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Juwara L, Yang YA, Velly AM, Saha-Chaudhuri P. Privacy-preserving analysis of time-to-event data under nested case-control sampling. Stat Methods Med Res 2024; 33:96-111. [PMID: 38093410 PMCID: PMC10863373 DOI: 10.1177/09622802231215804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2024]
Abstract
Analyses of distributed data networks of rare diseases are constrained by legitimate privacy and ethical concerns. Analytical centers (e.g. research institutions) are thus confronted with the challenging task of obtaining data from recruiting sites that are often unable or unwilling to share personal records of participants. For time-to-event data, recently popularized disclosure techniques with privacy guarantees (e.g., Differentially Private Generative Adversarial Networks) are generally computationally expensive or inaccessible to applied researchers. To perform the widely used Cox proportional hazards regression, we propose an easy-to-implement privacy-preserving data analysis technique by pooling (i.e. aggregating) individual records of covariates at recruiting sites under the nested case-control sampling framework before sharing the pooled nested case-control subcohort. We show that the pooled hazard ratio estimators, under the pooled nested case-control subsamples from the contributing sites, are maximum likelihood estimators and provide consistent estimates of the individual level full cohort HRs. Furthermore, a sampling technique for generating pseudo-event times for individual subjects that constitute the pooled nested case-control subsamples is proposed. Our method is demonstrated using extensive simulations and analysis of the National Lung Screening Trial data. The utility of our proposed approach is compared to the gold standard (full cohort) and synthetic data generated using classification and regression trees. The proposed pooling technique performs to near-optimal levels comparable to full cohort analysis or synthetic data; the efficiency improves in rare event settings when more controls are matched on during nested case-control subcohort sampling.
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Affiliation(s)
- Lamin Juwara
- Quantitative Life Sciences, McGill University, Montreal, Canada
- Lady Davis Institute for Medical Research, Montreal, Quebec, Canada
| | - Yi Archer Yang
- Quantitative Life Sciences, McGill University, Montreal, Canada
- Department of Mathematics and Statistis, McGill University, Montreal, Quebec, Canada
| | - Ana M Velly
- Lady Davis Institute for Medical Research, Montreal, Quebec, Canada
- Department of Dentistry, McGill University, Montreal, Quebec, Canada
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Lee M, Chen J, Zeleniuch-Jacquotte A, Liu M. Goodness-of-fit two-phase sampling designs for time-to-event outcomes: a simulation study based on New York University Women's Health Study for breast cancer. BMC Med Res Methodol 2023; 23:119. [PMID: 37208600 DOI: 10.1186/s12874-023-01950-4] [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: 09/28/2022] [Accepted: 05/11/2023] [Indexed: 05/21/2023] Open
Abstract
BACKGROUND Sub-cohort sampling designs such as a case-cohort study play a key role in studying biomarker-disease associations due to their cost effectiveness. Time-to-event outcome is often the focus in cohort studies, and the research goal is to assess the association between the event risk and risk factors. In this paper, we propose a novel goodness-of-fit two-phase sampling design for time-to-event outcomes when some covariates (e.g., biomarkers) can only be measured on a subgroup of study subjects. METHODS Assuming that an external model, which can be the well-established risk models such as the Gail model for breast cancer, Gleason score for prostate cancer, and Framingham risk models for heart diseases, or built from preliminary data, is available to relate the outcome and complete covariates, we propose to oversample subjects with worse goodness-of-fit (GOF) based on an external survival model and time-to-event. With the cases and controls sampled using the GOF two-phase design, the inverse sampling probability weighting method is used to estimate the log hazard ratio of both incomplete and complete covariates. We conducted extensive simulations to evaluate the efficiency gain of our proposed GOF two-phase sampling designs over case-cohort study designs. RESULTS Through extensive simulations based on a dataset from the New York University Women's Health Study, we showed that the proposed GOF two-phase sampling designs were unbiased and generally had higher efficiency compared to the standard case-cohort study designs. CONCLUSION In cohort studies with rare outcomes, an important design question is how to select informative subjects to reduce sampling costs while maintaining statistical efficiency. Our proposed goodness-of-fit two-phase design provides efficient alternatives to standard case-cohort designs for assessing the association between time-to-event outcome and risk factors. This method is conveniently implemented in standard software.
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Affiliation(s)
- Myeonggyun Lee
- Department of Population Health, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Jinbo Chen
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Anne Zeleniuch-Jacquotte
- Department of Population Health, New York University Grossman School of Medicine, New York, NY, 10016, USA
- Department of Environmental Medicine, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Mengling Liu
- Department of Population Health, New York University Grossman School of Medicine, New York, NY, 10016, USA.
- Department of Environmental Medicine, New York University Grossman School of Medicine, New York, NY, 10016, USA.
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3
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He JR, Hirst JE, Tikellis G, Phillips GS, Ramakrishnan R, Paltiel O, Ponsonby AL, Klebanoff M, Olsen J, Murphy MFG, Håberg SE, Lemeshow S, F Olsen S, Qiu X, Magnus P, Golding J, Ward MH, Wiemels JL, Rahimi K, Linet MS, Dwyer T. Common maternal infections during pregnancy and childhood leukaemia in the offspring: findings from six international birth cohorts. Int J Epidemiol 2022; 51:769-777. [PMID: 34519790 PMCID: PMC9425514 DOI: 10.1093/ije/dyab199] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Previous epidemiological studies have found positive associations between maternal infections and childhood leukaemia; however, evidence from prospective cohort studies is scarce. We aimed to examine the associations using large-scale prospective data. METHODS Data were pooled from six population-based birth cohorts in Australia, Denmark, Israel, Norway, the UK and the USA (recruitment 1950s-2000s). Primary outcomes were any childhood leukaemia and acute lymphoblastic leukaemia (ALL); secondary outcomes were acute myeloid leukaemia (AML) and any childhood cancer. Exposures included maternal self-reported infections [influenza-like illness, common cold, any respiratory tract infection, vaginal thrush, vaginal infections and urinary tract infection (including cystitis)] and infection-associated symptoms (fever and diarrhoea) during pregnancy. Covariate-adjusted hazard ratio (HR) and 95% confidence interval (CI) were estimated using multilevel Cox models. RESULTS Among 312 879 children with a median follow-up of 13.6 years, 167 leukaemias, including 129 ALL and 33 AML, were identified. Maternal urinary tract infection was associated with increased risk of any leukaemia [HR (95% CI) 1.68 (1.10-2.58)] and subtypes ALL [1.49 (0.87-2.56)] and AML [2.70 ([0.93-7.86)], but not with any cancer [1.13 (0.85-1.51)]. Respiratory tract infection was associated with increased risk of any leukaemia [1.57 (1.06-2.34)], ALL [1.43 (0.94-2.19)], AML [2.37 (1.10-5.12)] and any cancer [1.33 (1.09-1.63)]; influenza-like illness showed a similar pattern but with less precise estimates. There was no evidence of a link between other infections and any outcomes. CONCLUSIONS Urinary tract and respiratory tract infections during pregnancy may be associated with childhood leukaemia, but the absolute risk is small given the rarity of the outcome.
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Affiliation(s)
- Jian-Rong He
- Nuffield Department of Women’s and Reproductive Health, University of
Oxford, Oxford, UK
- Division of Birth Cohort Study, Guangzhou Women and Children’s Medical
Center, Guangzhou Medical University, Guangzhou, China
- George Institute for Global Health, University of Oxford,
Oxford, UK
| | - Jane E Hirst
- Nuffield Department of Women’s and Reproductive Health, University of
Oxford, Oxford, UK
- George Institute for Global Health, University of Oxford,
Oxford, UK
| | - Gabriella Tikellis
- Murdoch Children’s Research Institute, Royal Children’s Hospital,
University of Melbourne, Melbourne, VIC, Australia
| | - Gary S Phillips
- Retired from Center for Biostatistics, Department of Biomedical
Informatics, Ohio State University, Columbus, OH, USA
| | - Rema Ramakrishnan
- Nuffield Department of Women’s and Reproductive Health, University of
Oxford, Oxford, UK
- George Institute for Global Health, University of Oxford,
Oxford, UK
- University of New South Wales, Faculty of Medicine, Sydney,
NSW, Australia
| | - Ora Paltiel
- Braun School of Public Health, Hadassah-Hebrew University Medical
Center, Jerusalem, Israel
| | - Anne-Louise Ponsonby
- Murdoch Children’s Research Institute, Royal Children’s Hospital,
University of Melbourne, Melbourne, VIC, Australia
| | - Mark Klebanoff
- Center for Perinatal Research, Abigail Wexner Research Institute at
Nationwide Children's Hospital, Columbus, OH, USA
| | - Jørn Olsen
- Department of Clinical Epidemiology, Aarhus University,
Aarhus, Denmark
| | - Michael F G Murphy
- Nuffield Department of Women’s and Reproductive Health, University of
Oxford, Oxford, UK
| | - Siri E Håberg
- Centre for Fertility and Health, Norwegian Institute of Public
Health, Oslo, Norway
| | - Stanley Lemeshow
- Division of Biostatistics, College of Public Health, Ohio State
University, Columbus, OH, USA
| | - Sjurdur F Olsen
- Centre for Fetal Programming, Department of Epidemiology Research, Statens
Serum Institut, Copenhagen, Denmark
| | - Xiu Qiu
- Division of Birth Cohort Study, Guangzhou Women and Children’s Medical
Center, Guangzhou Medical University, Guangzhou, China
| | - Per Magnus
- Centre for Fertility and Health, Norwegian Institute of Public
Health, Oslo, Norway
| | - Jean Golding
- Centre for Academic Child Health, Population Health Sciences, Bristol
Medical School, University of Bristol, Bristol, UK
| | - Mary H Ward
- Occupational and Environmental Epidemiology Branch, Division of Cancer
Epidemiology and Genetics, National Cancer Institute, Rockville, MD,
USA
| | - Joseph L Wiemels
- Department of Preventative Medicine, University of Southern
California, Los Angeles, CA, USA
and
| | - Kazem Rahimi
- Nuffield Department of Women’s and Reproductive Health, University of
Oxford, Oxford, UK
- George Institute for Global Health, University of Oxford,
Oxford, UK
| | - Martha S Linet
- Division of Cancer Epidemiology and Genetics, National Cancer
Institute, Bethesda, MD, USA
| | - Terence Dwyer
- Corresponding author. Nuffield Department of Women’s and
Reproductive Health, University of Oxford, Oxford OX3 9DU, UK. E-mail:
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O'Brien KM, Lawrence KG, Keil AP. The Case for Case-Cohort: An Applied Epidemiologist's Guide to Reframing Case-Cohort Studies to Improve Usability and Flexibility. Epidemiology 2022; 33:354-361. [PMID: 35383643 PMCID: PMC9172927 DOI: 10.1097/ede.0000000000001469] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
When research questions require the use of precious samples, expensive assays or equipment, or labor-intensive data collection or analysis, nested case-control or case-cohort sampling of observational cohort study participants can often reduce costs. These study designs have similar statistical precision for addressing a singular research question, but case-cohort studies have broader efficiency and superior flexibility. Despite this, case-cohort designs are comparatively underutilized in the epidemiologic literature. Recent advances in statistical methods and software have made analyses of case-cohort data easier to implement, and advances from casual inference, such as inverse probability of sampling weights, have allowed the case-cohort design to be used with a variety of target parameters and populations. To provide an accessible link to this technical literature, we give a conceptual overview of case-cohort study analysis with inverse probability of sampling weights. We show how this general analytic approach can be leveraged to more efficiently study subgroups of interest or disease subtypes or to examine associations independent of case status. A brief discussion of how this framework could be extended to incorporate other related methodologic applications further demonstrates the broad cost-effectiveness and adaptability of case-cohort methods for a variety of modern epidemiologic applications in resource-limited settings.
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Affiliation(s)
- Katie M O'Brien
- From the Epidemiology Branch, National Institute of Environmental Health Sciences, NC
| | - Kaitlyn G Lawrence
- From the Epidemiology Branch, National Institute of Environmental Health Sciences, NC
| | - Alexander P Keil
- From the Epidemiology Branch, National Institute of Environmental Health Sciences, NC
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC
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Bruin MM, Deijkers RLM, Bus MPA, van Elzakker EPM, Bazuin R, Nelissen RG, Pijls BG. Inhaled Corticosteroids, Vitamin K Antagonists and Amlodipine Were Associated with an Increased Risk of Acute Periprosthetic Joint Infection in Patients with Total Hip Arthroplasty: A Retrospective Case–Cohort Study. J Clin Med 2022; 11:jcm11071842. [PMID: 35407449 PMCID: PMC8999352 DOI: 10.3390/jcm11071842] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/22/2022] [Accepted: 03/22/2022] [Indexed: 01/03/2023] Open
Abstract
The perioperative use of certain medication may influence the risk of developing a periprosthetic joint infection (PJI). Inhaled corticosteroids (ICSs) and cardiovascular drugs are widely used against pulmonary and cardiovascular diseases. While oral corticosteroids and anticoagulants have been shown to increase the risk of developing PJI, this is not clear for ICSs. In contrast, some cardiovascular drugs, such as amlodipine, nifedipine and statins, have been documented to show an antimicrobial effect, suggesting a synergistic effect with antibiotics in the treatment of (multi-resistant) microorganisms. We performed a case–cohort study to assess the association between the occurrence of PJI after THA and the use of inhaled corticosteroids, anticoagulants, or previously mentioned cardiovascular agents. In a cohort of 5512 primary THAs, we identified 75 patients with a PJI (1.4%), and randomly selected 302 controls. A weighted Cox proportional hazard regression model was used for the study design and to adjust for potential confounders (age, sex, smoking, and cardiovascular/pulmonary disease). We found ICS use (HR 2.6 [95% CI 1.1–5.9]), vitamin K antagonist use (HR 5.3 [95% CI 2.5–11]), and amlodipine use (HR 3.1 [95% CI 1.4–6.9]) to be associated with an increased risk of developing PJI after THA. The effect remained after correction for the mentioned possible confounders. The underlying diseases for which the medications are prescribed could also play a role in the mentioned association; we believe, however, that the usages of ICSs, vitamin K antagonists and amlodipine appear to be potential modifiable risk factors for PJI, and therefore have to be questioned during preoperative screening and consultation.
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Affiliation(s)
- Maarten M. Bruin
- Department of Orthopedic Surgery, Haga Ziekenhuis, 2545 AA The Hague, The Netherlands; (M.M.B.); (R.L.M.D.); (R.B.)
- Department of Orthopaedics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; (M.P.A.B.); (R.G.N.)
| | - Ruud L. M. Deijkers
- Department of Orthopedic Surgery, Haga Ziekenhuis, 2545 AA The Hague, The Netherlands; (M.M.B.); (R.L.M.D.); (R.B.)
| | - Michaël P. A. Bus
- Department of Orthopaedics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; (M.P.A.B.); (R.G.N.)
| | | | - Roos Bazuin
- Department of Orthopedic Surgery, Haga Ziekenhuis, 2545 AA The Hague, The Netherlands; (M.M.B.); (R.L.M.D.); (R.B.)
| | - Rob G. Nelissen
- Department of Orthopaedics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; (M.P.A.B.); (R.G.N.)
| | - Bart G. Pijls
- Department of Orthopedic Surgery, Haga Ziekenhuis, 2545 AA The Hague, The Netherlands; (M.M.B.); (R.L.M.D.); (R.B.)
- Department of Orthopaedics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; (M.P.A.B.); (R.G.N.)
- Correspondence:
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6
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Patson N, Mukaka M, Peterson I, Divala T, Kazembe L, Mathanga D, Laufer MK, Chirwa T. Effect of adverse events on non-adherence and study non-completion in malaria chemoprevention during pregnancy trial: A nested case control study. PLoS One 2022; 17:e0262797. [PMID: 35045119 PMCID: PMC8769307 DOI: 10.1371/journal.pone.0262797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 10/18/2021] [Indexed: 11/18/2022] Open
Abstract
Background
In drug trials, adverse events (AEs) burden can induce treatment non-adherence or discontinuation. The non-adherence and discontinuation induce selection bias, affecting drug safety interpretation. Nested case-control (NCC) study can efficiently quantify the impact of the AEs, although choice of sampling approach is challenging. We investigated whether NCC study with incidence density sampling is more efficient than NCC with path sampling under conditional logistic or weighted Cox models in assessing the effect of AEs on treatment non-adherence and participation in preventive antimalarial drug during pregnancy trial.
Methods
Using data from a trial of medication to prevent malaria in pregnancy that randomized 600 women to receive chloroquine or sulfadoxine-pyrimethamine during pregnancy, we conducted a NCC study assessing the role of prospectively collected AEs, as exposure of interest, on treatment non-adherence and study non-completion. We compared estimates from NCC study with incidence density against those from NCC with path sampling under conditional logistic and weighted Cox models.
Results
Out of 599 women with the outcomes of interest, 474 (79%) experienced at least one AE before delivery. For conditional logistic model, the hazard ratio for the effect of AE occurrence on treatment non-adherence was 0.70 (95% CI: 0.42, 1.17; p = 0.175) under incidence density sampling and 0.68 (95% CI: 0.41, 1.13; p = 0.137) for path sampling. For study non-completion, the hazard ratio was 1.02 (95% CI: 0.56, 1.83; p = 0.955) under incidence density sampling and 0.85 (95% CI: 0.45, 1.60; p = 0.619) under path sampling. We obtained similar hazard ratios and standard errors under incidence density sampling and path sampling whether weighted Cox or conditional logistic models were used.
Conclusion
NCC with incidence density sampling and NCC with path sampling are practically similar in efficiency whether conditional logistic or weighted Cox analytical methods although path sampling uses more unique controls to achieve the similar estimates.
Trial registration
ClinicalTrials.gov: NCT01443130.
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Affiliation(s)
- Noel Patson
- School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
- School of Public Health and Family Medicine, College of Medicine, University of Malawi, Blantyre, Malawi
- * E-mail:
| | - Mavuto Mukaka
- Mahidol Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
- Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Ingrid Peterson
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - Titus Divala
- TB Centre, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Helse Nord Tuberculosis Initiative, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Lawrence Kazembe
- Department of Biostatistics, University of Namibia, Windhoek, Namibia
| | - Don Mathanga
- School of Public Health and Family Medicine, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Miriam K. Laufer
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - Tobias Chirwa
- School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
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Steenland K, Winquist A. PFAS and cancer, a scoping review of the epidemiologic evidence. ENVIRONMENTAL RESEARCH 2021; 194:110690. [PMID: 33385391 PMCID: PMC7946751 DOI: 10.1016/j.envres.2020.110690] [Citation(s) in RCA: 124] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 12/24/2020] [Accepted: 12/25/2020] [Indexed: 05/19/2023]
Abstract
BACKGROUND The number of studies addressing per- and polyfluoroalkyl substances (PFAS) and cancer is increasing. Many communities have had water contaminated by PFAS, and cancer is one of the important community concerns related to PFAS exposure. OBJECTIVES We critically reviewed the evidence relating to PFAS and cancer from an epidemiologic standpoint to highlight directions for future research that would be the most likely to meaningfully increase knowledge. METHODS We conducted a search in PubMed for studies of cancer and PFAS (through 9/20/2020). We identified epidemiologic studies that provided a quantitative estimate for some measure of the association between PFAS and cancer. Here, we review that literature, including several aspects of epidemiologic study design that impact the usefulness of study results. RESULTS We identified 16 cohort (or case-cohort) studies, 10 case-control studies (4 nested within cohorts and 6 non-nested), 1 cross sectional study and 1 ecologic study. The cancer sites with the most evidence of an association with PFAS are testicular and kidney cancer. There are also some suggestions in a few studies of an association with prostate cancer, but the data are inconsistent. DISCUSSION Each study's design has strengths and limitations. Weaknesses in study design and methods can, in some cases, lead to questionable associations, but in other cases can make it more difficult to detect true associations, if they are present. Overall, the evidence for an association between cancer and PFAS remains sparse. A variety of studies with different strengths and weaknesses can be helpful to clarify associations between PFAS and cancer. Long term follow-up of large-sized cohorts with large exposure contrasts are most likely to be informative.
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Affiliation(s)
- Kyle Steenland
- Rollins School of Public Health, Emory University, 1518 Clifton Road NE, Atlanta, GA, 30322, USA
| | - Andrea Winquist
- National Center for Environmental Health, Centers for Disease Control and Prevention, 4770 Buford Highway, MS S 106-6, Atlanta, GA, 30341, USA.
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8
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Lee M, Zeleniuch-Jacquotte A, Liu M. Empirical evaluation of sub-cohort sampling designs for risk prediction modeling. J Appl Stat 2020; 48:1374-1401. [DOI: 10.1080/02664763.2020.1861225] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Myeonggyun Lee
- Department of Population Health, NYU School of Medicine, New York, NY, USA
| | - Anne Zeleniuch-Jacquotte
- Department of Population Health, NYU School of Medicine, New York, NY, USA
- Department of Environmental Medicine, NYU School of Medicine, New York, NY, USA
| | - Mengling Liu
- Department of Population Health, NYU School of Medicine, New York, NY, USA
- Department of Environmental Medicine, NYU School of Medicine, New York, NY, USA
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Li W, Li R, Feng Z, Ning J. Semiparametric isotonic regression analysis for risk assessment under nested case-control and case-cohort designs. Stat Methods Med Res 2020; 29:2328-2343. [PMID: 31868119 PMCID: PMC7306447 DOI: 10.1177/0962280219893389] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Two-phase sampling designs, including nested case-control and case-cohort designs, are frequently utilized in large cohort studies involving expensive biomarkers. To analyze data from two-phase designs with a binary outcome, parametric models such as logistic regression are often adopted. However, when the model assumptions are not valid, parametric models may lead to biased estimation and risk evaluation. In this paper, we propose a robust semiparametric regression model for binary outcomes and an easy-to-implement computational procedure that combines the pool-adjacent violators algorithm with inverse probability weighting. The asymptotic properties are established, including consistency and the convergence rate. Simulation studies show that the proposed method performs well and is more robust than logistic regression methods. We demonstrate the application of the proposed method to real data from the Prostate, Lung, Colorectal, and Ovarian (PLCO) Cancer Screening Trial.
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Affiliation(s)
- Wen Li
- Department of Biostatistics and Data Science, The University of Texas Health Science Center, Houston, TX, USA
| | - Ruosha Li
- Department of Biostatistics and Data Science, The University of Texas Health Science Center, Houston, TX, USA
| | - Ziding Feng
- Fred Hutchinson Cancer Research Center, Seattle, Washington, DC, USA
| | - Jing Ning
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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Mortier P, Vilagut G, Puértolas Gracia B, De Inés Trujillo A, Alayo Bueno I, Ballester Coma L, Blasco Cubedo MJ, Cardoner N, Colls C, Elices M, Garcia-Altes A, Gené Badia M, Gómez Sánchez J, Martín Sánchez M, Morros R, Prat Pubill B, Qin P, Mehlum L, Kessler RC, Palao D, Pérez Sola V, Alonso J. Catalonia Suicide Risk Code Epidemiology (CSRC-Epi) study: protocol for a population-representative nested case-control study of suicide attempts in Catalonia, Spain. BMJ Open 2020; 10:e037365. [PMID: 32660952 PMCID: PMC7359191 DOI: 10.1136/bmjopen-2020-037365] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 05/02/2020] [Accepted: 05/29/2020] [Indexed: 11/15/2022] Open
Abstract
INTRODUCTION Suicide attempts represent an important public health burden. Centralised electronic health record (EHR) systems have high potential to provide suicide attempt surveillance, to inform public health action aimed at reducing risk for suicide attempt in the population, and to provide data-driven clinical decision support for suicide risk assessment across healthcare settings. To exploit this potential, we designed the Catalonia Suicide Risk Code Epidemiology (CSRC-Epi) study. Using centralised EHR data from the entire public healthcare system of Catalonia, Spain, the CSRC-Epi study aims to estimate reliable suicide attempt incidence rates, identify suicide attempt risk factors and develop validated suicide attempt risk prediction tools. METHODS AND ANALYSIS The CSRC-Epi study is registry-based study, specifically, a two-stage exposure-enriched nested case-control study of suicide attempts during the period 2014-2019 in Catalonia, Spain. The primary study outcome consists of first and repeat attempts during the observation period. Cases will come from a case register linked to a suicide attempt surveillance programme, which offers in-depth psychiatric evaluations to all Catalan residents who present to clinical care with any suspected risk for suicide. Predictor variables will come from centralised EHR systems representing all relevant healthcare settings. The study's sampling frame will be constructed using population-representative administrative lists of Catalan residents. Inverse probability weights will restore representativeness of the original population. Analysis will include the calculation of age-standardised and sex-standardised suicide attempt incidence rates. Logistic regression will identify suicide attempt risk factors on the individual level (ie, relative risk) and the population level (ie, population attributable risk proportions). Machine learning techniques will be used to develop suicide attempt risk prediction tools. ETHICS AND DISSEMINATION This protocol is approved by the Parc de Salut Mar Clinical Research Ethics Committee (2017/7431/I). Dissemination will include peer-reviewed scientific publications, scientific reports for hospital and government authorities, and updated clinical guidelines. TRIAL REGISTRATION NUMBER NCT04235127.
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Affiliation(s)
- Philippe Mortier
- Health Services Research Group, IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Gemma Vilagut
- Health Services Research Group, IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Beatriz Puértolas Gracia
- Health Services Research Group, IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Ana De Inés Trujillo
- Health Services Research Group, IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
- Department of Social Psychology, Autonomous University of Barcelona (UAB), Cerdanyola del Vallès, Barcelona, Spain
| | - Itxaso Alayo Bueno
- Health Services Research Group, IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Laura Ballester Coma
- Health Services Research Group, IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Department of Psychology, University of Girona (UdG), Girona, Spain
| | - María Jesús Blasco Cubedo
- Health Services Research Group, IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Department of Health & Experimental Sciences, Pompeu Fabra University (UPF), Barcelona, Spain
| | - Narcís Cardoner
- Depression and Anxiety Program, Department of Mental Health, Parc Taulí Sabadell, Hospital Universitari, Sabadell, Spain
- Department of Psychiatry and Legal Medicine, Universitat Autònoma de Barcelona (UAB), Cerdanyola Del Vallès, Barcelona, Spain
- Centro de Investigación en Red de Salud Mental, CIBERSAM, Madrid, Spain
- Institut d'Investigació i Innovació Parc Taulí (I3PT), Sabadell, Barcelona, Spain
| | - Cristina Colls
- Agència de Qualitat i Avaluació Sanitàries de Catalunya - Health Evaluation and Quality Agency of Catalonia (AQuAS), Catalan Health Department, Barcelona, Spain
| | - Matilde Elices
- Centro de Investigación en Red de Salud Mental, CIBERSAM, Madrid, Spain
- Neurosciences Research Programme, IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | - Anna Garcia-Altes
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Agència de Qualitat i Avaluació Sanitàries de Catalunya - Health Evaluation and Quality Agency of Catalonia (AQuAS), Catalan Health Department, Barcelona, Spain
- Institut d'Investigació Biomèdica (IIB Sant Pau), Barcelona, Spain
| | - Manel Gené Badia
- Legal Medicine Unit, Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - Javier Gómez Sánchez
- Health Services Research Group, IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | - Mario Martín Sánchez
- Preventive Medicine and Public Health Training Unit PSMar-UPF-ASPB, Parc de Salut Mar, Agència de Salut Pública de Barcelona, Pompeu Fabra University, Barcelona, Spain
| | - Rosa Morros
- Fundació Institut Universitari per a la recerca a l'Atenció Primària de Salut Jordi Gol i Gurina (IDIAPJGol), Barcelona, Spain
- Departament de Farmacologia, de Terapèutica i de Toxicologia, Universitat Autònoma de Barcelona, Barcelona, Spain
- Institut Català de la Salut (ICS), Metropolitana Nord, Barcelona, Spain
| | - Bibiana Prat Pubill
- Master Plan on Mental Health and Addictions, Ministry of Health, Catalan Government, Barcelona, Spain
| | - Ping Qin
- National Centre for Suicide Research and Prevention, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Lars Mehlum
- National Centre for Suicide Research and Prevention, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Ronald C Kessler
- Department of Health Care Policy, Harvard Medical School, Boston, MA, USA
| | - Diego Palao
- Depression and Anxiety Program, Department of Mental Health, Parc Taulí Sabadell, Hospital Universitari, Sabadell, Spain
- Department of Psychiatry and Legal Medicine, Universitat Autònoma de Barcelona (UAB), Cerdanyola Del Vallès, Barcelona, Spain
- Centro de Investigación en Red de Salud Mental, CIBERSAM, Madrid, Spain
- Institut d'Investigació i Innovació Parc Taulí (I3PT), Sabadell, Barcelona, Spain
| | - Víctor Pérez Sola
- Department of Psychiatry and Legal Medicine, Universitat Autònoma de Barcelona (UAB), Cerdanyola Del Vallès, Barcelona, Spain
- Centro de Investigación en Red de Salud Mental, CIBERSAM, Madrid, Spain
- Neurosciences Research Programme, IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
- Institut de Neuropsiquiatria i Addiccions, Hospital del Mar, Barcelona, Spain
| | - Jordi Alonso
- Health Services Research Group, IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Department of Health & Experimental Sciences, Pompeu Fabra University (UPF), Barcelona, Spain
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11
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Liu S, Zhou B, Wang Y, Wang K, Zhang Z, Niu W. Pre-pregnancy Maternal Weight and Gestational Weight Gain Increase the Risk for Childhood Asthma and Wheeze: An Updated Meta-Analysis. Front Pediatr 2020; 8:134. [PMID: 32309270 PMCID: PMC7145976 DOI: 10.3389/fped.2020.00134] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 03/10/2020] [Indexed: 01/09/2023] Open
Abstract
Background: Mounting evidence suggests that childhood asthma is closely associated with maternal weight before pregnancy and gestational weight gain (GWG), yet the results are not often reproducible. Objectives: We conducted a comprehensive meta-analysis, aiming to evaluate the association of pre-pregnancy maternal obesity or overweight and high GWG with the risk for childhood asthma and wheeze. Methods: Literature search, quality assessment, and data extraction were completed independently and in duplicate. Effect-size estimates are expressed as odds ratio (OR) with 95% confidence interval (CI). Results: Twenty-two observational studies involving 145,574 mother-child pairs were meta-analyzed. In overall analyses, maternal obesity or overweight in pre-pregnancy significantly increased the risk of both childhood asthma and wheeze (adjusted OR: 1.41 and 1.13, 95% CI: 1.26-1.59 and 1.07-1.20, both p < 0.001). Per 1 kg/m2 increment in maternal body mass index was associated with a significantly increased risk of childhood asthma and wheeze (adjusted OR: 1.03, 95% CI: 1.02-1.03, p < 0.001). Compared with normal GWG, very high GWG (adjusted OR: 1.24, 95% CI: 1.04-1.47, p: 0.018), moderate high GWG (adjusted OR: 1.12, 95% CI: 1.04-1.21, p: 0.004), and very low GWG (adjusted OR: 1.26, 95% CI: 1.08-1.47, p: 0.004) increased the risk of childhood asthma and wheeze. There was a low probability of publication bias. Conclusions: Our findings indicate that both pre-pregnancy maternal obesity or overweight and very to moderate high or low GWG render their offspring susceptible to a significantly increased risk of having childhood asthma and wheeze.
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Affiliation(s)
- Shufang Liu
- Graduate School, Beijing University of Chinese Medicine, Beijing, China.,Department of Pediatrics, China-Japan Friendship Hospital, Beijing, China
| | - Bo Zhou
- Graduate School, Beijing University of Chinese Medicine, Beijing, China.,Department of Pediatrics, China-Japan Friendship Hospital, Beijing, China
| | - Yunfeng Wang
- Department of Pediatrics, China-Japan Friendship Hospital, Beijing, China
| | - Kundi Wang
- Department of Pediatrics, China-Japan Friendship Hospital, Beijing, China
| | - Zhixin Zhang
- Department of Pediatrics, China-Japan Friendship Hospital, Beijing, China.,International Medical Services, China-Japan Friendship Hospital, Beijing, China
| | - Wenquan Niu
- Institute of Clinical Medical Sciences, China-Japan Friendship Hospital, Beijing, China
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12
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Zelic R, Zugna D, Bottai M, Andrén O, Fridfeldt J, Carlsson J, Davidsson S, Fiano V, Fiorentino M, Giunchi F, Grasso C, Lianas L, Mascia C, Molinaro L, Zanetti G, Richiardi L, Pettersson A, Akre O. Estimation of Relative and Absolute Risks in a Competing-Risks Setting Using a Nested Case-Control Study Design: Example From the ProMort Study. Am J Epidemiol 2019; 188:1165-1173. [PMID: 30976789 PMCID: PMC8210820 DOI: 10.1093/aje/kwz026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 01/28/2019] [Accepted: 01/29/2019] [Indexed: 12/16/2022] Open
Abstract
In this paper, we describe the Prognostic Factors for Mortality in Prostate Cancer (ProMort) study and use it to demonstrate how the weighted likelihood method can be used in nested case-control studies to estimate both relative and absolute risks in the competing-risks setting. ProMort is a case-control study nested within the National Prostate Cancer Register (NPCR) of Sweden, comprising 1,710 men diagnosed with low- or intermediate-risk prostate cancer between 1998 and 2011 who died from prostate cancer (cases) and 1,710 matched controls. Cause-specific hazard ratios and cumulative incidence functions (CIFs) for prostate cancer death were estimated in ProMort using weighted flexible parametric models and compared with the corresponding estimates from the NPCR cohort. We further drew 1,500 random nested case-control subsamples of the NPCR cohort and quantified the bias in the hazard ratio and CIF estimates. Finally, we compared the ProMort estimates with those obtained by augmenting competing-risks cases and by augmenting both competing-risks cases and controls. The hazard ratios for prostate cancer death estimated in ProMort were comparable to those in the NPCR. The hazard ratios for dying from other causes were biased, which introduced bias in the CIFs estimated in the competing-risks setting. When augmenting both competing-risks cases and controls, the bias was reduced.
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Affiliation(s)
- Renata Zelic
- Clinical Epidemiology Unit, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Daniela Zugna
- Cancer Epidemiology Unit, Department of Medical Sciences, University of Turin, Turin, Italy
- Centro di Riferimento per l’Epidemiologia e la Prevenzione Oncologica
| | - Matteo Bottai
- Unit of Biostatistics, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Ove Andrén
- Department of Urology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Jonna Fridfeldt
- Department of Urology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Jessica Carlsson
- Department of Urology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Sabina Davidsson
- Department of Urology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Valentina Fiano
- Cancer Epidemiology Unit, Department of Medical Sciences, University of Turin, Turin, Italy
- Centro di Riferimento per l’Epidemiologia e la Prevenzione Oncologica
| | - Michelangelo Fiorentino
- Pathology Service, Addarii Institute of Oncology, Sant’Orsola-Malpighi Hospital, Bologna, Italy
| | - Francesca Giunchi
- Pathology Service, Addarii Institute of Oncology, Sant’Orsola-Malpighi Hospital, Bologna, Italy
| | - Chiara Grasso
- Cancer Epidemiology Unit, Department of Medical Sciences, University of Turin, Turin, Italy
- Centro di Riferimento per l’Epidemiologia e la Prevenzione Oncologica
| | - Luca Lianas
- Data-Intensive Computing Division, Center for Advanced Studies, Research and Development in Sardinia, Pula, Italy
| | - Cecilia Mascia
- Data-Intensive Computing Division, Center for Advanced Studies, Research and Development in Sardinia, Pula, Italy
| | - Luca Molinaro
- Division of Pathology, Azienda Ospedaliero-Universitaria Città della Salute e della Scienza Hospital, Turin, Italy
| | - Gianluigi Zanetti
- Data-Intensive Computing Division, Center for Advanced Studies, Research and Development in Sardinia, Pula, Italy
| | - Lorenzo Richiardi
- Cancer Epidemiology Unit, Department of Medical Sciences, University of Turin, Turin, Italy
- Centro di Riferimento per l’Epidemiologia e la Prevenzione Oncologica
| | - Andreas Pettersson
- Clinical Epidemiology Unit, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Olof Akre
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Urology, Karolinska University Hospital, Stockholm, Sweden
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13
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Wang X, Chao L, Liu X, Xu X, Zhang Q. Association Between HLA Genotype and Cutaneous Adverse Reactions to Antiepileptic Drugs Among Epilepsy Patients in Northwest China. Front Neurol 2019; 10:1. [PMID: 30761061 PMCID: PMC6362303 DOI: 10.3389/fneur.2019.00001] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 01/03/2019] [Indexed: 11/13/2022] Open
Abstract
This study aimed to investigate the association between HLA genotypes and antiepileptic drug-induced cutaneous adverse reactions (AEDs-cADRs) among patients with epilepsy in Ningxia Hui Autonomous Region of Northwest China. Fifteen patients with AEDs-cADRs and 30 matched AEDs tolerant controls from anested case-control study were tested the HLA-A, HLA-B, and HLA-DRB1 genotype using the polymerase chain reaction sequence-based typing (PCR-SBT). Significant difference was not observed between AEDs-cADRs and AEDs tolerant groups in terms of HLA-A, HLA-B, and HLA-DRB1 genotype frequencies. Future studies using larger cohorts are needed to verify this observation.
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Affiliation(s)
- Xu Wang
- Department of Neurology, General Hospital of Ningxia Medical University, Yinchuan, China
| | - Lina Chao
- Department of Neurology, The First People's Hospital, Shizuishan, China
| | - Xiaojing Liu
- Department of Neurology, The First Hospital of Tongxiang, Tongxiang, China
| | - Xianrui Xu
- Department of Neurology, General Hospital of Ningxia Medical University, Yinchuan, China
| | - Qing Zhang
- Department of Neurology, General Hospital of Ningxia Medical University, Yinchuan, China.,Ningxia Key Laboratory of Cerebrocranial Diseases, The Incubation Base of National Key Laboratory, Yinchuan, China
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14
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Morton AM, Koch M, Mendivil CO, Furtado JD, Tjønneland A, Overvad K, Wang L, Jensen MK, Sacks FM. Apolipoproteins E and CIII interact to regulate HDL metabolism and coronary heart disease risk. JCI Insight 2018; 3:98045. [PMID: 29467335 DOI: 10.1172/jci.insight.98045] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 01/17/2018] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Subspecies of HDL contain apolipoprotein E (apoE) and/or apoCIII. Both proteins have properties that could affect HDL metabolism. The relation between HDL metabolism and risk of coronary heart disease (CHD) is not well understood. METHODS Eighteen participants were given a bolus infusion of [D3]L-leucine to label endogenous proteins on HDL. HDL was separated into subspecies containing apoE and/or apoCIII and then into 4 sizes. Metabolic rates for apoA-I in HDL subspecies and sizes were determined by interactive modeling. The concentrations of apoE in HDL that contain or lack apoCIII were measured in a prospective study in Denmark including 1,949 incident CHD cases during 9 years. RESULTS HDL containing apoE but not apoCIII is disproportionately secreted into the circulation, actively expands while circulating, and is quickly cleared. These are key metabolic steps in reverse cholesterol transport, which may protect against atherosclerosis. ApoCIII on HDL strongly attenuates these metabolic actions of HDL apoE. In the epidemiological study, the relation between HDL apoE concentration and CHD significantly differed depending on whether apoCIII was present. HDL apoE was associated significantly with lower risk of CHD only in the HDL subspecies lacking apoCIII. CONCLUSIONS ApoE and apoCIII on HDL interact to affect metabolism and CHD. ApoE promotes metabolic steps in reverse cholesterol transport and is associated with lower risk of CHD. ApoCIII, when coexisting with apoE on HDL, abolishes these benefits. Therefore, differences in metabolism of HDL subspecies pertaining to reverse cholesterol transport are reflected in differences in association with CHD. TRIAL REGISTRATION Clinicaltrials.gov NCT01399632. FUNDING This work was supported by NIH grant R01HL095964 to FMS and by a grant to the Harvard Clinical and Translational Science Center (8UL1TR0001750) from the National Center for Advancing Translational Science.
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Affiliation(s)
- Allyson M Morton
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Manja Koch
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Carlos O Mendivil
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA.,Department of Medicine, Universidad de los Andes, Bogotá, Colombia.,Section of Endocrinology, Department of Internal Medicine, Fundación Santa Fe de Bogotá, Bogotá, Colombia
| | - Jeremy D Furtado
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | | | - Kim Overvad
- Department of Cardiology, Aalborg University Hospital, Aalborg, Denmark.,Section for Epidemiology, Department of Public Health, Aarhus University, Aarhus, Denmark
| | - Liyun Wang
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Majken K Jensen
- 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
| | - Frank M Sacks
- 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.,Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
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15
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Delcoigne B, Colzani E, Prochazka M, Gagliardi G, Hall P, Abrahamowicz M, Czene K, Reilly M. Breaking the matching in nested case–control data offered several advantages for risk estimation. J Clin Epidemiol 2017; 82:79-86. [DOI: 10.1016/j.jclinepi.2016.11.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 11/22/2016] [Accepted: 11/28/2016] [Indexed: 10/20/2022]
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16
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Ren J, Murphy G, Fan J, Dawsey SM, Taylor PR, Selhub J, Qiao Y, Abnet CC. Prospective study of serum B vitamins levels and oesophageal and gastric cancers in China. Sci Rep 2016; 6:35281. [PMID: 27748414 PMCID: PMC5066215 DOI: 10.1038/srep35281] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 09/08/2016] [Indexed: 01/27/2023] Open
Abstract
B vitamins play an essential role in DNA synthesis and methylation, and may protect against oesophageal and gastric cancers. In this case-cohort study, subjects were enrolled from the General Population Nutrition Intervention Trial in Linxian, China. Subjects included 498 oesophageal squamous cell carcinomas (OSCCs), 255 gastric cardia adenocarcinomas (GCAs), and an age- and sex-matched sub-cohort of 947 individuals. Baseline serum riboflavin, pyridoxal phosphate (PLP), folate, vitamin B12, and flavin mononucleotide (FMN) were measured for all subjects. We estimated the associations with Cox proportional hazard models, with adjustment for potential confounders. Compared to those in the lowest quartile of serum riboflavin, those in the highest had a 44% lower risk of OSCC (HR: 0.56, 95% CI: 0.41 to 0.75). Serum vitamin B12 as a continuous variable was observed to be significantly inversely associated with OSCC (HR: 0.95, 95% CI: 0.89 to 1.01, P for score test = 0.041). Higher serum FMN levels were significantly associated with increased risk of OSCC (HR: 1.08, 95% CI: 1.01 to 1.16) and GCA (HR: 1.09, 95% CI: 1.00 to 1.20). Our study prompted that B vitamins have the potential role as chemopreventive agents for upper gastrointestinal cancers.
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Affiliation(s)
- Jiansong Ren
- Program Office for Cancer Screening in Urban China, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Gwen Murphy
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Jinhu Fan
- Department of Epidemiology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Sanford M. Dawsey
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Philip R. Taylor
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Jacob Selhub
- Jean Mayer U.S. Department of Agriculture Human Nutrition Research Center on Aging at Tufts University, Boston, Massachusetts, USA
| | - Youlin Qiao
- Department of Epidemiology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Christian C. Abnet
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
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17
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Delcoigne B, Hagenbuch N, Schelin ME, Salim A, Lindström LS, Bergh J, Czene K, Reilly M. Feasibility of reusing time-matched controls in an overlapping cohort. Stat Methods Med Res 2016; 27:1818-1829. [PMID: 27659169 DOI: 10.1177/0962280216669744] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The methods developed for secondary analysis of nested case-control data have been illustrated only in simplified settings in a common cohort and have not found their way into biostatistical practice. This paper demonstrates the feasibility of reusing prior nested case-control data in a realistic setting where a new outcome is available in an overlapping cohort where no new controls were gathered and where all data have been anonymised. Using basic information about the background cohort and sampling criteria, the new cases and prior data are "aligned" to identify the common underlying study base. With this study base, a Kaplan-Meier table of the prior outcome extracts the risk sets required to calculate the weights to assign to the controls to remove the sampling bias. A weighted Cox regression, implemented in standard statistical software, provides unbiased hazard ratios. Using the method to compare cases of contralateral breast cancer to available controls from a prior study of metastases, we identified a multifocal tumor as a risk factor that has not been reported previously. We examine the sensitivity of the method to an imperfect weighting scheme and discuss its merits and pitfalls to provide guidance for its use in medical research studies.
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Affiliation(s)
- Bénédicte Delcoigne
- 1 Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Niels Hagenbuch
- 1 Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Maria Ec Schelin
- 2 Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Agus Salim
- 3 Department of Mathematics and Statistics, La Trobe University, Victoria, Australia
| | - Linda S Lindström
- 1 Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.,4 Department of Surgery, University of California, San Francisco, CA, USA
| | - Jonas Bergh
- 1 Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Kamila Czene
- 1 Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Marie Reilly
- 1 Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
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18
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19
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Rivera CL, Lumley T. Using the entire history in the analysis of nested case cohort samples. Stat Med 2016; 35:3213-28. [DOI: 10.1002/sim.6917] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 01/20/2016] [Accepted: 01/31/2016] [Indexed: 11/10/2022]
Affiliation(s)
- C. L. Rivera
- Department of Biostatistics; Harvard School of Public Health; 677 Huntington Avenue, Kresge 803B Boston MA 02115 U.S.A
| | - T. Lumley
- Department of Biostatistics; Harvard School of Public Health; 677 Huntington Avenue, Kresge 803B Boston MA 02115 U.S.A
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20
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Rivera C, Lumley T. Using the whole cohort in the analysis of countermatched samples. Biometrics 2015; 72:382-91. [PMID: 26393818 DOI: 10.1111/biom.12419] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2015] [Revised: 07/01/2015] [Accepted: 08/01/2015] [Indexed: 11/29/2022]
Abstract
We present a technique for using calibrated weights to incorporate whole-cohort information in the analysis of a countermatched sample. Following Samuelsen's approach for matched case-control sampling, we derive expressions for the marginal sampling probabilities, so that the data can be treated as an unequally-sampled case-cohort design. Pseudolikelihood estimating equations are used to find the estimates. The sampling weights can be calibrated, allowing all whole-cohort variables to be used in estimation; in contrast, the partial likelihood analysis makes use only of a single discrete surrogate for exposure. Using a survey-sampling approach rather than a martingale approach simplifies the theory; in particular, the sampling weights need not be a predictable process. Our simulation results show that pseudolikelihood estimation gives lower efficiency than partial likelihood estimation, but that the gain from calibration of weights can more than compensate for this loss. If there is a good surrogate for exposure, countermatched sampling still outperforms case-cohort and two-phase case-control sampling even when calibrated weights are used. Findings are illustrated with data from the National Wilms' Tumour Study and the Welsh nickel refinery workers study.
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Affiliation(s)
- C Rivera
- Department of statistics, University of Auckland, Auckland, NZ
| | - T Lumley
- Department of statistics, University of Auckland, Auckland, NZ
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21
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Jones E, Sweeting MJ, Sharp SJ, Thompson SG. A method making fewer assumptions gave the most reliable estimates of exposure-outcome associations in stratified case-cohort studies. J Clin Epidemiol 2015; 68:1397-405. [PMID: 26051242 PMCID: PMC4669309 DOI: 10.1016/j.jclinepi.2015.04.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Revised: 04/09/2015] [Accepted: 04/16/2015] [Indexed: 01/13/2023]
Abstract
Objective A case–cohort study is an efficient epidemiological study design for estimating exposure–outcome associations. When sampling of the subcohort is stratified, several methods of analysis are possible, but it is unclear how they compare. Our objective was to compare five analysis methods using Cox regression for this type of data, ranging from a crude model that ignores the stratification to a flexible one that allows nonproportional hazards and varying covariate effects across the strata. Study Design and Setting We applied the five methods to estimate the association between physical activity and incident type 2 diabetes using data from a stratified case–cohort study and also used artificial data sets to exemplify circumstances in which they can give different results. Results In the diabetes study, all methods except the method that ignores the stratification gave similar results for the hazard ratio associated with physical activity. In the artificial data sets, the more flexible methods were shown to be necessary when certain assumptions of the simpler models failed. The most flexible method gave reliable results for all the artificial data sets. Conclusion The most flexible method is computationally straightforward, and appropriate whether or not key assumptions made by the simpler models are valid.
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Affiliation(s)
- Edmund Jones
- Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Worts' Causeway, Cambridge, CB1 8RN, UK.
| | - Michael J Sweeting
- Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Worts' Causeway, Cambridge, CB1 8RN, UK
| | - Stephen J Sharp
- Medical Research Council Epidemiology Unit, University of Cambridge School of Clinical Medicine, Box 285, Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
| | - Simon G Thompson
- Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Worts' Causeway, Cambridge, CB1 8RN, UK
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Kim RS, Kaplan RC. Analysis of secondary outcomes in nested case-control study designs. Stat Med 2014; 33:4215-26. [PMID: 24919979 DOI: 10.1002/sim.6231] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Revised: 05/01/2014] [Accepted: 05/22/2014] [Indexed: 11/09/2022]
Abstract
One of the main perceived advantages of using a case-cohort design compared with a nested case-control design in an epidemiologic study is the ability to evaluate with the same subcohort outcomes other than the primary outcome of interest. In this paper, we show that valid inferences about secondary outcomes can also be achieved in nested case-control studies by using the inclusion probability weighting method in combination with an approximate jackknife standard error that can be computed using existing software. Simulation studies demonstrate that when the sample size is sufficient, this approach yields valid type 1 error and coverage rates for the analysis of secondary outcomes in nested case-control designs. Interestingly, the statistical power of the nested case-control design was comparable with that of the case-cohort design when the primary and secondary outcomes were positively correlated. The proposed method is illustrated with the data from a cohort in Cardiovascular Health Study to study the association of C-reactive protein levels and the incidence of congestive heart failure.
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Affiliation(s)
- Ryung S Kim
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York, 10461, U.S.A
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