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Tang Z, Liang D, Deubler EL, Sarnat JA, Chow SS, Diver WR, Wang Y. Lung cancer metabolomics: a pooled analysis in the Cancer Prevention Studies. BMC Med 2024; 22:262. [PMID: 38915026 PMCID: PMC11197282 DOI: 10.1186/s12916-024-03473-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 06/10/2024] [Indexed: 06/26/2024] Open
Abstract
BACKGROUND A better understanding of lung cancer etiology and the development of screening biomarkers have important implications for lung cancer prevention. METHODS We included 623 matched case-control pairs from the Cancer Prevention Study (CPS) cohorts. Pre-diagnosis blood samples were collected between 1998 and 2001 in the CPS-II Nutrition cohort and 2006 and 2013 in the CPS-3 cohort and were sent for metabolomics profiling simultaneously. Cancer-free controls at the time of case diagnosis were 1:1 matched to cases on date of birth, blood draw date, sex, and race/ethnicity. Odds ratios (ORs) and 95% confidence intervals (CIs) were estimated using conditional logistic regression, controlling for confounders. The Benjamini-Hochberg method was used to correct for multiple comparisons. RESULTS Sphingomyelin (d18:0/22:0) (OR: 1.32; 95% CI: 1.15, 1.53, FDR = 0.15) and taurodeoxycholic acid 3-sulfate (OR: 1.33; 95% CI: 1.14, 1.55, FDR = 0.15) were positively associated with lung cancer risk. Participants diagnosed within 3 years of blood draw had a 55% and 48% higher risk of lung cancer per standard deviation increase in natural log-transformed sphingomyelin (d18:0/22:0) and taurodeoxycholic acid 3-sulfate level, while 26% and 28% higher risk for those diagnosed beyond 3 years, compared to matched controls. Lipid and amino acid metabolism accounted for 47% to 80% of lung cancer-associated metabolites at P < 0.05 across all participants and subgroups. Notably, ever-smokers exhibited a higher proportion of lung cancer-associated metabolites (P < 0.05) in xenobiotic- and lipid-associated pathways, whereas never-smokers showed a more pronounced involvement of amino acid- and lipid-associated metabolic pathways. CONCLUSIONS This is the largest prospective study examining untargeted metabolic profiles regarding lung cancer risk. Sphingomyelin (d18:0/22:0), a sphingolipid, and taurodeoxycholic acid 3-sulfate, a bile salt, may be risk factors and potential screening biomarkers for lung cancer. Lipid and amino acid metabolism may contribute significantly to lung cancer etiology which varied by smoking status.
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Affiliation(s)
- Ziyin Tang
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Donghai Liang
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA.
| | - Emily L Deubler
- Department of Population Science, American Cancer Society, Atlanta, GA, USA
| | - Jeremy A Sarnat
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Sabrina S Chow
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - W Ryan Diver
- Department of Population Science, American Cancer Society, Atlanta, GA, USA
- Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Ying Wang
- Department of Population Science, American Cancer Society, Atlanta, GA, USA.
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Lee J, Ogino S, Wang M. Weighting estimation in the cause-specific Cox regression with partially missing causes of failure. Stat Med 2024; 43:2575-2591. [PMID: 38659326 DOI: 10.1002/sim.10084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 02/25/2024] [Accepted: 04/05/2024] [Indexed: 04/26/2024]
Abstract
Complex diseases are often analyzed using disease subtypes classified by multiple biomarkers to study pathogenic heterogeneity. In such molecular pathological epidemiology research, we consider a weighted Cox proportional hazard model to evaluate the effect of exposures on various disease subtypes under competing-risk settings in the presence of partially or completely missing biomarkers. The asymptotic properties of the inverse and augmented inverse probability-weighted estimating equation methods are studied with a general pattern of missing data. Simulation studies have been conducted to demonstrate the double robustness of the estimators. For illustration, we applied this method to examine the association between pack-years of smoking before the age of 30 and the incidence of colorectal cancer subtypes defined by a combination of four tumor molecular biomarkers (statuses of microsatellite instability, CpG island methylator phenotype, BRAF mutation, and KRAS mutation) in the Nurses' Health Study cohort.
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Affiliation(s)
- Jooyoung Lee
- Department of Applied Statistics, Chung-Ang University, Seoul, Korea
| | - Shuji Ogino
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
- Cancer Immunology and Cancer Epidemiology Programs, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Program in Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Eli and Edythe L Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Molin Wang
- Department of Epidemiology, 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
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
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Kanbayti IH, Alzahrani MA, Yeslam YO, Habib NH, Hadadi I, Almaimoni Y, Alahmadi A, Ekpo EU. Association between Family History of Breast Cancer and Breast Density in Saudi Premenopausal Women Participating in Mammography Screening. Clin Pract 2024; 14:164-172. [PMID: 38391399 PMCID: PMC10887693 DOI: 10.3390/clinpract14010013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 12/24/2023] [Accepted: 01/11/2024] [Indexed: 02/24/2024] Open
Abstract
BACKGROUND Mammographic density and family history of breast cancer (FHBC) are well-established independent factors affecting breast cancer risk; however, the association between these two risk factors in premenopausal-screened women remains unclear. The aim of this study is to investigate the relationship between mammographic density and FHBC among Saudi premenopausal-screened women. METHODS A total of 446 eligible participants were included in the study. Mammographic density was assessed qualitatively using the Breast Imaging Reporting and Data System (BIRADS 4th edition). Logistic regression models were built to investigate the relationship between mammographic density and FHBC. RESULTS Women with a family history of breast cancer demonstrated an 87% greater chance of having dense tissue than women without a family history of breast cancer (95% CI: 1.14-3.08; p = 0.01). Having a positive family history for breast cancer in mothers was significantly associated with dense tissue (adjusted odds ratio (OR): 5.6; 95% CI: 1.3-24.1; p = 0.02). CONCLUSION Dense breast tissue in Saudi premenopausal women undergoing screening may be linked to FHBC. If this conclusion is replicated in larger studies, then breast cancer risk prediction models must carefully consider these breast cancer risk factors.
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Affiliation(s)
- Ibrahem Hussain Kanbayti
- Radiologic Sciences Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mayada A Alzahrani
- Radiologic Sciences Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Yara O Yeslam
- Radiologic Sciences Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Noora H Habib
- Radiologic Sciences Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ibrahim Hadadi
- Department of Radiological Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | - Yousef Almaimoni
- Radiologic Sciences Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Adnan Alahmadi
- Radiologic Sciences Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ernest U Ekpo
- Medical Image Optimization and Perception Group (MIOPeG), Faculty of Medicine and Health, The University of Sydney, Campus C4 75 East Street, Sydney, NSW 2141, Australia
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Woodward AA, Urbanowicz RJ, Naj AC, Moore JH. Genetic heterogeneity: Challenges, impacts, and methods through an associative lens. Genet Epidemiol 2022; 46:555-571. [PMID: 35924480 PMCID: PMC9669229 DOI: 10.1002/gepi.22497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 07/06/2022] [Accepted: 07/19/2022] [Indexed: 01/07/2023]
Abstract
Genetic heterogeneity describes the occurrence of the same or similar phenotypes through different genetic mechanisms in different individuals. Robustly characterizing and accounting for genetic heterogeneity is crucial to pursuing the goals of precision medicine, for discovering novel disease biomarkers, and for identifying targets for treatments. Failure to account for genetic heterogeneity may lead to missed associations and incorrect inferences. Thus, it is critical to review the impact of genetic heterogeneity on the design and analysis of population level genetic studies, aspects that are often overlooked in the literature. In this review, we first contextualize our approach to genetic heterogeneity by proposing a high-level categorization of heterogeneity into "feature," "outcome," and "associative" heterogeneity, drawing on perspectives from epidemiology and machine learning to illustrate distinctions between them. We highlight the unique nature of genetic heterogeneity as a heterogeneous pattern of association that warrants specific methodological considerations. We then focus on the challenges that preclude effective detection and characterization of genetic heterogeneity across a variety of epidemiological contexts. Finally, we discuss systems heterogeneity as an integrated approach to using genetic and other high-dimensional multi-omic data in complex disease research.
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Affiliation(s)
- Alexa A. Woodward
- Department of Biostatistics, Epidemiology and InformaticsUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Ryan J. Urbanowicz
- Department of Computational BiomedicineCedars‐Sinai Medical CenterLos AngelesCaliforniaUSA
| | - Adam C. Naj
- Department of Biostatistics, Epidemiology and InformaticsUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Jason H. Moore
- Department of Computational BiomedicineCedars‐Sinai Medical CenterLos AngelesCaliforniaUSA
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Zheng J, Dong X, Newton CC, Hsu L. A Generalized Integration Approach to Association Analysis with Multi-category Outcome: An Application to a Tumor Sequencing Study of Colorectal Cancer and Smoking. J Am Stat Assoc 2022; 118:29-42. [PMID: 37193510 PMCID: PMC10168026 DOI: 10.1080/01621459.2022.2105703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 07/06/2022] [Accepted: 07/14/2022] [Indexed: 10/16/2022]
Abstract
Cancer is a heterogeneous disease, and rapid progress in sequencing and -omics technologies has enabled researchers to characterize tumors comprehensively. This has stimulated an intensive interest in studying how risk factors are associated with various tumor heterogeneous features. The Cancer Prevention Study-II (CPS-II) cohort is one of the largest prospective studies, particularly valuable for elucidating associations between cancer and risk factors. In this paper, we investigate the association of smoking with novel colorectal tumor markers obtained from targeted sequencing. However, due to cost and logistic difficulties, only a limited number of tumors can be assayed, which limits our capability for studying these associations. Meanwhile, there are extensive studies for assessing the association of smoking with overall cancer risk and established colorectal tumor markers. Importantly, such summary information is readily available from the literature. By linking this summary information to parameters of interest with proper constraints, we develop a generalized integration approach for polytomous logistic regression model with outcome characterized by tumor features. The proposed approach gains the efficiency through maximizing the joint likelihood of individual-level tumor data and external summary information under the constraints that narrow the parameter searching space. We apply the proposed method to the CPS-II data and identify the association of smoking with colorectal cancer risk differing by the mutational status of APC and RNF43 genes, neither of which is identified by the conventional analysis of CPS-II individual data only. These results help better understand the role of smoking in the etiology of colorectal cancer.
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Affiliation(s)
- Jiayin Zheng
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Xinyuan Dong
- Department of Biostatistics, University of Washington, Seattle, WA
| | | | - Li Hsu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA
- Department of Biostatistics, University of Washington, Seattle, WA
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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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Hurson AN, Abubakar M, Hamilton AM, Conway K, Hoadley KA, Love MI, Olshan AF, Perou CM, Garcia-Closas M, Troester MA. TP53 Pathway Function, Estrogen Receptor Status, and Breast Cancer Risk Factors in the Carolina Breast Cancer Study. Cancer Epidemiol Biomarkers Prev 2022; 31:124-131. [PMID: 34737209 PMCID: PMC8755611 DOI: 10.1158/1055-9965.epi-21-0661] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 08/25/2021] [Accepted: 10/26/2021] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND TP53 and estrogen receptor (ER) both play essential roles in breast cancer development and progression, with recent research revealing cross-talk between TP53 and ER signaling pathways. Although many studies have demonstrated heterogeneity of risk factor associations across ER subtypes, associations by TP53 status have been inconsistent. METHODS This case-case analysis included incident breast cancer cases (47% Black) from the Carolina Breast Cancer Study (1993-2013). Formalin-fixed paraffin-embedded tumor samples were classified for TP53 functional status (mutant-like/wild-type-like) using a validated RNA signature. For IHC-based TP53 status, mutant-like was classified as at least 10% positivity. We used two-stage polytomous logistic regression to evaluate risk factor heterogeneity due to RNA-based TP53 and/or ER, adjusting for each other and for PR, HER2, and grade. We then compared this with the results when using IHC-based TP53 classification. RESULTS The RNA-based classifier identified 55% of tumors as TP53 wild-type-like and 45% as mutant-like. Several hormone-related factors (oral contraceptive use, menopausal status, age at menopause, and pre- and postmenopausal body mass index) were associated with TP53 mutant-like status, whereas reproductive factors (age at first birth and parity) and smoking were associated with ER status. Multiparity was associated with both TP53 and ER. When classifying TP53 status using IHC methods, no associations were observed with TP53. Associations observed with RNA-based TP53 remained after accounting for basal-like subtype. CONCLUSIONS This case-case study found breast cancer risk factors associated with RNA-based TP53 and ER. IMPACT RNA-based TP53 and ER represent an emerging etiologic schema of interest in breast cancer prevention research.
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Affiliation(s)
- Amber N Hurson
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Division of Cancer Epidemiology and Genetics, NCI, Rockville, Maryland
| | - Mustapha Abubakar
- Division of Cancer Epidemiology and Genetics, NCI, Rockville, Maryland
| | - Alina M Hamilton
- Department of Pathology and Laboratory Medicine, The University of North Carolina, Chapel Hill, North Carolina
| | - Kathleen Conway
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Katherine A Hoadley
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Michael I Love
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Andrew F Olshan
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Charles M Perou
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | | | - Melissa A Troester
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.
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Premenopausal Breast Cancer Risk Factors and Associations with Molecular Subtypes: A Case-Control Study. Int J Breast Cancer 2021; 2021:5560559. [PMID: 34659834 PMCID: PMC8519716 DOI: 10.1155/2021/5560559] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 09/16/2021] [Indexed: 11/17/2022] Open
Abstract
Background Breast cancer (BC) is the most prevalent cancer in women and the leading cause of women's cancer-related deaths and morbidity worldwide. In Rwanda, BC incidence is increasing with an unacceptably high mortality rate in premenopausal women. Objectives The purpose was to identify modifiable BC risk factors and assess associations between common breast cancer risks factors and molecular subtypes in premenopausal women in Rwanda. Methods This was a case-control study. Premenopausal women with histological confirmation of BC and frequency-matched for age controls were recruited. A preestablished questionnaire was administered to both cases and controls for sociodemographics, BC probable risk factors, and clinical and pathological characteristics. BC was classified into luminal A, luminal B, HER2-type, basal-like (triple negative), and unclassified molecular subtypes by immunohistochemistry (IHC). Odds ratio (OR) and 95% confidence interval (CI) were estimated using multivariate logistic regression analysis. Results 340 participants were recruited into the study (170 cases vs. 170 controls). The median age was 39 years. The majority of cases presented at advanced stages of the disease (51.2% in stages III and IV) and had invasive ductal carcinoma (98.2%). 60.6% had subtypes of poor prognosis (HER2 enriched 14.7%, triple negative 12.9%, and unclassified 32.9%). Alcohol intake (AOR = 3.73, 95%CI 2.19 - 6.32, p < 0.001), obesity/overweight in adolescence or early adulthood (AOR = 10.86, 95%CI 4.82 - 24.4, p < 0.001), history of primary infertility (AOR = 33.8, 95%CI 3.5 - 321.5, p = 0.002), nulliparity (AOR = 3.75, 95%CI 1.61 - 8.75, p = 0.002), and a history of benign breast disease (AOR = 6.06, 95%CI 1.19 - 30.73, p = 0.03) were associated with the occurrence of premenopausal breast cancer. There was no significant difference between risk factor stratification per molecular subtype. Conclusion Several reproductive, environmental, and lifestyle risk factors have been identified to be associated with premenopausal BC. Among them, alcohol intake and obesity/overweight during adolescence/early adulthood can be modified. Interventions targeting alcohol consumption and obesity/overweight in adolescents and young adults may decrease the incidence of premenopausal breast cancer.
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Zabor EC, Seshan VE, Wang S, Begg CB. Validity of a method for identifying disease subtypes that are etiologically heterogeneous. Stat Methods Med Res 2021; 30:2045-2056. [PMID: 34319833 DOI: 10.1177/09622802211032704] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
A focus of cancer epidemiologic research has become the identification of risk factors that influence specific subtypes of disease, a phenomenon known as etiologic heterogeneity. In previous work we developed a novel strategy to cluster tumor markers and identify disease subtypes that differ maximally with respect to known risk factors for use in the context of case-control studies. The method relies on the premise that unsupervised k-means clustering will find candidate solutions that are closely aligned with the sought-after etiologically distinct clusters, which may not be true in the presence of clusters of tumor markers that are not related to risk of disease. In this article, we investigate in detail the ability of the method to identify the "true" clusters in the presence of clusters that are unrelated to risk factors, what we term "counterfeit" clusters. We find that our method works when the strength of structure is larger in the clusters that truly represent etiologic heterogeneity than in the counterfeit clusters, but when this condition is not met, or when there are many tumor markers that simply represent noise, the method will not find the correct solution without first performing variable selection to identify the tumor markers most strongly related to the risk factors. We illustrate the results using data from a breast cancer case-control study.
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Affiliation(s)
- Emily C Zabor
- Department of Quantitative Health Sciences & Taussig Cancer Institute, 2569Cleveland Clinic, Cleveland Clinic, Cleveland, OH, USA
| | - Venkatraman E Seshan
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Shuang Wang
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Colin B Begg
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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Roberts JM, Rich-Edwards JW, McElrath TF, Garmire L, Myatt L. Subtypes of Preeclampsia: Recognition and Determining Clinical Usefulness. Hypertension 2021; 77:1430-1441. [PMID: 33775113 DOI: 10.1161/hypertensionaha.120.14781] [Citation(s) in RCA: 113] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The concept that preeclampsia is a multisystemic syndrome is appreciated in both research and clinical care. Our understanding of pathophysiology recognizes the role of inflammation, oxidative and endoplasm reticulum stress, and angiogenic dysfunction. Yet, we have not progressed greatly toward clinically useful prediction nor had substantial success in prevention or treatment. One possibility is that the maternal syndrome may be reached through different pathophysiological pathways, that is, subtypes of preeclampsia, that in their specificity yield more clinical utility. For example, early and late onset preeclampsia are increasingly acknowledged as different pathophysiological processes leading to a common presentation. Other subtypes of preeclampsia are supported by disparate clinical outcomes, long-range prognosis, organ systems involved, and risk factors. These insights have been supplemented by discovery-driven methods, which cluster preeclampsia cases into groups indicating different pathophysiologies. In this presentation, we review likely subtypes based on current knowledge and suggest others. We present a consideration of the requirements for a clinically meaningful preeclampsia subtype. A useful subtype should (1) identify a specific pathophysiological pathway or (2) specifically indicate maternal or fetal outcome, (3) be recognizable in a clinically useful time frame, and (4) these results should be reproducible and generalizable (but at varying frequency) including in low resource settings. We recommend that the default consideration be that preeclampsia includes several subtypes rather than trying to force all cases into a single pathophysiological pathway. The recognition of subtypes and deciphering their different pathophysiologies will provide specific targets for prevention, prediction, and treatment directing personalized care.
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Affiliation(s)
- James M Roberts
- Magee-Womens Research Institute, Department of Obstetrics Gynecology and Reproductive Sciences, Epidemiology and Clinical and Translational Research, University of Pittsburgh (J.M.R.)
| | - Janet W Rich-Edwards
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Harvard University, Boston, MA (J.W.R.-E.).,Division of Women's Health, Department of Medicine (J.W.R.-E.), Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Thomas F McElrath
- Division of Maternal-Fetal Medicine (T.F.M.), Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Lana Garmire
- Department of Computational Medicine and Bioinformatics, Medical School, University of Michigan (L.G.)
| | - Leslie Myatt
- Department of Obstetrics and Gynecology, Moore Institute of Nutrition and Wellness, Oregon Health and Science University (L.M.)
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Benefield HC, Zabor EC, Shan Y, Allott EH, Begg CB, Troester MA. Evidence for Etiologic Subtypes of Breast Cancer in the Carolina Breast Cancer Study. Cancer Epidemiol Biomarkers Prev 2019; 28:1784-1791. [PMID: 31395590 PMCID: PMC6825567 DOI: 10.1158/1055-9965.epi-19-0365] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 06/12/2019] [Accepted: 08/01/2019] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Distinctions in the etiology of triple-negative versus luminal breast cancer have become well established using immunohistochemical surrogates [notably estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2)]. However, it is unclear whether established immunohistochemical subtypes are the sole or definitive means of etiologically subdividing breast cancers. METHODS We evaluated clinical biomarkers and tumor suppressor p53 with risk factor data from cases and controls in the Carolina Breast Cancer Study, a population-based study of incident breast cancers. For each individual marker and combinations of markers, we calculated an aggregate measure to distinguish the etiologic heterogeneity of different classification schema. To compare schema, we estimated subtype-specific case-control odds ratios for individual risk factors and fit age-at-incidence curves with two-component mixture models. We also evaluated subtype concordance of metachronous contralateral breast tumors in the California Cancer Registry. RESULTS ER was the biomarker that individually explained the greatest variability in risk factor profiles. However, further subdivision by p53 significantly increased the degree of etiologic heterogeneity. Age at diagnosis, nulliparity, and race were heterogeneously associated with ER/p53 subtypes. The ER-/p53+ subtype exhibited a similar risk factor profile and age-at-incidence distribution to the triple-negative subtype. CONCLUSIONS Clinical marker-based intrinsic subtypes have established value, yet other schema may also yield important etiologic insights. IMPACT Novel environmental or genetic risk factors may be identifiable by considering different etiologic schema, including cross-classification based on ER/p53.
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Affiliation(s)
- Halei C Benefield
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.
| | - Emily C Zabor
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Yue Shan
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Emma H Allott
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, United Kingdom
| | - Colin B Begg
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Melissa A Troester
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
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Kresovich JK, Erdal S, Chen HY, Gann PH, Argos M, Rauscher GH. Metallic air pollutants and breast cancer heterogeneity. ENVIRONMENTAL RESEARCH 2019; 177:108639. [PMID: 31419716 PMCID: PMC6717519 DOI: 10.1016/j.envres.2019.108639] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 08/07/2019] [Accepted: 08/07/2019] [Indexed: 05/23/2023]
Abstract
BACKGROUND Emerging evidence suggests airborne metals may be associated with breast cancer risk. However, breast cancer is heterogenous and associations with heavy metals vary by subtype. Heavy metals possess both carcinogenic and xenoestrogenic properties which may be related to different tumor etiologies. Therefore, we tested for etiologic heterogeneity, using a case-series approach, to determine whether associations between residential airborne metal concentrations and breast cancer differed by tumor subtype. METHODS Between 2005 and 2008, we enrolled incident breast cancer cases into the Breast Cancer Care in Chicago study. Tumor estrogen and progesterone receptors status was determined by medical record abstraction and confirmed immunohistochemically (N = 696; 147 ER/PR-negative). The 2002 USEPA's National Air Toxics Assessment census-tract estimates of metal concentrations (antimony, arsenic, beryllium, cadmium, chromium, cobalt, lead, manganese, mercury, nickel and selenium) were matched to participants' residences of the same year. Adjusted logistic regression models were used to examine whether the airborne heavy metal associations differed by tumor ER/PR status. Principal component analysis was performed to assess associations by metal co-exposures. RESULTS Comparing the highest and lowest quintiles, higher concentrations of antimony (odds ratio[OR]: 1.8, 95% confidence interval[CI]: 0.9, 3.7, P-trend: 0.05), cadmium (OR: 2.3, 95% CI: 1.2, 4.4, P-trend: 0.04) and cobalt (OR: 2.0, 95% CI: 0.9, 4.4, P-trend: 0.04) were associated with ER/PR-negative breast cancer. Mixture analysis using principal components suggested co-exposures to multiple airborne heavy metals may drive associations with tumor receptor status. CONCLUSIONS Among women diagnosed with breast cancer, metallic air pollutants were associated with increased odds of developing ER/PR-negative breast cancer.
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Affiliation(s)
- Jacob K Kresovich
- Division of Epidemiology and Biostatisitics, University of Illinois at Chicago School of Public Health, Chicago, IL, 60612, USA.
| | - Serap Erdal
- Division of Environmental and Occupational Health Sciences, University of Illinois at Chicago School of Public Health, Chicago, IL, 60612, USA
| | - Hua Yun Chen
- Division of Epidemiology and Biostatisitics, University of Illinois at Chicago School of Public Health, Chicago, IL, 60612, USA
| | - Peter H Gann
- Division of Epidemiology and Biostatisitics, University of Illinois at Chicago School of Public Health, Chicago, IL, 60612, USA; Department of Pathology, University of Illinois at Chicago College of Medicine, Chicago, IL, 60612, USA
| | - Maria Argos
- Division of Epidemiology and Biostatisitics, University of Illinois at Chicago School of Public Health, Chicago, IL, 60612, USA
| | - Garth H Rauscher
- Division of Epidemiology and Biostatisitics, University of Illinois at Chicago School of Public Health, Chicago, IL, 60612, USA
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13
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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: 67] [Impact Index Per Article: 13.4] [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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14
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Nevo D, Nishihara R, Ogino S, Wang M. The competing risks Cox model with auxiliary case covariates under weaker missing-at-random cause of failure. LIFETIME DATA ANALYSIS 2018; 24:425-442. [PMID: 28779227 PMCID: PMC5797530 DOI: 10.1007/s10985-017-9401-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 07/23/2017] [Indexed: 05/08/2023]
Abstract
In the analysis of time-to-event data with multiple causes using a competing risks Cox model, often the cause of failure is unknown for some of the cases. The probability of a missing cause is typically assumed to be independent of the cause given the time of the event and covariates measured before the event occurred. In practice, however, the underlying missing-at-random assumption does not necessarily hold. Motivated by colorectal cancer molecular pathological epidemiology analysis, we develop a method to conduct valid analysis when additional auxiliary variables are available for cases only. We consider a weaker missing-at-random assumption, with missing pattern depending on the observed quantities, which include the auxiliary covariates. We use an informative likelihood approach that will yield consistent estimates even when the underlying model for missing cause of failure is misspecified. The superiority of our method over naive methods in finite samples is demonstrated by simulation study results. We illustrate the use of our method in an analysis of colorectal cancer data from the Nurses' Health Study cohort, where, apparently, the traditional missing-at-random assumption fails to hold.
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Affiliation(s)
- Daniel Nevo
- Departments of Biostatistics and Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
| | - Reiko Nishihara
- Departments of Epidemiology and Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Shuji Ogino
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Division of MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Womens Hospital and Harvard Medical School, Boston, MA, USA
| | - Molin Wang
- Departments of Biostatistics and Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
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15
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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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16
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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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17
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Zabor EC, Begg CB. A comparison of statistical methods for the study of etiologic heterogeneity. Stat Med 2017; 36:4050-4060. [PMID: 28748599 DOI: 10.1002/sim.7405] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 06/14/2017] [Accepted: 06/16/2017] [Indexed: 01/08/2023]
Abstract
Cancer epidemiologic research has traditionally been guided by the premise that certain diseases share an underlying etiology, or cause. However, with the rise of molecular and genomic profiling, attention has increasingly focused on identifying subtypes of disease. As subtypes are identified, it is natural to ask the question of whether they share a common etiology or in fact arise from distinct sets of risk factors. In this context, epidemiologic questions of interest include (1) whether a risk factor of interest has the same effect across all subtypes of disease and (2) whether risk factor effects differ across levels of each individual tumor marker of which the subtypes are comprised. A number of statistical models have been proposed to address these questions. In an effort to determine the similarities and differences among the proposed methods, and to identify any advantages or disadvantages, we use a simplified data example to elucidate the interpretation of model parameters and available hypothesis tests, and we perform a simulation study to assess bias in effect size, type I error, and power. The results show that when the number of tumor markers is small enough that the cross-classification of markers can be evaluated in the traditional polytomous logistic regression framework, then the statistical properties are at least as good as the more complex modeling approaches that have been proposed. The potential advantage of more complex methods is in the ability to accommodate multiple tumor markers in a model of reduced parametric dimension.
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Affiliation(s)
- Emily C Zabor
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, 485 Lexington Ave, 2nd floor, New York, NY 10017, USA.,Department of Biostatistics, Mailman School of Public Health, Columbia University, 722 W 168th St, New York, NY 10032, USA
| | - Colin B Begg
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, 485 Lexington Ave, 2nd floor, New York, NY 10017, USA
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18
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Mauguen A, Zabor EC, Thomas NE, Berwick M, Seshan VE, Begg CB. Defining Cancer Subtypes With Distinctive Etiologic Profiles: An Application to the Epidemiology of Melanoma. J Am Stat Assoc 2017; 112:54-63. [PMID: 28603323 DOI: 10.1080/01621459.2016.1191499] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
We showcase a novel analytic strategy to identify sub-types of cancer that possess distinctive causal factors, i.e. sub-types that are "etiologically" distinct. The method involves the integrated analysis of two types of study design: an incident series of cases with double primary cancers with detailed information on tumor characteristics that can be used to define the sub-types; a case-series of incident cases with information on known risk factors that can be used to investigate the specific risk factors that distinguish the sub-types. The methods are applied to a rich melanoma dataset with detailed information on pathologic tumor factors, and comprehensive information on known genetic and environmental risk factors for melanoma. Identification of the optimal sub-typing solution is accomplished using a novel clustering analysis that seeks to maximize a measure that characterizes the distinctiveness of the distributions of risk factors across the sub-types and that is a function of the correlations of tumor factors in the case-specific tumor pairs. This analysis is challenged by the presence of extensive missing data. If successful, studies of this nature offer the opportunity for efficient study design to identify unknown risk factors whose effects are concentrated in defined sub-types.
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Affiliation(s)
- Audrey Mauguen
- Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, NY
| | - Emily C Zabor
- Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, NY
| | - Nancy E Thomas
- Department of Dermatology, University of North Carolina, Chapel Hill, NC.,Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC
| | - Marianne Berwick
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC
| | - Venkatraman E Seshan
- Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, NY
| | - Colin B Begg
- Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, NY
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19
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Campbell PT, Rebbeck TR, Nishihara R, Beck AH, Begg CB, Bogdanov AA, Cao Y, Coleman HG, Freeman GJ, Heng YJ, Huttenhower C, Irizarry RA, Kip NS, Michor F, Nevo D, Peters U, Phipps AI, Poole EM, Qian ZR, Quackenbush J, Robins H, Rogan PK, Slattery ML, Smith-Warner SA, Song M, VanderWeele TJ, Xia D, Zabor EC, Zhang X, Wang M, Ogino S. Proceedings of the third international molecular pathological epidemiology (MPE) meeting. Cancer Causes Control 2017; 28:167-176. [PMID: 28097472 PMCID: PMC5303153 DOI: 10.1007/s10552-016-0845-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 12/20/2016] [Indexed: 02/07/2023]
Abstract
Molecular pathological epidemiology (MPE) is a transdisciplinary and relatively new scientific discipline that integrates theory, methods, and resources from epidemiology, pathology, biostatistics, bioinformatics, and computational biology. The underlying objective of MPE research is to better understand the etiology and progression of complex and heterogeneous human diseases with the goal of informing prevention and treatment efforts in population health and clinical medicine. Although MPE research has been commonly applied to investigating breast, lung, and colorectal cancers, its methodology can be used to study most diseases. Recent successes in MPE studies include: (1) the development of new statistical methods to address etiologic heterogeneity; (2) the enhancement of causal inference; (3) the identification of previously unknown exposure-subtype disease associations; and (4) better understanding of the role of lifestyle/behavioral factors on modifying prognosis according to disease subtype. Central challenges to MPE include the relative lack of transdisciplinary experts, educational programs, and forums to discuss issues related to the advancement of the field. To address these challenges, highlight recent successes in the field, and identify new opportunities, a series of MPE meetings have been held at the Dana-Farber Cancer Institute in Boston, MA. Herein, we share the proceedings of the Third International MPE Meeting, held in May 2016 and attended by 150 scientists from 17 countries. Special topics included integration of MPE with immunology and health disparity research. This meeting series will continue to provide an impetus to foster further transdisciplinary integration of divergent scientific fields.
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Affiliation(s)
- Peter T Campbell
- Epidemiology Research Program, American Cancer Society, 250 Williams Street NW, Atlanta, GA, 30303, USA.
| | - Timothy R Rebbeck
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Reiko Nishihara
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Andrew H Beck
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Boston, MA, USA
- Department of Pathology, Harvard Medical School, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Colin B Begg
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alexei A Bogdanov
- Department of Radiology, University of Massachusetts Medical School, Worcester, 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 and Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Helen G Coleman
- Epidemiology and Health Services Research Group, Centre for Public Health, Queens University Belfast, Belfast, Northern Ireland
| | - Gordon J Freeman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Yujing J Heng
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Boston, MA, USA
- Department of Pathology, Harvard Medical School, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Microbial Systems and Communities, Genome Sequencing and Analysis Program, The Broad Institute, Cambridge, MA, USA
| | - Rafael A Irizarry
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - N Sertac Kip
- Laboratory Medicine and Pathology, Geisinger Health System, Danville, PA, USA
| | - Franziska Michor
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Daniel Nevo
- Department of Epidemiology, 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
| | - Ulrike Peters
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA, USA
| | - Amanda I Phipps
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA, USA
| | - Elizabeth M Poole
- 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
| | - Zhi Rong Qian
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - John Quackenbush
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Harlan Robins
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Peter K Rogan
- Department of Biochemistry, University of Western Ontario, London, Canada
| | | | - Stephanie A Smith-Warner
- 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
| | - Mingyang Song
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Tyler J VanderWeele
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Daniel Xia
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Emily C Zabor
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Xuehong Zhang
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Molin Wang
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Shuji Ogino
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
- Division of 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 Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA.
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20
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Nishi A, Milner DA, Giovannucci EL, Nishihara R, Tan AS, Kawachi I, Ogino S. Integration of molecular pathology, epidemiology and social science for global precision medicine. Expert Rev Mol Diagn 2015; 16:11-23. [PMID: 26636627 PMCID: PMC4713314 DOI: 10.1586/14737159.2016.1115346] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The precision medicine concept and the unique disease principle imply that each patient has unique pathogenic processes resulting from heterogeneous cellular genetic and epigenetic alterations and interactions between cells (including immune cells) and exposures, including dietary, environmental, microbial and lifestyle factors. As a core method field in population health science and medicine, epidemiology is a growing scientific discipline that can analyze disease risk factors and develop statistical methodologies to maximize utilization of big data on populations and disease pathology. The evolving transdisciplinary field of molecular pathological epidemiology (MPE) can advance biomedical and health research by linking exposures to molecular pathologic signatures, enhancing causal inference and identifying potential biomarkers for clinical impact. The MPE approach can be applied to any diseases, although it has been most commonly used in neoplastic diseases (including breast, lung and colorectal cancers) because of availability of various molecular diagnostic tests. However, use of state-of-the-art genomic, epigenomic and other omic technologies and expensive drugs in modern healthcare systems increases racial, ethnic and socioeconomic disparities. To address this, we propose to integrate molecular pathology, epidemiology and social science. Social epidemiology integrates the latter two fields. The integrative social MPE model can embrace sociology, economics and precision medicine, address global health disparities and inequalities, and elucidate biological effects of social environments, behaviors and networks. We foresee advancements of molecular medicine, including molecular diagnostics, biomedical imaging and targeted therapeutics, which should benefit individuals in a global population, by means of an interdisciplinary approach of integrative MPE and social health science.
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Affiliation(s)
- Akihiro Nishi
- Yale Institute for Network Science, New Haven, CT, USA (AN); Department of Sociology, Yale University, New Haven, CT, USA (AN); Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA (DAM, SO); Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA (DAM); Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA (ELG, RN, SO); Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA (ELG, RN); Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA (ELG); Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA (RN); Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA (RN, AST, SO); Department of Social and Behavioral Sciences, Harvard T.H. Chan School of Public Health, Boston, MA, USA (AST, IK)
| | - Danny A Milner
- Yale Institute for Network Science, New Haven, CT, USA (AN); Department of Sociology, Yale University, New Haven, CT, USA (AN); Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA (DAM, SO); Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA (DAM); Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA (ELG, RN, SO); Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA (ELG, RN); Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA (ELG); Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA (RN); Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA (RN, AST, SO); Department of Social and Behavioral Sciences, Harvard T.H. Chan School of Public Health, Boston, MA, USA (AST, IK)
| | - Edward L. Giovannucci
- Yale Institute for Network Science, New Haven, CT, USA (AN); Department of Sociology, Yale University, New Haven, CT, USA (AN); Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA (DAM, SO); Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA (DAM); Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA (ELG, RN, SO); Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA (ELG, RN); Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA (ELG); Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA (RN); Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA (RN, AST, SO); Department of Social and Behavioral Sciences, Harvard T.H. Chan School of Public Health, Boston, MA, USA (AST, IK)
| | - Reiko Nishihara
- Yale Institute for Network Science, New Haven, CT, USA (AN); Department of Sociology, Yale University, New Haven, CT, USA (AN); Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA (DAM, SO); Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA (DAM); Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA (ELG, RN, SO); Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA (ELG, RN); Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA (ELG); Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA (RN); Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA (RN, AST, SO); Department of Social and Behavioral Sciences, Harvard T.H. Chan School of Public Health, Boston, MA, USA (AST, IK)
| | - Andy S. Tan
- Yale Institute for Network Science, New Haven, CT, USA (AN); Department of Sociology, Yale University, New Haven, CT, USA (AN); Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA (DAM, SO); Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA (DAM); Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA (ELG, RN, SO); Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA (ELG, RN); Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA (ELG); Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA (RN); Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA (RN, AST, SO); Department of Social and Behavioral Sciences, Harvard T.H. Chan School of Public Health, Boston, MA, USA (AST, IK)
| | - Ichiro Kawachi
- Yale Institute for Network Science, New Haven, CT, USA (AN); Department of Sociology, Yale University, New Haven, CT, USA (AN); Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA (DAM, SO); Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA (DAM); Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA (ELG, RN, SO); Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA (ELG, RN); Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA (ELG); Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA (RN); Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA (RN, AST, SO); Department of Social and Behavioral Sciences, Harvard T.H. Chan School of Public Health, Boston, MA, USA (AST, IK)
| | - Shuji Ogino
- Yale Institute for Network Science, New Haven, CT, USA (AN); Department of Sociology, Yale University, New Haven, CT, USA (AN); Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA (DAM, SO); Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA (DAM); Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA (ELG, RN, SO); Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA (ELG, RN); Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA (ELG); Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA (RN); Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA (RN, AST, SO); Department of Social and Behavioral Sciences, Harvard T.H. Chan School of Public Health, Boston, MA, USA (AST, IK)
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21
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Wang M, Spiegelman D, Kuchiba A, Lochhead P, Kim S, Chan AT, Poole EM, Tamimi R, Tworoger SS, Giovannucci E, Rosner B, Ogino S. Statistical methods for studying disease subtype heterogeneity. Stat Med 2015; 35:782-800. [PMID: 26619806 DOI: 10.1002/sim.6793] [Citation(s) in RCA: 207] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 09/08/2015] [Accepted: 10/13/2015] [Indexed: 12/31/2022]
Abstract
A fundamental goal of epidemiologic research is to investigate the relationship between exposures and disease risk. Cases of the disease are often considered a single outcome and assumed to share a common etiology. However, evidence indicates that many human diseases arise and evolve through a range of heterogeneous molecular pathologic processes, influenced by diverse exposures. Pathogenic heterogeneity has been considered in various neoplasms such as colorectal, lung, prostate, and breast cancers, leukemia and lymphoma, and non-neoplastic diseases, including obesity, type II diabetes, glaucoma, stroke, cardiovascular disease, autism, and autoimmune disease. In this article, we discuss analytic options for studying disease subtype heterogeneity, emphasizing methods for evaluating whether the association of a potential risk factor with disease varies by disease subtype. Methods are described for scenarios where disease subtypes are categorical and ordinal and for cohort studies, matched and unmatched case-control studies, and case-case study designs. For illustration, we apply the methods to a molecular pathological epidemiology study of alcohol intake and colon cancer risk by tumor LINE-1 methylation subtypes. User-friendly software to implement the methods is publicly available.
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Affiliation(s)
- Molin Wang
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, U.S.A.,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, U.S.A.,Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, U.S.A
| | - Donna Spiegelman
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, U.S.A.,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, U.S.A.,Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, U.S.A.,Department of Global Health and Population, Harvard T.H. Chan School of Public Health, Boston, MA, U.S.A
| | - Aya Kuchiba
- Department of Biostatistics, National Cancer Center, Tokyo, Japan
| | - Paul Lochhead
- Division of Gastroenterology, Massachusetts General Hospital, Boston, MA, U.S.A
| | - Sehee Kim
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, U.S.A
| | - Andrew T Chan
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, U.S.A.,Division of Gastroenterology, Massachusetts General Hospital, Boston, MA, U.S.A
| | - Elizabeth M Poole
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, U.S.A
| | - Rulla Tamimi
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, U.S.A.,Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, U.S.A
| | - Shelley S Tworoger
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, U.S.A.,Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, U.S.A
| | - Edward Giovannucci
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, U.S.A.,Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, U.S.A.,Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, U.S.A
| | - Bernard Rosner
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, U.S.A.,Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, U.S.A
| | - Shuji Ogino
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, U.S.A.,Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, U.S.A.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, U.S.A
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22
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Wang M, Kuchiba A, Ogino S. A Meta-Regression Method for Studying Etiological Heterogeneity Across Disease Subtypes Classified by Multiple Biomarkers. Am J Epidemiol 2015; 182:263-70. [PMID: 26116215 DOI: 10.1093/aje/kwv040] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 02/04/2015] [Indexed: 12/22/2022] Open
Abstract
In interdisciplinary biomedical, epidemiologic, and population research, it is increasingly necessary to consider pathogenesis and inherent heterogeneity of any given health condition and outcome. As the unique disease principle implies, no single biomarker can perfectly define disease subtypes. The complex nature of molecular pathology and biology necessitates biostatistical methodologies to simultaneously analyze multiple biomarkers and subtypes. To analyze and test for heterogeneity hypotheses across subtypes defined by multiple categorical and/or ordinal markers, we developed a meta-regression method that can utilize existing statistical software for mixed-model analysis. This method can be used to assess whether the exposure-subtype associations are different across subtypes defined by 1 marker while controlling for other markers and to evaluate whether the difference in exposure-subtype association across subtypes defined by 1 marker depends on any other markers. To illustrate this method in molecular pathological epidemiology research, we examined the associations between smoking status and colorectal cancer subtypes defined by 3 correlated tumor molecular characteristics (CpG island methylator phenotype, microsatellite instability, and the B-Raf protooncogene, serine/threonine kinase (BRAF), mutation) in the Nurses' Health Study (1980-2010) and the Health Professionals Follow-up Study (1986-2010). This method can be widely useful as molecular diagnostics and genomic technologies become routine in clinical medicine and public health.
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23
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Begg CB, Orlow I, Zabor EC, Arora A, Sharma A, Seshan VE, Bernstein JL. Identifying Etiologically Distinct Sub-Types of Cancer: A Demonstration Project Involving Breast Cancer. Cancer Med 2015; 4:1432-9. [PMID: 25974664 PMCID: PMC4567028 DOI: 10.1002/cam4.456] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Revised: 03/03/2015] [Accepted: 03/04/2015] [Indexed: 12/19/2022] Open
Abstract
With the advent of increasingly detailed molecular portraits of tumor specimens, much attention has been directed toward identifying clinically distinct subtypes of cancer. Subtyping of tumors can also be accomplished with the goal of identifying distinct etiologies. We demonstrate the use of new methodologies to identify genes that distinguish etiologically heterogeneous subtypes of breast cancer using data from the case-control Cancer and Steroid Hormone Study. Tumor specimens were evaluated using a breast cancer expression panel of 196 genes. Using a statistical measure that distinguishes the degree of etiologic heterogeneity in tumor subtypes, each gene is ranked on the basis of its ability to distinguish etiologically distinct subtypes. This is accomplished independently using case-control comparisons and by examining the concordance odds ratios in double primaries. The estrogen receptor gene, and others in this pathway with expression levels that correlated strongly with estrogen receptor levels, demonstrate high degrees of etiologic heterogeneity in both methods. Our results are consistent with a growing literature that confirms the distinct etiologies of breast cancers classified on the basis of estrogen receptor expression levels. This proof-of-principle project demonstrates the viability of new strategies to identify genomic features that distinguish subtypes of cancer from an etiologic perspective.
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Affiliation(s)
- Colin B Begg
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York City, New York
| | - Irene Orlow
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York City, New York
| | - Emily C Zabor
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York City, New York
| | - Arshi Arora
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York City, New York
| | - Ajay Sharma
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York City, New York
| | - Venkatraman E Seshan
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York City, New York
| | - Jonine L Bernstein
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York City, New York
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24
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Ogino S, Campbell PT, Nishihara R, Phipps AI, Beck AH, Sherman ME, Chan AT, Troester MA, Bass AJ, Fitzgerald KC, Irizarry RA, Kelsey KT, Nan H, Peters U, Poole EM, Qian ZR, Tamimi RM, Tchetgen Tchetgen EJ, Tworoger SS, Zhang X, Giovannucci EL, van den Brandt PA, Rosner BA, Wang M, Chatterjee N, Begg CB. Proceedings of the second international molecular pathological epidemiology (MPE) meeting. Cancer Causes Control 2015; 26:959-72. [PMID: 25956270 DOI: 10.1007/s10552-015-0596-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 04/27/2015] [Indexed: 02/07/2023]
Abstract
Disease classification system increasingly incorporates information on pathogenic mechanisms to predict clinical outcomes and response to therapy and intervention. Technological advancements to interrogate omics (genomics, epigenomics, transcriptomics, proteomics, metabolomics, metagenomics, interactomics, etc.) provide widely open opportunities in population-based research. Molecular pathological epidemiology (MPE) represents integrative science of molecular pathology and epidemiology. This unified paradigm requires multidisciplinary collaboration between pathology, epidemiology, biostatistics, bioinformatics, and computational biology. Integration of these fields enables better understanding of etiologic heterogeneity, disease continuum, causal inference, and the impact of environment, diet, lifestyle, host factors (including genetics and immunity), and their interactions on disease evolution. Hence, the Second International MPE Meeting was held in Boston in December 2014, with aims to: (1) develop conceptual and practical frameworks; (2) cultivate and expand opportunities; (3) address challenges; and (4) initiate the effort of specifying guidelines for MPE. The meeting mainly consisted of presentations of method developments and recent data in various malignant neoplasms and tumors (breast, prostate, ovarian and colorectal cancers, renal cell carcinoma, lymphoma, and leukemia), followed by open discussion sessions on challenges and future plans. In particular, we recognized need for efforts to further develop statistical methodologies. This meeting provided an unprecedented opportunity for interdisciplinary collaboration, consistent with the purposes of the Big Data to Knowledge, Genetic Associations and Mechanisms in Oncology, and Precision Medicine Initiative of the US National Institute of Health. The MPE meeting series can help advance transdisciplinary population science and optimize training and education systems for twenty-first century medicine and public health.
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Affiliation(s)
- Shuji Ogino
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, 450 Brookline Ave., Room M422, Boston, MA, 02215, USA,
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25
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Wild CP, Bucher JR, de Jong BWD, Dillner J, von Gertten C, Groopman JD, Herceg Z, Holmes E, Holmila R, Olsen JH, Ringborg U, Scalbert A, Shibata T, Smith MT, Ulrich C, Vineis P, McLaughlin J. Translational cancer research: balancing prevention and treatment to combat cancer globally. J Natl Cancer Inst 2015; 107:353. [PMID: 25515230 PMCID: PMC4334834 DOI: 10.1093/jnci/dju353] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 08/28/2014] [Accepted: 09/26/2014] [Indexed: 12/21/2022] Open
Abstract
Cancer research is drawing on the human genome project to develop new molecular-targeted treatments. This is an exciting but insufficient response to the growing, global burden of cancer, particularly as the projected increase in new cases in the coming decades is increasingly falling on developing countries. The world is not able to treat its way out of the cancer problem. However, the mechanistic insights from basic science can be harnessed to better understand cancer causes and prevention, thus underpinning a complementary public health approach to cancer control. This manuscript focuses on how new knowledge about the molecular and cellular basis of cancer, and the associated high-throughput laboratory technologies for studying those pathways, can be applied to population-based epidemiological studies, particularly in the context of large prospective cohorts with associated biobanks to provide an evidence base for cancer prevention. This integrated approach should allow a more rapid and informed translation of the research into educational and policy interventions aimed at risk reduction across a population.
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Affiliation(s)
- Christopher P Wild
- Director's Office, Sections of Mechanisms of Carcinogenesis and Nutrition and Metabolism, International Agency for Research on Cancer, Lyon, France (CPW, ZH, RH, AS); National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA (JRB); Department of Pathology, Erasmus Medical Centre, Rotterdam, The Netherlands (BWDdJ); Department of Medical Epidemiology & Biostatistics, BioBanking & Molecular Resource Infrastructure, Karolinska Institute, Stockholm, Sweden (JD); Radiation Medicine Center, Karolinska Institute, Stockholm, Sweden (CvG); Department of Environmental Health Sciences, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA (JDG); Department of Surgery and Cancer, Imperial College London, London, UK (EH); Danish Cancer Society Research Centre, Copenhagen, Denmark (JHO); Cancer Center Karolinska, Karolinska University Hospital Solna, Stockholm, Sweden (UR); Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan (TS); School of Public Health, University of California, Berkeley, CA, USA (MTS); Division of Preventive Oncology, National Center for Tumor Diseases and German Cancer Research Center, Heidelberg, Germany (CU); Department of Epidemiology & Biostatistics, Imperial College London, London, UK (PV); Dalla Lana School of Public Health, University of Toronto, Toronto, Canada (JM).
| | - John R Bucher
- Director's Office, Sections of Mechanisms of Carcinogenesis and Nutrition and Metabolism, International Agency for Research on Cancer, Lyon, France (CPW, ZH, RH, AS); National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA (JRB); Department of Pathology, Erasmus Medical Centre, Rotterdam, The Netherlands (BWDdJ); Department of Medical Epidemiology & Biostatistics, BioBanking & Molecular Resource Infrastructure, Karolinska Institute, Stockholm, Sweden (JD); Radiation Medicine Center, Karolinska Institute, Stockholm, Sweden (CvG); Department of Environmental Health Sciences, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA (JDG); Department of Surgery and Cancer, Imperial College London, London, UK (EH); Danish Cancer Society Research Centre, Copenhagen, Denmark (JHO); Cancer Center Karolinska, Karolinska University Hospital Solna, Stockholm, Sweden (UR); Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan (TS); School of Public Health, University of California, Berkeley, CA, USA (MTS); Division of Preventive Oncology, National Center for Tumor Diseases and German Cancer Research Center, Heidelberg, Germany (CU); Department of Epidemiology & Biostatistics, Imperial College London, London, UK (PV); Dalla Lana School of Public Health, University of Toronto, Toronto, Canada (JM)
| | - Bas W D de Jong
- Director's Office, Sections of Mechanisms of Carcinogenesis and Nutrition and Metabolism, International Agency for Research on Cancer, Lyon, France (CPW, ZH, RH, AS); National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA (JRB); Department of Pathology, Erasmus Medical Centre, Rotterdam, The Netherlands (BWDdJ); Department of Medical Epidemiology & Biostatistics, BioBanking & Molecular Resource Infrastructure, Karolinska Institute, Stockholm, Sweden (JD); Radiation Medicine Center, Karolinska Institute, Stockholm, Sweden (CvG); Department of Environmental Health Sciences, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA (JDG); Department of Surgery and Cancer, Imperial College London, London, UK (EH); Danish Cancer Society Research Centre, Copenhagen, Denmark (JHO); Cancer Center Karolinska, Karolinska University Hospital Solna, Stockholm, Sweden (UR); Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan (TS); School of Public Health, University of California, Berkeley, CA, USA (MTS); Division of Preventive Oncology, National Center for Tumor Diseases and German Cancer Research Center, Heidelberg, Germany (CU); Department of Epidemiology & Biostatistics, Imperial College London, London, UK (PV); Dalla Lana School of Public Health, University of Toronto, Toronto, Canada (JM)
| | - Joakim Dillner
- Director's Office, Sections of Mechanisms of Carcinogenesis and Nutrition and Metabolism, International Agency for Research on Cancer, Lyon, France (CPW, ZH, RH, AS); National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA (JRB); Department of Pathology, Erasmus Medical Centre, Rotterdam, The Netherlands (BWDdJ); Department of Medical Epidemiology & Biostatistics, BioBanking & Molecular Resource Infrastructure, Karolinska Institute, Stockholm, Sweden (JD); Radiation Medicine Center, Karolinska Institute, Stockholm, Sweden (CvG); Department of Environmental Health Sciences, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA (JDG); Department of Surgery and Cancer, Imperial College London, London, UK (EH); Danish Cancer Society Research Centre, Copenhagen, Denmark (JHO); Cancer Center Karolinska, Karolinska University Hospital Solna, Stockholm, Sweden (UR); Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan (TS); School of Public Health, University of California, Berkeley, CA, USA (MTS); Division of Preventive Oncology, National Center for Tumor Diseases and German Cancer Research Center, Heidelberg, Germany (CU); Department of Epidemiology & Biostatistics, Imperial College London, London, UK (PV); Dalla Lana School of Public Health, University of Toronto, Toronto, Canada (JM)
| | - Christina von Gertten
- Director's Office, Sections of Mechanisms of Carcinogenesis and Nutrition and Metabolism, International Agency for Research on Cancer, Lyon, France (CPW, ZH, RH, AS); National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA (JRB); Department of Pathology, Erasmus Medical Centre, Rotterdam, The Netherlands (BWDdJ); Department of Medical Epidemiology & Biostatistics, BioBanking & Molecular Resource Infrastructure, Karolinska Institute, Stockholm, Sweden (JD); Radiation Medicine Center, Karolinska Institute, Stockholm, Sweden (CvG); Department of Environmental Health Sciences, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA (JDG); Department of Surgery and Cancer, Imperial College London, London, UK (EH); Danish Cancer Society Research Centre, Copenhagen, Denmark (JHO); Cancer Center Karolinska, Karolinska University Hospital Solna, Stockholm, Sweden (UR); Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan (TS); School of Public Health, University of California, Berkeley, CA, USA (MTS); Division of Preventive Oncology, National Center for Tumor Diseases and German Cancer Research Center, Heidelberg, Germany (CU); Department of Epidemiology & Biostatistics, Imperial College London, London, UK (PV); Dalla Lana School of Public Health, University of Toronto, Toronto, Canada (JM)
| | - John D Groopman
- Director's Office, Sections of Mechanisms of Carcinogenesis and Nutrition and Metabolism, International Agency for Research on Cancer, Lyon, France (CPW, ZH, RH, AS); National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA (JRB); Department of Pathology, Erasmus Medical Centre, Rotterdam, The Netherlands (BWDdJ); Department of Medical Epidemiology & Biostatistics, BioBanking & Molecular Resource Infrastructure, Karolinska Institute, Stockholm, Sweden (JD); Radiation Medicine Center, Karolinska Institute, Stockholm, Sweden (CvG); Department of Environmental Health Sciences, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA (JDG); Department of Surgery and Cancer, Imperial College London, London, UK (EH); Danish Cancer Society Research Centre, Copenhagen, Denmark (JHO); Cancer Center Karolinska, Karolinska University Hospital Solna, Stockholm, Sweden (UR); Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan (TS); School of Public Health, University of California, Berkeley, CA, USA (MTS); Division of Preventive Oncology, National Center for Tumor Diseases and German Cancer Research Center, Heidelberg, Germany (CU); Department of Epidemiology & Biostatistics, Imperial College London, London, UK (PV); Dalla Lana School of Public Health, University of Toronto, Toronto, Canada (JM)
| | - Zdenko Herceg
- Director's Office, Sections of Mechanisms of Carcinogenesis and Nutrition and Metabolism, International Agency for Research on Cancer, Lyon, France (CPW, ZH, RH, AS); National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA (JRB); Department of Pathology, Erasmus Medical Centre, Rotterdam, The Netherlands (BWDdJ); Department of Medical Epidemiology & Biostatistics, BioBanking & Molecular Resource Infrastructure, Karolinska Institute, Stockholm, Sweden (JD); Radiation Medicine Center, Karolinska Institute, Stockholm, Sweden (CvG); Department of Environmental Health Sciences, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA (JDG); Department of Surgery and Cancer, Imperial College London, London, UK (EH); Danish Cancer Society Research Centre, Copenhagen, Denmark (JHO); Cancer Center Karolinska, Karolinska University Hospital Solna, Stockholm, Sweden (UR); Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan (TS); School of Public Health, University of California, Berkeley, CA, USA (MTS); Division of Preventive Oncology, National Center for Tumor Diseases and German Cancer Research Center, Heidelberg, Germany (CU); Department of Epidemiology & Biostatistics, Imperial College London, London, UK (PV); Dalla Lana School of Public Health, University of Toronto, Toronto, Canada (JM)
| | - Elaine Holmes
- Director's Office, Sections of Mechanisms of Carcinogenesis and Nutrition and Metabolism, International Agency for Research on Cancer, Lyon, France (CPW, ZH, RH, AS); National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA (JRB); Department of Pathology, Erasmus Medical Centre, Rotterdam, The Netherlands (BWDdJ); Department of Medical Epidemiology & Biostatistics, BioBanking & Molecular Resource Infrastructure, Karolinska Institute, Stockholm, Sweden (JD); Radiation Medicine Center, Karolinska Institute, Stockholm, Sweden (CvG); Department of Environmental Health Sciences, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA (JDG); Department of Surgery and Cancer, Imperial College London, London, UK (EH); Danish Cancer Society Research Centre, Copenhagen, Denmark (JHO); Cancer Center Karolinska, Karolinska University Hospital Solna, Stockholm, Sweden (UR); Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan (TS); School of Public Health, University of California, Berkeley, CA, USA (MTS); Division of Preventive Oncology, National Center for Tumor Diseases and German Cancer Research Center, Heidelberg, Germany (CU); Department of Epidemiology & Biostatistics, Imperial College London, London, UK (PV); Dalla Lana School of Public Health, University of Toronto, Toronto, Canada (JM)
| | - Reetta Holmila
- Director's Office, Sections of Mechanisms of Carcinogenesis and Nutrition and Metabolism, International Agency for Research on Cancer, Lyon, France (CPW, ZH, RH, AS); National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA (JRB); Department of Pathology, Erasmus Medical Centre, Rotterdam, The Netherlands (BWDdJ); Department of Medical Epidemiology & Biostatistics, BioBanking & Molecular Resource Infrastructure, Karolinska Institute, Stockholm, Sweden (JD); Radiation Medicine Center, Karolinska Institute, Stockholm, Sweden (CvG); Department of Environmental Health Sciences, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA (JDG); Department of Surgery and Cancer, Imperial College London, London, UK (EH); Danish Cancer Society Research Centre, Copenhagen, Denmark (JHO); Cancer Center Karolinska, Karolinska University Hospital Solna, Stockholm, Sweden (UR); Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan (TS); School of Public Health, University of California, Berkeley, CA, USA (MTS); Division of Preventive Oncology, National Center for Tumor Diseases and German Cancer Research Center, Heidelberg, Germany (CU); Department of Epidemiology & Biostatistics, Imperial College London, London, UK (PV); Dalla Lana School of Public Health, University of Toronto, Toronto, Canada (JM)
| | - Jørgen H Olsen
- Director's Office, Sections of Mechanisms of Carcinogenesis and Nutrition and Metabolism, International Agency for Research on Cancer, Lyon, France (CPW, ZH, RH, AS); National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA (JRB); Department of Pathology, Erasmus Medical Centre, Rotterdam, The Netherlands (BWDdJ); Department of Medical Epidemiology & Biostatistics, BioBanking & Molecular Resource Infrastructure, Karolinska Institute, Stockholm, Sweden (JD); Radiation Medicine Center, Karolinska Institute, Stockholm, Sweden (CvG); Department of Environmental Health Sciences, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA (JDG); Department of Surgery and Cancer, Imperial College London, London, UK (EH); Danish Cancer Society Research Centre, Copenhagen, Denmark (JHO); Cancer Center Karolinska, Karolinska University Hospital Solna, Stockholm, Sweden (UR); Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan (TS); School of Public Health, University of California, Berkeley, CA, USA (MTS); Division of Preventive Oncology, National Center for Tumor Diseases and German Cancer Research Center, Heidelberg, Germany (CU); Department of Epidemiology & Biostatistics, Imperial College London, London, UK (PV); Dalla Lana School of Public Health, University of Toronto, Toronto, Canada (JM)
| | - Ulrik Ringborg
- Director's Office, Sections of Mechanisms of Carcinogenesis and Nutrition and Metabolism, International Agency for Research on Cancer, Lyon, France (CPW, ZH, RH, AS); National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA (JRB); Department of Pathology, Erasmus Medical Centre, Rotterdam, The Netherlands (BWDdJ); Department of Medical Epidemiology & Biostatistics, BioBanking & Molecular Resource Infrastructure, Karolinska Institute, Stockholm, Sweden (JD); Radiation Medicine Center, Karolinska Institute, Stockholm, Sweden (CvG); Department of Environmental Health Sciences, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA (JDG); Department of Surgery and Cancer, Imperial College London, London, UK (EH); Danish Cancer Society Research Centre, Copenhagen, Denmark (JHO); Cancer Center Karolinska, Karolinska University Hospital Solna, Stockholm, Sweden (UR); Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan (TS); School of Public Health, University of California, Berkeley, CA, USA (MTS); Division of Preventive Oncology, National Center for Tumor Diseases and German Cancer Research Center, Heidelberg, Germany (CU); Department of Epidemiology & Biostatistics, Imperial College London, London, UK (PV); Dalla Lana School of Public Health, University of Toronto, Toronto, Canada (JM)
| | - Augustin Scalbert
- Director's Office, Sections of Mechanisms of Carcinogenesis and Nutrition and Metabolism, International Agency for Research on Cancer, Lyon, France (CPW, ZH, RH, AS); National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA (JRB); Department of Pathology, Erasmus Medical Centre, Rotterdam, The Netherlands (BWDdJ); Department of Medical Epidemiology & Biostatistics, BioBanking & Molecular Resource Infrastructure, Karolinska Institute, Stockholm, Sweden (JD); Radiation Medicine Center, Karolinska Institute, Stockholm, Sweden (CvG); Department of Environmental Health Sciences, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA (JDG); Department of Surgery and Cancer, Imperial College London, London, UK (EH); Danish Cancer Society Research Centre, Copenhagen, Denmark (JHO); Cancer Center Karolinska, Karolinska University Hospital Solna, Stockholm, Sweden (UR); Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan (TS); School of Public Health, University of California, Berkeley, CA, USA (MTS); Division of Preventive Oncology, National Center for Tumor Diseases and German Cancer Research Center, Heidelberg, Germany (CU); Department of Epidemiology & Biostatistics, Imperial College London, London, UK (PV); Dalla Lana School of Public Health, University of Toronto, Toronto, Canada (JM)
| | - Tatsuhiro Shibata
- Director's Office, Sections of Mechanisms of Carcinogenesis and Nutrition and Metabolism, International Agency for Research on Cancer, Lyon, France (CPW, ZH, RH, AS); National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA (JRB); Department of Pathology, Erasmus Medical Centre, Rotterdam, The Netherlands (BWDdJ); Department of Medical Epidemiology & Biostatistics, BioBanking & Molecular Resource Infrastructure, Karolinska Institute, Stockholm, Sweden (JD); Radiation Medicine Center, Karolinska Institute, Stockholm, Sweden (CvG); Department of Environmental Health Sciences, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA (JDG); Department of Surgery and Cancer, Imperial College London, London, UK (EH); Danish Cancer Society Research Centre, Copenhagen, Denmark (JHO); Cancer Center Karolinska, Karolinska University Hospital Solna, Stockholm, Sweden (UR); Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan (TS); School of Public Health, University of California, Berkeley, CA, USA (MTS); Division of Preventive Oncology, National Center for Tumor Diseases and German Cancer Research Center, Heidelberg, Germany (CU); Department of Epidemiology & Biostatistics, Imperial College London, London, UK (PV); Dalla Lana School of Public Health, University of Toronto, Toronto, Canada (JM)
| | - Martyn T Smith
- Director's Office, Sections of Mechanisms of Carcinogenesis and Nutrition and Metabolism, International Agency for Research on Cancer, Lyon, France (CPW, ZH, RH, AS); National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA (JRB); Department of Pathology, Erasmus Medical Centre, Rotterdam, The Netherlands (BWDdJ); Department of Medical Epidemiology & Biostatistics, BioBanking & Molecular Resource Infrastructure, Karolinska Institute, Stockholm, Sweden (JD); Radiation Medicine Center, Karolinska Institute, Stockholm, Sweden (CvG); Department of Environmental Health Sciences, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA (JDG); Department of Surgery and Cancer, Imperial College London, London, UK (EH); Danish Cancer Society Research Centre, Copenhagen, Denmark (JHO); Cancer Center Karolinska, Karolinska University Hospital Solna, Stockholm, Sweden (UR); Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan (TS); School of Public Health, University of California, Berkeley, CA, USA (MTS); Division of Preventive Oncology, National Center for Tumor Diseases and German Cancer Research Center, Heidelberg, Germany (CU); Department of Epidemiology & Biostatistics, Imperial College London, London, UK (PV); Dalla Lana School of Public Health, University of Toronto, Toronto, Canada (JM)
| | - Cornelia Ulrich
- Director's Office, Sections of Mechanisms of Carcinogenesis and Nutrition and Metabolism, International Agency for Research on Cancer, Lyon, France (CPW, ZH, RH, AS); National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA (JRB); Department of Pathology, Erasmus Medical Centre, Rotterdam, The Netherlands (BWDdJ); Department of Medical Epidemiology & Biostatistics, BioBanking & Molecular Resource Infrastructure, Karolinska Institute, Stockholm, Sweden (JD); Radiation Medicine Center, Karolinska Institute, Stockholm, Sweden (CvG); Department of Environmental Health Sciences, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA (JDG); Department of Surgery and Cancer, Imperial College London, London, UK (EH); Danish Cancer Society Research Centre, Copenhagen, Denmark (JHO); Cancer Center Karolinska, Karolinska University Hospital Solna, Stockholm, Sweden (UR); Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan (TS); School of Public Health, University of California, Berkeley, CA, USA (MTS); Division of Preventive Oncology, National Center for Tumor Diseases and German Cancer Research Center, Heidelberg, Germany (CU); Department of Epidemiology & Biostatistics, Imperial College London, London, UK (PV); Dalla Lana School of Public Health, University of Toronto, Toronto, Canada (JM)
| | - Paolo Vineis
- Director's Office, Sections of Mechanisms of Carcinogenesis and Nutrition and Metabolism, International Agency for Research on Cancer, Lyon, France (CPW, ZH, RH, AS); National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA (JRB); Department of Pathology, Erasmus Medical Centre, Rotterdam, The Netherlands (BWDdJ); Department of Medical Epidemiology & Biostatistics, BioBanking & Molecular Resource Infrastructure, Karolinska Institute, Stockholm, Sweden (JD); Radiation Medicine Center, Karolinska Institute, Stockholm, Sweden (CvG); Department of Environmental Health Sciences, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA (JDG); Department of Surgery and Cancer, Imperial College London, London, UK (EH); Danish Cancer Society Research Centre, Copenhagen, Denmark (JHO); Cancer Center Karolinska, Karolinska University Hospital Solna, Stockholm, Sweden (UR); Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan (TS); School of Public Health, University of California, Berkeley, CA, USA (MTS); Division of Preventive Oncology, National Center for Tumor Diseases and German Cancer Research Center, Heidelberg, Germany (CU); Department of Epidemiology & Biostatistics, Imperial College London, London, UK (PV); Dalla Lana School of Public Health, University of Toronto, Toronto, Canada (JM)
| | - John McLaughlin
- Director's Office, Sections of Mechanisms of Carcinogenesis and Nutrition and Metabolism, International Agency for Research on Cancer, Lyon, France (CPW, ZH, RH, AS); National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA (JRB); Department of Pathology, Erasmus Medical Centre, Rotterdam, The Netherlands (BWDdJ); Department of Medical Epidemiology & Biostatistics, BioBanking & Molecular Resource Infrastructure, Karolinska Institute, Stockholm, Sweden (JD); Radiation Medicine Center, Karolinska Institute, Stockholm, Sweden (CvG); Department of Environmental Health Sciences, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA (JDG); Department of Surgery and Cancer, Imperial College London, London, UK (EH); Danish Cancer Society Research Centre, Copenhagen, Denmark (JHO); Cancer Center Karolinska, Karolinska University Hospital Solna, Stockholm, Sweden (UR); Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan (TS); School of Public Health, University of California, Berkeley, CA, USA (MTS); Division of Preventive Oncology, National Center for Tumor Diseases and German Cancer Research Center, Heidelberg, Germany (CU); Department of Epidemiology & Biostatistics, Imperial College London, London, UK (PV); Dalla Lana School of Public Health, University of Toronto, Toronto, Canada (JM)
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26
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Begg CB, Seshan VE, Zabor EC, Furberg H, Arora A, Shen R, Maranchie JK, Nielsen ME, Rathmell WK, Signoretti S, Tamboli P, Karam JA, Choueiri TK, Hakimi AA, Hsieh JJ. Genomic investigation of etiologic heterogeneity: methodologic challenges. BMC Med Res Methodol 2014; 14:138. [PMID: 25532962 PMCID: PMC4292824 DOI: 10.1186/1471-2288-14-138] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 11/27/2014] [Indexed: 11/13/2022] Open
Abstract
Background The etiologic heterogeneity of cancer has traditionally been investigated by comparing risk factor frequencies within candidate sub-types, defined for example by histology or by distinct tumor markers of interest. Increasingly tumors are being profiled for molecular features much more extensively. This greatly expands the opportunities for defining distinct sub-types. In this article we describe an exploratory analysis of the etiologic heterogeneity of clear cell kidney cancer. Data are available on the primary known risk factors for kidney cancer, while the tumors are characterized on a genome-wide basis using expression, methylation, copy number and mutational profiles. Methods We use a novel clustering strategy to identify sub-types. This is accomplished independently for the expression, methylation and copy number profiles. The goals are to identify tumor sub-types that are etiologically distinct, to identify the risk factors that define specific sub-types, and to endeavor to characterize the key genes that appear to represent the principal features of the distinct sub-types. Results The analysis reveals strong evidence that gender represents an important factor that distinguishes disease sub-types. The sub-types defined using expression data and methylation data demonstrate considerable congruence and are also clearly correlated with mutations in important cancer genes. These sub-types are also strongly correlated with survival. The complexity of the data presents many analytical challenges including, prominently, the risk of false discovery. Conclusions Genomic profiling of tumors offers the opportunity to identify etiologically distinct sub-types, paving the way for a more refined understanding of cancer etiology. Electronic supplementary material The online version of this article (doi:10.1186/1471-2288-14-138) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Colin B Begg
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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