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Toyama KS, Crochet P, Leblois R. Sampling schemes and drift can bias admixture proportions inferred by
structure. Mol Ecol Resour 2020; 20:1769-1785. [DOI: 10.1111/1755-0998.13234] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 07/17/2020] [Accepted: 07/24/2020] [Indexed: 11/27/2022]
Affiliation(s)
- Ken S. Toyama
- Department of Ecology and Evolutionary Biology University of Toronto Toronto ON Canada
| | - Pierre‐André Crochet
- CEFE CNRS University of Montpellier Université Paul Valéry Montpellier 3 EPHE IRD Montpellier France
| | - Raphaël Leblois
- CBGP INRAE CIRAD IRD Montpellier SupAgro University of Montpellier Montpellier France
- Institut de Biologie Computationnelle University of Montpellier Montpellier France
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Mitchell KA, Shah E, Bowman ED, Zingone A, Nichols N, Pine SR, Kittles RA, Ryan BM. Relationship between West African ancestry with lung cancer risk and survival in African Americans. Cancer Causes Control 2019; 30:1259-1268. [PMID: 31468279 PMCID: PMC8274945 DOI: 10.1007/s10552-019-01212-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Accepted: 07/30/2019] [Indexed: 01/12/2023]
Abstract
PURPOSE African Americans, especially men, have a higher incidence of lung cancer compared with all other racial and ethnic groups in the US. Self-reported race is frequently used in genomic research studies to capture an individual's race or ethnicity. However, it is clear from studies of genetic admixture that human genetic variation does not segregate into the same biologically discrete categories as socially defined categories of race. Previous studies have suggested that the degree of West African ancestry among African Americans can contribute to cancer risk in this population, though few studies have addressed this question in lung cancer. METHODS Using a genetic ancestry panel of 100 SNPs, we estimated West African, European, and Native American ancestry in 1,407 self-described African Americans and 2,413 European Americans. RESULTS We found that increasing West African ancestry was associated with increased risk of lung cancer among African American men (ORQ5 vs Q1 = 2.55 (1.45-4.48), p = 0.001), while no association was observed in African American women (ORQ5 vs Q1 = 0.90 (0.51-1.59), p = 0.56). This relationship diminished following adjustment for income and education. CONCLUSIONS Genetic ancestry is not a major contributor to lung cancer risk or survival disparities.
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Affiliation(s)
- Khadijah A Mitchell
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Ebony Shah
- Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Elise D Bowman
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Adriana Zingone
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Noah Nichols
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Sharon R Pine
- Rutgers Cancer Institute of New Jersey, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08854, USA
| | - Rick A Kittles
- Division of Health Equities, Department of Populations Sciences, City of Hope Comprehensive Cancer Center, Duarte, CA, 91010, USA
| | - Bríd M Ryan
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA.
- Laboratory of Human Carcinogenesis, Center for Cancer Research, NCI, Building 37, Room 3060C, Bethesda, MD, 20892, USA.
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Algee-Hewitt BFB. Geographic substructure in craniometric estimates of admixture for contemporary American populations. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2017. [DOI: 10.1002/ajpa.23267] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Aldrich MC, Selvin S, Wrensch MR, Sison JD, Hansen HM, Quesenberry CP, Seldin MF, Barcellos LF, Buffler PA, Wiencke JK. Socioeconomic status and lung cancer: unraveling the contribution of genetic admixture. Am J Public Health 2013; 103:e73-80. [PMID: 23948011 DOI: 10.2105/ajph.2013.301370] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
OBJECTIVES We examined the relationship between genetic ancestry, socioeconomic status (SES), and lung cancer among African Americans and Latinos. METHODS We evaluated SES and genetic ancestry in a Northern California lung cancer case-control study (1998-2003) of African Americans and Latinos. Lung cancer case and control participants were frequency matched on age, gender, and race/ethnicity. We assessed case-control differences in individual admixture proportions using the 2-sample t test and analysis of covariance. Logistic regression models examined associations among genetic ancestry, socioeconomic characteristics, and lung cancer. RESULTS Decreased Amerindian ancestry was associated with higher education among Latino control participants and greater African ancestry was associated with decreased education among African lung cancer case participants. Education was associated with lung cancer among both Latinos and African Americans, independent of smoking, ancestry, age, and gender. Genetic ancestry was not associated with lung cancer among African Americans. CONCLUSIONS Findings suggest that socioeconomic factors may have a greater impact than genetic ancestry on lung cancer among African Americans. The genetic heterogeneity and recent dynamic migration and acculturation of Latinos complicate recruitment; thus, epidemiological analyses and findings should be interpreted cautiously.
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Affiliation(s)
- Melinda C Aldrich
- At the time of the study, Melinda C. Aldrich was with the Division of Epidemiology, School of Public Health, University of California, Berkeley. Steve Selvin is with the Division of Biostatistics, School of Public Health, University of California, Berkeley. Margaret R. Wrensch, Helen M. Hansen, and John K. Wiencke are with the Department of Neurologic Surgery, University of California, San Francisco. Jennette D. Sison was with the Department of Neurologic Surgery, University of California, San Francisco. Charles P. Quesenberry Jr, is with the Division of Research, Kaiser Permanente, Oakland, CA. Michael F. Seldin is with the Departments of Biological Chemistry and Medicine, University of California, Davis. Lisa F. Barcellos and Patricia A. Buffler are with the Division of Epidemiology, School of Public Health, University of California, Berkeley
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Bhavnani SK, Bellala G, Victor S, Bassler KE, Visweswaran S. The role of complementary bipartite visual analytical representations in the analysis of SNPs: a case study in ancestral informative markers. J Am Med Inform Assoc 2013; 19:e5-e12. [PMID: 22718038 PMCID: PMC3392853 DOI: 10.1136/amiajnl-2011-000745] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Objective Several studies have shown how sets of single-nucleotide polymorphisms (SNPs) can help to classify subjects on the basis of their continental origins, with applications to case–control studies and population genetics. However, most of these studies use dimensionality-reduction methods, such as principal component analysis, or clustering methods that result in unipartite (either subjects or SNPs) representations of the data. Such analyses conceal important bipartite relationships, such as how subject and SNP clusters relate to each other, and the genotypes that determine their cluster memberships. Methods To overcome the limitations of current methods of analyzing SNP data, the authors used three bipartite analytical representations (bipartite network, heat map with dendrograms, and Circos ideogram) that enable the simultaneous visualization and analysis of subjects, SNPs, and subject attributes. Results The results demonstrate (1) novel insights into SNP data that are difficult to derive from purely unipartite views of the data, (2) the strengths and limitations of each method, revealing the role that each play in revealing novel insights, and (3) implications for how the methods can be used for the analysis of SNPs in genomic studies associated with disease. Conclusion The results suggest that bipartite representations can reveal new patterns in SNP data compared with existing unipartite representations. However, the novel insights require multiple representations to discover, verify, and comprehend the complex relationships. The results therefore motivate the need for a complementary visual analytical framework that guides the use of multiple bipartite representations to analyze complex relationships in SNP data.
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Affiliation(s)
- Suresh K Bhavnani
- Institute for Translational Sciences, University of Texas Medical Branch, Galveston, Texas 77555-0129, USA.
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Hoyos-Giraldo LS, Escobar-Hoyos LF, Reyes-Carvajal I, García JJ, Córdoba L, Gómez AS, García-Vallejo F, Cajas-Salazar N, Carvajal S, Bedoya G. The Effect of Genetic Admixture in an Association Study: Genetic Polymorphisms and Chromosome Aberrations in a Colombian Population Exposed to Organic Solvents. Ann Hum Genet 2013; 77:308-20. [DOI: 10.1111/ahg.12019] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2012] [Accepted: 12/06/2012] [Indexed: 11/28/2022]
Affiliation(s)
- Luz Stella Hoyos-Giraldo
- Department of Biology, Research Group Genetic Toxicology and Cytogenetics, Faculty of Natural Sciences and Education; Universidad del Cauca; Popayán Cauca Colombia
| | - Luisa F. Escobar-Hoyos
- Department of Biology, Research Group Genetic Toxicology and Cytogenetics, Faculty of Natural Sciences and Education; Universidad del Cauca; Popayán Cauca Colombia
- Department of Pharmacological Sciences and Pathology; Stony Brook University; Stony Brook NY USA
| | - Ingrid Reyes-Carvajal
- Department of Biology, Research Group Genetic Toxicology and Cytogenetics, Faculty of Natural Sciences and Education; Universidad del Cauca; Popayán Cauca Colombia
| | - Jharley J. García
- Laboratory of Molecular Genetics, Institute of Biology; Universidad de Antioquia; Medellin Colombia
| | - Liliana Córdoba
- Laboratory of Molecular Genetics, Institute of Biology; Universidad de Antioquia; Medellin Colombia
| | - Adalberto Sánchez Gómez
- Laboratory of Molecular Biology and Pathogenesis; Department of Physiologic Sciences; Faculty of Health, Universidad del Valle; Cali Valle del Cauca Colombia
| | - Felipe García-Vallejo
- Laboratory of Molecular Biology and Pathogenesis; Department of Physiologic Sciences; Faculty of Health, Universidad del Valle; Cali Valle del Cauca Colombia
| | - Nohelia Cajas-Salazar
- Department of Biology, Research Group Genetic Toxicology and Cytogenetics, Faculty of Natural Sciences and Education; Universidad del Cauca; Popayán Cauca Colombia
| | - Silvio Carvajal
- Department of Biology, Research Group Genetic Toxicology and Cytogenetics, Faculty of Natural Sciences and Education; Universidad del Cauca; Popayán Cauca Colombia
| | - Gabriel Bedoya
- Laboratory of Molecular Genetics, Institute of Biology; Universidad de Antioquia; Medellin Colombia
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Worsham MJ, Divine G, Kittles RA. Race as a social construct in head and neck cancer outcomes. Otolaryngol Head Neck Surg 2011; 144:381-9. [PMID: 21493200 DOI: 10.1177/0194599810393884] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
OBJECTIVE The authors examined ancestry informative markers (AIMs) to estimate the amount of population admixture and control for this heterogeneity for stage and survival in a primary head and neck squamous cell carcinoma (HNSCC) cohort. STUDY DESIGN Historical cohort study. SETTING Integrated health care system. SUBJECTS The cohort comprised 358 patients with HNSCC who self-reported race as Caucasian American (CA), African American (AA), or other. METHODS DNA was interrogated for West African (WA) and European genetic background by genotyping AIMs. Associations of race (self-report or WA ancestry) with stage and survival were analyzed using logistic regression and Cox regression modeling. A subgroup analysis for diagnosis (late vs early stage) and survival (time to death) and WA ancestry was performed for self-reported AAs. RESULTS There were significant associations between stage and self-reported race (P = .04 [univariate]) and with cancer site (oropharynx: P = .014; hypopharynx: P = .026 [multivariate]). For prognosis, there were significant multivariate associations between stage (P = .002), age (>65 years, P < .001), and cancer site (hypopharynx: P < .001; oral cavity: P = .049), but self-reported race was not associated with overall survival. Interestingly, there was no association with degree of WA ancestry and stage or survival. In the subgroup analysis of genetic ancestry among self-reported AAs, cancer site remained an independent risk factor for stage (other site: P = .026) and survival (oropharynx: P = .036). Late stage persisted as an independent variable for poor survival (P = .032). CONCLUSIONS Stratification within AAs by WA ancestry revealed no correlation with stage or survival, suggesting that HNSCC outcomes with race may be owing to social/behavior factors rather than biological differences.
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Affiliation(s)
- Maria J Worsham
- Department of Otolaryngology/Head and Neck Surgery, Henry Ford Health System, Detroit, MI 48202, USA.
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Kumar R, Seibold MA, Aldrich MC, Williams LK, Reiner AP, Colangelo L, Galanter J, Gignoux C, Hu D, Sen S, Choudhry S, Peterson EL, Rodriguez-Santana J, Rodriguez-Cintron W, Nalls MA, Leak TS, O'Meara E, Meibohm B, Kritchevsky SB, Li R, Harris TB, Nickerson DA, Fornage M, Enright P, Ziv E, Smith LJ, Liu K, Burchard EG. Genetic ancestry in lung-function predictions. N Engl J Med 2010; 363:321-30. [PMID: 20647190 PMCID: PMC2922981 DOI: 10.1056/nejmoa0907897] [Citation(s) in RCA: 191] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
BACKGROUND Self-identified race or ethnic group is used to determine normal reference standards in the prediction of pulmonary function. We conducted a study to determine whether the genetically determined percentage of African ancestry is associated with lung function and whether its use could improve predictions of lung function among persons who identified themselves as African American. METHODS We assessed the ancestry of 777 participants self-identified as African American in the Coronary Artery Risk Development in Young Adults (CARDIA) study and evaluated the relation between pulmonary function and ancestry by means of linear regression. We performed similar analyses of data for two independent cohorts of subjects identifying themselves as African American: 813 participants in the Health, Aging, and Body Composition (HABC) study and 579 participants in the Cardiovascular Health Study (CHS). We compared the fit of two types of models to lung-function measurements: models based on the covariates used in standard prediction equations and models incorporating ancestry. We also evaluated the effect of the ancestry-based models on the classification of disease severity in two asthma-study populations. RESULTS African ancestry was inversely related to forced expiratory volume in 1 second (FEV(1)) and forced vital capacity in the CARDIA cohort. These relations were also seen in the HABC and CHS cohorts. In predicting lung function, the ancestry-based model fit the data better than standard models. Ancestry-based models resulted in the reclassification of asthma severity (based on the percentage of the predicted FEV(1)) in 4 to 5% of participants. CONCLUSIONS Current predictive equations, which rely on self-identified race alone, may misestimate lung function among subjects who identify themselves as African American. Incorporating ancestry into normative equations may improve lung-function estimates and more accurately categorize disease severity. (Funded by the National Institutes of Health and others.)
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Affiliation(s)
- Rajesh Kumar
- Division of Allergy and Immunology, Children's Memorial Hospital, 2300 Children's Plaza, Box 60, Chicago IL 60614, USA.
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Via M, Ziv E, Burchard EG. Recent advances of genetic ancestry testing in biomedical research and direct to consumer testing. Clin Genet 2010; 76:225-35. [PMID: 19793051 DOI: 10.1111/j.1399-0004.2009.01263.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
In the post-Human Genome Project era, the debate on the concept of race/ethnicity and its implications for biomedical research are dependent on two critical issues: whether and how to classify individuals and whether biological factors play a role in health disparities. The advent of reliable estimates of genetic (or biogeographic) ancestry has provided this debate with a quantitative and more objective tool. The estimation of genetic ancestry allows investigators to control for population stratification in association studies and helps to detect biological causation behind population-specific differences in disease and drug response. New techniques such as admixture mapping can specifically detect population-specific risk alleles for a disease in admixed populations. However, researchers have to be mindful of the correlation between genetic ancestry and socioeconomic and environmental factors that could underlie these differences. More importantly, researchers must avoid the stigmatization of individuals based on perceived or real genetic risks. The latter point will become increasingly sensitive as several 'for profit companies' are offering ancestry and genetic testing directly to consumers and the consequences of the spread of the services of these companies are still unforeseeable.
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Affiliation(s)
- M Via
- Institute for Human Genetics, University of California, San Francisco, CA 94143-2911, USA.
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