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Tao J, Helali AE, Ho JC, Lam WWT, Pang H. An Evaluation of Gene-Diet Interaction Statistical Methods and Discovery of rs7175421-Whole Grain Interaction in Lung Cancer. Nutr Cancer 2022; 75:219-227. [PMID: 35930377 DOI: 10.1080/01635581.2022.2104878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Dietary factors show different effects on genetically diverse populations. Scientific research uses gene-environment interaction models to study the effects of dietary factors on genetically diverse populations for lung cancer risk. However, previous study designs have not investigated the degree of type I error inflation and, in some instances, have not corrected for multiple testing. Using a motivating investigation of diet-gene interaction and lung cancer risk, we propose a training and testing strategy and perform real-world simulations to select the appropriate statistical methods to reduce false-positive discoveries. The simulation results show that the unconstrained maximum likelihood (UML) method controls the type I error better than the constrained maximum likelihood (CML). The empirical Bayesian (EB) method can compete with the UML method in achieving statistical power and controlling type I error. We observed a significant interaction between SNP rs7175421 with dietary whole grain in lung cancer prevention, with an effect size (standard error) of -0.312 (0.112) for EB estimate. SNP rs7175421 may interact with dietary whole grains in modulating lung cancer risk. Evaluating statistical methods for gene-diet interaction analysis can help balance the statistical power and type I error.
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Affiliation(s)
- Jun Tao
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong, China
| | - Aya El Helali
- Department of Clinical Oncology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong, China
| | - James C Ho
- Department of Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong, China
| | - Wendy W T Lam
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong, China.,Jockey Club Institute of Cancer Care, The University of Hong Kong, Pok Fu Lam, Hong Kong, China
| | - Herbert Pang
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong, China.,Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, North Carolina, USA
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Mbemi A, Khanna S, Njiki S, Yedjou CG, Tchounwou PB. Impact of Gene-Environment Interactions on Cancer Development. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:E8089. [PMID: 33153024 PMCID: PMC7662361 DOI: 10.3390/ijerph17218089] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 10/26/2020] [Accepted: 10/30/2020] [Indexed: 12/24/2022]
Abstract
Several epidemiological and experimental studies have demonstrated that many human diseases are not only caused by specific genetic and environmental factors but also by gene-environment interactions. Although it has been widely reported that genetic polymorphisms play a critical role in human susceptibility to cancer and other chronic disease conditions, many single nucleotide polymorphisms (SNPs) are caused by somatic mutations resulting from human exposure to environmental stressors. Scientific evidence suggests that the etiology of many chronic illnesses is caused by the joint effect between genetics and the environment. Research has also pointed out that the interactions of environmental factors with specific allelic variants highly modulate the susceptibility to diseases. Hence, many scientific discoveries on gene-environment interactions have elucidated the impact of their combined effect on the incidence and/or prevalence rate of human diseases. In this review, we provide an overview of the nature of gene-environment interactions, and discuss their role in human cancers, with special emphases on lung, colorectal, bladder, breast, ovarian, and prostate cancers.
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Affiliation(s)
- Ariane Mbemi
- NIH/NIMHD RCMI-Center for Health Disparities Research, Jackson State University, 1400 Lynch Street, Box 18750, Jackson, MS 39217, USA; (A.M.); (S.N.)
- Department of Biology, College of Science, Engineering and Technology, Jackson State University, 1400 Lynch Street, Box 18540, Jackson, MS 39217, USA
| | - Sunali Khanna
- Department of Oral Medicine and Radiology, Nair Hospital Dental College, Municipal Corporation of Greater Mumbai, Mumbai 400 008, India;
| | - Sylvianne Njiki
- NIH/NIMHD RCMI-Center for Health Disparities Research, Jackson State University, 1400 Lynch Street, Box 18750, Jackson, MS 39217, USA; (A.M.); (S.N.)
- Department of Biology, College of Science, Engineering and Technology, Jackson State University, 1400 Lynch Street, Box 18540, Jackson, MS 39217, USA
| | - Clement G. Yedjou
- Department of Biological Sciences, College of Science and Technology, Florida Agricultural and Mechanical University, 1610 S. Martin Luther King Blvd., Tallahassee, FL 32307, USA;
| | - Paul B. Tchounwou
- NIH/NIMHD RCMI-Center for Health Disparities Research, Jackson State University, 1400 Lynch Street, Box 18750, Jackson, MS 39217, USA; (A.M.); (S.N.)
- Department of Biology, College of Science, Engineering and Technology, Jackson State University, 1400 Lynch Street, Box 18540, Jackson, MS 39217, USA
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Kim S, Wang M, Tyrer JP, Jensen A, Wiensch A, Liu G, Lee AW, Ness RB, Salvatore M, Tworoger SS, Whittemore AS, Anton-Culver H, Sieh W, Olson SH, Berchuck A, Goode EL, Goodman MT, Doherty JA, Chenevix-Trench G, Rossing MA, Webb PM, Giles GG, Terry KL, Ziogas A, Fortner RT, Menon U, Gayther SA, Wu AH, Song H, Brooks-Wilson A, Bandera EV, Cook LS, Cramer DW, Milne RL, Winham SJ, Kjaer SK, Modugno F, Thompson PJ, Chang-Claude J, Harris HR, Schildkraut JM, Le ND, Wentzensen N, Trabert B, Høgdall E, Huntsman D, Pike MC, Pharoah PD, Pearce CL, Mukherjee B. A comprehensive gene-environment interaction analysis in Ovarian Cancer using genome-wide significant common variants. Int J Cancer 2019; 144:2192-2205. [PMID: 30499236 PMCID: PMC6399057 DOI: 10.1002/ijc.32029] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 10/24/2018] [Indexed: 12/18/2022]
Abstract
As a follow-up to genome-wide association analysis of common variants associated with ovarian carcinoma (cancer), our study considers seven well-known ovarian cancer risk factors and their interactions with 28 genome-wide significant common genetic variants. The interaction analyses were based on data from 9971 ovarian cancer cases and 15,566 controls from 17 case-control studies. Likelihood ratio and Wald tests for multiplicative interaction and for relative excess risk due to additive interaction were used. The top multiplicative interaction was noted between oral contraceptive pill (OCP) use (ever vs. never) and rs13255292 (p value = 3.48 × 10-4 ). Among women with the TT genotype for this variant, the odds ratio for OCP use was 0.53 (95% CI = 0.46-0.60) compared to 0.71 (95%CI = 0.66-0.77) for women with the CC genotype. When stratified by duration of OCP use, women with 1-5 years of OCP use exhibited differential protective benefit across genotypes. However, no interaction on either the multiplicative or additive scale was found to be statistically significant after multiple testing correction. The results suggest that OCP use may offer increased benefit for women who are carriers of the T allele in rs13255292. On the other hand, for women carrying the C allele in this variant, longer (5+ years) use of OCP may reduce the impact of carrying the risk allele of this SNP. Replication of this finding is needed. The study presents a comprehensive analytic framework for conducting gene-environment analysis in ovarian cancer.
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Affiliation(s)
- Sehee Kim
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Miao Wang
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Jonathan P. Tyrer
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Allan Jensen
- Department of Virus, Lifestyle and Genes, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Ashley Wiensch
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Gang Liu
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Alice W. Lee
- Department of Health Science, California State University, Fullerton, Fullerton, CA, USA
| | - Roberta B. Ness
- University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Maxwell Salvatore
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Shelley S. Tworoger
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
- Research Institute and Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Alice S. Whittemore
- Department of Health Research and Policy - Epidemiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
| | - Hoda Anton-Culver
- Department of Epidemiology, Genetic Epidemiology Research Institute, University of California Irvine, Irvine, CA, USA
| | - Weiva Sieh
- Department of Genetics and Genomic Sciences, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sara H. Olson
- Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Andrew Berchuck
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, USA
| | - Ellen L. Goode
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Marc T. Goodman
- Cancer Prevention and Control, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Community and Population Health Research Institute, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jennifer Anne Doherty
- Department of Population Health Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Georgia Chenevix-Trench
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Mary Anne Rossing
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Penelope M. Webb
- Population Health Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Graham G. Giles
- Cancer Epidemiology & Intelligence Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, Victoria, Australia
| | - Kathryn L. Terry
- Obstetrics and Gynecology Epidemiology Center, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Argyrios Ziogas
- Department of Epidemiology, Genetic Epidemiology Research Institute, University of California Irvine, Irvine, CA, USA
| | - Renée T. Fortner
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Usha Menon
- Gynaecological Cancer Research Centre, Women’s Cancer, Institute for Women’s Health, University College London, London, UK
| | - Simon A. Gayther
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Anna H. Wu
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Honglin Song
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Angela Brooks-Wilson
- Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, Canada
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC, Canada
| | - Elisa V. Bandera
- Cancer Prevention and Control Program, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Linda S. Cook
- University of New Mexico Health Sciences Center, University of New Mexico, Albuquerque, NM, USA
- Division of Cancer Care, Department of Population Health Research, Alberta Health Services, Calgary, AB, Canada
| | - Daniel W. Cramer
- Obstetrics and Gynecology Epidemiology Center, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Roger L. Milne
- Cancer Epidemiology & Intelligence Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Stacey J. Winham
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Susanne K. Kjaer
- Department of Virus, Lifestyle and Genes, Danish Cancer Society Research Center, Copenhagen, Denmark
- Department of Gynaecology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Francesmary Modugno
- Ovarian Cancer Center of Excellence, Womens Cancer Research Program, Magee-Womens Research Institute and Hillman Cancer Center, Pittsburgh, PA, USA
- Division of Gynecologic Oncology, Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Pamela J. Thompson
- Cancer Prevention and Control, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Research Group Genetic Cancer Epidemiology, University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Holly R. Harris
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Nhu D. Le
- Cancer Control Research, BC Cancer Agency, Vancouver, BC, Canada
| | - Nico Wentzensen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Britton Trabert
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Estrid Høgdall
- Department of Virus, Lifestyle and Genes, Danish Cancer Society Research Center, Copenhagen, Denmark
- Molecular Unit, Department of Pathology, Herlev Hospital, University of Copenhagen, Copenhagen, Denmark
| | - David Huntsman
- British Columbia’s Ovarian Cancer Research (OVCARE) program, Vancouver General Hospital, BC Cancer Agency and University of British Columbia
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Malcolm C. Pike
- Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Paul D.P. Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Celeste Leigh Pearce
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Center for Cancer Prevention and Translational Genomics, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Bhramar Mukherjee
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
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