1
|
Pérez-Jeldres T, Magne F, Ascui G, Alvares D, Orellana M, Alvarez-Lobos M, Hernandez-Rocha C, Azocar L, Aguilar N, Espino A, Estela R, Escobar S, Zazueta A, Baez P, Silva V, De La Vega A, Arriagada E, Pavez-Ovalle C, Díaz-Asencio A, Travisany D, Miquel JF, Villablanca EJ, Kronenberg M, Bustamante ML. Amerindian ancestry proportion as a risk factor for inflammatory bowel diseases: results from a Latin American Andean cohort. Front Med (Lausanne) 2023; 10:1258395. [PMID: 37964883 PMCID: PMC10642057 DOI: 10.3389/fmed.2023.1258395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 09/27/2023] [Indexed: 11/16/2023] Open
Abstract
Background and aims Latin American populations remain underrepresented in genetic studies of inflammatory bowel diseases (IBDs). Most genetic association studies of IBD rely on Caucasian, African, and Asian individuals. These associations have yet to be evaluated in detail in the Andean region of South America. We explored the contribution of IBD-reported genetic risk variants to a Chilean cohort and the ancestry contribution to IBD in this cohort. Methods A total of 192 Chilean IBD patients were genotyped using Illumina's Global Screening Array. Genotype data were combined with similar information from 3,147 Chilean controls. The proportions of Aymara, African, European, and Mapuche ancestries were estimated using the software ADMIXTURE. We calculated the odds ratios (ORs) and 95% confidence intervals (CIs) for gender, age, and ancestry proportions. We also explored associations with previously reported IBD-risk variants independently and in conjunction with genetic ancestry. Results The first and third quartiles of the proportion of Mapuche ancestry in IBD patients were 24.7 and 34.2%, respectively, and the corresponding OR was 2.30 (95%CI 1.52-3.48) for the lowest vs. the highest group. Only one variant (rs7210086) of the 180 reported IBD-risk SNPs was associated with IBD risk in the Chilean cohort (adjusted P = 0.01). This variant is related to myeloid cells. Conclusion The type and proportion of Native American ancestry in Chileans seem to be associated with IBD risk. Variants associated with IBD risk in this Andean region were related to myeloid cells and the innate immune response.
Collapse
Affiliation(s)
- Tamara Pérez-Jeldres
- Department of Gastroenterology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
- Department of Gastroenterology, Hospital San Borja Arriarán, Santiago, Chile
| | - Fabien Magne
- Department of Microbiology, Faculty of Medicine, Institute of Biomedical Sciences (ICBM), Universidad de Chile, Santiago, Chile
| | - Gabriel Ascui
- La Jolla Institute for Immunology, San Diego, CA, United States
| | - Danilo Alvares
- MRC Biostatistics Unit, University of Cambridge, Cambridge, United Kingdom
| | - Matias Orellana
- Department of Computer Science, Faculty of Physical Sciences and Mathematics, Universidad de Chile, Santiago, Chile
| | - Manuel Alvarez-Lobos
- Department of Gastroenterology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Cristian Hernandez-Rocha
- Department of Gastroenterology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Lorena Azocar
- Department of Gastroenterology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Nataly Aguilar
- Department of Gastroenterology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Alberto Espino
- Department of Gastroenterology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Ricardo Estela
- Department of Gastroenterology, Hospital San Borja Arriarán, Santiago, Chile
| | - Sergio Escobar
- Department of Gastroenterology, Hospital San Borja Arriarán, Santiago, Chile
| | - Alejandra Zazueta
- Department of Microbiology, Faculty of Medicine, Institute of Biomedical Sciences (ICBM), Universidad de Chile, Santiago, Chile
| | - Pablo Baez
- Center of Medical Informatics and Telemedicine, University of Chile, Santiago, Chile
| | - Verónica Silva
- Department of Gastroenterology, Hospital San Borja Arriarán, Santiago, Chile
| | - Andres De La Vega
- Department of Gastroenterology, Hospital San Borja Arriarán, Santiago, Chile
| | - Elizabeth Arriagada
- Department of Gastroenterology, Hospital San Borja Arriarán, Santiago, Chile
| | - Carolina Pavez-Ovalle
- Department of Gastroenterology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | | | - Dante Travisany
- Núcleo de Investigación en Data Science, Facultad de Ingeniería y Negocios, Universidad de las Américas, Santiago, Chile
| | - Juan Francisco Miquel
- Department of Gastroenterology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Eduardo J. Villablanca
- Division of Immunology and Allergy, Department of Medicine, Solna, Karolinska Institutet and University Hospital, Stockholm, Sweden
| | - Mitchell Kronenberg
- La Jolla Institute for Immunology, San Diego, CA, United States
- Department of Molecular Biology, University of California San Diego, La Jolla, CA, United States
| | - María Leonor Bustamante
- Department of Human Genetic, Faculty of Medicine, Institute of Biomedical Sciences (ICBM), Universidad de Chile, Santiago, Chile
- Fundación Diagnosis, Santiago, Chile
| |
Collapse
|
2
|
Zollner L, Torres D, Briceno I, Gilbert M, Torres-Mejía G, Dennis J, Bolla MK, Wang Q, Hamann U, Lorenzo Bermejo J. Native American ancestry and breast cancer risk in Colombian and Mexican women: ruling out potential confounding through ancestry-informative markers. Breast Cancer Res 2023; 25:111. [PMID: 37784177 PMCID: PMC10544431 DOI: 10.1186/s13058-023-01713-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 09/18/2023] [Indexed: 10/04/2023] Open
Abstract
BACKGROUND Latin American and Hispanic women are less likely to develop breast cancer (BC) than women of European descent. Observational studies have found an inverse relationship between the individual proportion of Native American ancestry and BC risk. Here, we use ancestry-informative markers to rule out potential confounding of this relationship, estimating the confounder-free effect of Native American ancestry on BC risk. METHODS AND STUDY POPULATION We used the informativeness for assignment measure to select robust instrumental variables for the individual proportion of Native American ancestry. We then conducted separate Mendelian randomization (MR) analyses based on 1401 Colombian women, most of them from the central Andean regions of Cundinamarca and Huila, and 1366 Mexican women from Mexico City, Monterrey and Veracruz, supplemented by sensitivity and stratified analyses. RESULTS The proportion of Colombian Native American ancestry showed a putatively causal protective effect on BC risk (inverse variance-weighted odds ratio [OR] = 0.974 per 1% increase in ancestry proportion, 95% confidence interval [CI] 0.970-0.978, p = 3.1 × 10-40). The corresponding OR for Mexican Native American ancestry was 0.988 (95% CI 0.987-0.990, p = 1.4 × 10-44). Stratified analyses revealed a stronger association between Native American ancestry and familial BC (Colombian women: OR = 0.958, 95% CI 0.952-0.964; Mexican women: OR = 0.973, 95% CI 0.969-0.978), and stronger protective effects on oestrogen receptor (ER)-positive BC than on ER-negative and triple-negative BC. CONCLUSIONS The present results point to an unconfounded protective effect of Native American ancestry on BC risk in both Colombian and Mexican women which appears to be stronger for familial and ER-positive BC. These findings provide a rationale for personalised prevention programmes that take genetic ancestry into account, as well as for future admixture mapping studies.
Collapse
Affiliation(s)
- Linda Zollner
- Statistical Genetics Research Group, Institute of Medical Biometry, Heidelberg University, Heidelberg, Germany
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
- Division of Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Diana Torres
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
- Institute of Human Genetics, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Ignacio Briceno
- Instituto de Genética Humana, Universidad de la Sabana, Bogotá, Colombia
| | - Michael Gilbert
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
| | - Gabriela Torres-Mejía
- Center for Population Health Research, National Institute of Public Health, Cuernavaca, Morelos, Mexico
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Manjeet K Bolla
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Qin Wang
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany.
| | - Justo Lorenzo Bermejo
- Statistical Genetics Research Group, Institute of Medical Biometry, Heidelberg University, Heidelberg, Germany
- Department of Biostatistics for Precision Oncology, Institut de Cancérologie Strasbourg Europe, Strasbourg, France
| |
Collapse
|
3
|
Ang KC, Canfield VA, Foster TC, Harbaugh TD, Early KA, Harter RL, Reid KP, Leong SL, Kawasawa Y, Liu D, Hawley JW, Cheng KC. Native American genetic ancestry and pigmentation allele contributions to skin color in a Caribbean population. eLife 2023; 12:e77514. [PMID: 37294081 PMCID: PMC10371226 DOI: 10.7554/elife.77514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 06/08/2023] [Indexed: 06/10/2023] Open
Abstract
Our interest in the genetic basis of skin color variation between populations led us to seek a Native American population with genetically African admixture but low frequency of European light skin alleles. Analysis of 458 genomes from individuals residing in the Kalinago Territory of the Commonwealth of Dominica showed approximately 55% Native American, 32% African, and 12% European genetic ancestry, the highest Native American genetic ancestry among Caribbean populations to date. Skin pigmentation ranged from 20 to 80 melanin units, averaging 46. Three albino individuals were determined to be homozygous for a causative multi-nucleotide polymorphism OCA2NW273KV contained within a haplotype of African origin; its allele frequency was 0.03 and single allele effect size was -8 melanin units. Derived allele frequencies of SLC24A5A111T and SLC45A2L374F were 0.14 and 0.06, with single allele effect sizes of -6 and -4, respectively. Native American genetic ancestry by itself reduced pigmentation by more than 20 melanin units (range 24-29). The responsible hypopigmenting genetic variants remain to be identified, since none of the published polymorphisms predicted in prior literature to affect skin color in Native Americans caused detectable hypopigmentation in the Kalinago.
Collapse
Affiliation(s)
- Khai C Ang
- Department of Pathology, Penn State College of MedicineHersheyUnited States
- Jake Gittlen Laboratories for Cancer Research, Penn State College of MedicineHersheyUnited States
| | - Victor A Canfield
- Department of Pathology, Penn State College of MedicineHersheyUnited States
- Jake Gittlen Laboratories for Cancer Research, Penn State College of MedicineHersheyUnited States
| | - Tiffany C Foster
- Department of Pathology, Penn State College of MedicineHersheyUnited States
- Jake Gittlen Laboratories for Cancer Research, Penn State College of MedicineHersheyUnited States
| | - Thaddeus D Harbaugh
- Department of Pathology, Penn State College of MedicineHersheyUnited States
- Jake Gittlen Laboratories for Cancer Research, Penn State College of MedicineHersheyUnited States
| | - Kathryn A Early
- Department of Pathology, Penn State College of MedicineHersheyUnited States
- Jake Gittlen Laboratories for Cancer Research, Penn State College of MedicineHersheyUnited States
| | - Rachel L Harter
- Department of Pathology, Penn State College of MedicineHersheyUnited States
| | - Katherine P Reid
- Department of Pathology, Penn State College of MedicineHersheyUnited States
- Jake Gittlen Laboratories for Cancer Research, Penn State College of MedicineHersheyUnited States
| | - Shou Ling Leong
- Department of Family & Community Medicine, Penn State College of MedicineHersheyUnited States
| | - Yuka Kawasawa
- Department of Biochemistry and Molecular Biology, Penn State College of MedicineHersheyUnited States
- Department of Pharmacology, Penn State College of MedicineHersheyUnited States
- Institute of Personalized Medicine, Penn State College of MedicineHersheyUnited States
| | - Dajiang Liu
- Department of Biochemistry and Molecular Biology, Penn State College of MedicineHersheyUnited States
- Department of Public Health Sciences, Penn State College of MedicineHersheyUnited States
| | | | - Keith C Cheng
- Department of Pathology, Penn State College of MedicineHersheyUnited States
- Jake Gittlen Laboratories for Cancer Research, Penn State College of MedicineHersheyUnited States
- Department of Biochemistry and Molecular Biology, Penn State College of MedicineHersheyUnited States
- Department of Pharmacology, Penn State College of MedicineHersheyUnited States
| |
Collapse
|
4
|
McElhoe JA, Wilton PR, Parson W, Holland MM. Exploring statistical weight estimates for mitochondrial DNA matches involving heteroplasmy. Int J Legal Med 2022; 136:671-685. [PMID: 35243529 DOI: 10.1007/s00414-022-02774-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 01/12/2022] [Indexed: 11/26/2022]
Abstract
Massively parallel sequencing (MPS) of mitochondrial (mt) DNA allows forensic laboratories to report heteroplasmy on a routine basis. Statistical approaches will be needed to determine the relative frequency of observing an mtDNA haplotype when including the presence of a heteroplasmic site. Here, we examined 1301 control region (CR) sequences, collected from individuals in four major population groups (European, African, Asian, and Latino), and covering 24 geographically distributed haplogroups, to assess the rates of point heteroplasmy (PHP) on an individual and nucleotide position (np) basis. With a minor allele frequency (MAF) threshold of 2%, the data was similar across population groups, with an overall PHP rate of 37.7%, and the majority of heteroplasmic individuals (77.3%) having only one site of heteroplasmy. The majority (75.2%) of identified PHPs had an MAF of 2-10%, and were observed at 12.6% of the nps across the CR. Both the broad and phylogenetic testing suggested that in many cases the low number of observations of heteroplasmy at any one np results in a lack of statistical association. The posterior frequency estimates, which skew conservative to a degree depending on the sample size in a given haplogroup, had a mean of 0.152 (SD 0.134) and ranged from 0.031 to 0.83. As expected, posterior frequency estimates decreased in accordance with 1/n as the sample size (n) increased. This provides a proposed conservative statistical framework for assessing haplotype/heteroplasmy matches when applying an MPS technique in forensic cases and will allow for continual refinement as more data is generated, both within the CR and across the mitochondrial genome.
Collapse
Affiliation(s)
- Jennifer A McElhoe
- Department of Biochemistry & Molecular Biology, Forensic Science Program, The Pennsylvania State University, University Park, 014 Thomas Building, State College, PA, 16802, USA.
| | - Peter R Wilton
- Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA
- 23andMe Inc, Sunnyvale, CA, 94086, USA
| | - Walther Parson
- Department of Biochemistry & Molecular Biology, Forensic Science Program, The Pennsylvania State University, University Park, 014 Thomas Building, State College, PA, 16802, USA
- Institute of Legal Medicine, Medical University of Innsbruck, Müllerstraße 44, 6020, Innsbruck, Austria
| | - Mitchell M Holland
- Department of Biochemistry & Molecular Biology, Forensic Science Program, The Pennsylvania State University, University Park, 014 Thomas Building, State College, PA, 16802, USA
| |
Collapse
|
5
|
Hunley K, Moes E, Edgar H, Healy M, Mosley C, Dixon A. Colonialism, ethnogenesis, and biogeographic ancestry in the US Southwest. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2021; 176:559-571. [PMID: 34338305 DOI: 10.1002/ajpa.24380] [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: 12/22/2020] [Revised: 07/08/2021] [Accepted: 07/14/2021] [Indexed: 11/12/2022]
Abstract
OBJECTIVE Differences between self-perceived biogeographic ancestry and estimates derived from DNA are potentially informative about the formation of ethnic identities in different sociohistorical contexts. Here, we compared self-estimates and DNA-estimates in New Mexico, where notions of shared ancestry and ethnic identity have been shaped by centuries of migration and admixture. MATERIALS AND METHODS We asked 507 New Mexicans of Spanish-speaking descent (NMS) to list their ethnic identity and to estimate their percentages of European and Native American ancestry. We then compared self-estimates to estimates derived from 291,917 single nucleotide polymorphisms (SNPs), and we examined how differences between the estimates varied by ethnic identity. RESULTS Most NMS (94%) predicted that they had non-zero percentages of European and Native American ancestry. Self-estimates and SNP-estimates were positively correlated (rEuropean = 0.38, rNative-American = 0.36, p < 0.001). The correlations belie systematic patterns of underestimation and overestimation based on ethnic identity. NMS with ancestral ties to 20th century immigrants, who identified as Mexican or Mexican American, often underestimated their European ancestry (self-estimate < SNP-estimate) and overestimated their Native American ancestry. The pattern was reversed for NMS who emphasized deep connections to colonial New Mexico and identified as Spanish or Spanish American. DISCUSSION While NMS accurately predicted that they had European and Native American ancestry, they predicted ancestry percentages with only moderate accuracy. Differences between self-estimated and SNP-estimated ancestry were associated with ethnic identities that were shaped by migration to the region over the past 400 years. We connect ethnic identities and patterns of ancestry estimation to resistance to colonial hegemony and discuss the implications of our results for the construction of ethnic identities, now and in the past.
Collapse
Affiliation(s)
- Keith Hunley
- Department of Anthropology, University of New Mexico, Albuquerque, New Mexico, USA
| | - Emily Moes
- Department of Anthropology, University of New Mexico, Albuquerque, New Mexico, USA
| | - Heather Edgar
- Department of Anthropology, University of New Mexico, Albuquerque, New Mexico, USA
| | - Meghan Healy
- Department of Anthropology, University of New Mexico, Albuquerque, New Mexico, USA
| | - Carmen Mosley
- Department of Anthropology, University of New Mexico, Albuquerque, New Mexico, USA
| | - Aurelia Dixon
- Department of Anthropology, University of New Mexico, Albuquerque, New Mexico, USA
| |
Collapse
|
6
|
Behavioral and Psychological Outcomes Associated with Skin Cancer Genetic Testing in Albuquerque Primary Care. Cancers (Basel) 2021; 13:cancers13164053. [PMID: 34439206 PMCID: PMC8394482 DOI: 10.3390/cancers13164053] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 07/28/2021] [Accepted: 08/03/2021] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Genetic information is publicly available but research examining the best use of such information has not engaged diverse members of the public. We examined public reactions to melanoma genetic testing (using the melanocortin-1 receptor [MC1R] gene) in a study randomizing (like the flip of a coin) 600 diverse primary care patients to a MC1R test offer or usual care. We found that testing did not improve sun protection and skin cancer screening, nor did it lead worry to increase. However, groups less aware of their skin cancer risk, including those who thought their risk was “unlikely” at the start of the study, showed significant improvements in sun protection at three months. In conclusion, testing might be very helpful for certain people who have the most to learn about their risk, who may become motivated to protect themselves from the damaging effects of the sun as a result of skin cancer genetic testing. Abstract Public availability of genetic information is increasing; thus, efforts to improve diversity in basic and translational research in genomics is a top priority. Given the increasing U.S. incidence and mortality of melanoma, and the prevalence of common melanocortin-1 receptor (MC1R) gene melanoma risk variants in the general population, we examined genomic testing of MC1R for skin cancer risk in a randomized controlled trial in Albuquerque, New Mexico primary care. Participants were 48% Hispanic and were randomized 5:1 to a MC1R test invitation or usual care. We assessed 3 month sun protection, skin cancer screening, and skin cancer worry outcomes associated with testing, and key effect moderators (e.g., cancer risk perceptions, and skin cancer risk factors). Our findings indicate that the primary outcomes were unchanged by the MC1R test offer, test acceptance, and level of risk feedback. Moderator analyses showed that those with lower risk perception, and those with skin that readily tans, significantly increased their sun protection in response to higher than average risk feedback. Risk feedback did not prompt cancer worry, and average risk feedback did not erode existing sun protection. This study paves the way for the development of tailored strategies to address low skin cancer risk awareness in this understudied context of public health genomics.
Collapse
|
7
|
Jablonski NG. Skin color and race. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2021; 175:437-447. [PMID: 33372701 PMCID: PMC8247429 DOI: 10.1002/ajpa.24200] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 10/23/2020] [Accepted: 11/30/2020] [Indexed: 12/19/2022]
Abstract
Skin color is the primary physical criterion by which people have been classified into groups in the Western scientific tradition. From the earliest classifications of Linnaeus, skin color labels were not neutral descriptors, but connoted meanings that influenced the perceptions of described groups. In this article, the history of the use of skin color is reviewed to show how the imprint of history in connection with a single trait influenced subsequent thinking about human diversity. Skin color was the keystone trait to which other physical, behavioral, and culture characteristics were linked. To most naturalists and philosophers of the European Enlightenment, skin color was influenced by the external environment and expressed an inner state of being. It was both the effect and the cause. Early investigations of skin color and human diversity focused on understanding the central polarity between "white" Europeans and nonwhite others, with most attention devoted to explaining the origin and meaning of the blackness of Africans. Consistently negative associations with black and darkness influenced philosophers David Hume and Immanuel Kant to consider Africans as less than fully human and lacking in personal agency. Hume and Kant's views on skin color, the integrity of separate races, and the lower status of Africans provided support to diverse political, economic, and religious constituencies in Europe and the Americas interested in maintaining the transatlantic slave trade and upholding chattel slavery. The mental constructs and stereotypes of color-based races remained, more strongly in some places than others, after the abolition of the slave trade and of slavery. The concept of color-based hierarchies of people arranged from the superior light-colored people to inferior dark-colored ones hardened during the late seventeenth century and have been reinforced by diverse forces ever since. These ideas manifest themselves as racism, colorism, and in the development of implicit bias. Current knowledge of the evolution of skin color and of the historical development of color-based race concepts should inform all levels of formal and informal education. Awareness of the influence of color memes and race ideation in general on human behavior and the conduct of science is important.
Collapse
Affiliation(s)
- Nina G. Jablonski
- Department of AnthropologyThe Pennsylvania State UniversityState CollegePennsylvaniaUSA
| |
Collapse
|
8
|
Spradley MK. Use of craniometric data to facilitate migrant identifications at the United States/Mexico border. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2021; 175:486-496. [PMID: 33555056 DOI: 10.1002/ajpa.24241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 11/30/2020] [Accepted: 12/05/2020] [Indexed: 11/12/2022]
Abstract
OBJECTIVES Thousands of migrants have died along the United States/Mexico border and many remain unidentified. The purpose of this research is to test whether estimations of population affinity, derived from craniometric data, can facilitate identification of migrant remains and provide a geographic region of origin rather than the broad label Hispanic. The appropriateness of current forensic reference data will also be assessed. METHODS A case study combined with craniometric data from positively identified and unidentified migrants from the Pima County Office of the Medical Examiner (n = 489) in Arizona and operation identification (n = 201) in Texas were compared to skeletal data representing Guatemalan (n = 87) and Mexican (n = 65) Mayans. Biological distance and discriminant function analyses were used to assess overall population relationships and classificatory models for forensic anthropological application. RESULTS The majority of evidence indicates that estimations of population affinity can assist in the facilitation identification of migrant remains, even when a broad classification is used. Biological distances among the groups suggest that positively identified Guatemalan and Mexican migrants are similar to one another but differ from Guatemalan and Mexican Mayans. CONCLUSIONS Population affinity estimations can aid migrant identification, and current reference data used in forensic anthropological practice should be replaced with data from positive identifications. Estimates of geographic origin may be more useful than the broad generic term Hispanic for narrowing down the search for a missing person, but more data and research is needed to achieve this goal. Although, the utility of geographic origin estimates relies on transnational data centralization and sharing, which is not always the case.
Collapse
|
9
|
Genetic Structural Differentiation Analyses of Intercontinental Populations and Ancestry Inference of the Chinese Hui Group Based on a Novel Developed Autosomal AIM-InDel Genotyping System. BIOMED RESEARCH INTERNATIONAL 2020; 2020:2124370. [PMID: 32908873 PMCID: PMC7468629 DOI: 10.1155/2020/2124370] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 05/04/2020] [Indexed: 01/08/2023]
Abstract
In the present study, we investigated the genetic polymorphisms of 39 ancestry informative marker-insertion/deletion (AIM-InDel) loci in the Chinese Hui group using a previously self-developed panel, further clarified the genetic relationships between the Hui group and other reference populations, and assessed the ancestry inference efficiency of the AIM-InDel panel based on the worldwide population data from 1000 Genomes Phase 3. The results of the locus-specific informativeness (In) and pairwise fixation index (Fst) values, multidimensional scaling analysis, and success ratio of estimation with cross-validation showed that the novel panel could well reveal the genetic structural differentiations of the East Asian, European, African, and South Asian populations. Besides, the biogeographical ancestry origin inference both at the individual and population levels was conducted on the Chinese Hui group by principal component analysis and STRUCTURE analysis, and the results revealed that the Hui group had the East Asian origin, and the East Asian component ratio of Hui group was approximately 88.87%. Furthermore, the population genetic analyses among the Hui group and reference populations were performed based on the insertion allele frequency heat map, population pairwise Fst values and phylogenetic tree, and the results indicated that the Hui group was genetically closer to East Asian populations, especially two Chinese Han populations (CHS and CHB populations).
Collapse
|
10
|
Díaz-Peña R, Boekstegers F, Silva RS, Jaime S, Hosgood HD, Miravitlles M, Agustí À, Lorenzo Bermejo J, Olloquequi J. Amerindian Ancestry Influences Genetic Susceptibility to Chronic Obstructive Pulmonary Disease. J Pers Med 2020; 10:jpm10030093. [PMID: 32824824 PMCID: PMC7565405 DOI: 10.3390/jpm10030093] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 08/10/2020] [Accepted: 08/12/2020] [Indexed: 12/21/2022] Open
Abstract
The contribution of genetic ancestry on chronic obstructive pulmonary disease (COPD) predisposition remains unclear. To explore this relationship, we analyzed the associations between 754,159 single nucleotide polymorphisms (SNPs) and risk of COPD (n = 214 cases, 193 healthy controls) in Talca, Chile, considering the genetic ancestry and established risk factors. The proportion of Mapuche ancestry (PMA) was based on a panel of 45 Mapuche reference individuals. Five PRDM15 SNPs and two PPP1R12B SNPs were associate with COPD risk (p = 0.05 to 5×10-4) in those individuals with lower PMA. Based on linkage disequilibrium and sliding window analyses, an adjacent PRDM15 SNPs were associated with COPD risk in the lower PMA group (p = 10-3 to 3.77×10-8). Our study is the first to report an association between PPP1R12B and COPD risk, as well as effect modification between ethnicity and PRDM15 SNPs in determining COPD risk. Our results are biologically plausible given that PPP1R12B and PRDM15 are involved in immune dysfunction and autoimmunity, providing mechanistic evidence for COPD pathogenesis and highlighting the importance to conduct more genome wide association studies (GWAS) in admixed populations with Amerindian descent.
Collapse
Affiliation(s)
- Roberto Díaz-Peña
- Laboratory of Cellular and Molecular Pathology, Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Talca 3460000, Chile;
- Liquid Biopsy Analysis Unit, Oncomet, Health Research Institute of Santiago (IDIS), 15706 Santiago de Compostela, Spain
| | - Felix Boekstegers
- Statistical Genetics Group, Institute of Medical Biometry and Informatics, University of Heidelberg, 69126 Heidelberg, Germany; (F.B.); (J.L.B.)
| | - Rafael S. Silva
- Unidad Respiratorio, Centro de Diagnóstico Terapéutico, Hospital Regional de Talca, Talca 3460000, Chile; (R.S.S.); (S.J.)
| | - Sergio Jaime
- Unidad Respiratorio, Centro de Diagnóstico Terapéutico, Hospital Regional de Talca, Talca 3460000, Chile; (R.S.S.); (S.J.)
| | - H. Dean Hosgood
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA;
| | - Marc Miravitlles
- Pneumology Department, Hospital Universitari Vall d’Hebron/Vall d’Hebron Institut de Recerca (VHIR), CIBER Enfermedades Respiratorias (CIBERES), 08035 Barcelona, Spain;
| | - Àlvar Agustí
- Respiratory Institute, Hospital Clínic, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona, CIBER Enfermedades Respiratorias (CIBERES), 08036 Barcelona, Spain;
| | - Justo Lorenzo Bermejo
- Statistical Genetics Group, Institute of Medical Biometry and Informatics, University of Heidelberg, 69126 Heidelberg, Germany; (F.B.); (J.L.B.)
| | - Jordi Olloquequi
- Laboratory of Cellular and Molecular Pathology, Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Talca 3460000, Chile;
- Correspondence: ; Tel.: +56-71-273-5728
| |
Collapse
|
11
|
Impacts of personal DNA ancestry testing. J Community Genet 2020; 12:37-52. [PMID: 32789669 DOI: 10.1007/s12687-020-00481-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 07/29/2020] [Indexed: 11/27/2022] Open
Abstract
Consumer uptake of direct-to-consumer (DTC) DNA ancestry testing is accelerating, yet few empirical studies have examined test impacts on recipients despite the DTC ancestry industry being two decades old. Participants in a longitudinal cohort study of response to health-related DTC genomic testing also received personal DNA ancestry testing at no additional cost. Baseline survey data from the primary study were analyzed together with responses to an additional follow-up survey focused on the response to ancestry results. Ancestry results were generated for 3466 individuals. Of those, 1317 accessed their results, and 322 individuals completed an ancestry response survey, in other words, approximately one in ten who received ancestry testing responded to the survey. Self-reported race/ethnicity was predictive of those most likely to view their results. While 46% of survey responders (N = 147) reported their ancestry results as surprising or unexpected, less than 1% (N = 3) were distressed by them. Importantly, however, 21% (N = 67) reported that their results reshaped their personal identity. Most (81%; N = 260) planned to share results with family, and 12% (N = 39) intended to share results with a healthcare provider. Many (61%; N = 196) reported test benefits (e.g., health insights), while 12% (N = 38) reported negative aspects (e.g., lack of utility). Over half (N = 162) reported being more likely to have other genetic tests in the future. DNA ancestry testing affected individuals with respect to personal identity, intentions to share genetic information with family and healthcare providers, and the likelihood to engage with other genetic tests in the future. These findings have implications for medical care and research, specifically, provider readiness to engage with genetic ancestry information.
Collapse
|
12
|
Micheletti SJ, Bryc K, Ancona Esselmann SG, Freyman WA, Moreno ME, Poznik GD, Shastri AJ, Beleza S, Mountain JL, Agee M, Aslibekyan S, Auton A, Bell R, Clark S, Das S, Elson S, Fletez-Brant K, Fontanillas P, Gandhi P, Heilbron K, Hicks B, Hinds D, Huber K, Jewett E, Jiang Y, Kleinman A, Lin K, Litterman N, McCreight J, McIntyre M, McManus K, Mozaffari S, Nandakumar P, Noblin L, Northover C, O’Connell J, Petrakovitz A, Pitts S, Shelton J, Shringarpure S, Tian C, Tung J, Tunney R, Vacic V, Wang X, Zare A. Genetic Consequences of the Transatlantic Slave Trade in the Americas. Am J Hum Genet 2020; 107:265-277. [PMID: 32707084 PMCID: PMC7413858 DOI: 10.1016/j.ajhg.2020.06.012] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 06/15/2020] [Indexed: 01/07/2023] Open
Abstract
According to historical records of transatlantic slavery, traders forcibly deported an estimated 12.5 million people from ports along the Atlantic coastline of Africa between the 16th and 19th centuries, with global impacts reaching to the present day, more than a century and a half after slavery's abolition. Such records have fueled a broad understanding of the forced migration from Africa to the Americas yet remain underexplored in concert with genetic data. Here, we analyzed genotype array data from 50,281 research participants, which-combined with historical shipping documents-illustrate that the current genetic landscape of the Americas is largely concordant with expectations derived from documentation of slave voyages. For instance, genetic connections between people in slave trading regions of Africa and disembarkation regions of the Americas generally mirror the proportion of individuals forcibly moved between those regions. While some discordances can be explained by additional records of deportations within the Americas, other discordances yield insights into variable survival rates and timing of arrival of enslaved people from specific regions of Africa. Furthermore, the greater contribution of African women to the gene pool compared to African men varies across the Americas, consistent with literature documenting regional differences in slavery practices. This investigation of the transatlantic slave trade, which is broad in scope in terms of both datasets and analyses, establishes genetic links between individuals in the Americas and populations across Atlantic Africa, yielding a more comprehensive understanding of the African roots of peoples of the Americas.
Collapse
|
13
|
Hunley K, Edgar H, Healy M, Mosley C. Colonialism and the co-evolution of ethnic and genetic structure in New Mexico. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2020; 171:509-519. [PMID: 31930496 DOI: 10.1002/ajpa.23997] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 10/24/2019] [Accepted: 12/14/2019] [Indexed: 01/18/2023]
Abstract
OBJECTIVE Socially constructed ethnic identities are frequently rooted in beliefs about common descent that form when people with disparate cultures, languages, and biology come into contact. This study explores connections between beliefs about common descent, as represented by ethnic nomenclatures, and histories of migration and isolation ascertained from genomic data in New Mexicans of Spanish-speaking descent (NMS). MATERIALS AND METHODS We interviewed 507 NMS who further identified using one of seven ethnic terms that they associated with beliefs about connections to past ancestors. For groups of individuals who identified using each term, we estimated biogeographic ancestry, fit admixture models to ancestry distributions, and partitioned genetic distance into admixture and drift components. RESULTS Regardless of which ethnic term they used, all NMS had appreciable Native American (avg. 27%) and European ancestry (avg.71%). However, individuals who identified using terms associated with beliefs connecting them to colonial-period Spanish ancestors had significantly higher European ancestry than individuals who identified using terms associated with ancestral connections to post-colonial-period migrants from Mexico. Model-fitting analyses show that this ancestry difference reflects post-colonial gene flow with non-NMS European Americans, not colonial-period gene flow with Spaniards. Drift, not admixture, accounted for most of the genetic distance between NMS who expressed connections to Mexican versus Spanish ancestors, reflecting relative isolation of New Mexico and Mexico through the 19th century. DISCUSSION Patterns of genomic diversity in NMS are consistent with beliefs about common descent in showing that New Mexico was isolated for generations following initial colonization. They are inconsistent with these beliefs in showing that all NMS have substantial European and Native American ancestry, and in showing that a proportion of European ancestry derives from post-colonial-period admixture with non-NMS European Americans. Our findings provide insights into the construction of ethnic identity in contexts of migration and isolation in New Mexico and, potentially, throughout human prehistory.
Collapse
Affiliation(s)
- Keith Hunley
- Department of Anthropology, University of New Mexico, Albuquerque, New Mexico
| | - Heather Edgar
- Department of Anthropology, University of New Mexico, Albuquerque, New Mexico
| | - Meghan Healy
- Department of Anthropology, University of New Mexico, Albuquerque, New Mexico
| | - Carmen Mosley
- Department of Anthropology, University of New Mexico, Albuquerque, New Mexico
| |
Collapse
|
14
|
Hay JL, Zielaskowski K, Meyer White K, Kaphingst K, Robers E, Guest D, Sussman A, Talamantes Y, Schwartz M, Rodríguez VM, Li Y, Schofield E, Bigney J, Hunley K, Buller D, Berwick M. Interest and Uptake of MC1R Testing for Melanoma Risk in a Diverse Primary Care Population: A Randomized Clinical Trial. JAMA Dermatol 2019; 154:684-693. [PMID: 29801061 DOI: 10.1001/jamadermatol.2018.0592] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Importance Germline variants in the MC1R gene are common and confer moderate melanoma risk in those with varied skin types. Approaches to precision skin cancer prevention that include genetic information may promote risk awareness and risk reduction in the general population, including Hispanics. Objective To examine prevalence of interest in and uptake of MC1R testing in the general population and examine patterns across demographic and skin cancer risk factors. Design, Setting, and Participants A randomized clinical trial examined interest in and uptake of MC1R testing among patients at University of New Mexico General Internal Medicine clinics. Study participants were randomized to either a usual-care condition (National Cancer Institute skin cancer pamphlet for diverse skin types) or an MC1R test offer. Participants were registered clinic patients (≥6 months) and English or Spanish fluent. Of the 600 participants recruited to the overall trial, the present study included those 499 participants randomized to the MC1R test offer. Interventions Participants were presented with the option to log onto the study website to read 3 educational modules presenting the rationale, benefits, and drawbacks of MC1R testing. Main Outcomes and Measures Main outcomes include website log on (yes vs no), saliva test kit request (yes vs no), and saliva test kit return for MC1R testing (yes vs no). Demographic and skin cancer risk factors were examined as potential predictors of test interest and uptake. Results Of the 499 participants (220 [44%] non-Hispanic white, 242 [48%] Hispanic, 396 [79%] female; mean [SD] age, 54 [14.3] years), 232 (46%) elected to learn about MC1R testing by logging onto the website; 204 (88%) of those who logged on decided to request testing; and 167 (82%) of those who requested testing returned the kit. The strongest predictors of website log on were race/ethnicity and education (non-Hispanic whites were more likely to log on [odds ratio for Hispanics vs non-Hispanic whites, 0.5; 95% CI, 0.3-0.7], as were more highly educated individuals [odds ratio for more than high school vs high school or less, 2.7; 95% CI, 1.7-4.3]). The strongest predictor of ordering the test was sunburn history (odds ratio, 5.4; 95% CI, 2.3-12.9 vs no sunburn history). Conclusions and Relevance There were moderately high levels of MC1R test interest and uptake in this diverse sample. Addressing potential barriers to testing may be warranted as genomic information becomes integrated into general population approaches to the precision prevention of skin cancer. Trial Registration ClinicalTrials.gov identifier: NCT03130569.
Collapse
Affiliation(s)
- Jennifer L Hay
- Department of Psychiatry and Behavioral Sciences, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kate Zielaskowski
- Clinical Research Finance, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kirsten Meyer White
- Division of Epidemiology, Department of Internal Medicine, University of New Mexico, Albuquerque
| | - Kimberly Kaphingst
- Department of Communication, University of Utah, Salt Lake City.,Huntsman Cancer Institute, University of Utah, Salt Lake City
| | - Erika Robers
- New Mexico Translation and Transcription, Albuquerque
| | - Dolores Guest
- CRTC Population Sciences Academic Unit, University of New Mexico, Albuquerque
| | - Andrew Sussman
- Department of Family and Community Medicine, University of New Mexico, Albuquerque
| | - Yvonne Talamantes
- CRTC Population Sciences Academic Unit, University of New Mexico, Albuquerque
| | - Matthew Schwartz
- CRTC Population Sciences Academic Unit, University of New Mexico, Albuquerque
| | | | - Yuelin Li
- Department of Psychiatry and Behavioral Sciences, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Elizabeth Schofield
- Department of Psychiatry and Behavioral Sciences, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jessica Bigney
- Department of General Internal Medicine, University of New Mexico, Albuquerque
| | - Keith Hunley
- Department of Anthropology, University of New Mexico, Albuquerque
| | | | - Marianne Berwick
- Department of Internal Medicine, University of New Mexico, Albuquerque.,Department of Dermatology, University of New Mexico, Albuquerque
| |
Collapse
|
15
|
Dutil J, Chen Z, Monteiro AN, Teer JK, Eschrich SA. An Interactive Resource to Probe Genetic Diversity and Estimated Ancestry in Cancer Cell Lines. Cancer Res 2019; 79:1263-1273. [PMID: 30894373 DOI: 10.1158/0008-5472.can-18-2747] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 11/08/2018] [Accepted: 12/26/2018] [Indexed: 12/21/2022]
Abstract
Recent work points to a lack of diversity in genomics studies from genome-wide association studies to somatic (tumor) genome analyses. Yet, population-specific genetic variation has been shown to contribute to health disparities in cancer risk and outcomes. Immortalized cancer cell lines are widely used in cancer research, from mechanistic studies to drug screening. Larger collections of cancer cell lines better represent the genomic heterogeneity found in primary tumors. Yet, the genetic ancestral origin of cancer cell lines is rarely acknowledged and often unknown. Using genome-wide genotyping data from 1,393 cancer cell lines from the Catalogue of Somatic Mutations in Cancer (COSMIC) and Cancer Cell Line Encyclopedia (CCLE), we estimated the genetic ancestral origin for each cell line. Our data indicate that cancer cell line collections are not representative of the diverse ancestry and admixture characterizing human populations. We discuss the implications of genetic ancestry and diversity of cellular models for cancer research and present an interactive tool, Estimated Cell Line Ancestry (ECLA), where ancestry can be visualized with reference populations of the 1000 Genomes Project. Cancer researchers can use this resource to identify cell line models for their studies by taking ancestral origins into consideration.
Collapse
Affiliation(s)
- Julie Dutil
- Cancer Biology Division, Ponce Research Institute, Ponce Health Sciences University, Ponce, Puerto Rico.
| | - Zhihua Chen
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Alvaro N Monteiro
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Jamie K Teer
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Steven A Eschrich
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida.
| |
Collapse
|
16
|
Torres D, Lorenzo Bermejo J, Garcia Mesa K, Gilbert M, Briceño I, Pohl-Zeidler S, González Silos R, Boekstegers F, Plass C, Hamann U. Interaction between genetic ancestry and common breast cancer susceptibility variants in Colombian women. Int J Cancer 2019; 144:2181-2191. [PMID: 30485434 DOI: 10.1002/ijc.32023] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 11/05/2018] [Indexed: 01/31/2023]
Abstract
Latino women show lower incidences of breast cancer (BC) than non-Hispanic whites. Large-scale genetic association studies have identified variants robustly associated with BC risk in European women. We examine here the relevance of these variants to Colombian BC and possible interactions with genetic ancestry. Native American, European and African proportions were estimated for 1022 Colombian BC cases and 1023 controls. Logistic regression was applied to assess the association between 78 variants and BC risk and interactions between the variants and ancestry proportions. We constructed a multifactorial risk score combining established BC risk factors, associated risk variants and individual ancestry proportions. Each 1% increase in the Native American proportion translated into a 2.2% lower BC risk (95% CI: 1.4-2.9). Thirteen variants were associated with BC in Colombian women, with allele frequencies and risk effects partially different from European women. Ancestry proportions moderated the risk effects of two variants. The ability of Native American proportions to separate Colombian cases and controls (area-under-the-curve (AUC) = 0.61) was similar to the discriminative ability of family history of BC in first-degree female relatives (AUC = 0.58) or the combined effect of all 13 associated risk variants (AUC = 0.57). Our findings demonstrate ample potential for individualized BC prevention in Hispanic women taking advantage of individual Native American proportions, information on established susceptibility factors and recently identified common risk variants.
Collapse
Affiliation(s)
- Diana Torres
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Institute of Human Genetics, Pontificia Universidad Javeriana, Bogota, Colombia
| | - Justo Lorenzo Bermejo
- Institute of Medical Biometry and Informatics, University of Heidelberg, Heidelberg, Germany
| | - Karen Garcia Mesa
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Institute of Medical Biometry and Informatics, University of Heidelberg, Heidelberg, Germany
| | - Michael Gilbert
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ignacio Briceño
- Institute of Human Genetics, Pontificia Universidad Javeriana, Bogota, Colombia.,Universidad de la Sabana, Bogota, Colombia
| | - Svenja Pohl-Zeidler
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Rosa González Silos
- Institute of Medical Biometry and Informatics, University of Heidelberg, Heidelberg, Germany
| | - Felix Boekstegers
- Institute of Medical Biometry and Informatics, University of Heidelberg, Heidelberg, Germany
| | - Christoph Plass
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| |
Collapse
|
17
|
Quillen EE, Norton HL, Parra EJ, Lona-Durazo F, Ang KC, Illiescu FM, Pearson LN, Shriver MD, Lasisi T, Gokcumen O, Starr I, Lin YL, Martin AR, Jablonski NG. Shades of complexity: New perspectives on the evolution and genetic architecture of human skin. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2018; 168 Suppl 67:4-26. [PMID: 30408154 DOI: 10.1002/ajpa.23737] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 09/17/2018] [Accepted: 09/20/2018] [Indexed: 02/06/2023]
Abstract
Like many highly variable human traits, more than a dozen genes are known to contribute to the full range of skin color. However, the historical bias in favor of genetic studies in European and European-derived populations has blinded us to the magnitude of pigmentation's complexity. As deliberate efforts are being made to better characterize diverse global populations and new sequencing technologies, better measurement tools, functional assessments, predictive modeling, and ancient DNA analyses become more widely accessible, we are beginning to appreciate how limited our understanding of the genetic bases of human skin color have been. Novel variants in genes not previously linked to pigmentation have been identified and evidence is mounting that there are hundreds more variants yet to be found. Even for genes that have been exhaustively characterized in European populations like MC1R, OCA2, and SLC24A5, research in previously understudied groups is leading to a new appreciation of the degree to which genetic diversity, epistatic interactions, pleiotropy, admixture, global and local adaptation, and cultural practices operate in population-specific ways to shape the genetic architecture of skin color. Furthermore, we are coming to terms with how factors like tanning response and barrier function may also have influenced selection on skin throughout human history. By examining how our knowledge of pigmentation genetics has shifted in the last decade, we can better appreciate how far we have come in understanding human diversity and the still long road ahead for understanding many complex human traits.
Collapse
Affiliation(s)
- Ellen E Quillen
- Department of Internal Medicine, Section of Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina.,Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Heather L Norton
- Department of Anthropology, University of Cincinnati, Cincinnati, Ohio
| | - Esteban J Parra
- Department of Anthropology, University of Toronto - Mississauga, Mississauga, Ontario, Canada
| | - Frida Lona-Durazo
- Department of Anthropology, University of Toronto - Mississauga, Mississauga, Ontario, Canada
| | - Khai C Ang
- Department of Pathology and Jake Gittlen Laboratories for Cancer Research, Penn State College of Medicine, Hershey, Pennsylvania
| | - Florin Mircea Illiescu
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom.,Centro de Estudios Interculturales e Indígenas - CIIR, P. Universidad Católica de Chile, Santiago, Chile
| | - Laurel N Pearson
- Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania
| | - Mark D Shriver
- Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania
| | - Tina Lasisi
- Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania
| | - Omer Gokcumen
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, New York
| | - Izzy Starr
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, New York
| | - Yen-Lung Lin
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, New York
| | - Alicia R Martin
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Nina G Jablonski
- Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania
| |
Collapse
|
18
|
Healy M, Edgar H, Mosley C, Hunley K. Associations between ethnic identity, regional history, and genomic ancestry in New Mexicans of Spanish-speaking descent. BIODEMOGRAPHY AND SOCIAL BIOLOGY 2018; 64:152-170. [PMID: 30570413 DOI: 10.1080/19485565.2018.1545563] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
This study examines associations between ethnic identity, regional history, and genomic ancestry in New Mexicans of Spanish-speaking descent (NMS). In structured interviews, we asked 507 NMS to select from a list of eight ethnic identity terms identified in previous research. We estimated genomic ancestry for each individual from 291,917 single nucleotide polymorphisms (SNPs) and compared genomic ancestry, age, and birthplace between groups of individuals who identified using each ethnic identity term. Eighty-eight per cent of NMS who identified as "Hispanic," "Nuevomexicano/a," and "Spanish," on average, were born in New Mexico, as were the vast majority of their parents and grandparents. Thirty-three per cent of NMS who identified as "Mexican" and "Mexican American" were born in Mexico, as were 59 per cent of their parents and 67 per cent of their grandparents. Average Native American and African ancestry proportions in "Hispanic" (0.26, 0.02, respectively), "Spanish" (0.25, 0.01), and "Nuevomexicano/a" (0.24, 0.01) NMS were significantly lower than in "Mexican American" (0.37, 0.04) NMS. Significant age differences between older "Spanish" and younger "Nuevomexicano/a" individuals, combined with widespread use of the term "Hispanic," may reflect ongoing nomenclature changes. Patterns of correspondence between ethnic identity, ethnic nomenclatures, and genomic ancestry reflect historical patterns of migration, colonization, and cultural change.
Collapse
Affiliation(s)
- Meghan Healy
- a Department of Anthropology , University of New Mexico , Albuquerque , New Mexico
| | - Heather Edgar
- a Department of Anthropology , University of New Mexico , Albuquerque , New Mexico
| | - Carmen Mosley
- a Department of Anthropology , University of New Mexico , Albuquerque , New Mexico
| | - Keith Hunley
- a Department of Anthropology , University of New Mexico , Albuquerque , New Mexico
| |
Collapse
|
19
|
Kahn JM, Cole PD, Blonquist TM, Stevenson K, Jin Z, Barrera S, Davila R, Roberts E, Neuberg DS, Athale UH, Clavell LA, Laverdiere C, Leclerc JM, Michon B, Schorin MA, Welch JJ, Sallan SE, Silverman LB, Kelly KM. An investigation of toxicities and survival in Hispanic children and adolescents with ALL: Results from the Dana-Farber Cancer Institute ALL Consortium protocol 05-001. Pediatr Blood Cancer 2018; 65:10.1002/pbc.26871. [PMID: 29090520 PMCID: PMC5766393 DOI: 10.1002/pbc.26871] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 09/26/2017] [Accepted: 09/29/2017] [Indexed: 12/15/2022]
Abstract
PURPOSE This study compared the relative incidence of treatment-related toxicities and the event-free and overall survival between Hispanic and non-Hispanic children undergoing therapy for acute lymphoblastic leukemia (ALL) on Dana-Farber Cancer Institute ALL Consortium protocol 05-001. PATIENTS AND METHODS Secondary analysis of prospectively collected data from a phase III multicenter study in children and adolescents of 1-18 years with previously untreated ALL. RESULTS Between 2005 and 2011, 794 eligible patients enrolled on DFCI 05-001, 730 of whom were included in this analysis (19% [N = 150] Hispanic, 73% [N = 580] non-Hispanic). Hispanic patients were more likely to be ≥10 years of age (32% vs. 24%, P = 0.045) at diagnosis. Toxicity analyses revealed that Hispanic patients had significantly lower cumulative incidence of bone fracture (P < 0.001) and osteonecrosis (ON; P = 0.047). In multivariable risk regression, the risk of ON was significantly lower in Hispanic patients ≥10 years (HR 0.23; P = 0.006). Hispanic patients had significantly lower 5-year event-free survival (EFS) (79.4%; 95% CI: 71.6-85.2) and overall survival (OS) (89.2%; 95% CI: 82.7-93.4) than non-Hispanic patients (EFS: 87.5%; 95% CI: 84.5-90.0, P = 0.004; OS: 92.7%; 95% CI: 90.2-94.6, P = 0.006). Exploratory analyses revealed differences between Hispanic and non-Hispanic patients in the frequency of common variants in genes related to toxicity or ALL outcome. CONCLUSION Hispanic children treated for ALL on DFCI 05-001 had fewer bone-related toxicities and inferior survival than non-Hispanic patients. While disease biology is one explanatory variable for outcome disparities, these findings suggest that biologic and non-biologic mechanisms affecting drug delivery and exposure in this population may be important contributing factors as well.
Collapse
Affiliation(s)
- Justine M. Kahn
- Division of Pediatric Hematology/Oncology/Stem Cell Transplantation, Columbia University Medical Center, NewYork-Presbyterian Morgan Stanley Children’s Hospital, New York, NY, USA
| | - Peter D. Cole
- Division of Pediatric Hematology/Oncology, Children’s Hospital at Montefiore, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Traci M. Blonquist
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Kristen Stevenson
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Zhezhen Jin
- Department of Biostatistics, Columbia University Medical Center, New York, New York, USA
| | - Sergio Barrera
- Department of Economics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Randy Davila
- Department of Psychology, University of California, Davis, Davis, California, USA
| | - Emily Roberts
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, USA
| | - Donna S. Neuberg
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Uma H. Athale
- Division of Pediatric Hematology/Oncology, McMaster University, Hamilton, ON, Canada
| | - Luis A. Clavell
- Division of Pediatric Oncology, San Jorge Children’s Hospital, San Juan, Puerto Rico
| | - Caroline Laverdiere
- Division of Hematology and Oncology, Hospital Sainte-Justine, University of Montreal, Montreal, Canada
| | - Jean-Marie Leclerc
- Division of Hematology and Oncology, Hospital Sainte-Justine, University of Montreal, Montreal, Canada
| | - Bruno Michon
- Division of Hematology-Oncology, Centre Hospitalier de l’Université Laval, Quebec City, Canada
| | | | - Jennifer J.G. Welch
- Division of Pediatric Hematology-Oncology, Hasbro Children’s Hospital, Warren Alpert Medical School of Brown University, Providence, RI, USA
| | - Stephen E. Sallan
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Division of Hematology/Oncology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Lewis B. Silverman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Division of Hematology/Oncology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Kara M. Kelly
- Division of Pediatric Hematology/Oncology/Stem Cell Transplantation, Columbia University Medical Center, NewYork-Presbyterian Morgan Stanley Children’s Hospital, New York, NY, USA,Roswell Park Cancer Institute and Women and Children’s Hospital, University at Buffalo School of Medicine and Biomedical Sciences, Buffalo, NY, USA
| |
Collapse
|
20
|
Healy ME, Hill D, Berwick M, Edgar H, Gross J, Hunley K. Social-group identity and population substructure in admixed populations in New Mexico and Latin America. PLoS One 2017; 12:e0185503. [PMID: 28977000 PMCID: PMC5627912 DOI: 10.1371/journal.pone.0185503] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 09/13/2017] [Indexed: 12/13/2022] Open
Abstract
We examined the relationship between continental-level genetic ancestry and racial and ethnic identity in an admixed population in New Mexico with the goal of increasing our understanding of how racial and ethnic identity influence genetic substructure in admixed populations. Our sample consists of 98 New Mexicans who self-identified as Hispanic or Latino (NM-HL) and who further categorized themselves by race and ethnic subgroup membership. The genetic data consist of 270 newly-published autosomal microsatellites from the NM-HL sample and previously published data from 57 globally distributed populations, including 13 admixed samples from Central and South America. For these data, we 1) summarized the major axes of genetic variation using principal component analyses, 2) performed tests of Hardy Weinberg equilibrium, 3) compared empirical genetic ancestry distributions to those predicted under a model of admixture that lacked substructure, 4) tested the hypotheses that individuals in each sample had 100%, 0%, and the sample-mean percentage of African, European, and Native American ancestry. We found that most NM-HL identify themselves and their parents as belonging to one of two groups, conforming to a region-specific narrative that distinguishes recent immigrants from Mexico from individuals whose families have resided in New Mexico for generations and who emphasize their Spanish heritage. The “Spanish” group had significantly lower Native American ancestry and higher European ancestry than the “Mexican” group. Positive FIS values, PCA plots, and heterogeneous ancestry distributions suggest that most Central and South America admixed samples also contain substructure, and that this substructure may be related to variation in social identity. Genetic substructure appears to be common in admixed populations in the Americas and may confound attempts to identify disease-causing genes and to understand the social causes of variation in health outcomes and social inequality.
Collapse
Affiliation(s)
- Meghan E. Healy
- Department of Anthropology, University of New Mexico, Albuquerque, NM, United States of America
| | - Deirdre Hill
- Department of Internal Medicine, University of New Mexico, Albuquerque, NM, United States of America
| | - Marianne Berwick
- Department of Internal Medicine, University of New Mexico, Albuquerque, NM, United States of America
| | - Heather Edgar
- Department of Anthropology, University of New Mexico, Albuquerque, NM, United States of America
| | - Jessica Gross
- Department of Anthropology, University of New Mexico, Albuquerque, NM, United States of America
| | - Keith Hunley
- Department of Anthropology, University of New Mexico, Albuquerque, NM, United States of America
- * E-mail:
| |
Collapse
|
21
|
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]
|
22
|
Hay JL, Berwick M, Zielaskowski K, White KA, Rodríguez VM, Robers E, Guest DD, Sussman A, Talamantes Y, Schwartz MR, Greb J, Bigney J, Kaphingst KA, Hunley K, Buller DB. Implementing an Internet-Delivered Skin Cancer Genetic Testing Intervention to Improve Sun Protection Behavior in a Diverse Population: Protocol for a Randomized Controlled Trial. JMIR Res Protoc 2017; 6:e52. [PMID: 28442450 PMCID: PMC5424125 DOI: 10.2196/resprot.7158] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Revised: 02/08/2017] [Accepted: 02/08/2017] [Indexed: 11/13/2022] Open
Abstract
Background Limited translational genomic research currently exists to guide the availability, comprehension, and appropriate use of personalized genomics in diverse general population subgroups. Melanoma skin cancers are preventable, curable, common in the general population, and disproportionately increasing in Hispanics. Objective Variants in the melanocortin-1 receptor (MC1R) gene are present in approximately 50% of the population, are major factors in determining sun sensitivity, and confer a 2-to-3-fold increase in melanoma risk in the general population, even in populations with darker skin. Therefore, feedback regarding MC1R risk status may raise risk awareness and protective behavior in the general population. Methods We are conducting a randomized controlled trial examining Internet presentation of the risks and benefits of personalized genomic testing for MC1R gene variants that are associated with increased melanoma risk. We will enroll a total of 885 participants (462 participants are currently enrolled), who will be randomized 6:1 to personalized genomic testing for melanoma risk versus waiting list control. Control participants will be offered testing after outcome assessments. Participants will be balanced across self-reported Hispanic versus non-Hispanic ethnicity (n=750 in personalized genomic testing for melanoma risk arm; n=135 in control arm), and will be recruited from a general population cohort in Albuquerque, New Mexico, which is subject to year-round sun exposure. Baseline surveys will be completed in-person with study staff and follow-up measures will be completed via telephone. Results Aim 1 of the trial will examine the personal utility of personalized genomic testing for melanoma risk in terms of short-term (3-month) sun protection and skin screening behaviors, family and physician communication, and melanoma threat and control beliefs (ie, putative mediators of behavior change). We will also examine potential unintended consequences of testing among those who receive average-risk personalized genomic testing for melanoma risk findings, and examine predictors of sun protection at 3 months as the outcome. These findings will be used to develop messages for groups that receive average-risk feedback. Aim 2 will compare rates of test consideration in Hispanics versus non-Hispanics, including consideration of testing pros and cons and registration of a decision to either accept or decline testing. Aim 3 will examine personalized genomic testing for melanoma risk feedback comprehension, recall, satisfaction, and cancer-related distress in those who undergo testing, and whether these outcomes differ by ethnicity (Hispanic vs non-Hispanic), or sociocultural or demographic factors. Final outcome data collection is anticipated to be complete by October 2017, at which point data analysis will commence. Conclusions This study has important implications for personalized genomics in the context of melanoma risk, and may be broadly applicable as a model for delivery of personalized genomic feedback for other health conditions.
Collapse
Affiliation(s)
- Jennifer L Hay
- Memorial Sloan Kettering Cancer Center, Department of Psychiatry & Behavioral Sciences, New York, NY, United States
| | | | - Kate Zielaskowski
- Memorial Sloan Kettering Cancer Center, Department of Psychiatry & Behavioral Sciences, New York, NY, United States
| | | | | | - Erika Robers
- University of New Mexico, Albuquerque, NM, United States
| | | | - Andrew Sussman
- University of New Mexico, Albuquerque, NM, United States
| | | | | | - Jennie Greb
- University of New Mexico, Albuquerque, NM, United States
| | - Jessica Bigney
- University of New Mexico, Albuquerque, NM, United States
| | | | - Keith Hunley
- University of New Mexico, Albuquerque, NM, United States
| | | |
Collapse
|
23
|
Langlois C, Abadi A, Peralta-Romero J, Alyass A, Suarez F, Gomez-Zamudio J, Burguete-Garcia AI, Yazdi FT, Cruz M, Meyre D. Evaluating the transferability of 15 European-derived fasting plasma glucose SNPs in Mexican children and adolescents. Sci Rep 2016; 6:36202. [PMID: 27782183 PMCID: PMC5080582 DOI: 10.1038/srep36202] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 10/12/2016] [Indexed: 12/15/2022] Open
Abstract
Genome wide association studies (GWAS) have identified single-nucleotide polymorphisms (SNPs) that are associated with fasting plasma glucose (FPG) in adult European populations. The contribution of these SNPs to FPG in non-Europeans and children is unclear. We studied the association of 15 GWAS SNPs and a genotype score (GS) with FPG and 7 metabolic traits in 1,421 Mexican children and adolescents from Mexico City. Genotyping of the 15 SNPs was performed using TaqMan Open Array. We used multivariate linear regression models adjusted for age, sex, body mass index standard deviation score, and recruitment center. We identified significant associations between 3 SNPs (G6PC2 (rs560887), GCKR (rs1260326), MTNR1B (rs10830963)), the GS and FPG level. The FPG risk alleles of 11 out of the 15 SNPs (73.3%) displayed significant or non-significant beta values for FPG directionally consistent with those reported in adult European GWAS. The risk allele frequencies for 11 of 15 (73.3%) SNPs differed significantly in Mexican children and adolescents compared to European adults from the 1000G Project, but no significant enrichment in FPG risk alleles was observed in the Mexican population. Our data support a partial transferability of European GWAS FPG association signals in children and adolescents from the admixed Mexican population.
Collapse
Affiliation(s)
- Christine Langlois
- Department of Clinical Epidemiology and Biostatistics, McMaster University, Hamilton, ON, Canada
| | - Arkan Abadi
- Department of Clinical Epidemiology and Biostatistics, McMaster University, Hamilton, ON, Canada
| | - Jesus Peralta-Romero
- Medical Research Unit in Biochemistry, Hospital de Especialidades, Centro Médico Nacional Siglo XXI del Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Akram Alyass
- Department of Clinical Epidemiology and Biostatistics, McMaster University, Hamilton, ON, Canada
| | - Fernando Suarez
- Medical Research Unit in Biochemistry, Hospital de Especialidades, Centro Médico Nacional Siglo XXI del Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Jaime Gomez-Zamudio
- Medical Research Unit in Biochemistry, Hospital de Especialidades, Centro Médico Nacional Siglo XXI del Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Ana I. Burguete-Garcia
- Centro de investigación sobre enfermedades infecciosas. Instituto Nacional de Salud Pública. Cuernavaca, Morelos, Mexico
| | - Fereshteh T. Yazdi
- Department of Clinical Epidemiology and Biostatistics, McMaster University, Hamilton, ON, Canada
| | - Miguel Cruz
- Medical Research Unit in Biochemistry, Hospital de Especialidades, Centro Médico Nacional Siglo XXI del Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - David Meyre
- Department of Clinical Epidemiology and Biostatistics, McMaster University, Hamilton, ON, Canada
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
| |
Collapse
|
24
|
Algee-Hewitt BF. Population inference from contemporary American craniometrics. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2016; 160:604-24. [DOI: 10.1002/ajpa.22959] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 12/06/2015] [Accepted: 01/20/2016] [Indexed: 11/11/2022]
Affiliation(s)
- Bridget F.B. Algee-Hewitt
- Department of Biology; Stanford University; Stanford CA 94305
- Departments of Anthropology and Scientific Computing; Florida State University; Tallahassee FL 32306
| |
Collapse
|
25
|
Marden JR, Walter S, Kaufman JS, Glymour MM. African Ancestry, Social Factors, and Hypertension Among Non-Hispanic Blacks in the Health and Retirement Study. BIODEMOGRAPHY AND SOCIAL BIOLOGY 2016; 62:19-35. [PMID: 27050031 DOI: 10.1080/19485565.2015.1108836] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The biomedical literature contains much speculation about possible genetic explanations for the large and persistent black-white disparities in hypertension, but profound social inequalities are also hypothesized to contribute to this outcome. Our goal is to evaluate whether socioeconomic status (SES) differences provide a plausible mechanism for associations between African ancestry and hypertension in a U.S. cohort of older non-Hispanic blacks. We included only non-Hispanic black participants (N = 998) from the Health and Retirement Study who provided genetic data. We estimated percent African ancestry based on 84,075 independent single nucleotide polymorphisms using ADMIXTURE V1.23, imposing K = 4 ancestral populations, and categorized into quartiles. Hypertension status was self-reported in the year 2000. We used linear probability models (adjusted for age, sex, and southern birth) to predict prevalent hypertension with African ancestry quartile, before and after accounting for a small set of SES measures. Respondents with the highest quartile of African ancestry had 8 percentage points' (RD = 0.081; 95% CI: -0.001, 0.164) higher prevalence of hypertension compared to the lowest quartile. Adjustment for childhood disadvantage, education, income, and wealth explained over one-third (RD = 0.050; 95% CI: -0.034, 0.135) of the disparity. Explanations for the residual disparity remain unspecified and may include other indicators of SES or diet, lifestyle, and psychosocial mechanisms.
Collapse
Affiliation(s)
- Jessica R Marden
- a Department of Social and Behavioral Sciences , Harvard School of Public Health , Boston , Massachusetts , USA
| | - Stefan Walter
- b Department of Epidemiology and Biostatistics , University of California at San Francisco , San Francisco , California , USA
| | - Jay S Kaufman
- c Department of Epidemiology and Biostatistics , McGill University , Montreal , Quebec , Canada
| | - M Maria Glymour
- a Department of Social and Behavioral Sciences , Harvard School of Public Health , Boston , Massachusetts , USA
- b Department of Epidemiology and Biostatistics , University of California at San Francisco , San Francisco , California , USA
| |
Collapse
|
26
|
Pontoriero AC, Trinks J, Hulaniuk ML, Caputo M, Fortuny L, Pratx LB, Frías A, Torres O, Nuñez F, Gadano A, Argibay P, Corach D, Flichman D. Influence of ethnicity on the distribution of genetic polymorphisms associated with risk of chronic liver disease in South American populations. BMC Genet 2015. [PMID: 26219465 PMCID: PMC4518515 DOI: 10.1186/s12863-015-0255-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The global burden of chronic liver disease is rising. Besides environmental, behavioral, viral and metabolic factors, genetic polymorphisms in patatin-like phospholipase-3 (PNPLA3) and vitamin D receptor (VDR) genes have been related to the development of chronic liver disease and progression towards liver cancer. Although their prevalence differs remarkably among ethnic groups, the frequency of these polymorphisms in South American populations -whose genetic background is highly admixed- has been poorly studied. Hence, the aim of this study was to characterize polymorphisms related to chronic liver disease and their association with the genetic ancestry of South American populations. RESULTS DNA samples from 258 healthy unrelated male volunteers were analyzed. The frequencies of G and C alleles of rs738409 polymorphism (PNPLA3 gene) were 74 % and 26 %, respectively; whereas the bAt (CCA) haplotype (VDR gene) was observed in 32.5 % of the samples. The GG genotype of PNPLA3 rs738409 and the bAt (CCA) haplotype -associated with an increased risk of chronic liver disease and progression towards liver cancer- were significantly more frequent among samples exhibiting maternal and paternal Native American haplogroups (63.7 % and 64.6 %), intermediate among admixed samples (45.1 % and 44.9 %; p = 0.03) and the lowest for Non-native American ancestry (30.1 % and 29.6 %; p = 0.001 and p = 0.0008). CONCLUSIONS These results suggest that individuals with Native American ancestry might have a high risk of chronic liver disorders and cancer. Furthermore, these data not only support the molecular evaluation of ancestry in multi-ethnic population studies, but also suggest that the characterization of these variants in South American populations may be useful for establishing public health policies aimed at high risk ethnic communities.
Collapse
Affiliation(s)
- Ana Cecilia Pontoriero
- Instituto de Ciencias Básicas y Medicina Experimental (ICBME), Hospital Italiano de Buenos Aires, Potosí 4240, C1199ACL, Buenos Aires, Argentina.
| | - Julieta Trinks
- Instituto de Ciencias Básicas y Medicina Experimental (ICBME), Hospital Italiano de Buenos Aires, Potosí 4240, C1199ACL, Buenos Aires, Argentina. .,National Scientific and Technical Research Council (CONICET), Av. Rivadavia 1917, C1033AAJ, Buenos Aires, Argentina.
| | - María Laura Hulaniuk
- Instituto de Ciencias Básicas y Medicina Experimental (ICBME), Hospital Italiano de Buenos Aires, Potosí 4240, C1199ACL, Buenos Aires, Argentina.
| | - Mariela Caputo
- National Scientific and Technical Research Council (CONICET), Av. Rivadavia 1917, C1033AAJ, Buenos Aires, Argentina. .,Servicio de Huellas Digitales Genéticas, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 954, C1113AAD, Buenos Aires, Argentina.
| | - Lisandro Fortuny
- Servicio de Medicina Transfusional, Hospital Italiano de Buenos Aires, Juan D. Perón 4190, C1181ACH, Buenos Aires, Argentina.
| | - Leandro Burgos Pratx
- Servicio de Medicina Transfusional, Hospital Italiano de Buenos Aires, Juan D. Perón 4190, C1181ACH, Buenos Aires, Argentina.
| | - Analía Frías
- Servicio de Medicina Transfusional, Hospital Materno Infantil "Ramón Sardá", Esteban de Luca 2151, C1246ABQ, Buenos Aires, Argentina.
| | - Oscar Torres
- Servicio de Medicina Transfusional, Hospital Materno Infantil "Ramón Sardá", Esteban de Luca 2151, C1246ABQ, Buenos Aires, Argentina.
| | - Félix Nuñez
- Servicio de Medicina Transfusional, Hospital Italiano de Buenos Aires, Juan D. Perón 4190, C1181ACH, Buenos Aires, Argentina.
| | - Adrián Gadano
- Servicio de Hepatología, Hospital Italiano de Buenos Aires, Juan D. Perón 4190, C1181ACH, Buenos Aires, Argentina.
| | - Pablo Argibay
- Instituto de Ciencias Básicas y Medicina Experimental (ICBME), Hospital Italiano de Buenos Aires, Potosí 4240, C1199ACL, Buenos Aires, Argentina. .,National Scientific and Technical Research Council (CONICET), Av. Rivadavia 1917, C1033AAJ, Buenos Aires, Argentina.
| | - Daniel Corach
- National Scientific and Technical Research Council (CONICET), Av. Rivadavia 1917, C1033AAJ, Buenos Aires, Argentina. .,Servicio de Huellas Digitales Genéticas, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 954, C1113AAD, Buenos Aires, Argentina.
| | - Diego Flichman
- National Scientific and Technical Research Council (CONICET), Av. Rivadavia 1917, C1033AAJ, Buenos Aires, Argentina. .,Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 954, C1113AAD, Buenos Aires, Argentina.
| |
Collapse
|
27
|
Gómez-Puerta JA, Barbhaiya M, Guan H, Feldman CH, Alarcón GS, Costenbader KH. Racial/Ethnic variation in all-cause mortality among United States medicaid recipients with systemic lupus erythematosus: a Hispanic and asian paradox. Arthritis Rheumatol 2015; 67:752-60. [PMID: 25590668 DOI: 10.1002/art.38981] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 11/25/2014] [Indexed: 12/12/2022]
Abstract
OBJECTIVE The incidence of systemic lupus erythematosus (SLE) is disproportionately high in nonwhite patients compared with white patients. However, variation in mortality according to race/ethnicity has not been well studied. The aim of this study was to examine all-cause mortality according to race/ethnicity among SLE patients enrolled in Medicaid. METHODS We used Medicaid Analytic eXtract data, with billing claims from 47 US states and Washington, DC, to identify individuals ages 18-65 years who were enrolled in Medicaid for ≥3 months in 2000-2006. Individuals were classified as having SLE if they had ≥3 visits ≥30 days apart with an International Classification of Diseases, Ninth Revision (ICD-9) code for SLE (710.0). Among the individuals with SLE, those with lupus nephritis (LN) were identified by the presence of ≥2 ICD-9 claims for glomerulonephritis, proteinuria, or renal failure. We calculated mortality rates per 1,000 person-years, with 95% confidence intervals (95% CIs), according to race/ethnicity. Multivariable Cox proportional hazards regression models were used to estimate mortality risks, adjusting for age, sex, demographics, and comorbidities. RESULTS Among 42,221 prevalent cases of SLE, 8,191 prevalent cases of LN were identified. Blacks represented 40.1%, whites 38.4%, and Hispanics 15.3%. Overall SLE mortality rates per 1,000 person-years were highest among Native American (27.52), white (20.17), and black (24.13) patients and were lower among Hispanic (7.12) or Asian (5.18) patients. After multivariable adjustment, Hispanic and Asian patients had lower mortality risks (hazard ratio [HR] 0.48 [95% CI 0.40-0.59] and 0.59 [95% CI 0.40-0.86], respectively) compared with whites. Conversely, the risk of death was significantly higher among Native American (HR 1.40 [95% CI 1.04-1.90]) and black (HR 1.21 [95% CI 1.10-1.33]) patients compared with white patients. Among patients with LN, mortality risks were lower in Hispanic and Asian patients compared with white patients. CONCLUSION After accounting for demographic and clinical factors, mortality among Asian and Hispanic Medicaid patients with SLE was lower than that among black, white, or Native American patients.
Collapse
|
28
|
Bryc K, Durand EY, Macpherson JM, Reich D, Mountain JL. The genetic ancestry of African Americans, Latinos, and European Americans across the United States. Am J Hum Genet 2015; 96:37-53. [PMID: 25529636 PMCID: PMC4289685 DOI: 10.1016/j.ajhg.2014.11.010] [Citation(s) in RCA: 431] [Impact Index Per Article: 47.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 11/17/2014] [Indexed: 12/11/2022] Open
Abstract
Over the past 500 years, North America has been the site of ongoing mixing of Native Americans, European settlers, and Africans (brought largely by the trans-Atlantic slave trade), shaping the early history of what became the United States. We studied the genetic ancestry of 5,269 self-described African Americans, 8,663 Latinos, and 148,789 European Americans who are 23andMe customers and show that the legacy of these historical interactions is visible in the genetic ancestry of present-day Americans. We document pervasive mixed ancestry and asymmetrical male and female ancestry contributions in all groups studied. We show that regional ancestry differences reflect historical events, such as early Spanish colonization, waves of immigration from many regions of Europe, and forced relocation of Native Americans within the US. This study sheds light on the fine-scale differences in ancestry within and across the United States and informs our understanding of the relationship between racial and ethnic identities and genetic ancestry.
Collapse
Affiliation(s)
- Katarzyna Bryc
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; 23andMe, Inc., Mountain View, CA 94043, USA.
| | | | | | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | |
Collapse
|
29
|
Mustapic M, Maihofer AX, Mahata M, Chen Y, Baker DG, O'Connor DT, Nievergelt CM. The catecholamine biosynthetic enzyme dopamine β-hydroxylase (DBH): first genome-wide search positions trait-determining variants acting additively in the proximal promoter. Hum Mol Genet 2014; 23:6375-84. [PMID: 24986918 DOI: 10.1093/hmg/ddu332] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Dopamine beta-hydroxylase (DBH) is the biosynthetic enzyme catalyzing formation of norepinephrine. Changes in DBH expression or activity have been implicated in the pathogenesis of cardiovascular and neuropsychiatric disorders. Genetic determination of DBH enzymatic activity and its secretion are only incompletely understood. We began with a genome-wide association search for loci contributing to DBH activity in human plasma. Initially, in a population sample of European ancestry, we identified the proximal DBH promoter as a region harboring three common trait-determining variants (top hit rs1611115, P = 7.2 × 10(-51)). We confirmed their effects on transcription and showed that the three variants each acted additively on gene expression. Results were replicated in a population sample of Native American descent (top hit rs1611115, P = 4.1 × 10(-15)). Jointly, DBH variants accounted for 57% of DBH trait variation. We further identified a genome-wide significant SNP at the LOC338797 locus on chromosome 12 as trans-quantitative trait locus (QTL) (rs4255618, P = 4.62 × 10(-8)). Conditional analyses on DBH identified a third genomic region contributing to DBH variation: a likely cis-QTL adjacent to DBH in SARDH (rs7040170, P = 1.31 × 10(-14)) on chromosome 9q. We conclude that three common SNPs in the DBH promoter act additively to control phenotypic variation in DBH levels, and that two additional novel loci (SARDH and LOC338797) may also contribute to the expression of this catecholamine biosynthetic trait. Identification of DBH variants with strong effects makes it possible to take advantage of Mendelian randomization approaches to test causal effects of this intermediate trait on disease.
Collapse
Affiliation(s)
- Maja Mustapic
- Department of Psychiatry and Department of Medicine, University of California at San Diego, La Jolla, CA 92093, USA, Ruđer Bošković Institute, Zagreb HR-10000, Croatia
| | | | - Manjula Mahata
- Department of Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Yuqing Chen
- Department of Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Dewleen G Baker
- Department of Psychiatry and VA San Diego Healthcare System, VA Center of Excellence for Stress and Mental Health (CESAMH), La Jolla, CA 92161, USA and
| | - Daniel T O'Connor
- Department of Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Caroline M Nievergelt
- Department of Psychiatry and VA San Diego Healthcare System, VA Center of Excellence for Stress and Mental Health (CESAMH), La Jolla, CA 92161, USA and
| |
Collapse
|
30
|
Levin AM, Adrianto I, Datta I, Iannuzzi MC, Trudeau S, McKeigue P, Montgomery CG, Rybicki BA. Performance of HLA allele prediction methods in African Americans for class II genes HLA-DRB1, -DQB1, and -DPB1. BMC Genet 2014; 15:72. [PMID: 24935557 PMCID: PMC4074844 DOI: 10.1186/1471-2156-15-72] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Accepted: 06/11/2014] [Indexed: 12/23/2022] Open
Abstract
Background The expense of human leukocyte antigen (HLA) allele genotyping has motivated the development of imputation methods that use dense single nucleotide polymorphism (SNP) genotype data and the region’s haplotype structure, but the performance of these methods in admixed populations (such as African Americans) has not been adequately evaluated. We compared genotype-based—derived from both genome-wide genotyping and targeted sequencing—imputation results to existing allele data for HLA–DRB1, −DQB1, and –DPB1. Results In European Americans, the newly-developed HLA Genotype Imputation with Attribute Bagging (HIBAG) method outperformed HLA*IMP:02. In African Americans, HLA*IMP:02 performed marginally better than HIBAG pre-built models, but HIBAG models constructed using a portion of our African American sample with both SNP genotyping and four-digit HLA class II allele typing had consistently higher accuracy than HLA*IMP:02. However, HIBAG was significantly less accurate in individuals heterozygous for local ancestry (p ≤0.04). Accuracy improved in models with equal numbers of African and European chromosomes. Variants added by targeted sequencing and SNP imputation further improved both imputation accuracy and the proportion of high quality calls. Conclusion Combining the HIBAG approach with local ancestry and dense variant data can produce highly-accurate HLA class II allele imputation in African Americans.
Collapse
Affiliation(s)
- Albert M Levin
- Department of Public Health Sciences, Henry Ford Health System, 1 Ford Place, 3E, 48202 Detroit, MI, USA.
| | | | | | | | | | | | | | | |
Collapse
|
31
|
Nelson BD, Bishop JR, Sarapas C, Kittles RA, Shankman SA. Asians demonstrate reduced sensitivity to unpredictable threat: a preliminary startle investigation using genetic ancestry in a multiethnic sample. ACTA ACUST UNITED AC 2014; 14:615-23. [PMID: 24708496 DOI: 10.1037/a0035776] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Research has indicated that individuals of Asian descent, relative to other racial groups, demonstrate reduced emotional responding and lower prevalence rates of several anxiety disorders. It is unclear though whether these group differences extend to biomarkers of anxiety disorders and whether genetic differences play a role. This study compared self-identified Caucasian, Latino, and Asian persons (total N = 174) on startle response during a baseline period and while anticipating unpredictable threat-a putative biomarker for certain anxiety disorders--as well as predictable threat. In addition, the association between genetic ancestry and startle response was examined within each racial group to determine potential genetic influences on responding. For the baseline period, Asian participants exhibited a smaller startle response relative to Caucasian and Latino participants, who did not differ. Within each racial group, genetic ancestry was associated with baseline startle. Furthermore, genetic ancestry mediated racial group differences in baseline startle. For the threat conditions, a Race × Condition interaction indicated that Asian participants exhibited reduced startle potentiation to unpredictable, but not predicable, threat relative to Caucasian and Latino participants, who did not differ. However, genetic ancestry was not associated with threat-potentiated startle in any racial group. This study adds to the growing literature on racial differences in emotional responding and provides preliminary evidence suggesting that genetic ancestry may play an important role. Moreover, reduced sensitivity to unpredictable threat may reflect a mechanism for why individuals of Asian descent are at less risk for particular anxiety disorders relative to other racial groups.
Collapse
|
32
|
Jablonski NG, Chaplin G. The evolution of skin pigmentation and hair texture in people of African ancestry. Dermatol Clin 2014; 32:113-21. [PMID: 24679998 DOI: 10.1016/j.det.2013.11.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Our species, Homo sapiens, evolved in Africa, and humanity's highest levels of genetic diversity are maintained there today. Underlying genetic diversity combined with the great range of solar regimes and climatic conditions found in Africa has contributed to a wide range of human integumentary phenotypes within the continent. Millions of Africans have moved, voluntarily and involuntarily, to other continents in the past 2000 years, and the range of integumentary phenotypes among admixed African diaspora populations is enormous. In this contribution, we do not catalog this variation, but provide basic evolutionary background as to how it developed in the first place.
Collapse
Affiliation(s)
- Nina G Jablonski
- Department of Anthropology, The Pennsylvania State University, 409 Carpenter Building, University Park, PA 16802, USA.
| | - George Chaplin
- Department of Anthropology, The Pennsylvania State University, 409 Carpenter Building, University Park, PA 16802, USA; Department of Geography, The Pennsylvania State University, 409 Carpenter Building, University Park, PA 16802, USA
| |
Collapse
|
33
|
Norden-Krichmar TM, Gizer IR, Libiger O, Wilhelmsen KC, Ehlers CL, Schork NJ. Correlation analysis of genetic admixture and social identification with body mass index in a Native American community. Am J Hum Biol 2014; 26:347-60. [PMID: 24757035 DOI: 10.1002/ajhb.22521] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 01/16/2014] [Accepted: 01/21/2014] [Indexed: 12/30/2022] Open
Abstract
OBJECTIVES Body mass index (BMI) is a well-known measure of obesity with a multitude of genetic and non-genetic determinants. Identifying the underlying factors associated with BMI is difficult because of its multifactorial etiology that varies as a function of geoethnic background and socioeconomic setting. Thus, we pursued a study exploring the influence of the degree of Native American admixture on BMI (as well as weight and height individually) in a community sample of Native Americans (n = 846) while accommodating a variety of socioeconomic and cultural factors. METHODS Participants' degree of Native American (NA) ancestry was estimated using a genome-wide panel of markers. The participants also completed an extensive survey of cultural and social identity measures: the Indian Culture Scale (ICS) and the Orthogonal Cultural Identification Scale (OCIS). Multiple linear regression was used to examine the relation between these measures and BMI. RESULTS Our results suggest that BMI is correlated positively with the proportion of NA ancestry. Age was also significantly associated with BMI, while gender and socioeconomic measures (education and income) were not. For the two cultural identity measures, the ICS showed a positive correlation with BMI, while OCIS was not associated with BMI. CONCLUSIONS Taken together, these results suggest that genetic and cultural environmental factors, rather than socioeconomic factors, account for a substantial proportion of variation in BMI in this population. Further, significant correlations between degree of NA ancestry and BMI suggest that admixture mapping may be appropriate to identify loci associated with BMI in this population.
Collapse
Affiliation(s)
- Trina M Norden-Krichmar
- Scripps Translational Science Institute and The Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California, 92037
| | | | | | | | | | | |
Collapse
|
34
|
Developing a novel panel of genome-wide ancestry informative markers for bio-geographical ancestry estimates. Forensic Sci Int Genet 2014; 8:187-94. [DOI: 10.1016/j.fsigen.2013.09.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Revised: 09/06/2013] [Accepted: 09/09/2013] [Indexed: 01/13/2023]
|
35
|
Campos-Sánchez R, Raventós H, Barrantes R. Ancestry Informative Markers Clarify the Regional Admixture Variation in the Costa Rican Population. Hum Biol 2013; 85:721-40. [DOI: 10.3378/027.085.0505] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/29/2013] [Indexed: 11/05/2022]
|
36
|
Libiger O, Schork NJ. A Method for Inferring an Individual's Genetic Ancestry and Degree of Admixture Associated with Six Major Continental Populations. Front Genet 2013; 3:322. [PMID: 23335941 PMCID: PMC3543981 DOI: 10.3389/fgene.2012.00322] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Accepted: 12/24/2012] [Indexed: 01/27/2023] Open
Abstract
The determination of the ancestry and genetic backgrounds of the subjects in genetic and general epidemiology studies is a crucial component in the analysis of relevant outcomes or associations. Although there are many methods for differentiating ancestral subgroups among individuals based on genetic markers only a few of these methods provide actual estimates of the fraction of an individual’s genome that is likely to be associated with different ancestral populations. We propose a method for assigning ancestry that works in stages to refine estimates of ancestral population contributions to individual genomes. The method leverages genotype data in the public domain obtained from individuals with known ancestries. Although we showcase the method in the assessment of ancestral genome proportions leveraging largely continental populations, the strategy can be used for assessing within-continent or more subtle ancestral origins with the appropriate data.
Collapse
Affiliation(s)
- Ondrej Libiger
- Department of Molecular and Experimental Medicine, The Scripps Research Institute and the Scripps Translational Science Institute La Jolla, CA, USA
| | | |
Collapse
|
37
|
Henn BM, Botigué LR, Gravel S, Wang W, Brisbin A, Byrnes JK, Fadhlaoui-Zid K, Zalloua PA, Moreno-Estrada A, Bertranpetit J, Bustamante CD, Comas D. Genomic ancestry of North Africans supports back-to-Africa migrations. PLoS Genet 2012; 8:e1002397. [PMID: 22253600 PMCID: PMC3257290 DOI: 10.1371/journal.pgen.1002397] [Citation(s) in RCA: 219] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2011] [Accepted: 10/11/2011] [Indexed: 01/20/2023] Open
Abstract
North African populations are distinct from sub-Saharan Africans based on cultural, linguistic, and phenotypic attributes; however, the time and the extent of genetic divergence between populations north and south of the Sahara remain poorly understood. Here, we interrogate the multilayered history of North Africa by characterizing the effect of hypothesized migrations from the Near East, Europe, and sub-Saharan Africa on current genetic diversity. We present dense, genome-wide SNP genotyping array data (730,000 sites) from seven North African populations, spanning from Egypt to Morocco, and one Spanish population. We identify a gradient of likely autochthonous Maghrebi ancestry that increases from east to west across northern Africa; this ancestry is likely derived from “back-to-Africa” gene flow more than 12,000 years ago (ya), prior to the Holocene. The indigenous North African ancestry is more frequent in populations with historical Berber ethnicity. In most North African populations we also see substantial shared ancestry with the Near East, and to a lesser extent sub-Saharan Africa and Europe. To estimate the time of migration from sub-Saharan populations into North Africa, we implement a maximum likelihood dating method based on the distribution of migrant tracts. In order to first identify migrant tracts, we assign local ancestry to haplotypes using a novel, principal component-based analysis of three ancestral populations. We estimate that a migration of western African origin into Morocco began about 40 generations ago (approximately 1,200 ya); a migration of individuals with Nilotic ancestry into Egypt occurred about 25 generations ago (approximately 750 ya). Our genomic data reveal an extraordinarily complex history of migrations, involving at least five ancestral populations, into North Africa. Proposed migrations between North Africa and neighboring regions have included Paleolithic gene flow from the Near East, an Arabic migration across the whole of North Africa 1,400 years ago (ya), and trans-Saharan transport of slaves from sub-Saharan Africa. Historical records, archaeology, and mitochondrial and Y-chromosome DNA have been marshaled in support of one theory or another, but there is little consensus regarding the overall genetic background of North African populations or their origin and expansion. We characterize the patterns of genetic variation in North Africa using ∼730,000 single nucleotide polymorphisms from across the genome for seven populations. We observe two distinct, opposite gradients of ancestry: an east-to-west increase in likely autochthonous North African ancestry and an east-to-west decrease in likely Near Eastern Arabic ancestry. The indigenous North African ancestry may have been more common in Berber populations and appears most closely related to populations outside of Africa, but divergence between Maghrebi peoples and Near Eastern/Europeans likely precedes the Holocene (>12,000 ya). We also find significant signatures of sub-Saharan African ancestry that vary substantially among populations. These sub-Saharan ancestries appear to be a recent introduction into North African populations, dating to about 1,200 years ago in southern Morocco and about 750 years ago into Egypt, possibly reflecting the patterns of the trans-Saharan slave trade that occurred during this period.
Collapse
Affiliation(s)
- Brenna M Henn
- Department of Genetics, Stanford University, Stanford, CA, USA
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
38
|
Gomez-Rubio P, Klimentidis YC, Cantu-Soto E, Meza-Montenegro MM, Billheimer D, Lu Z, Chen Z, Klimecki WT. Indigenous American ancestry is associated with arsenic methylation efficiency in an admixed population of northwest Mexico. JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH. PART A 2012; 75:36-49. [PMID: 22047162 PMCID: PMC3572940 DOI: 10.1080/15287394.2011.615107] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Many studies provide evidence relating lower human arsenic (As) methylation efficiency, represented by high percent urinary monomethylarsonic acid (MMA(V)), with several As-induced diseases, possibly due to the fact that MMA(V) serves as a proxy for MMA(III), the most toxic As metabolite. Some epidemiological studies suggested that indigenous Americans (AME) methylate As more efficiently; however, data supporting this have been equivocal. The aim of this study was to characterize the association between AME ancestry and As methylation efficiency using a panel of ancestry informative genetic markers to determine individual ancestry proportions in an admixed population (composed of two or more isolated ancestral populations) of 746 individuals environmentally exposed to As in northwest Mexico. Total urinary As (TAs) mean and range were 170.4 and 2.3-1053.5 μg/L, while percent AME (%AME) mean and range were 72.4 and 23-100. Adjusted (gender, age, AS3MT 7388/M287T haplotypes, body mass index [BMI], and TAs) multiple regression model showed that higher AME ancestry is significantly associated with lower percentage of urinary As excreted as MMA(V) (%uMMA) in this population (p < .01). Data also demonstrated a significant interaction between BMI and gender, indicating negative association between BMI and %uMMA, stronger in women than men (p < .01). Moreover, age and the AS3MT variants 7388 (intronic) and M287T (nonsynonymous) were also significantly associated with As methylation efficiency (p < .01). This study highlights the importance of BMI and indigenous American ancestry in some of the observed variability in As methylation efficiency, underscoring the need to be considered in epidemiology studies, particularly those carried out in admixed populations.
Collapse
Affiliation(s)
- Paulina Gomez-Rubio
- Department of Pharmacology and Toxicology, University of Arizona, Tucson, Arizona
| | - Yann C. Klimentidis
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, Alabama
| | - Ernesto Cantu-Soto
- Department of Environmental Sciences, Instituto Tecnologico de Sonora, Ciudad Obregon, Sonora, Mexico
| | - Maria M. Meza-Montenegro
- Department of Environmental Sciences, Instituto Tecnologico de Sonora, Ciudad Obregon, Sonora, Mexico
| | - Dean Billheimer
- Department of Agricultural and Biosystems Engineering, University of Arizona, Tucson, Arizona
| | - Zhenqiang Lu
- Arizona Statistical Consulting Laboratory, University of Arizona, Tucson, Arizona
| | - Zhao Chen
- Division of Epidemiology and Biostatistics, Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson, Arizona
| | - Walter T. Klimecki
- Department of Pharmacology and Toxicology, University of Arizona, Tucson, Arizona
- To whom correspondence should be addressed: Walter Klimecki, DVM, Ph.D., 1657 E Helen St, RM319, Thomas Keating Bldg. Tucson, AZ 85721, Tel. 520-626-7470, Fax. 520-626-2466,
| |
Collapse
|
39
|
Quillen EE, Bauchet M, Bigham AW, Delgado-Burbano ME, Faust FX, Klimentidis YC, Mao X, Stoneking M, Shriver MD. OPRM1 and EGFR contribute to skin pigmentation differences between Indigenous Americans and Europeans. Hum Genet 2011; 131:1073-80. [DOI: 10.1007/s00439-011-1135-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Accepted: 12/14/2011] [Indexed: 12/26/2022]
|
40
|
Brehm JM, Hagiwara K, Tesfaigzi Y, Bruse S, Mariani TJ, Bhattacharya S, Boutaoui N, Ziniti JP, Soto-Quiros ME, Avila L, Cho MH, Himes B, Litonjua AA, Jacobson F, Bakke P, Gulsvik A, Anderson WH, Lomas DA, Forno E, Datta S, Silverman EK, Celedón JC. Identification of FGF7 as a novel susceptibility locus for chronic obstructive pulmonary disease. Thorax 2011; 66:1085-90. [PMID: 21921092 PMCID: PMC3348619 DOI: 10.1136/thoraxjnl-2011-200017] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
RATIONALE Traditional genome-wide association studies (GWASs) of large cohorts of subjects with chronic obstructive pulmonary disease (COPD) have successfully identified novel candidate genes, but several other plausible loci do not meet strict criteria for genome-wide significance after correction for multiple testing. OBJECTIVES The authors hypothesise that by applying unbiased weights derived from unique populations we can identify additional COPD susceptibility loci. Methods The authors performed a homozygosity haplotype analysis on a group of subjects with and without COPD to identify regions of conserved homozygosity haplotype (RCHHs). Weights were constructed based on the frequency of these RCHHs in case versus controls, and used to adjust the p values from a large collaborative GWAS of COPD. RESULTS The authors identified 2318 RCHHs, of which 576 were significantly (p<0.05) over-represented in cases. After applying the weights constructed from these regions to a collaborative GWAS of COPD, the authors identified two single nucleotide polymorphisms (SNPs) in a novel gene (fibroblast growth factor-7 (FGF7)) that gained genome-wide significance by the false discovery rate method. In a follow-up analysis, both SNPs (rs12591300 and rs4480740) were significantly associated with COPD in an independent population (combined p values of 7.9E-7 and 2.8E-6, respectively). In another independent population, increased lung tissue FGF7 expression was associated with worse measures of lung function. CONCLUSION Weights constructed from a homozygosity haplotype analysis of an isolated population successfully identify novel genetic associations from a GWAS on a separate population. This method can be used to identify promising candidate genes that fail to meet strict correction for multiple testing.
Collapse
Affiliation(s)
- John M. Brehm
- Division of Pediatric Pulmonary Medicine, Allergy, and Immunology, Children’s Hospital of Pittsburgh of UPMC, Pittsburgh, PA
- Channing Laboratory, Brigham and Women’s Hospital, Boston, Massachusetts
- Division of Pulmonary/Critical Care Medicine, Brigham and Women’s Hospital, Boston, Massachusetts
- Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Koichi Hagiwara
- Saitama Medical University Hospital and Institute, Saitama, Japan
| | - Y Tesfaigzi
- Lovelace Respiratory Research Institute, Albuquerque, NM
| | - S Bruse
- Lovelace Respiratory Research Institute, Albuquerque, NM
| | | | | | - Nadia Boutaoui
- Division of Pediatric Pulmonary Medicine, Allergy, and Immunology, Children’s Hospital of Pittsburgh of UPMC, Pittsburgh, PA
| | - John P. Ziniti
- Channing Laboratory, Brigham and Women’s Hospital, Boston, Massachusetts
| | | | - Lydiana Avila
- Division of Pediatric Pulmonology, Hospital Nacional de Niños, San José, Costa Rica
| | - Michael H. Cho
- Channing Laboratory, Brigham and Women’s Hospital, Boston, Massachusetts
- Division of Pulmonary/Critical Care Medicine, Brigham and Women’s Hospital, Boston, Massachusetts
- Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts
| | - Blanca Himes
- Channing Laboratory, Brigham and Women’s Hospital, Boston, Massachusetts
| | - Augusto A. Litonjua
- Channing Laboratory, Brigham and Women’s Hospital, Boston, Massachusetts
- Division of Pulmonary/Critical Care Medicine, Brigham and Women’s Hospital, Boston, Massachusetts
- Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Francine Jacobson
- Department of Radiology, Brigham and Women’s Hospital, Boston, Massachusetts
| | - Per Bakke
- Haukeland University Hospital and Institute of Medicine, University of Bergen, Bergen, Norway
| | - Amund Gulsvik
- Haukeland University Hospital and Institute of Medicine, University of Bergen, Bergen, Norway
| | - Wayne H Anderson
- GlaxoSmithKline Research and Development, Research Triangle Park, North Carolina, USA
| | - David A. Lomas
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Erick Forno
- Division of Pediatric Pulmonology, Dept. of Pediatrics, University of Miami, Miami, FL
| | - Soma Datta
- Channing Laboratory, Brigham and Women’s Hospital, Boston, Massachusetts
| | - Edwin K. Silverman
- Channing Laboratory, Brigham and Women’s Hospital, Boston, Massachusetts
- Division of Pulmonary/Critical Care Medicine, Brigham and Women’s Hospital, Boston, Massachusetts
- Center for Genomic Medicine, Brigham and Women’s Hospital, Boston, Massachusetts
- Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts
| | - Juan C. Celedón
- Division of Pediatric Pulmonary Medicine, Allergy, and Immunology, Children’s Hospital of Pittsburgh of UPMC, Pittsburgh, PA
- Channing Laboratory, Brigham and Women’s Hospital, Boston, Massachusetts
- Division of Pulmonary/Critical Care Medicine, Brigham and Women’s Hospital, Boston, Massachusetts
- Center for Genomic Medicine, Brigham and Women’s Hospital, Boston, Massachusetts
- Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| |
Collapse
|
41
|
Leite TKM, Fonseca RMC, de França NM, Parra EJ, Pereira RW. Genomic ancestry, self-reported "color" and quantitative measures of skin pigmentation in Brazilian admixed siblings. PLoS One 2011; 6:e27162. [PMID: 22073278 PMCID: PMC3206941 DOI: 10.1371/journal.pone.0027162] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Accepted: 10/11/2011] [Indexed: 01/03/2023] Open
Abstract
A current concern in genetic epidemiology studies in admixed populations is that population stratification can lead to spurious results. The Brazilian census classifies individuals according to self-reported “color”, but several studies have demonstrated that stratifying according to “color” is not a useful strategy to control for population structure, due to the dissociation between self-reported “color” and genomic ancestry. We report the results of a study in a group of Brazilian siblings in which we measured skin pigmentation using a reflectometer, and estimated genomic ancestry using 21 Ancestry Informative Markers (AIMs). Self-reported “color”, according to the Brazilian census, was also available for each participant. This made it possible to evaluate the relationship between self-reported “color” and skin pigmentation, self-reported “color” and genomic ancestry, and skin pigmentation and genomic ancestry. We observed that, although there were significant differences between the three “color” groups in genomic ancestry and skin pigmentation, there was considerable dispersion within each group and substantial overlap between groups. We also saw that there was no good agreement between the “color” categories reported by each member of the sibling pair: 30 out of 86 sibling pairs reported different “color”, and in some cases, the sibling reporting the darker “color” category had lighter skin pigmentation. Socioeconomic status was significantly associated with self-reported “color” and genomic ancestry in this sample. This and other studies show that subjective classifications based on self-reported “color”, such as the one that is used in the Brazilian census, are inadequate to describe the population structure present in recently admixed populations. Finally, we observed that one of the AIMs included in the panel (rs1426654), which is located in the known pigmentation gene SLC24A5, was strongly associated with skin pigmentation in this sample.
Collapse
Affiliation(s)
- Tailce K. M. Leite
- Programa de Pós-Graduação em Educação Física, Universidade Católica de Brasília, Brasília, Distrito Federal, Brazil
| | - Rômulo M. C. Fonseca
- Programa de Pós-Graduação em Educação Física, Universidade Católica de Brasília, Brasília, Distrito Federal, Brazil
| | - Nanci M. de França
- Programa de Pós-Graduação em Educação Física, Universidade Católica de Brasília, Brasília, Distrito Federal, Brazil
| | - Esteban J. Parra
- Department of Anthropology, University of Toronto at Mississauga, Mississauga, Ontario, Canada
| | - Rinaldo W. Pereira
- Programa de Pós-Graduação em Educação Física, Universidade Católica de Brasília, Brasília, Distrito Federal, Brazil
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Distrito Federal, Brazil
- * E-mail:
| |
Collapse
|
42
|
Kumar R, Tsai HJ, Hong X, Gignoux C, Pearson C, Ortiz K, Fu M, Pongracic JA, Burchard EG, Bauchner H, Wang X. African ancestry, early life exposures, and respiratory morbidity in early childhood. Clin Exp Allergy 2011; 42:265-74. [PMID: 22093077 DOI: 10.1111/j.1365-2222.2011.03873.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2011] [Revised: 08/19/2011] [Accepted: 08/23/2011] [Indexed: 12/24/2022]
Abstract
BACKGROUND Racial disparities persist in early childhood wheezing and cannot be completely explained by known risk factors. OBJECTIVE To evaluate the associations of genetic ancestry and self-identified race with early childhood recurrent wheezing, accounting for socio-economic status (SES) and early life exposures. METHODS We studied 1034 children in an urban, multi-racial, prospective birth cohort. Multivariate logistic regression was used to evaluate the association of genetic ancestry as opposed to self-identified race with recurrent wheezing (>3 episodes). Sequential models accounted for demographic, socio-economic factors and early life risk factors. Genetic ancestry, estimated using 150 ancestry informative markers, was expressed in deciles. RESULTS Approximately 6.1% of subjects (mean age 3.1 years) experienced recurrent wheezing. After accounting for SES and demographic factors, African ancestry (OR: 1.16, 95% CI: 1.02-1.31) was significantly associated with recurrent wheezing. By self-reported race, hispanic subjects had a borderline decrease in risk of wheeze compared with African Americans (OR: 0.44, 95% CI: 0.19-1.00), whereas white subjects (OR: 0.46, 95% CI: 0.14-1.57) did not have. After further adjustment for known confounders and early life exposures, both African (OR: 1.19, 95% CI: 1.05-1.34) and European ancestry (OR: 0.84, 95% CI: 0.74-0.94) retained a significant association with recurrent wheezing, as compared with self-identified race (OR(whites) : 0.31, 95% CI: 0.09-1.14; OR(hispanic) : 0.47, 95% CI: 0.20-1.08). There were no significant interactions between ancestry and early life factors on recurrent wheezing. CONCLUSIONS AND CLINICAL RELEVANCE In contrast to self-identified race, African ancestry remained a significant, independent predictor of early childhood wheezing after accounting for early life and other known risk factors associated with lung function changes and asthma. Genetic ancestry may be a powerful way to evaluate wheezing disparities and a proxy for differentially distributed genetic and early life risk factors associated with childhood recurrent wheezing.
Collapse
Affiliation(s)
- R Kumar
- Division of Allergy and Immunology, Children's Memorial Hospital, Chicago, IL 60614, USA.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
43
|
Teruel BM, Rodríguez JJL, McKeigue P, Mesa T TC, Fuentes E, Cepero A AV, Hernandez MAG, Copeland J R M JRM, Ferri CP, Prince MJ. Interactions between genetic admixture, ethnic identity, APOE genotype and dementia prevalence in an admixed Cuban sample; a cross-sectional population survey and nested case-control study. BMC MEDICAL GENETICS 2011; 12:43. [PMID: 21435264 PMCID: PMC3079615 DOI: 10.1186/1471-2350-12-43] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2010] [Accepted: 03/24/2011] [Indexed: 01/27/2023]
Abstract
Background The prevalence and incidence of dementia are low in Nigeria, but high among African-Americans. In these populations there is a high frequency of the risk-conferring APOE-e4 allele, but the risk ratio is less than in Europeans. In an admixed population of older Cubans we explored the effects of ethnic identity and genetic admixture on APOE genotype, its association with dementia, and dementia prevalence. Methods A cross-sectional catchment area survey of 2928 residents aged 65 and over, with a nested case-control study of individual admixture. Dementia diagnosis was established using 10/66 Dementia and DSM-IV criteria. APOE genotype was determined in 2520 participants, and genetic admixture in 235 dementia cases and 349 controls. Results Mean African admixture proportions were 5.8% for 'white', 28.6% for 'mixed' and 49.6% for 'black' ethnic identities. All three groups were substantially admixed with considerable overlap. African admixture was linearly related to number of APOE-e4 alleles. One or more APOE-e4 alleles was associated with dementia in 'white' and 'black' but not 'mixed' groups but neither this, nor the interaction between APOE-e4 and African admixture (PR 0.52, 95% CI 0.13-2.08) were statistically significant. Neither ethnic identity nor African admixture was associated with dementia prevalence when assessed separately. However, considering their joint effects African versus European admixture was independently associated with a higher prevalence, and 'mixed' or 'black' identity with a lower prevalence of dementia. Conclusions APOE genotype is strongly associated with ancestry. Larger studies are needed to confirm whether the concentration of the high-risk allele in those with African ancestry is offset by an attenuation of its effect. Counter to our hypothesis, African admixture may be associated with higher risk of dementia. Although strongly correlated, effects of admixture and ethnic identity should be distinguished when assessing genetic and environmental contributions to disease risk in mixed ancestry populations.
Collapse
|
44
|
Sanders AR, Levinson DF, Duan J, Dennis JM, Li R, Kendler KS, Rice JP, Shi J, Mowry BJ, Amin F, Silverman JM, Buccola NG, Byerley WF, Black DW, Freedman R, Cloninger CR, Gejman PV. The Internet-based MGS2 control sample: self report of mental illness. Am J Psychiatry 2010; 167:854-65. [PMID: 20516154 PMCID: PMC6385597 DOI: 10.1176/appi.ajp.2010.09071050] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
OBJECTIVE The Molecular Genetics of Schizophrenia (MGS2) project recruited an adult control sample of non-Hispanic European-ancestry (N=3,364) and African American (N=1,301) subjects. METHOD Subjects gave consent to deposit phenotypic data and blood samples into a repository for general research use, with full anonymization of the sample. The authors compared the control sample with population census data for demographic data and with previous population surveys for anthropometrics and prevalences of psychiatric disorders as estimated by an Internet-administered questionnaire. RESULTS The full MGS2 control sample includes 4,665 subjects (European-ancestry: N=3,364; African American: N=1,301), of whom 3,626 were included in the MGS2 genome-wide association study (GWAS). The sample is generally demographically representative of the U.S. population, except for being older and more female, educated, and affluent, although all strata are represented. Self-reported ancestry was consistent with genotypic and census data. Lifetime prevalences for depressive, anxiety, and substance use diagnoses were higher than in previous population-based surveys, probably due to use of an abbreviated self-report instrument. However, patterns such as sex ratios, comorbidity, and demographic associations were consistent with previous reports. DNA quality for the Internet collected/evaluated control sample was comparable to that of the face-to-face case sample. CONCLUSIONS The Internet-based methods facilitated the rapid collection of large and anonymized non-Hispanic European-ancestry and African American control samples that have been validated as being generally representative for many aspects of demography, ancestry, and morbidity. Utilization of clinical screening data shared with the scientific community may permit investigators to select appropriate controls for some studies.
Collapse
Affiliation(s)
- Alan R Sanders
- Center for Psychiatric Genetics, Department of Psychiatry and Behavioral Sciences, NorthShore University HealthSystem, Evanston, Ill 60201-3137, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
45
|
Chernin G, Heeringa SF, Vega-Warner V, Schoeb DS, Nürnberg P, Hildebrandt F. Adequate use of allele frequencies in Hispanics--a problem elucidated in nephrotic syndrome. Pediatr Nephrol 2010; 25:261-6. [PMID: 19876656 PMCID: PMC2899680 DOI: 10.1007/s00467-009-1315-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/22/2009] [Revised: 08/13/2009] [Accepted: 08/13/2009] [Indexed: 01/19/2023]
Abstract
Previous studies in children with focal segmental glomerulosclerosis (FSGS) and nephrotic syndrome (NS) in the USA have revealed inter-ethnic differences in their clinical presentation and outcome. However, ethnicity was based on self-identification rather than on molecular genetic data. Here, we show that genetic heterogeneity exists in self-identified Hispanic (Spanish-American) patients with steroid-resistant nephrotic syndrome (SRNS), as patients may be either of Caucasian or Mesoamerican (Native-American) genetic background. Twenty-one self-identified Hispanic patients with SRNS from 18 families were initially evaluated for mutations in the NPHS2 and WT1 genes. All patients resided and were cared for in the USA. We performed a total genome search for linkage in all Hispanic patients using 250K single nucleotide polymorphism microarrays, comparing Caucasian with Mesoamerican allele frequencies to determine regions of homozygosity by descent and to establish the correct allele frequency for each family. We found that only ten families (56%) of the 18 self-identified Hispanic families are genetically of Mesoamerican descent, whereas the other eight families (44%) are of Caucasian descent. Due to the small number of families examined, we were unable to draw any conclusion on the prevalence of NPHS2 and WT1 in this ethnic group, but the data do suggest that self-identification of ethnicity in Hispanic-American patients is not an adequate basis for genetic studies, as this cohort may represent not only patients of Mesoamerican origin but also patients of Caucasian origin. Thus, one needs to critically review previous studies of FSGS/SRNS patients that involved Hispanic patients as a group. Future larger studies may employ a total genome search for linkage to test self-identified Hispanic ethnicity for true Mesoamerican versus Caucasian ethnicity in order to generate valid genetic data.
Collapse
Affiliation(s)
- Gil Chernin
- Departments of Pediatrics and of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Saskia F. Heeringa
- Departments of Pediatrics and of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Virginia Vega-Warner
- Departments of Pediatrics and of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Dominik S. Schoeb
- Departments of Pediatrics and of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Peter Nürnberg
- Center for Genomics (CCG) and Institute for Genetics, Universität zu Köln, Cologne, Germany
| | - Friedhelm Hildebrandt
- Departments of Pediatrics and of Human Genetics, University of Michigan, Ann Arbor, MI, USA. Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA. University of Michigan Health System, 8220C MSRB III, 1150 West Medical Center Drive, Ann Arbor, MI 48109-5646, USA
| |
Collapse
|
46
|
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.
Collapse
Affiliation(s)
- M Via
- Institute for Human Genetics, University of California, San Francisco, CA 94143-2911, USA.
| | | | | |
Collapse
|
47
|
Looker AC, Melton LJ, Harris TB, Borrud LG, Shepherd JA. Prevalence and trends in low femur bone density among older US adults: NHANES 2005-2006 compared with NHANES III. J Bone Miner Res 2010; 25:64-71. [PMID: 19580459 PMCID: PMC3312738 DOI: 10.1359/jbmr.090706] [Citation(s) in RCA: 183] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2009] [Accepted: 05/14/2009] [Indexed: 01/13/2023]
Abstract
Hip fracture incidence appears to be declining in the United States, but changes in bone mineral density (BMD) of the population have not been evaluated. We used femur BMD data from the National Health and Nutrition Examination Survey (NHANES) 2005-2006 to estimate the prevalence of low femoral BMD in adults age 50 years and older and compared it with estimates from NHANES III (1988-1994). Dual-energy X-ray absorptiometry systems (pencil-beam geometry in NHANES III, fan-beam geometry in NHANES 2005-2006) were used to measure femur BMD, and World Health Organization (WHO) definitions of low BMD were used to categorize skeletal status. In 2005-2006, 49% of older US women had osteopenia and 10% had osteoporosis at the femur neck. In men, 30% had femur neck osteopenia and 2% had femur neck osteoporosis. An estimated 5.3 million older men and women had osteoporosis at the femur neck, and 34.5 million more had osteopenia in 2005-2006. When compared with NHANES III, the age-adjusted prevalence of femur neck osteoporosis in NHANES 2005-2006 was lower in men (by 3 percentage units) and women (by 7 percentage units) overall and among non-Hispanic whites. Changes in body mass index or osteoporosis medication use between surveys did not fully explain the decline in osteoporosis. Owing to the increase in the number of older adults in the US population, however, more older adults had low femur neck BMD (osteoporosis + osteopenia) in 2005-2006 than in 1988-1994. Thus, despite the decline in prevalence, the estimated number of affected older adults in 2005-2006 remained high.
Collapse
Affiliation(s)
- Anne C Looker
- National Center for Health Statistics, Centers for Disease Control and Prevention, Hyattsville, MD 20782, USA.
| | | | | | | | | |
Collapse
|
48
|
Ducci F, Roy A, Shen PH, Yuan Q, Yuan NP, Hodgkinson CA, Goldman LR, Goldman D. Association of substance use disorders with childhood trauma but not African genetic heritage in an African American cohort. Am J Psychiatry 2009; 166:1031-40. [PMID: 19605534 PMCID: PMC2768270 DOI: 10.1176/appi.ajp.2009.08071068] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
OBJECTIVE Genetic variation influences differential vulnerability to addiction within populations. However, it remains unclear whether differences in frequencies of vulnerability alleles contribute to disparities between populations and to what extent ancestry correlates with differential exposure to environmental risk factors, including poverty and trauma. METHOD The authors used 186 ancestry-informative markers to measure African ancestry in 407 addicts and 457 comparison subjects self-identified as African Americans. The reference group was 1,051 individuals from the Human Genome Diversity Cell Line Panel, which includes 51 diverse populations representing most worldwide genetic diversity. RESULTS African Americans varied in degrees of African, European, Middle Eastern, and Central Asian genetic heritage. The overall level of African ancestry was actually smaller among cocaine, opiate, and alcohol addicts (proportion=0.76-0.78) than nonaddicted African American comparison subjects (proportion=0.81). African ancestry was associated with living in impoverished neighborhoods, a factor previously associated with risk. There was no association between African ancestry and exposure to childhood abuse or neglect, a factor that strongly predicted all types of addictions. CONCLUSIONS These results suggest that African genetic heritage does not increase the likelihood of genetic risk for addictions. They highlight the complex interrelation between genetic ancestry and social, economic, and environmental conditions and the strong relation of those factors to addiction. Studies of epidemiological samples characterized for genetic ancestry and social, psychological, demographic, economic, cultural, and historical factors are needed to better disentangle the effects of genetic and environmental factors underlying interpopulation differences in vulnerability to addiction and other health disparities.
Collapse
Affiliation(s)
- Francesca Ducci
- Division of Psychological Medicine, PO63, Institute of Psychiatry, De Crespigny Park, London SE5 8AF, UK.
| | | | | | | | | | | | | | | |
Collapse
|
49
|
Foster MW. Looking for race in all the wrong places: analyzing the lack of productivity in the ongoing debate about race and genetics. Hum Genet 2009; 126:355-62. [DOI: 10.1007/s00439-009-0674-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2009] [Accepted: 04/17/2009] [Indexed: 12/25/2022]
|
50
|
Klimentidis YC, Shriver MD. Estimating genetic ancestry proportions from faces. PLoS One 2009; 4:e4460. [PMID: 19223962 PMCID: PMC2635957 DOI: 10.1371/journal.pone.0004460] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2008] [Accepted: 12/10/2008] [Indexed: 01/09/2023] Open
Abstract
Ethnicity can be a means by which people identify themselves and others. This type of identification mediates many kinds of social interactions and may reflect adaptations to a long history of group living in humans. Recent admixture in the US between groups from different continents, and the historically strong emphasis on phenotypic differences between members of these groups, presents an opportunity to examine the degree of concordance between estimates of group membership based on genetic markers and on visually-based estimates of facial features. We first measured the degree of Native American, European, African and East Asian genetic admixture in a sample of 14 self-identified Hispanic individuals, chosen to cover a broad range of Native American and European genetic admixture proportions. We showed frontal and side-view photographs of the 14 individuals to 241 subjects living in New Mexico, and asked them to estimate the degree of NA admixture for each individual. We assess the overall concordance for each observer based on an aggregated measure of the difference between the observer and the genetic estimates. We find that observers reach a significantly higher degree of concordance than expected by chance, and that the degree of concordance as well as the direction of the discrepancy in estimates differs based on the ethnicity of the observer, but not on the observers' age or sex. This study highlights the potentially high degree of discordance between physical appearance and genetic measures of ethnicity, as well as how perceptions of ethnic affiliation are context-specific. We compare our findings to those of previous studies and discuss their implications.
Collapse
Affiliation(s)
- Yann C Klimentidis
- Department of Anthropology, University of New Mexico, Albuquerque, NM, USA.
| | | |
Collapse
|