Regional admixture mapping and structured association testing: Conceptual unification and an extensible general linear model

PLoS Genetics

Volumn 2, Issue 8, 2006, Pages 1254-1264

  Redden, David T ^a   Divers, Jasmin ^a   Vaughan, Laura Kelly ^a   Tiwari, Hemant K ^a   Beasley, T Mark ^a   Fernández, José R ^a   Kimberly, Robert P ^b   Feng, Rui ^a   Padilla, Miguel A ^a   Liu, Nianjun ^a   Miller, Michael B ^c   Allison, David B ^a  

^a UNIVERSITY OF ALABAMA AT BIRMINGHAM   (United States)

^b The University of Alabama at Birmingham   (United States)

^c UNIVERSITY OF MINNESOTA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; GENE LOCUS; GENE MAPPING; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENETIC LINKAGE; GENETIC TRAIT; GENOTYPE; MEASUREMENT ERROR; METHODOLOGY; PHENOTYPE; PLESIOMORPHY; POPULATION RESEARCH; STATISTICAL MODEL; BIOLOGICAL MODEL; COMPUTER PROGRAM; COMPUTER SIMULATION; FEMALE; GENE LINKAGE DISEQUILIBRIUM; HUMAN; MALE; POPULATION GENETICS; QUANTITATIVE TRAIT LOCUS;

ANIMALIA;

COMPUTER SIMULATION; FEMALE; GENETICS, POPULATION; HUMANS; LINEAR MODELS; LINKAGE DISEQUILIBRIUM; MALE; MODELS, GENETIC; PHENOTYPE; QUANTITATIVE TRAIT LOCI; SOFTWARE;

EID: 33748031741     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.0020137     Document Type: Article

References (70)

1. Lee WC, Yen YC (2003) Admixture mapping using interval transmission/ disequilibrium tests. Ann Hum Genet 67: 580-588.
2. Smith MW, O'Brien SJ (2005) Mapping by admixture linkage disequilibrium: Advances, limitations and guidelines. Nat Rev Genet 6: 623-632.
3. Chen HS, Zhu X, Zhao H, Zhang S (2003) Qualitative semi-parametric test for genetic associations in case-control designs under structured populations. Ann Hum Genet 67: 250-264.
4. Halder I, Shriver M (2003) Measuring and using admixture to study the genetics of complex diseases. Hum Genet 1: 52-62.
5. Cardon LR, Palmer LJ (2003) Population stratification and spurious allelic association. Lancet 361: 598-604.
6. McKeigue PM, Carpenter JR, Parra EJ, Shriver MD (2000) Estimation of admixture and detection of linkage in admixed populations by a Bayesian approach: Application to African-American populations. Ann Hum Genet 64: 171-186.
7. Hoggart CJ, Parra EJ, Shriver MD, Bonilla C, Kittles RA, et al. (2003) Control of confounding of genetic associations in stratified populations. Am J Hum Genet 72: 1492-1504.
8. Falush D, Stephens M, Pritchard JK (2003) Inference of population structure using multilocus genotype data: Linked loci and correlated allele frequencies. Genetics 164: 1567-1587.
9. Hanis CL, Chakraborty R, Ferrell RE, Schull WJ (1986) Individual admixture estimates - Disease associations and individual risk of Diabetes and gallbladder-disease among Mexican-Americans in Starr County, Texas. Am J Phys Anthropol 70: 433-441.
10. Tang H, Peng J, Wang P, Risch NJ (2005) Estimation of individual admixture: Analytical and study design considerations. Genet Epidemiol 28: 289-301.
11. Satten GA, Flanders WD, Yang QH (2001) Accounting for unmeasured population substructure in case-control studies of genetic association using a novel latent-class model. Am J Hum Genet 68: 466-477.
12. Purcell S, Sham P (2004) Properties of structured association approaches to detecting population stratification. Hum Hered 58: 93-107.
13. Patterson N, Hattangadi N, Lane B, Lohmueller KE, Hafler DA, et al. (2004) Methods for high-density admixture mapping of disease genes. Am J Hum Genet 74: 979-1000.
14. Pritchard JK, Donnelly P (2001) Case-control studies of association in structured or admixed populations. Theor Popul Biol 60: 227-237.
15. Purcell S (2003) Sample selection and complex effects in quantitative trait loci analysis [dissertation]. London: University of London. 409 p.
16. Zhu XF, Cooper RS, Elston RC (2004) Linkage analysis of a complex disease through use of admixed populations. Am J Hum Genet 74: 1136-1153.
17. Nievergelt C, Schork N (2005) Admixture Mapping As a Gene Discovery Approach for Complex Human Traits and Diseases. Curr Hypertens Rep 7: 31-37.
18. Devlin B, Roeder K (1999) Genomic control for association studies. Biometrics 55: 997-1004.
19. Bacanu SA, Devlin B, Roeder K (2000) The power of genomic control. Am J Hum Genet 66: 1933-1944.
20. Kohler K, Bickeboller H (2006) Case-control association tests correcting for population stratification. Ann Hum Genet 70: 98-115.
21. Kohler K, Bickeboller H (2005) Structured Association tests in case-control studies. Ann Hum Genet 69: 768.
22. Pritchard JK, Stephens M, Rosenberg NA, Donnelly P (2000) Association mapping in structured populations. Am J Hum Genet 67: 170-181.
23. Stephens JC, Briscoe D, Obrien SJ (1994) Mapping by admixture linkage disequilibrium in human-populations - Limits and guidelines. Am J Hum Genet 55: 809-824.
24. Pfaff CL, Parra EJ, Bonilla C, Hiester K, McKeigue PM, et al. (2001) Population structure in admired populations: Effect of admixture dynamics on the pattern of linkage disequilibrium. Am J Hum Genet 68: 198-207.
25. McKeigue PM (1997) Mapping genes underlying ethnic differences in disease risk by linkage disequilibrium in recently admired populations. Am J Hum Genet 60: 188-196.
26. McKeigue PM (1998) Mapping genes that underlie ethnic differences in disease risk: Methods for detecting linkage in admixed populations, by conditioning on parental admixture. Am J Hum Genet 63: 241-251.
27. Montana G, Pritchard JK (2004) Statistical tests for admixture mapping with case-control and cases-only data. Am J Hum Genet 75: 771-789.
28. Zhang C, Chen K, Seldin MF, Li HZ (2004) A hidden Markov modeling approach for admixture mapping based on case-control data. Genet Epidemiol 27: 225-239.
29. McKeigue PM (2000) Multipoint admixture mapping. Genet Epidemiol 19: 464-465.
30. Cockett NE, Jackson SP, Shay TL, Farnir F, Berghmans S, et al. (1996) Polar overdominance at the Ovine callipyge locus. Science 273: 236-238.
31. Kim JJ, Farnir F, Savell J, Taylor JF (2003) Detection of quantitative trait loci for growth and beef carcass fatness traits in a cross between Bos taurus (Angus) and Bos indicus (Brahman) cattle. J Anim Sci 81: 1933-1942.
32. Kim KS, Kim LL, Dekkers LCM, Rothschild MF (2004) Polar overdominant inheritance of a DLK1 polymorphism is associated with growth and fatness in pigs. Mamm Genome 15: 552-559.
33. Luo LJ, Li ZK, Mei HW, Shu QY, Tabien R, et al. (2001) Overdominant epistatic loci are the primary genetic basis of inbreeding depression and heterosis in rice. II. Grain yield components. Genetics 158: 1755-1771.
34. Li ZK, Luo LJ, Mei HW, Wang DL, Shu QY, Tabien R, et al. (2001) Overdominant epistatic loci are the primary genetic basis of inbreeding depression and heterosis in rice. I. Biomass and grain yield. Genetics 158: 1737-1753.
35. Rebbeck TR, Martinez ME, Sellers TA, Shields PG, Wild CP, Potter JD (2004) Genetic variation and cancer: Improving the environment for publication of association studies. Cancer Epidemiol Biomarkers Prev 13: 1985-1986.
36. Mickey RM, Greenland S (1989) The impact of confounder selection criteria on effect estimation. Am J Epidemiol 129: 125-137.
37. Deng HW, Chen WM, Recker RR (2001) Population admixture: Detection by Hardy-Weinberg test and its quantitative effects on linkage-disequilibrium methods for localizing genes underlying complex traits. Genetics 157: 885-897.
38. McCullagh P, Nelder J (1989) Generalized linear models. London: Chapman and Hall. 511 p.
39. Heo M, Faith MS, Mott JW, Gorman BS, Redden DT, Allison DB (2003) Hierarchical linear models for the development of growth curves: An example with body mass index in overweight/obese adults. Stat Med 22: 1911-1942.
40. Sullivan L, Dukes K, Losina E (1999) Tutorial in biostatistics. An introduction to hierarchical linear modeling. Stat Med 18: 855-888.
41. Fox J (1991) Regression diagnostics. Newbury Park (California): Sage Publications. 92 p.
42. Rousseeuw PJ, Leroy AM (1987) Robust regression and outlier detection. New York: John Wiley & Sons, Inc. 329 p.
43. Almasy L, Blangero J (2004) Exploring positional candidate genes: Linkage conditional on measured genotype. Behav Genet 34: 173-177.
44. Li MY, Boehnke M, Abecasis GR (2005) Joint modeling of linkage and association: Identifying SNPs responsible for a linkage signal. Am J Hum Genet 76: 934-949.
45. Li C, Scott LJ, Boehnke M (2004) Assessing whether an allele can account in part for a linkage signal: The Genotype-IBD Sharing Test (GIST). Am J Hum Genet 74: 418-431.
46. Lee WC, Yen YC (2003) Admixture mapping using interval transmission/disequilibrium tests. Ann Hum Genet 67: 580-588.
47. Lin S, Chakravarti A, Cutler DJ (2004) Exhaustive allelic transmission disequilibrium tests as a new approach to genome-wide association studies. Nat Genet 36: 1181-1188.
48. Kang SJ, Finch SJ, Haynes C, Gordon D (2004) Quantifying the percent increase in minimum sample size for SNP genotyping errors in genetic model-based association studies. Hum Hered 58: 139-144.
49. Edwards BJ, Haynes C, Levenstein MA, Finch SJ, Gordon D (2005) Power and sample size calculations in the presence of phenotype errors for case/control genetic association studies. BMC Genet 6: 18.
50. Liu B (1997) Statistical genomics: Linkage, mapping, and QTL analysis. Boca Raton: CRC Press. 611 p.
51. Becher H (1992) The concept of residual confounding in regression-models and some applications. Stat Med 11: 1747-1758.
52. Cheng CL, Schneeweiss H, Thamerus M (2000) A small sample estimator for a polynomial regression with errors in the variables. J R Stat Soc Ser B Stat Methodol 62: 699-709.
53. Cheng CL, Van Ness J (1999) Statistical regression with measurement error. New York: Oxford University Press. 262 p.
54. Carroll RJ, Kuchenhoff H, Lombard F, Stefanski LA (1996) Asymptotics for the SIMEX estimator in nonlinear measurement error models. J Am Stat Assoc 91: 242-250.
55. Lin XH, Carroll RJ (2000) Nonparametric function estimation for clustered data when the predictor is measured without/with error. J Am Stat Assoc 95: 520-534.
56. Carroll RJ, Ruppert D, Stefanski LA (1998) Measurement error in nonlinear models. London: Chapman & Hall/CRC. 305 p.
57. Stefanski LA, Cook JR (1995) Simulation extrapolation: The measurement error jackknife. J Am Stat Assoc 90: 1247-1256.
58. Gustafson P (2004) Measurement error and misclassification in statistics and epidemiology: Impacts and Bayesian adjustments. London: Champlan & Hall/CRC. 188 p.
59. Rubin DB (1996) Multiple imputation after 18+ years. J Am Stat Assoc 91: 473-489.
60. Zhang SL, Zhu XF, Zhao HY (2003) On a semiparametric test to detect associations between quantitative traits and candidate genes using unrelated individuals. Genet Epidemiol 24: 44-56.
61. McKeigue PM (2005) Prospects for admixture mapping of complex traits. Am J Hum Genet 76: 1-7.
62. Reich D, Patterson N (2005) Will admixture mapping work to find disease genes? Philos Trans R Soc Lond B Biol Sci 360: 1605-1607.
63. Slager SL, Schaid DJ, Wang L, Thibodeau SN (2003) Candidate-gene association studies with pedigree data: Controlling for environmental covariates. Genet Epidemiol 24: 273-283.
64. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155: 945-959.
65. Neale MC, Cardon LR (1992) Methodology for genetic studies of twins and families. Boston: Kluwer Academic Publishers. 496 p.
66. Lara-Castro C, Hunter GR, Lovejoy JC, Gower BA, Fernandez JR (2005) Apolipoprotein A-II polymorphism and visceral adiposity in African-American and white women. Obes Res 13: 507-512.
67. Bonilla C, Shriver MD, Parra EJ, Jones A, Fernandez JR (2004) Ancestral proportions and their association with skin pigmentation and bone mineral density in Puerto Rican women from New York city. Hum Genet 115: 57-68.
68. Gower BA, Fernandez JR, Beasley TM, Shriver MD, Goran MI (2003) Using genetic admixture to explain racial differences in insulin-related phenotypes. Diabetes 52: 1047-1051.
69. Sasieni PD (1997) From genotypes to genes: Doubling the sample size. Biometrics 53: 1253-1261.
70. Cook JR, Stefanski LA (1994) Simulation-extrapolation estimation in parametric measurement error models. J Am Stat Assoc 89: 1314-1328.