Characterizing race/ethnicity and genetic ancestry for 100,000 subjects in the genetic epidemiology research on adult health and aging (GERA) cohort

Genetics

Volumn 200, Issue 4, 2015, Pages 1285-1295

  Banda, Yambazi ^a   Kvale, Mark N ^a   Hoffmann, Thomas J ^a,b   Hesselson, Stephanie E ^a   Ranatunga, Dilrini ^c   Tang, Hua ^d   Sabatti, Chiara ^d   Croen, Lisa A ^c   Dispensa, Brad P ^a   Henderson, Mary ^c   Iribarren, Carlos ^c   Jorgenson, Eric ^c   Kushi, Lawrence H ^c   Ludwig, Dana ^c   Olberg, Diane ^c   Quesenberry, Charles P ^c   Rowell, Sarah ^c   Sadler, Marianne ^c   Sakoda, Lori C ^c   Sciortino, Stanley ^c   Shen, Ling ^c   Smethurst, David ^c   Somkin, Carol P ^c   Van Den Eeden, Stephen K ^c   Walter, Lawrence ^c   Whitmer, Rachel A ^c   Kwok, Pui Yan ^a   Schaefer, Catherine ^c   Risch, Neil ^a,b,c   more..

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c DIVISION OF RESEARCH   (United States)

^d STANFORD UNIVERSITY   (United States)

Author keywords

Admixture; Population structure; Principal components; Race ethnicity; RPGEH GERA

Indexed keywords

ADULT; AFRICAN; AFRICAN AMERICAN; AGED; AGING; AMERICAN INDIAN; ANCESTRY GROUP; ARTICLE; ASHKENAZI JEW; ASIAN; CAUCASIAN; COHORT ANALYSIS; ETHNICITY; EUROPEAN; FEMALE; GENETIC EPIDEMIOLOGY; GENOTYPE; HISPANIC; HUMAN; HUMAN GENOME DIVERSITY PROJECT; HUMAN GENOME PROJECT; MALE; MIDDLE AGED; MINORITY GROUP; POPULATION GENETIC STRUCTURE; POPULATION GENETICS; PRINCIPAL COMPONENT ANALYSIS; PRIORITY JOURNAL; SELF REPORT; SINGLE NUCLEOTIDE POLYMORPHISM; ETHNIC GROUP; GENETICS; GENOMICS; HEALTH; MOLECULAR EPIDEMIOLOGY; PEDIGREE;

ADULT; AGING; COHORT STUDIES; CONTINENTAL POPULATION GROUPS; ETHNIC GROUPS; FEMALE; GENOMICS; HEALTH; HUMANS; MALE; MIDDLE AGED; MOLECULAR EPIDEMIOLOGY; PEDIGREE; PRINCIPAL COMPONENT ANALYSIS;

EID: 84939422197     PISSN: 00166731     EISSN: 19432631     Source Type: Journal    
DOI: 10.1534/genetics.115.178616     Document Type: Article

References (39)

1. Barbujani, G., and G. Bertorelle, 2001 Genetics and the population history of Europe. Proc. Natl. Acad. Sci. USA 98: 22–25.
2. Bauchet, M., B. McEvoy, L. N. Pearson, E. E. Quillen, T. Sarkisian et al., 2007 Measuring European population stratification with microarray genotype data. Am. J. Hum. Genet. 80: 948–956.
3. Belle, E. M., P. A. Landry, and G. Barbujani, 2006 Origins and evolution of the Europeans’ genome: evidence from multiple microsatellite loci. Proc. Biol. Sci. 273: 1595–1602.
4. Bonilla, C., E. J. Parra, C. L. Pfaff, S. Dios, J. A. Marshall et al., 2004 Admixture in the Hispanics of the San Luis Valley, Colorado, and its implications for complex trait gene mapping. Ann. Hum. Genet. 68: 139–153.
5. Burchard, E. G., E. Ziv, N. Coyle, S. L. Gomez, H. Tang et al., 2003 The importance of race and ethnic background in biomedical research and clinical practice.N. Engl. J. Med. 348: 1170–1175.
6. Cavalli-Sforza, L. L., 2005 The Human Genome Diversity Project: past, present and future. Nat. Rev. Genet. 6: 333–340.
7. Cavalli-Sforza, L. L., P. Menozzi, and A. Piazza, 1993 Demic expansions and human evolution. Science 259: 639–646.
8. Cavalli-Sforza, L. L., P. Menozzi, and A. Piazza, 1996 The History and Geography of Human Genes. Princeton University Press, Princeton, NJ, pp xiii and 413.
9. Cooper, R. S., J. S. Kaufman, and R. Ward, 2003 Race and genomics. N. Engl. J. Med. 348: 1166–1170.
10. Fernandez, J. R., M. D. Shriver, T. M. Beasley, N. Rafla-Demetrious, E. Parra et al., 2003 Association of African genetic admixture with resting metabolic rate and obesity among women. Obes. Res. 11: 904–911.
11. Hodgson, J. A., C. J. Mulligan, A. Al-Meeri, and R. L. Raaum, 2014 Early back-to-Africa migration into the Horn of Africa. PLoS Genet. 10: e1004393.
12. Hoffmann, T. J., M. N. Kvale, S. E. Hesselson, Y. Zhan, C. Aquino et al., 2011a Next generation genome-wide association tool: design and coverage of a high-throughput European-optimized SNP array. Genomics 98: 79–89.
13. Hoffmann, T. J., Y. Zhan, M. N. Kvale, S. E. Hesselson, J. Gollub et al., 2011b Design and coverage of high throughput genotyping arrays optimized for individuals of East Asian, African American, and Latino race/ethnicity using imputation and a novel hybrid SNP selection algorithm. Genomics 98: 422–430.
14. HUGO Pan-Asian SNP Consortium; M. A. Abdulla, I. Ahmed, A. Assawamakin, J. Bhak, S. K. Brahmachari et al., 2009 Mapping human genetic diversity in Asia. Science 326: 1541–1545.
15. Jakobsson, M., S. W. Scholz, P. Scheet, J. R. Gibbs, J. M. VanLiere et al., 2008 Genotype, haplotype and copy-number variation in worldwide human populations. Nature 451: 998–1003.
16. Krieger, N., D. L. Rowley, A. A. Herman, B. Avery, and M. T. Phillips, 1993 Racism, sexism, and social class: implications for studies of health, disease, and well-being. Am. J. Prev. Med. 9: 82–122.
17. Kvale, M. N., S. E. Hesselson, T. J. Hoffmann, Y. Cao, D. Chan et al., 2015 Genotyping informatics and quality control for 100,000 subjects in the Genetic Epidemiology Research on Adult Health and Aging (GERA) cohort. DOI: 10.1534/genetics.115.178905.
18. Li, J. Z., D. M. Absher, H. Tang, A. M. Southwick, A. M. Casto et al., 2008 Worldwide human relationships inferred from genomewide patterns of variation. Science 319: 1100–1104.
19. Lohmueller, K. E., A. R. Indap, S. Schmidt, A. R. Boyko, R. D. Hernandez et al., 2008 Proportionally more deleterious genetic variation in European than in African populations. Nature 451: 994–997.
20. Manichaikul, A., J. C. Mychaleckyj, S. S. Rich, K. Daly, M. Sale et al., 2010 Robust relationship inference in genome-wide association studies. Bioinformatics 26: 2867–2873.
21. Menozzi, P., A. Piazza, and L. Cavalli-Sforza, 1978 Synthetic maps of human gene frequencies in Europeans. Science 201: 786–792.
22. Novembre, J., T. Johnson, K. Bryc, Z. Kutalik, A. R. Boyko et al., 2008 Genes mirror geography within Europe. Nature 456: 98–101.
23. Parra, E. J., A. Marcini, J. Akey, J. Martinson, M. A. Batzer et al., 1998 Estimating African American admixture proportions by use of population-specific alleles. Am. J. Hum. Genet. 63: 1839–1851.
24. Patterson, N., A. L. Price, and D. Reich, 2006 Population structure and eigenanalysis. PLoS Genet. 2: e190.
25. Price, A. L., J. Butler, N. Patterson, C. Capelli, V. L. Pascali et al., 2008 Discerning the ancestry of European Americans in genetic association studies. PLoS Genet. 4: e236.
26. Reich, D., K. Thangaraj, N. Patterson, A. L. Price, and L. Singh, 2009 Reconstructing Indian population history. Nature 461: 489–494.
27. Risch, N., E. Burchard, E. Ziv, and H. Tang, 2002 Categorization of humans in biomedical research: genes, race and disease. Genome Biol. 3: comment2007.
28. Seldin, M. F., R. Shigeta, P. Villoslada, C. Selmi, J. Tuomilehto et al., 2006 European population substructure: clustering of northern and southern populations. PLoS Genet. 2: e143.
29. Sokal, R. R., N. L. Oden, and C. Wilson, 1991 Genetic evidence for the spread of agriculture in Europe by demic diffusion. Nature 351: 143–145.
30. Su, B., J. Xiao, P. Underhill, R. Deka, W. Zhang et al., 1999 Ychromosome evidence for a northward migration of modern humans into Eastern Asia during the last Ice Age. Am. J. Hum. Genet. 65: 1718–1724.
31. Tang, H., J. Peng, P. Wang, and N. J. Risch, 2005 Estimation of individual admixture: analytical and study design considerations. Genet. Epidemiol. 28: 289–301.
32. Tang, H., E. Jorgenson, M. Gadde, S. L. Kardia, D. C. Rao et al., 2006 Racial admixture and its impact on BMI and blood pressure in African and Mexican Americans. Hum. Genet. 119: 624–633.
33. Tang, H., S. Choudhry, R. Mei, M. Morgan, W. Rodriguez-Cintron et al., 2007 Recent genetic selection in the ancestral admixture of Puerto Ricans. Am. J. Hum. Genet. 81: 626–633.
34. Tian, C., P. K. Gregersen, and M. F. Seldin, 2008a Accounting for ancestry: population substructure and genome-wide association studies. Hum. Mol. Genet. 17: R143–R150.
35. Tian, C., R. Kosoy, A. Lee, M. Ransom, J. W. Belmont et al., 2008b Analysis of East Asia genetic substructure using genomewide SNP arrays. PLoS One 3: e3862.
36. Tian, C., R. M. Plenge, M. Ransom, A. Lee, P. Villoslada et al., 2008c Analysis and application of European genetic substructure using 300 K SNP information. PLoS Genet. 4: e4.
37. Tishkoff, S. A., F. A. Reed, F. R. Friedlaender, C. Ehret, A. Ranciaro et al., 2009 The genetic structure and history of Africans and African Americans. Science 324: 1035–1044.
38. Wellcome Trust Case Consortium, 2007 Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 447: 661–678.
39. Zakharia, F., A. Basu, D. Absher, T. L. Assimes, A. S. Go et al., 2009 Characterizing the admixed African ancestry of African Americans. Genome Biol. 10: R141.