Examining population stratification via individual ancestry estimates versus self-reported race

Cancer Epidemiology Biomarkers and Prevention

Volumn 14, Issue 6, 2005, Pages 1545-1551

  Barnholtz Sloan, Jill S ^a,b   Chakraborty, Ranajit ^c   Sellers, Thomas A ^a   Schwartz, Ann G ^d  

^a H LEE MOFFITT CANCER CENTER AND RESEARCH INSTITUTE   (United States)

^b UNIVERSITY OF SOUTH FLORIDA   (United States)

^c UNIVERSITY OF CINCINNATI COLLEGE OF MEDICINE   (United States)

^d WAYNE STATE UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AFRICAN AMERICAN; ARTICLE; CANCER RISK; CAUCASIAN; CONTROLLED STUDY; GENE LOCUS; GENETIC MARKER; GENETIC RISK; GENOTYPE; HUMAN; LUNG CANCER; MAJOR CLINICAL STUDY; ONSET AGE; POPULATION RESEARCH; PRIORITY JOURNAL; RACE DIFFERENCE; SELF REPORT; SHORT TANDEM REPEAT;

AFRICAN CONTINENTAL ANCESTRY GROUP; CASE-CONTROL STUDIES; EUROPEAN CONTINENTAL ANCESTRY GROUP; GENOTYPE; GLUTATHIONE TRANSFERASE; HUMANS; LUNG NEOPLASMS; MODELS, THEORETICAL; PEDIGREE; REPRODUCIBILITY OF RESULTS; RISK ASSESSMENT; TANDEM REPEAT SEQUENCES;

EID: 20444364178     PISSN: 10559965     EISSN: None     Source Type: Journal    
DOI: 10.1158/1055-9965.EPI-04-0832     Document Type: Article

References (59)

1. Wiencke JK. Opinion: impact of race/ethnicity on molecular pathways in human cancer. Nat Rev Cancer 2004;4:79-84.
2. Holden C. Race and medicine. Science 2003;302:594-6.
3. Ferlay J, Bray F, Pisani P, Parkin DM. GLOBOCAN 2002: cancer incidence, mortality and prevalence worldwide; IARC Cancer Base No. 5. version 2.0. Lyon: IARC Press; 2004.
4. Ries LAG, Eisner MP, Kosary CL, et al. SEER cancer statistics review, 1975-2000, http://seer.cancer.gov/csr/. Bethesda (MD): National Cancer Institute; 2003.
5. Wacholder S, Rothman N, Caporaso N. Population stratification in epidemiologic studies of common genetic variants and cancer: quantification of bias. J Natl Cancer Inst 2000;92:1151-8.
6. McKeigue PM, Carpenter JR, Parra EJ, Shriver MD. Estimation of admixture and detection of linkage in admixed populations by a Bayesian approach: application to African-American populations. Ann Hum Genet 2000;64:171-86.
7. Shriver MD, Smith MW, Jin L, et al. Ethnic-affiliation estimation by use of population-specific DNA markers. Am J Hum Genet 1997;60: 957-64.
8. Pritchard JK, Rosenberg NA. Use of unlinked genetic markers to detect population stratification in association studies. Am J Hum Genet 1999; 65:220-8.
9. Pritchard JK, Stephens M, Donnelly P. Inference of population structure using multilocus genotype data. Genetics 2000;155:945-59.
10. Devlin B, Roeder K, Wasserman L. Genomic control, a new approach to genetic-based association studies. Theor Popul Biol 2001;60:155-66.
11. Stephens JC, Briscoe D, O'Brien SJ. Mapping by admixture linkage disequilibrium in human populations: limits and guidelines. Am J Hum Genet 1994;55:809-24.
12. Hoggart CJ, Parra EJ, Shriver MD, et al. Control of confounding of genetic associations in stratified populations. Am J Hum Genet 2003;72:6.
13. Bonilla C, Shriver MD, Parra EJ, Jones A, Fernandez JR. Ancestral proportions and their association with skin pigmentation and bone mineral density in Puerto Rican women from New York City. Hum Genet 2004; 115:57-68. Epub 2004 Apr 30.
14. Shriver MD, Parra EJ, Dios S, et al. Skin pigmentation, biogeographical ancestry and admixture mapping. Hum Genet 2003;112:387-99.
15. Gower BA, Fernandez JR, Beasley TM, Shriver MD, Goran MI. Using genetic admixture to explain racial differences in insulin-related phenotypes. Diabetes 2003;52:1047-51.
16. Chakraborty R, Kamboh MI, Nwankwo M, Ferrell RE. Caucasian genes in American Blacks: new data. Am J Hum Genet 1992;50:145-55.
17. Wilson JF, Weale ME, Smith AC, et al. Population genetic structure of variable drug response. Nat Genet 2001;29:265-9.
18. USCB. U.S. Census Bureau, Population Division: annual estimates of the population by race alone or in combination and Hispanic or Latino origin for the United States and States. Washington (DC): U.S. Government Printing Office; 2003.
19. Rosenberg NA, Pritchard JK, Weber JL, et al. Genetic structure of human populations. Science 2002;298:2381-5.
20. Chakraborty R, Weiss KM. Admixture as a tool for finding linked genes and detecting that difference from allelic association between loci. Proc Natl Acad Sci U S A 1988;85:9119-23.
21. Parra EJ, Marcini A, Akey J, et al. Estimating African American admixture proportions by use of population-specific alleles. Am J Hum Genet 1998;63: 1839-51.
22. Chakraborty R. Gene admixture in human populations: models and predictions. Yearbook of Physical Anthropology 1986;29:1-43.
23. Benhamou S, Lee WJ, Alexandrie AK, et al. Meta- and pooled analyses of the effects of glutathione S-transferase M1 polymorphisms and smoking on lung cancer risk. Carcinogenesis 2002;23:1343-50.
24. Houlston RS. Glutathione S-transferase M1 status and lung cancer risk: a meta-analysis. Cancer Epidemiol Biomarkers Prev 1999;8:675-82.
25. Seidegard J, DePierre JW, Pero RW. Hereditary interindividual differences in the glutathione transferase activity towards trans-stilbene oxide in resting human mononuclear leukocytes are due to a particular isozyme(s). Carcinogenesis 1985;6:1211-6.
26. Seidegard J, Pero RW. The hereditary transmission of high glutathione transferase activity towards trans-stilbene oxide in human mononuclear leukocytes. Hum Genet 1985;69:66-8.
27. Taioli E, Gaspari L, Benhamou S, et al. Polymorphisms in CYP1A1, GSTM1, GSTT1 and lung cancer below the age of 45 years. Int J Epidemiol 2003;32:60-3.
28. Lo YM, Lau TK, Chan LY, Leung TN, Chang AM. Quantitative analysis of the bidirectional fetomaternal transfer of nucleated cells and plasma DNA. Clin Chem 2000;46:1301-9.
29. Chen CL, Liu Q, Relling MV. Simultaneous characterization of glutathione S-transferase M1 and T1 polymorphisms by polymerase chain reaction in American whites and blacks. Pharmacogenetics 1996;6:187-91.
30. Budowle B, Moretti TR, Niezgoda S, Brown BL. CODIS and PCR-based short tandem repeat loci: law enforcement tools. Second European Symposium on Human Identification 1998. Madison (WI): Promega Corporation; 1998. p. 73-88.
31. Pepinski W, Janica J, Skawronska M, Koc-Zorawska E, Niemcunowicz-Janica A, Solryszewski I. Population genetics for the CODIS core STR loci in the population of Northeastern Poland. J Forensic Sci 2003;48:1197-8.
32. Sun G, McGarvey ST, Bayoumi R, et al. Global genetic variation at nine short tandem repeat loci and implications on forensic genetics. Eur J Hum Genet 2003;11:39-49.
33. Tofanelli S, Boschi I, Bertoneri S, et al. Variation at 16 STR loci in Rwandans (Hutu) and implications on profile frequency estimation in Bantu-speakers. Int J Legal Med 2003;117:121-6. Epub 2003 Feb 15.
34. MIEPIC. Michigan EPIC: about immigration in Michigan. Grand Rapids (MI): Center for Michigan History Studies; 2004.
35. Falush D, Stephens M, Pritchard JK. Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 2003;164:1567-87.
36. Lange K. Mathematical and statistical methods for genetic analysis. New York: Springer-Verlag, Inc.; 1997.
37. Edwards AWF. Likelihood. Baltimore: Johns Hopkins University Press; 1992.
38. Akaike H. Information theory and an extension of the maximum likelihood principle. In: CF Petrov BN, editor. Second international symposium on information theory. Budapest: Akademiai Kiado; 1973. p. 267-81.
39. SAS. Statistical analysis software, version 9.1. Cary (NC); 2003.
40. Collins-Schramm HE, Kittles RA, Operario DJ, et al. Markers that discriminate between European and African ancestry show limited variation within Africa. Hum Genet 2002;111:566-9.
41. Collins-Schramm HE, Phillips CM, Operario DJ, et al. Ethnic-difference markers for use in mapping by admixture linkage disequilibrium. Am J Hum Genet 2002;70:737-50.
42. Parkin DM, Whelan SL, Ferlay J, Teppo L, Thomas DB. Cancer incidence in five continents. Volume VIII. IARC Scientific Publication No. 155. Lyon: IARC Press; 2003.
43. Hartl DL, Clark AG. Principles of population genetics. 2nd ed. Sunderland (MA): Sinauer Associates, Inc.; 1989.
44. Cavalli-Sforza LL, Menozzi P, Piazza A. The history and geography of human genes. Princeton: Princeton University Press; 1994.
45. Sokal RR, Harding RM, Oden NL. Spatial patterns of human gene frequencies in Europe. Am J Phys Anthropol 1989;80:267-94.
46. Bamshad M, Wooding S, Salisbury BA, Stephens JC. Deconstructing the relationship between genetics and race. Nat Rev Genet 2004;5:598-609.
47. Khlat M, Cazes MH, Genin E, Guiguet M. Robustness of case-control studies of genetic factors to population stratification: magnitude of bias and type I error. Cancer Epidemiol Biomarkers Prev 2004;13:1660-4.
48. Thomas DC, Witte JS. Point: population stratification: a problem for case-control studies of candidate-gene associations? Cancer Epidemiol Biomarkers Prev 2002;11:505-12.
49. Marchini J, Cardon LR, Phillips MS, Donnelly P. The effects of human population structure on large genetic association studies. Nat Genet 2004;36:512-7. Epub 2004 Mar 28.
50. Reich DE, Goldstein DB. Detecting association in a case-control study while correcting for population stratification. Genet Epidemiol 2001;20:4-16.
51. Cavalli-Sforza LL, Feldman MW. The application of molecular genetic approaches to the study of human evolution. Nat Genet 2003;33 Suppl: 266-75.
52. USCB. U.S. Census Bureau (USCB). Current population reports, Series. Population profile of the United States: 1997. Washington (DC): U.S. Government Printing Office, 1998. p. 23-194.
53. Reed TE. Caucasian genes in American Negroes. Science 1969;165:762-8.
54. Smith MW, Lautenberger JA, Shin HD, et al. Markers for mapping by admixture linkage disequilibrium in African American and Hispanic populations. Am J Hum Genet 2001;69:1080-94.
55. Rosenberg NA, Li LM, Ward R, Pritchard JK. Informativeness of genetic markers for inference of ancestry. Am J Hum Genet 2003;73:6.
56. Pfaff CL, Barnholtz-Sloan J, Wagner JK, Long JC. Information on ancestry from genetic markers. Genet Epidemiol 2004;26:305-15.
57. Gill P. Population genetics of short tandem repeat (STR) loci. Genetica 1995; 96:69-87.
58. Budowle B, Shea B, Niezgoda S, Chakraborty R. CODIS STR loci data from 41 sample populations. J Forensic Sci 2001;46:453-89.
59. Chakraborty R, Stivers DN, Su B, Zhong Y, Budowle B. The utility of short tandem repeat loci beyond human identification: implications for development of new DNA typing systems. Electrophoresis 1999;20: 1682-96.