR) 2.4), even higher in those with non-respiratory syncytial virus bronchiolitis (RR 3.1) and persisted into late-onset wheeze (RR 1.7).
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Affiliation(s)
- Robin Marlow
- Population Health Sciences, University of Bristol, Bristol, UK
| | - Adam Finn
- Population Health Sciences, University of Bristol, Bristol, UK
| | - John Henderson
- Population Health Sciences, University of Bristol, Bristol, UK
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6
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Hamada T, Nowak JA, Milner DA, Song M, Ogino S. Integration of microbiology, molecular pathology, and epidemiology: a new paradigm to explore the pathogenesis of microbiome-driven neoplasms. J Pathol 2019; 247:615-628. [PMID: 30632609 PMCID: PMC6509405 DOI: 10.1002/path.5236] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 12/24/2018] [Accepted: 01/06/2019] [Indexed: 02/06/2023]
Abstract
Molecular pathological epidemiology (MPE) is an integrative transdisciplinary field that addresses heterogeneous effects of exogenous and endogenous factors (collectively termed 'exposures'), including microorganisms, on disease occurrence and consequences, utilising molecular pathological signatures of the disease. In parallel with the paradigm of precision medicine, findings from MPE research can provide aetiological insights into tailored strategies of disease prevention and treatment. Due to the availability of molecular pathological tests on tumours, the MPE approach has been utilised predominantly in research on cancers including breast, lung, prostate, and colorectal carcinomas. Mounting evidence indicates that the microbiome (inclusive of viruses, bacteria, fungi, and parasites) plays an important role in a variety of human diseases including neoplasms. An alteration of the microbiome may be not only a cause of neoplasia but also an informative biomarker that indicates or mediates the association of an epidemiological exposure with health conditions and outcomes. To adequately educate and train investigators in this emerging area, we herein propose the integration of microbiology into the MPE model (termed 'microbiology-MPE'), which could improve our understanding of the complex interactions of environment, tumour cells, the immune system, and microbes in the tumour microenvironment during the carcinogenic process. Using this approach, we can examine how lifestyle factors, dietary patterns, medications, environmental exposures, and germline genetics influence cancer development and progression through impacting the microbial communities in the human body. Further integration of other disciplines (e.g. pharmacology, immunology, nutrition) into microbiology-MPE would expand this developing research frontier. With the advent of high-throughput next-generation sequencing technologies, researchers now have increasing access to large-scale metagenomics as well as other omics data (e.g. genomics, epigenomics, proteomics, and metabolomics) in population-based research. The integrative field of microbiology-MPE will open new opportunities for personalised medicine and public health. Copyright © 2019 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Tsuyoshi Hamada
- Department of Oncologic Pathology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, USA
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Jonathan A Nowak
- Department of Pathology Program in MPE Molecular Pathological Epidemiology, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Danny A Milner
- American Society for Clinical Pathology, Chicago, Illinois, USA
| | - Mingyang Song
- Departments of Epidemiology and Nutrition, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Shuji Ogino
- Department of Oncologic Pathology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, USA
- Department of Pathology Program in MPE Molecular Pathological Epidemiology, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
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7
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8
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Myte R, Gylling B, Häggström J, Häggström C, Zingmark C, Löfgren Burström A, Palmqvist R, Van Guelpen B. Metabolic factors and the risk of colorectal cancer by KRAS and BRAF mutation status. Int J Cancer 2019; 145:327-337. [PMID: 30613980 DOI: 10.1002/ijc.32104] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 11/29/2018] [Accepted: 12/18/2018] [Indexed: 02/06/2023]
Abstract
Factors related to energy metabolism and the metabolic syndrome, such as higher body mass index (BMI), blood glucose, or blood lipids, and blood pressure, are associated with an increased risk of colorectal cancer (CRC). However, CRC is a heterogeneous disease, developing through distinct pathways with differences in molecular characteristics and prognosis, and possibly also in risk factors. For subtypes defined by KRAS and BRAF mutation status, BMI is the only metabolic factor previously studied, with inconsistent findings. We investigated whether associations between BMI, blood glucose, blood lipids, and blood pressure and CRC risk differed by tumor KRAS and BRAF mutation status in 117,687 participants from two population-based cohorts within the Northern Sweden Health and Disease Study (NSHDS). Hazard ratios (HRs) for overall CRC and CRC subtypes by metabolic factors were estimated with Cox proportional hazards regression, using multiple imputation to handle missing exposure and tumor data. During a median follow-up of 15.6 years, we acquired 1,250 prospective CRC cases, of which 766 cases had complete baseline and molecular tumor data. Consistent with previous evidence, higher BMI, total cholesterol, triglyceride levels, and blood pressure were associated with an increased risk of overall CRC (HRs per 1 standard deviation increase: 1.07 to 1.12). These associations were similar regardless of CRC subtype by KRAS and BRAF mutation status (all pheterogeneity > 0.05). The same was true for subtypes based on microsatellite instability status. Poor metabolic health may therefore be a universal mechanism for colorectal cancer, acting across multiple developmental pathways.
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Affiliation(s)
- Robin Myte
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Björn Gylling
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
| | - Jenny Häggström
- Department of Statistics, Umeå School of Business and Economics, Umeå University, Umeå, Sweden
| | - Christel Häggström
- Department of Biobank Research, Umeå University, Umeå, Sweden.,Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Carl Zingmark
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
| | | | - Richard Palmqvist
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
| | - Bethany Van Guelpen
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden.,Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
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9
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Ogino S, Nowak JA, Hamada T, Milner DA, Nishihara R. Insights into Pathogenic Interactions Among Environment, Host, and Tumor at the Crossroads of Molecular Pathology and Epidemiology. ANNUAL REVIEW OF PATHOLOGY 2019; 14:83-103. [PMID: 30125150 PMCID: PMC6345592 DOI: 10.1146/annurev-pathmechdis-012418-012818] [Citation(s) in RCA: 156] [Impact Index Per Article: 31.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Evidence indicates that diet, nutrition, lifestyle, the environment, the microbiome, and other exogenous factors have pathogenic roles and also influence the genome, epigenome, transcriptome, proteome, and metabolome of tumor and nonneoplastic cells, including immune cells. With the need for big-data research, pathology must transform to integrate data science fields, including epidemiology, biostatistics, and bioinformatics. The research framework of molecular pathological epidemiology (MPE) demonstrates the strengths of such an interdisciplinary integration, having been used to study breast, lung, prostate, and colorectal cancers. The MPE research paradigm not only can provide novel insights into interactions among environment, tumor, and host but also opens new research frontiers. New developments-such as computational digital pathology, systems biology, artificial intelligence, and in vivo pathology technologies-will further transform pathology and MPE. Although it is necessary to address the rarity of transdisciplinary education and training programs, MPE provides an exemplary model of integrative scientific approaches and contributes to advancements in precision medicine, therapy, and prevention.
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Affiliation(s)
- Shuji Ogino
- Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women's Hospital, and Harvard Medical School, Boston, Massachusetts 02215, USA; , ,
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, and Harvard Medical School, Boston, Massachusetts 02215, USA;
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
| | - Jonathan A Nowak
- Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women's Hospital, and Harvard Medical School, Boston, Massachusetts 02215, USA; , ,
| | - Tsuyoshi Hamada
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, and Harvard Medical School, Boston, Massachusetts 02215, USA;
| | - Danny A Milner
- American Society for Clinical Pathology, Chicago, Illinois 60603, USA;
| | - Reiko Nishihara
- Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women's Hospital, and Harvard Medical School, Boston, Massachusetts 02215, USA; , ,
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA
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10
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Ogino S, Nowak JA, Hamada T, Phipps AI, Peters U, Milner DA, Giovannucci EL, Nishihara R, Giannakis M, Garrett WS, Song M. Integrative analysis of exogenous, endogenous, tumour and immune factors for precision medicine. Gut 2018; 67:1168-1180. [PMID: 29437869 PMCID: PMC5943183 DOI: 10.1136/gutjnl-2017-315537] [Citation(s) in RCA: 128] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 01/02/2018] [Accepted: 01/05/2018] [Indexed: 12/14/2022]
Abstract
Immunotherapy strategies targeting immune checkpoints such as the CTLA4 and CD274 (programmed cell death 1 ligand 1, PD-L1)/PDCD1 (programmed cell death 1, PD-1) T-cell coreceptor pathways are revolutionising oncology. The approval of pembrolizumab use for solid tumours with high-level microsatellite instability or mismatch repair deficiency by the US Food and Drug Administration highlights promise of precision immuno-oncology. However, despite evidence indicating influences of exogenous and endogenous factors such as diet, nutrients, alcohol, smoking, obesity, lifestyle, environmental exposures and microbiome on tumour-immune interactions, integrative analyses of those factors and immunity lag behind. Immune cell analyses in the tumour microenvironment have not adequately been integrated into large-scale studies. Addressing this gap, the transdisciplinary field of molecular pathological epidemiology (MPE) offers research frameworks to integrate tumour immunology into population health sciences, and link the exposures and germline genetics (eg, HLA genotypes) to tumour and immune characteristics. Multilevel research using bioinformatics, in vivo pathology and omics (genomics, epigenomics, transcriptomics, proteomics and metabolomics) technologies is possible with use of tissue, peripheral blood circulating cells, cell-free plasma, stool, sputum, urine and other body fluids. This immunology-MPE model can synergise with experimental immunology, microbiology and systems biology. GI neoplasms represent exemplary diseases for the immunology-MPE model, given rich microbiota and immune tissues of intestines, and the well-established carcinogenic role of intestinal inflammation. Proof-of-principle studies on colorectal cancer provided insights into immunomodulating effects of aspirin, vitamin D, inflammatory diets and omega-3 polyunsaturated fatty acids. The integrated immunology-MPE model can contribute to better understanding of environment-tumour-immune interactions, and effective immunoprevention and immunotherapy strategies for precision medicine.
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Affiliation(s)
- Shuji Ogino
- Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA,Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
| | - Jonathan A Nowak
- Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Tsuyoshi Hamada
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Amanda I Phipps
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA,Department of Epidemiology, University of Washington, Seattle, Washington, USA
| | - Ulrike Peters
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA,Department of Epidemiology, University of Washington, Seattle, Washington, USA
| | - Danny A Milner
- American Society for Clinical Pathology, Chicago, Illinois, USA
| | - Edward L Giovannucci
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA,Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA,Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Reiko Nishihara
- Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA,Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Marios Giannakis
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA,Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA,Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Wendy S Garrett
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA,Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Mingyang Song
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA,Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, Massachusetts, USA,Division of Gastroenterology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
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11
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Abstract
Characterizing the relations between exposures and diseases is the central tenet of epidemiology. Researchers may want to evaluate exposure-disease causation by assessing whether the disease under concern is induced by the various exposures – the so-called “attribution”. In this paper, the authors propose a method to attribute diseases to multiple pathways based on the causal-pie model. The method can also be used to evaluate the potential impact of an intervention strategy and to allocate responsibility in tort-law liability issues.
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Affiliation(s)
- Christine Chen
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan
| | - Wen-Chung Lee
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan.,Research Center for Genes, Environment and Human Health, College of Public Health, National Taiwan University, Taipei, Taiwan
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12
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Myte R, Gylling B, Häggström J, Schneede J, Löfgren-Burström A, Huyghe JR, Hallmans G, Meyer K, Johansson I, Ueland PM, Palmqvist R, Van Guelpen B. One-carbon metabolism biomarkers and genetic variants in relation to colorectal cancer risk by KRAS and BRAF mutation status. PLoS One 2018; 13:e0196233. [PMID: 29694444 PMCID: PMC5919009 DOI: 10.1371/journal.pone.0196233] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 04/09/2018] [Indexed: 12/20/2022] Open
Abstract
Disturbances in one-carbon metabolism, intracellular reactions involved in nucleotide synthesis and methylation, likely increase the risk of colorectal cancer (CRC). However, results have been inconsistent. To explore whether this inconsistency could be explained by intertumoral heterogeneity, we evaluated a comprehensive panel of one-carbon metabolism biomarkers and some single nucleotide polymorphisms (SNPs) in relation to the risk of molecular subtypes of CRC defined by mutations in the KRAS and BRAF oncogenes. This nested case-control study included 488 CRC cases and 947 matched controls from two population-based cohorts in the Northern Sweden Health and Disease Study. We analyzed 14 biomarkers and 17 SNPs in prediagnostic blood and determined KRAS and BRAF mutation status in tumor tissue. In a multivariate network analysis, no variable displayed a strong association with the risk of specific CRC subtypes. A non-synonymous SNP in the CTH gene, rs1021737, had a stronger association compared with other variables. In subsequent univariate analyses, participants with variant rs1021737 genotype had a decreased risk of KRAS-mutated CRC (OR per allele = 0.72, 95% CI = 0.50, 1.05), and an increased risk of BRAF-mutated CRC (OR per allele = 1.56, 95% CI = 1.07, 2.30), with weak evidence for heterogeneity (Pheterogeneity = 0.01). This subtype-specific SNP association was not replicated in a case-case analysis of 533 CRC cases from The Cancer Genome Atlas (P = 0.85). In conclusion, we found no support for clear subtype-specific roles of one-carbon metabolism biomarkers and SNPs in CRC development, making differences in CRC molecular subtype distributions an unlikely explanation for the varying results on the role of one-carbon metabolism in CRC development across previous studies. Further investigation of the CTH gene in colorectal carcinogenesis with regards to KRAS and BRAF mutations or other molecular characteristics of the tumor may be warranted.
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Affiliation(s)
- Robin Myte
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
- * E-mail:
| | - Björn Gylling
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
| | - Jenny Häggström
- Department of Statistics, Umeå School of Business and Economics, Umeå University, Umeå, Sweden
| | - Jörn Schneede
- Department of Clinical Pharmacology, Pharmacology and Clinical Neurosciences, Umeå University, Umeå, Sweden
| | | | - Jeroen R. Huyghe
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Göran Hallmans
- Department of Biobank Research, Public Health and Clinical Medicine, Umeå University, Umeå, Sweden
| | | | | | - Per Magne Ueland
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Laboratory of Clinical Biochemistry, Haukeland University Hospital, Bergen, Norway
| | - Richard Palmqvist
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
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13
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Liu L, Nevo D, Nishihara R, Cao Y, Song M, Twombly TS, Chan AT, Giovannucci EL, VanderWeele TJ, Wang M, Ogino S. Utility of inverse probability weighting in molecular pathological epidemiology. Eur J Epidemiol 2017; 33:381-392. [PMID: 29264788 DOI: 10.1007/s10654-017-0346-8] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 12/12/2017] [Indexed: 12/17/2022]
Abstract
As one of causal inference methodologies, the inverse probability weighting (IPW) method has been utilized to address confounding and account for missing data when subjects with missing data cannot be included in a primary analysis. The transdisciplinary field of molecular pathological epidemiology (MPE) integrates molecular pathological and epidemiological methods, and takes advantages of improved understanding of pathogenesis to generate stronger biological evidence of causality and optimize strategies for precision medicine and prevention. Disease subtyping based on biomarker analysis of biospecimens is essential in MPE research. However, there are nearly always cases that lack subtype information due to the unavailability or insufficiency of biospecimens. To address this missing subtype data issue, we incorporated inverse probability weights into Cox proportional cause-specific hazards regression. The weight was inverse of the probability of biomarker data availability estimated based on a model for biomarker data availability status. The strategy was illustrated in two example studies; each assessed alcohol intake or family history of colorectal cancer in relation to the risk of developing colorectal carcinoma subtypes classified by tumor microsatellite instability (MSI) status, using a prospective cohort study, the Nurses' Health Study. Logistic regression was used to estimate the probability of MSI data availability for each cancer case with covariates of clinical features and family history of colorectal cancer. This application of IPW can reduce selection bias caused by nonrandom variation in biospecimen data availability. The integration of causal inference methods into the MPE approach will likely have substantial potentials to advance the field of epidemiology.
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Affiliation(s)
- Li Liu
- Department of Oncologic Pathology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA.,Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, 450 Brookline Ave., Room SM1036, Boston, MA, 02215, USA.,Department of Epidemiology and Biostatistics, and the Ministry of Education Key Lab of Environment and Health, School of Public Health, Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
| | - Daniel Nevo
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 677 Huntington Ave., Boston, MA, 02215, USA.,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Reiko Nishihara
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, 450 Brookline Ave., Room SM1036, Boston, MA, 02215, USA.,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Yin Cao
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Division of Gastroenterology, Massachusetts General Hospital, Boston, MA, USA.,Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Mingyang Song
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Division of Gastroenterology, Massachusetts General Hospital, Boston, MA, USA.,Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Tyler S Twombly
- Department of Oncologic Pathology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Andrew T Chan
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Division of Gastroenterology, Massachusetts General Hospital, Boston, MA, USA.,Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Edward L Giovannucci
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Tyler J VanderWeele
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 677 Huntington Ave., Boston, MA, 02215, USA.,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Molin Wang
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 677 Huntington Ave., Boston, MA, 02215, USA. .,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA. .,Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
| | - Shuji Ogino
- Department of Oncologic Pathology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA. .,Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, 450 Brookline Ave., Room SM1036, Boston, MA, 02215, USA. .,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA. .,Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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14
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Ogino S, Jhun I, Mata DA, Soong TR, Hamada T, Liu L, Nishihara R, Giannakis M, Cao Y, Manson JE, Nowak JA, Chan AT. Integration of pharmacology, molecular pathology, and population data science to support precision gastrointestinal oncology. NPJ Precis Oncol 2017; 1. [PMID: 29552640 PMCID: PMC5856171 DOI: 10.1038/s41698-017-0042-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Precision medicine has a goal of customizing disease prevention and treatment strategies. Under the precision medicine paradigm, each patient has unique pathologic processes resulting from cellular genomic, epigenomic, proteomic, and metabolomic alterations, which are influenced by pharmacological, environmental, microbial, dietary, and lifestyle factors. Hence, to realize the promise of precision medicine, multi-level research methods that can comprehensively analyze many of these variables are needed. In order to address this gap, the integrative field of molecular pathology and population data science (i.e., molecular pathological epidemiology) has been developed to enable such multi-level analyses, especially in gastrointestinal cancer research. Further integration of pharmacology can improve our understanding of drug effects, and inform decision-making of drug use at both the individual and population levels. Such integrative research demonstrated potential benefits of aspirin in colorectal carcinoma with PIK3CA mutations, providing the basis for new clinical trials. Evidence also suggests that HPGD (15-PDGH) expression levels in normal colon and the germline rs6983267 polymorphism that relates to tumor CTNNB1 (β-catenin)/WNT signaling status may predict the efficacy of aspirin for cancer chemoprevention. As immune checkpoint blockade targeting the CD274 (PD-L1)/PDCD1 (PD-1) pathway for microsatellite instability-high (or mismatch repair-deficient) metastatic gastrointestinal or other tumors has become standard of care, potential modifying effects of dietary, lifestyle, microbial, and environmental factors on immunotherapy need to be studied to further optimize treatment strategies. With its broad applicability, our integrative approach can provide insights into the interactive role of medications, exposures, and molecular pathology, and guide the development of precision medicine.
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Affiliation(s)
- Shuji Ogino
- Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Iny Jhun
- Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Douglas A Mata
- Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Thing Rinda Soong
- Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Tsuyoshi Hamada
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Li Liu
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Reiko Nishihara
- Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Marios Giannakis
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Yin Cao
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA.,Division of Gastroenterology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - JoAnn E Manson
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Division of Preventive Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jonathan A Nowak
- Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Andrew T Chan
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA.,Division of Gastroenterology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.,Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
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15
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Hunter DJ. What is in a name? Does cancer subtyping help or hinder in epidemiology research? Eur J Epidemiol 2017; 32:349-351. [PMID: 28660398 DOI: 10.1007/s10654-017-0274-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 06/10/2017] [Indexed: 11/26/2022]
Affiliation(s)
- David J Hunter
- Nuffield Department of Population Health, University of Oxford, Oxford, UK.
- Harvard TH Chan School of Public Health, Boston, MA, USA.
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