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Marín D, Narváez DM, Sierra A, Molina JS, Ortiz I, Builes JJ, Morales O, Cuellar M, Corredor A, Villamil-Osorio M, Bejarano MA, Vidal D, Basagaña X, Anguita-Ruiz A, Maitre L, Domínguez A, Valencia A, Henao J, Abad JM, Lopera V, Amaya F, Aristizábal LM, Rodríguez-Villamizar LA, Ramos-Contreras C, López L, Hernández-Flórez LJ, Bangdiwala SI, Groot H, Rueda ZV. DNA damage and its association with early-life exposome: Gene-environment analysis in Colombian children under five years old. ENVIRONMENT INTERNATIONAL 2024; 190:108907. [PMID: 39121825 DOI: 10.1016/j.envint.2024.108907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 07/01/2024] [Accepted: 07/22/2024] [Indexed: 08/12/2024]
Abstract
Environmental exposures and gene-exposure interactions are the major causes of some diseases. Early-life exposome studies are needed to elucidate the role of environmental exposures and their complex interactions with biological mechanisms involved in childhood health. This study aimed to determine the contribution of early-life exposome to DNA damage and the modifying effect of genetic polymorphisms involved in air pollutants metabolism, antioxidant defense, and DNA repair. We conducted a cohort study in 416 Colombian children under five years. Blood samples at baseline were collected to measure DNA damage by the Comet assay and to determine GSTT1, GSTM1, CYP1A1, H2AX, OGG1, and SOD2 genetic polymorphisms. The exposome was estimated using geographic information systems, remote sensing, LUR models, and questionnaires. The association exposome-DNA damage was estimated using the Elastic Net linear regression with log link. Our results suggest that exposure to PM2.5 one year before the blood draw (BBD) (0.83, 95 %CI: 0.76; 0.91), soft drinks consumption (0.94, 0.89; 0.98), and GSTM1 null genotype (0.05, 0.01; 0.36) diminished the DNA damage, whereas exposure to PM2.5 one-week BBD (1.18, 1.06; 1.32), NO2 lag-5 days BBD (1.27, 1.18; 1.36), in-house cockroaches (1.10, 1.00; 1.21) at the recruitment, crowding at home (1.34, 1.08; 1.67) at the recruitment, cereal consumption (1.11, 1.04; 1.19) and H2AX (AG/GG vs. AA) (1.44, 1.11; 1.88) increased the DNA damage. The interactions between H2AX (AG/GG vs. AA) genotypes with crowding and PM2.5 one week BBD, GSTM1 (null vs. present) with humidity at the first year of life, and OGG1 (SC/CC vs. SS) with walkability at the first year of life were significant. The early-life exposome contributes to elucidating the effect of environmental exposures on DNA damage in Colombian children under five years old. The exposome-DNA damage effect appears to be modulated by genetic variants in DNA repair and antioxidant defense enzymes.
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Affiliation(s)
- Diana Marín
- Public Health Group, School of Medicine, Universidad Pontificia Bolivariana, Medellín, Colombia.
| | - Diana M Narváez
- Human Genetics Laboratory, School of Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Anamaría Sierra
- Human Genetics Laboratory, School of Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Juan Sebastián Molina
- Human Genetics Laboratory, School of Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Isabel Ortiz
- Systems Biology Group, School of Medicine, Universidad Pontificia Bolivariana, Medellín, Colombia
| | | | - Olga Morales
- Pediaciencias Group, School of Medicine, Universidad de Antioquia, Department of Pediatrics, Hospital San Vicente Fundación, Medellín, Colombia
| | - Martha Cuellar
- Pediaciencias Group, School of Medicine, Universidad de Antioquia, Department of Pediatrics, SOMER Clinic, Medellín, Colombia
| | - Andrea Corredor
- Department of Pediatrics, ONIROS Centro Especializado en Medicina integral del Sueño, Bogotá, Colombia
| | - Milena Villamil-Osorio
- Department of Pediatrics, Fundación Hospital Pediátrico la Misericordia, Bogotá, Colombia
| | | | - Dolly Vidal
- Hospital Universitario San José, Popayán, Colombia
| | - Xavier Basagaña
- ISGlobal, Universitat Pompeu Fabra (UPF), CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Augusto Anguita-Ruiz
- ISGlobal, Universitat Pompeu Fabra (UPF), CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Leá Maitre
- ISGlobal, Universitat Pompeu Fabra (UPF), CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Alan Domínguez
- ISGlobal, Universitat Pompeu Fabra (UPF), CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Ana Valencia
- Systems Biology Group, School of Medicine, Universidad Pontificia Bolivariana, Medellín, Colombia
| | - Julián Henao
- Medical and Experimental Mycology, School of Medicine, Universidad Pontificia Bolivariana, Medellín, Colombia
| | | | - Verónica Lopera
- Secretaría de Salud, Alcaldía de Medellín, Medellín, Colombia
| | - Ferney Amaya
- School of Engineering, Universidad Pontificia Bolivariana, Medellín, Colombia
| | - Luis M Aristizábal
- School of Engineering, Universidad Pontificia Bolivariana, Medellín, Colombia
| | | | | | - Lucelly López
- Public Health Group, School of Medicine, Universidad Pontificia Bolivariana, Medellín, Colombia
| | | | - Shrikant I Bangdiwala
- Department of Health Research Methods, Evidence and Impact, McMaster University, Hamilton, Canada; Statistics Department, Population Health Research Institute, McMaster University, Hamilton, Canada
| | - Helena Groot
- Human Genetics Laboratory, School of Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Zulma Vanessa Rueda
- Public Health Group, School of Medicine, Universidad Pontificia Bolivariana, Medellín, Colombia; Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
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The Impact of the FKBP5 Gene Polymorphisms on the Relationship between Traumatic Life Events and Psychotic-Like Experiences in Non-Clinical Adults. Brain Sci 2021; 11:brainsci11050561. [PMID: 33925151 PMCID: PMC8144983 DOI: 10.3390/brainsci11050561] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 04/24/2021] [Indexed: 01/30/2023] Open
Abstract
Common variations of the FKBP5 gene are implicated in psychotic disorders, by modulating the hypothalamic–pituitary–adrenal axis reactivity to stress. It has been demonstrated that some of them might moderate the effects of childhood trauma on psychosis proneness. However, these associations have not been investigated with respect to traumatic life events (TLEs). Therefore, we aimed to explore whether the FKBP5 polymorphisms moderate the effects of TLEs on the level of psychotic-like experiences (PLEs). A total of 535 non-clinical adults were approached for participation, and genotyping of six FKBP5 polymorphisms (rs3800373, rs9470080, rs4713902, rs737054, rs1360780 and rs9296158) was performed. The Prodromal Questionnaire-16 (PQ-16) and the Traumatic Events Checklist (TEC) were administered to assess PLEs and TLEs, respectively. Among the rs1360780 CC homozygotes, a history of physical abuse was associated with significantly higher PQ-16 scores. This difference was not significant in the rs1360780 T allele carriers. Similarly, a history of physical abuse was associated with significantly higher PQ-16 scores in the rs9296158 GG homozygotes but not in the rs9296158 A allele carriers. Finally, emotional neglect was related to significantly higher PQ-16 scores in the rs737054 T allele carriers but not in the rs737054 CC homozygotes. The present study indicates that variation in the FKBP5 gene might moderate the effects of lifetime traumatic events on psychosis proneness.
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Benn Torres J. Anthropological perspectives on genomic data, genetic ancestry, and race. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2019; 171 Suppl 70:74-86. [DOI: 10.1002/ajpa.23979] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 11/04/2019] [Accepted: 11/11/2019] [Indexed: 02/06/2023]
Affiliation(s)
- Jada Benn Torres
- Vanderbilt UniversityDepartment of Anthropology Nashville Tennessee
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4
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Gallo V, Egger M, McCormack V, Farmer PB, Ioannidis JPA, Kirsch-Volders M, Matullo G, Phillips DH, Schoket B, Stromberg U, Vermeulen R, Wild C, Porta M, Vineis P. STrengthening the Reporting of OBservational studies in Epidemiology - Molecular Epidemiology (STROBE-ME): an extension of the STROBE statement. Eur J Clin Invest 2012; 42:1-16. [PMID: 22023344 DOI: 10.1111/j.1365-2362.2011.02561.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Advances in laboratory techniques have led to a rapidly increasing use of biomarkers in epidemiological studies. Biomarkers of internal dose, early biological change, susceptibility and clinical outcomes are used as proxies for investigating interactions between external and/or endogenous agents and body components or processes. The need for improved reporting of scientific research led to influential statements of recommendations such as the STrengthening Reporting of OBservational studies in Epidemiology (STROBE) statement. The STROBE initiative established in 2004 aimed to provide guidance on how to report observational research. Its guidelines provide a user-friendly checklist of 22 items to be reported in epidemiological studies, with items specific to the three main study designs: cohort studies, case-control studies and cross-sectional studies. The present STrengthening the Reporting of OBservational studies in Epidemiology -Molecular Epidemiology (STROBE-ME) initiative builds on the STROBE statement implementing nine existing items of STROBE and providing 17 additional items to the 22 items of STROBE checklist. The additions relate to the use of biomarkers in epidemiological studies, concerning collection, handling and storage of biological samples; laboratory methods, validity and reliability of biomarkers; specificities of study design; and ethical considerations. The STROBE-ME recommendations are intended to complement the STROBE recommendations.
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Affiliation(s)
- Valentina Gallo
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK.
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5
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Gallo V, Egger M, McCormack V, Farmer PB, Ioannidis JPA, Kirsch-Volders M, Matullo G, Phillips DH, Schoket B, Stromberg U, Vermeulen R, Wild C, Porta M, Vineis P. STrengthening the Reporting of OBservational studies in Epidemiology - Molecular Epidemiology (STROBE-ME): An extension of the STROBE statement. Mutagenesis 2012; 27:17-29. [DOI: 10.1093/mutage/ger039] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023] Open
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6
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Gallo V, Egger M, McCormack V, Farmer PB, Ioannidis JPA, Kirsch-Volders M, Matullo G, Phillips DH, Schoket B, Stromberg U, Vermeulen R, Wild C, Porta M, Vineis P. STrengthening the Reporting of OBservational studies in Epidemiology--Molecular Epidemiology STROBE-ME: an extension of the STROBE statement. J Clin Epidemiol 2011; 64:1350-63. [PMID: 22030070 DOI: 10.1016/j.jclinepi.2011.07.010] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2010] [Revised: 05/17/2011] [Accepted: 05/24/2011] [Indexed: 11/30/2022]
Abstract
Advances in laboratory techniques have led to a rapidly increasing use of biomarkers in epidemiological studies. Biomarkers of internal dose, early biological change susceptibility and clinical outcomes are used as proxies for investigating the interactions between external and/or endogenous agents and body components or processes. The need for improved reporting of scientific research led to influential statements of recommendations such as the STrengthening Reporting of OBservational studies in Epidemiology (STROBE) statement. The STROBE initiative established in 2004 aimed to provide guidance on how to report observational research. Its guidelines provide a user-friendly checklist of 22 items to be reported in epidemiological studies, with items specific to the three main study designs: cohort studies, case-control studies and cross-sectional studies. The present STrengthening the Reporting of OBservational studies in Epidemiology -Molecular Epidemiology (STROBE-ME) initiative builds on the STROBE statement implementing 9 existing items of STROBE and providing 17 additional items to the 22 items of STROBE checklist. The additions relate to the use of biomarkers in epidemiological studies, concerning collection, handling and storage of biological samples; laboratory methods, validity and reliability of biomarkers; specificities of study design; and ethical considerations. The STROBE-ME recommendations are intended to complement the STROBE recommendations.
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Affiliation(s)
- Valentina Gallo
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK.
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STrengthening the Reporting of OBservational studies in Epidemiology - Molecular Epidemiology (STROBE-ME): an extension of the STROBE statement. Prev Med 2011; 53:377-87. [PMID: 22029945 DOI: 10.1016/j.ypmed.2011.08.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2011] [Revised: 07/14/2011] [Accepted: 08/07/2011] [Indexed: 11/21/2022]
Abstract
Advances in laboratory techniques have led to a rapidly increasing use of biomarkers in epidemiological studies. Biomarkers of internal dose, early biological change, susceptibility and clinical outcomes are used as proxies for investigating the interactions between external and/or endogenous agents and the body components or processes. The need for improved reporting of scientific research led to influential statements of recommendations such as the STrenghtening Reporting of Observational studies in Epidemiology (STROBE) statement. The STROBE initiative established in 2004 aimed to provide guidance on how to report observational research. Its guidelines provide a user-friendly checklist of 22 items to be reported in epidemiological studies, with items specific to the three main study designs: cohort studies, case-control studies and cross-sectional studies. The present STrengthening the Reporting of OBservational studies in Epidemiology - Molecular Epidemiology (STROBE-ME) initiative builds on the STROBE Statement implementing 9 existing items of STROBE and providing 17 additional items to the 22 items of STROBE checklist. The additions relate to the use of biomarkers in epidemiological studies, concerning collection, handling and storage of biological samples; laboratory methods, validity and reliability of biomarkers; specificities of study design; and ethical considerations. The STROBE-ME recommendations are intended to complement the STROBE recommendations.
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Gallo V, Egger M, McCormack V, Farmer PB, Ioannidis JPA, Kirsch-Volders M, Matullo G, Phillips DH, Schoket B, Stromberg U, Vermeulen R, Wild C, Porta M, Vineis P. STrengthening the reporting of OBservational studies in Epidemiology-Molecular Epidemiology (STROBE-ME): an extension of the STROBE statement. Eur J Epidemiol 2011; 26:797-810. [PMID: 22037796 DOI: 10.1007/s10654-011-9622-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Accepted: 09/30/2011] [Indexed: 11/26/2022]
Abstract
Advances in laboratory techniques have led to a rapidly increasing use of biomarkers in epidemiological studies. Biomarkers of internal dose, early biological change, susceptibility, and clinical outcomes are used as proxies for investigating the interactions between external and/or endogenous agents and the body components or processes. The need for improved reporting of scientific research led to influential statements of recommendations such as STrengthening Reporting of Observational studies in Epidemiology (STROBE) statement. The STROBE initiative established in 2004 aimed to provide guidance on how to report observational research. Its guidelines provide a user-friendly checklist of 22 items to be reported in epidemiological studies, with items specific to the three main study designs: cohort studies, case-control studies and cross-sectional studies. The present STrengthening the Reporting of OBservational studies in Epidemiology-Molecular Epidemiology (STROBE-ME) initiative builds on the STROBE Statement implementing 9 existing items of STROBE and providing 17 additional items to the 22 items of STROBE checklist. The additions relate to the use of biomarkers in epidemiological studies, concerning collection, handling and storage of biological samples; laboratory methods, validity and reliability of biomarkers; specificities of study design; and ethical considerations. The STROBE-ME recommendations are intended to complement the STROBE recommendations.
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Affiliation(s)
- Valentina Gallo
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, St Mary's Campus Norfolk Place, W2 1PG London, UK.
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9
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Gallo V, Egger M, McCormack V, Farmer PB, Ioannidis JPA, Kirsch-Volders M, Matullo G, Phillips DH, Schoket B, Stromberg U, Vermeulen R, Wild C, Porta M, Vineis P. STrengthening the Reporting of OBservational studies in Epidemiology--Molecular Epidemiology (STROBE-ME): an extension of the STROBE Statement. PLoS Med 2011; 8:e1001117. [PMID: 22039356 PMCID: PMC3201942 DOI: 10.1371/journal.pmed.1001117] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Valentina Gallo and colleagues provide detailed guidance to authors to help more accurately report the findings of epidemiological studies involving biomarkers. Their guidance covers issues regarding collection, handling and storage of biological samples; laboratory methods, validity and reliability of biomarkers; specificities of study design; and ethical considerations.
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Affiliation(s)
- Valentina Gallo
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, United Kingdom
- Social and Environmental Health Research, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Matthias Egger
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | | | - Peter B. Farmer
- Department of Cancer Studies and Molecular Medicine, University of Leicester, Leicester, United Kingdom
| | - John P. A. Ioannidis
- Stanford Prevention Research Centre, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Hygiene and Epidemiology, University of Ioannina School of Medicine, Ioannina, Greece
| | | | - Giuseppe Matullo
- HuGeF Human Genetics Foundation, Turin, Italy
- Department of Genetics, Biology and Biochemistry, University of Turin, Turin, Italy
| | | | | | - Ulf Stromberg
- Division of Occupational and Environmental Medicine, Lund University, Lund, Sweden
| | - Roel Vermeulen
- Institute for Risk Assessment Sciences (IRAS), Division Environmental Epidemiology, Utrecht University, Utrecht, the Netherlands
| | | | - Miquel Porta
- Institut Municipal d'Investigacio Medica (IMIM), Universitat Autonoma de Barcelona, Barcelona, Spain
| | - Paolo Vineis
- HuGeF Human Genetics Foundation, Turin, Italy
- MRC-HPA Centre for Environment and Health, School of Public Health, Imperial College London, London, United Kingdom
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Microarrays and Epidemiology: Ensuring the Impact and Accessibility of Research Findings: Table 1. Cancer Epidemiol Biomarkers Prev 2009; 18:1-4. [DOI: 10.1158/1055-9965.epi-08-0867] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Steck SE, Keku T, Butler LM, Galanko J, Massa B, Millikan RC, Sandler RS. Polymorphisms in methionine synthase, methionine synthase reductase and serine hydroxymethyltransferase, folate and alcohol intake, and colon cancer risk. JOURNAL OF NUTRIGENETICS AND NUTRIGENOMICS 2008; 1:196-204. [PMID: 19776626 DOI: 10.1159/000136651] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2007] [Accepted: 03/04/2008] [Indexed: 11/19/2022]
Abstract
BACKGROUND/AIMS We examined associations among folate and alcohol intake, single nucleotide polymorphisms (SNPs) in genes involved in one-carbon metabolism, and colon cancer risk. METHODS Colon cancer cases (294 African-Americans and 349 whites) were frequency matched to population controls (437 African-Americans and 611 whites) by age, race and sex from 33 North Carolina counties from 1996 to 2000. Folate and alcohol intakes were collected by dietary interview. Five SNPs were genotyped using DNA from whole blood: SHMT C1420T; MTRR A66G; MTR A2756G, and the previously-reported MTHFR C677T and MTHFR A1298C. Adjusted odds ratios (OR) and 95% CI were calculated using logistic regression. RESULTS An inverse association was observed for SHMT TT genotype as compared to CC genotype in whites (OR = 0.6, 95% CI = 0.4, 1.0), but not in African Americans. Inverse associations were observed for high folate intake in individuals carrying 0 or 1 variant allele [OR 0.2 (95% CI 0.06-0.8) for African-Americans; OR 0.2 (95% CI 0.1-0.6) for whites] compared to low folate intake. Modest interactions between these SNPs and alcohol or folate intakes were observed. CONCLUSIONS Our results are consistent with other findings and provide needed data on these associations among African-Americans.
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Affiliation(s)
- Susan E Steck
- Department of Nutrition, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, N.C., USA.
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12
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Butler LM, Millikan RC, Sinha R, Keku TO, Winkel S, Harlan B, Eaton A, Gammon MD, Sandler RS. Modification by N-acetyltransferase 1 genotype on the association between dietary heterocyclic amines and colon cancer in a multiethnic study. Mutat Res 2008; 638:162-74. [PMID: 18022202 PMCID: PMC2234436 DOI: 10.1016/j.mrfmmm.2007.10.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2007] [Revised: 10/03/2007] [Accepted: 10/04/2007] [Indexed: 05/25/2023]
Abstract
OBJECTIVE Colorectal cancer incidence is greater among African Americans, compared to whites in the U.S., and may be due in part to differences in diet, genetic variation at metabolic loci, and/or the joint effect of diet and genetic susceptibility. We examined whether our previously reported associations between meat-derived heterocyclic amine (HCA) intake and colon cancer were modified by N-acetyltransferase 1 (NAT1) or 2 (NAT2) genotypes and whether there were differences by race. METHODS In a population-based, case-control study of colon cancer, exposure to HCAs was assessed using a food-frequency questionnaire with a meat-cooking and doneness module, among African Americans (217 cases and 315 controls) and whites (290 cases and 534 controls). RESULTS There was no association with NAT1*10 versus NAT1-non*10 genotypes for colon cancer. Among whites, there was a positive association for NAT2-"rapid/intermediate" genotype [odds ratio (OR)=1.4; 95% confidence interval (CI)=1.0, 1.8], compared to the NAT2-"slow" that was not observed among African Americans. Colon cancer associations with HCA intake were modified by NAT1, but not NAT2, regardless of race. However, the "at-risk" NAT1 genotype differed by race. For example, among African Americans, the positive association with 2-amino-1-methyl-6-phenyl-imidazo[4,5-b]pyridine (PhIP) was confined to those with NAT1*10 genotype (OR=1.8; 95% CI=1.0, 3.3; P for interaction=0.02, comparing highest to lowest intake), but among whites, an association with 2-amino-3,8-dimethylimidazo[4,5-f]quinoxaline (MeIQx) was confined to those with NAT1-non*10 genotype (OR=1.9; 95% CI=1.1, 3.1; P for interaction=0.03). CONCLUSIONS Our data indicate modification by NAT1 for HCA and colon cancer associations, regardless of race. Although the at-risk NAT1 genotype differs by race, the magnitude of the individual HCA-related associations in both race groups are similar. Therefore, our data do not support the hypothesis that NAT1 by HCA interactions contribute to differences in colorectal cancer incidence between African Americans and whites.
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Affiliation(s)
- Lesley M Butler
- University of California-Davis, Department of Public Health Sciences, Division of Epidemiology, Davis, CA 95616, USA.
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Zhou Y, Li N, Zhuang W, Liu GJ, Wu TX, Yao X, Du L, Wei ML, Wu XT. P53 codon 72 polymorphism and gastric cancer: a meta-analysis of the literature. Int J Cancer 2007; 121:1481-6. [PMID: 17546594 DOI: 10.1002/ijc.22833] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Studies investigating the association between p53 codon 72 polymorphism and gastric cancer risk report conflicting results. The objective of this study was to quantitatively summarize the evidence for such a relationship. Two investigators independently searched the Medline and Embase databases. This meta-analysis included 12 case-control studies, which included 1,665 gastric cancer cases and 2,358 controls. The combined results based on all studies showed that there was no significant difference in genotype distribution [Arg/Arg odds ratio (OR) = 0.96, 95% confidence interval (CI) = 0.79, 1.16; Pro/Pro (OR = 1.21, 95% CI = 0.92, 1.58); Pro/Arg (OR = 0.95, 95% CI = 0.79, 1.14)] between gastric cancer and noncancer patients. When stratifying for race, results were similar except that patients with gastric cancer had a significantly lower frequency of Arg/Arg (OR = 0.84, 95% CI = 0.72, 0.99) than noncancer patients among Asians. Stratified the various studies by the location, stage, Lauren's classification, and histological differentiation of gastric cancer, we found that (i) patients with cardia gastric cancer had a significantly higher frequency of Pro/Pro (OR = 3.20, 95% CI = 1.46,7.01) than those with noncardia gastric cancer among Asians; (ii) patients with advanced (stage III/IV) gastric cancer had a significantly higher frequency of Arg/Arg (OR = 1.48, 95% CI = 1.01, 2.16) than those with early (stage I/II) gastric cancer among Asians; (iii) patients with poor differentiation had a significantly lower frequency of Pro/Pro (OR = 0.13, 95% CI = 0.03, 0.64) than those with well differentiation among Caucasians. This meta-analysis suggests that the p53 codon 72 polymorphism may be associated with gastric cancer among Asians, and that difference in genotype distribution may be associated with the location, stage, and histological differentiation of gastric cancer.
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Affiliation(s)
- Yong Zhou
- Department of Gastrointestinal Surgery, West China Hospital, Sichuan University, Chengdu, China
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15
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Duell EJ. The future of epidemiology. Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz 2006. [DOI: 10.1007/s00103-006-0083-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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16
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Duell EJ. The future of epidemiology: methodological challenges and multilevel inference. Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz 2006; 49:622-7. [PMID: 16715181 DOI: 10.1007/s00103-006-1293-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
A decade ago there was considerable debate about the appropriate objectives and paradigms of modern epidemiologic research. One concern put forth in these debates was that "risk factor epidemiology" might be forcing our field to focus more on individuals and less on populations and public health. Today, most epidemiologists acknowledge that public health is influenced by both population-level and individual-level determinants. Ecologic studies are valuable tools for generating hypotheses and addressing group-level determinants of disease risk. Traditional risk factor studies and genomic studies have helped establish the multifactorial concept of disease causation. Individual-level studies also have provided the biomedical community with hypotheses that have stimulated research into disease mechanisms that have led to reductions in morbidity and mortality for diseases such as HIV/AIDS, cardiovascular disease, and cancer. Current debates about the role of genomic data in epidemiology and public health mirror the debates about risk factor epidemiology one decade ago. Genomic variation is measured at the individual level, but how this variation is maintained in human populations is a group-level (population) phenomenon that is worthy of epidemiologic investigation in its own right. Multilevel epidemiology seeks to understand multiple levels of inference, from genes to individuals to populations and could combine hypothesis-driven research with aspects of data mining. Multilevel epidemiology calls for the study of health and disease determinants defined at the population level and individual level for a more comprehensive strategy to understanding human disease etiology. With the continued development of multilevel statistical methods and the advent of data mining, the technical constraints of the past will become less relevant to the next generation of epidemiologists who wish to embrace a more multilevel epidemiology.
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Affiliation(s)
- Eric J Duell
- Norris Cotton Cancer Center, Section of Biostatistics and Epidemiology, Center for the Evaluative Clinical Sciences, Department of Community and Family Medicine, Dartmouth Medical School, Lebanon, New Hampshire, USA.
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Buchanan AV, Weiss KM, Fullerton SM. Dissecting complex disease: the quest for the Philosopher's Stone? Int J Epidemiol 2006; 35:562-71. [PMID: 16540539 DOI: 10.1093/ije/dyl001] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Is the search for the causes of complex disease akin to the alchemist's vain quest for the Philosopher's Stone? Complex chronic diseases have tremendous public health impact in the industrialized world. Much effort has been expended on research into their causes, with the aim of predicting who will be affected or preventing effects before they arise, but progress has been halting at best. In this paper, we discuss possible reasons including the use of models and methods that fit point-source and Mendelian diseases but may not be as appropriate for complex diseases, reliance on causal criteria that may not be as relevant as they are for communicable diseases, and the biology of complex disease itself. Finally, we ask whether most complex diseases are even good candidates for the kind of prediction and prevention that we have come to expect based on experience with infectious and Mendelian disease.
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Affiliation(s)
- Anne V Buchanan
- Department of Anthropology, Penn State University, University Park, PA 16802, USA
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Pompanon F, Bonin A, Bellemain E, Taberlet P. Genotyping errors: causes, consequences and solutions. Nat Rev Genet 2005; 6:847-59. [PMID: 16304600 DOI: 10.1038/nrg1707] [Citation(s) in RCA: 665] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Although genotyping errors affect most data and can markedly influence the biological conclusions of a study, they are too often neglected. Errors have various causes, but their occurrence and effect can be limited by considering these causes in the production and analysis of the data. Procedures that have been developed for dealing with errors in linkage studies, forensic analyses and non-invasive genotyping should be applied more broadly to any genetic study. We propose a protocol for estimating error rates and recommend that these measures be systemically reported to attest the reliability of published genotyping studies.
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Affiliation(s)
- François Pompanon
- Laboratoire d'Ecologie Alpine, UMR CNRS 5553, Université Joseph Fourier, B.P. 53, 38041 Grenoble Cedex 9, France.
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Foster MW, Sharp RR. Will investments in large-scale prospective cohorts and biobanks limit our ability to discover weaker, less common genetic and environmental contributors to complex diseases? ENVIRONMENTAL HEALTH PERSPECTIVES 2005; 113:119-22. [PMID: 15687047 PMCID: PMC1277853 DOI: 10.1289/ehp.7343] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Increasing the size of prospective cohorts and biobanks is one approach to discovering previously unknown contributors to complex diseases, but it may come at the price of concealing contributors that are less common across all the participants in those larger studies and of limiting hypothesis generation. Prospective cohorts and biobanks constitute significant, long-term investments in research infrastructure that will have ongoing consequences for opportunities in biomedical research for the foreseeable future. Thus, it is important to think about how these major additions to research infrastructure can be designed to be more productive in generating hypotheses for novel environmental contributors to complex diseases and to help identify genetic and environmental contributors that may not be common across the larger samples but are more frequent within local or ancestral subsets. Incorporating open-ended inquiries and qualitative information about local communal and ecologic contexts and the political, economic, and other social structures that affect health status and outcome will enable qualitative hypothesis generation in those localized contexts, as well as the collection of more detailed genealogic and family health history information that may be useful in designing future studies. Using communities as building blocks for larger cohorts and biobanks presents some practical and ethical challenges but also enhances opportunities for interdisciplinary, multilevel investigations of the multifactorial contributors to complex diseases.
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Affiliation(s)
- Morris W Foster
- Department of Anthropology, University of Oklahoma, Norman, Oklahoma 73019, USA.
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Koushik A, Ghosh A, Duarte-Franco E, Forest P, Voyer H, Matlashewski G, Coutlée F, Franco EL. The p53 codon 72 polymorphism and risk of high-grade cervical intraepithelial neoplasia. ACTA ACUST UNITED AC 2005; 29:307-16. [PMID: 16122882 DOI: 10.1016/j.cdp.2005.06.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/24/2005] [Indexed: 11/16/2022]
Abstract
BACKGROUND The Arg/Arg genotype versus Arg/Pro or Pro/Pro at codon 72 of the p53 gene has been implicated in increasing susceptibility of the cervix to human papillomavirus (HPV) infection and thus altering cancer risk. However, research on this topic has been contentious, which prompted us to carry out a case-control study in the Montreal area. METHODS Cases were women with histologically-confirmed high-grade cervical intraepithelial neoplasia (HGCIN). Controls were women without a history of cervical abnormalities. From each woman, we obtained a cervical specimen for HPV testing and p53 genotyping, and a questionnaire was completed. DNA sequencing was used to minimize genotype misclassification. A subsample of specimens was also genotyped using the TaqMan assay. RESULTS There were 357 cases and 760 controls recruited between February 2001 and December 2003. The distribution of Arg/Arg, Arg/Pro and Pro/Pro was 55.2, 36.4 and 8.4%, respectively, among cases, and 52.1, 38.7 and 9.2%, among controls, corresponding to an odds ratio (OR) adjusted for ancestral origin of 1.16 (95% confidence interval (CI): 0.9-1.5) for Arg/Arg versus other genotypes. When restricted to high-risk HPV-positive women, the adjusted ORs were 1.40 (CI: 0.9-2.1) and 2.12 (CI: 1.1-4.2), for Arg/Arg versus other genotypes and versus Pro/Pro, respectively. The findings were comparable with analyses of genotype results that agreed between DNA sequencing and TaqMan. CONCLUSIONS In this study, we attempted to minimize selection bias, population stratification and genotype misclassification. The results suggest that the role of the p53 codon 72 polymorphism on HGCIN is weak at best. Further research may reveal if the polymorphism has a stronger influence on the risk of invasive cervical cancer.
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Affiliation(s)
- Anita Koushik
- Department of Epidemiology and Biostatistics, Division of Cancer Epidemiology, McGill University, 546 Pine Avenue West, Montréal, Que., Canada H2W1S6
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Akkina J, Reif J, Keefe T, Bachand A. Age at natural menopause and exposure to organochlorine pesticides in Hispanic women. JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH. PART A 2004; 67:1407-1422. [PMID: 15371229 DOI: 10.1080/15287390490483845] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
A cross-sectional study was conducted to evaluate the relationship between exposure to selected organochlorine pesticides (OCP) (p,p'-DDT, p',p'-DDE, dieldrin, hexachlorobenzene, beta-hexachlorocyclohexane [beta-HCH], oxychlordane, trans' nonachlor) and age at natural menopause in a sample of 219 menopausal women participating in the Hispanic Health and Nutrition Examination Survey in 1982-1984. Information on age at menopause, reproductive history, demographic variables, and potential confounding variables was collected via interview. Analysis of variance was employed to compare adjusted mean age at natural menopause among women by category of serum OCP level. Serum levels of p,p'-DDT, p,p'-DDE, beta-HCH, and trans-nonachlor were associated with a younger age at menopause. In particular, women with exposure levels in the highest exposure categories (serum p,p'-DDT > or = 6ppb, beta-HCH > or = 4ppb, or trans-nonachlor > or = 2ppb) had an adjusted mean age at menopause on average 5.7, 3.4, and 5.2 yr earlier, respectively, than women with serum levels of these pesticides below the detection limit. Women with serum p,p'-DDE levels greater than 23.6 ppb (highest quintile) had an adjusted mean age at menopause 1.7 yr earlier than women with serump,p'-DDE levels less than 5.5 ppb (lowest quintile). However, no consistent dose-response effect was apparent across low, medium, and high exposure categories. Interactions were detected for p,p'-DDT in combination with beta-HCH, trans-nonachlor, or oxychlordane, as well as beta-HCH in combination with oxychlordane.
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Affiliation(s)
- Judy Akkina
- U.S. Department of Agriculture, Animal Plant Health Inspection Service, Veterinary Services, Centers for Epidemiology and Animal Health, Fort Collins, Colorado 80526-8117, USA.
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Affiliation(s)
- Richard R Sharp
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX 77030, USA
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Koushik A, Platt RW, Franco EL. p53 Codon 72 Polymorphism and Cervical Neoplasia: A Meta-Analysis Review. Cancer Epidemiol Biomarkers Prev 2004; 13:11-22. [PMID: 14744727 DOI: 10.1158/1055-9965.epi-083-3] [Citation(s) in RCA: 111] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The Arg/Arg genotype versus Arg/Pro or Pro/Pro at codon 72 of the p53 gene has been implicated as a risk marker in cervical neoplasia. However, research on this topic has produced controversial results. We reviewed the published literature to summarize the association and to identify methodological features that may have contributed to the heterogeneity. Information on specific methodological features of studies addressing this topic published between 1998 and 2002 were obtained. Study-specific odds ratios (ORs) were combined in a meta-analysis, assuming random effects. To identify characteristics that significantly contributed to heterogeneity, we used meta-regression analysis. We identified 50 articles, of which 45 were included in the meta-analyses and regressions. No evidence of association or heterogeneity was detected for preinvasive lesions. For invasive cervical cancer with undefined histology, the Arg/Arg genotype was not found to affect risk (OR, 1.1; 95% confidence interval (CI), 0.9-1.3). However, a slightly increased risk was observed for squamous cell carcinoma (OR, 1.5; 95% CI, 1.2-1.9) and adenocarcinoma (OR, 1.7; 95% CI, 1.0-2.7). Meta-regression analysis identified that the most important factor contributing to heterogeneity among results for invasive lesions was departures from Hardy-Weinberg equilibrium in the control group. Summary ORs for studies in equilibrium were essentially null. A possible susceptibility role by the p53 codon 72 polymorphism at a late carcinogenetic stage in cervical cancer cannot be ruled out. However, various methodological features can contribute to departures from Hardy-Weinberg equilibrium and consequently to less than ideal circumstances for the examination of this polymorphism. Future investigations require appropriate attention to design and methodological issues.
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Affiliation(s)
- Anita Koushik
- Department of Epidemiology and Biostatistics, McGill University, Montréal, Québec, Canada
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Bataller R, North KE, Brenner DA. Genetic polymorphisms and the progression of liver fibrosis: a critical appraisal. Hepatology 2003; 37:493-503. [PMID: 12601343 DOI: 10.1053/jhep.2003.50127] [Citation(s) in RCA: 264] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Liver fibrosis is a highly dynamic process in which multiple genes interact with environmental factors. Recent human epidemiologic studies have identified possible polymorphisms in a number of candidate genes that influence the progression of liver fibrosis. These genetic factors could explain the broad spectrum of responses to the same etiologic agent found in patients with chronic liver diseases. Polymorphisms in genes encoding immunoregulatory proteins, proinflammatory cytokines, and fibrogenic factors may influence disease progression in patients with alcohol-induced liver disease, primary biliary cirrhosis, or chronic hepatitis C. However, some of the studies have yielded contradictory results. For example, conflicting results have been obtained in studies assessing the role of mutations in the hemochromatosis gene on fibrosis progression in patients with chronic hepatitis C. Large-scale, well-designed studies are required to clarify the actual role of this factor and other genetic variants in liver fibrosis.
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Affiliation(s)
- Ramón Bataller
- Department of Medicine, Biochemistry and Biophysics, University of North Carolina at Chapel Hill, School of Medicine, Chapel Hill, NC 27599, USA
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Abstract
Many promises have been made about the impact of the Human Genome Project on clinical practice and public health, yet despite massively funded efforts over the past decade, little headway has been made in elucidating the specific genetic factors which have major impact on the risk of developing common complex traits. There are two fundamental reasons for this abject failure as follows: 1) studies have been inadequately designed to identify such genetic risk factors; 2) the genetic factors that do exist are individually of small marginal importance, and are characterized by extensive heterogeneity. If 2) is the truth, there is little we can do about it, so we emphasize the importance of 1) in this article, while recognizing that 2) probably is not far from the truth. Genetic studies, in contrast to epidemiological studies, use confounding and ascertainment bias to help identify weak etiologic signal due to genes, since gene mapping is fundamentally a hypothesis-free science. This strategy makes it possible to identify genetic risk factors, but makes it impossible to quantify the size of their effect on risk. Classical epidemiological study designs are of minimal value for gene identification, but may be of use in estimation of the effect size of genetic risk factors once they are identified in more appropriately designed genetic studies. However, if the effects are so weak that we need this strong, systematic ascertainment bias to find them, their relevance to public health may be of questionable immediate value, raising many questions about the rhetoric and promises being made to the public as justification for 'big science' approaches to dissecting the hypothetical role of genes in complex traits.
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Affiliation(s)
- Joseph D Terwilliger
- Department of Psychiatry, Columbia Genome Center, Columbia University, New York, NY 10032, USA.
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