Informativeness of Genetic Markers for Inference of Ancestry

American Journal of Human Genetics

Volumn 73, Issue 6, 2003, Pages 1402-1422

  Rosenberg, Noah A ^a   Li, Lei M ^a   Ward, Ryk ^b   Pritchard, Jonathan K ^c  

^a UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

^b UNIVERSITY OF OXFORD   (United Kingdom)

^c UNIVERSITY OF CHICAGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DINUCLEOTIDE; MICROSATELLITE DNA;

ALLELE; ARTICLE; CALCULATION; CASE CONTROL STUDY; DECISION MAKING; ENTROPY; GENE MAPPING; GENETIC ASSOCIATION; GENETIC MARKER; HUMAN; INFORMATION SCIENCE; MICROSATELLITE MARKER; PHYLOGENY; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM;

EID: 0347362518     PISSN: 00029297     EISSN: None     Source Type: Journal    
DOI: 10.1086/380416     Document Type: Article

References (52)

1. Abramowitz MA, Stegun IA (1965) Handbook of mathematical functions. Dover, New York
2. Akey JM, Zhang G, Zhang K, Jin L, Shriver MD (2002) Interrogating a high-density SNP map for signatures of natural selection. Genome Res 12:1805-1814
3. Anderson EC, Thompson EA (2002) A model-based method for identifying species hybrids using multilocus genetic data. Genetics 160:1217-1229
4. Bamshad MJ, Wooding S, Watkins WS, Ostler CT, Batzer MA, Jorde LB (2003) Human population genetic structure and inference of group membership. Am J Hum Genet 72:578-589
5. Banks MA, Eichert W, Olsen JB (2003) Which genetic loci have greater population assignment power? Bioinformatics 19:1436-1438
6. Barron A, Rissanen J, Yu B (1998) The minimum description length principle in coding and modeling. IEEE Trans Inform Theory 44:2743-2760
7. Brenner CH (1998) Difficulties in the estimation of ethnic affiliation. Am J Hum Genet 62:1558-1560
8. Buchanan FC, Adams LJ, Littlejohn RP, Maddox JF, Crawford AM (1994). Determination of evolutionary relationships among sheep breeds using microsatellites. Genomics 22:397-403
9. Campbell D, Duchesne P, Bernatchez L (2003) AFLP utility for population assignment studies: analytical investigation and empirical comparison with microsatellites. Mol Ecol 12:1979-1991
10. Cann HM, de Toma C, Cazes L, Legrand M-F, Morel V, Piouffre L, Bodmer J, et al (2002) A human genome diversity cell line panel. Science 296:261-262
11. Chakraborty R, Weiss KM (1988) Admixture as a tool for finding linked genes and detecting that difference from allelic association between loci. Proc Natl Acad Sci USA 85:9119-9123
12. Collins-Schramm HE, Phillips CM, Operario DJ, Lee JS, Weber JL, Hanson RL, Knowler WC, et al (2002) Ethnic-difference markers for use in mapping by admixture linkage disequilibrium. Am J Hum Genet 70:737-750
13. Cornuet J-M, Piry S, Luikart G, Estoup A, Solignac M (1999) New methods employing multilocus genotypes to select or exclude populations as origins of individuals. Genetics 153:1989-2000
14. Cover TM, Thomas JA (1991) Elements of information theory. Wiley, New York
15. Davies N, Villablanca FX, Roderick GK (1999) Determining the source of individuals: multilocus genotyping in non-equilibrium population genetics. Trends Ecol Evol 14:17-21
16. Dean M, Stephens JC, Winkler C, Lomb DA, Ramsburg M, Boaze R, Stewart C, et al (1994) Polymorphic admixture typing in human ethnic populations. Am J Hum Genet 55:788-808
17. Elandt-Johnson RC (1971) Probability models and statistical methods in genetics. Wiley, New York
18. Excoffier L (2001) Analysis of population subdivision. In: Balding DJ, Bishop M, Cannings C (eds) Handbook of statistical genetics. John Wiley & Sons, Chichester, UK, pp 271-307
19. 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
20. Ghebranious N, Vaske D, Yu A, Zhao C, Marth G, Weber JL (2003) STRP screening sets for the human genome at 5 cM density. BMC Genomics 4:6
21. Gibbons JD (1985) Nonparametric statistical inference. 2nd ed. Marcel Dekker, New York
22. Gomulkiewicz R, Brodziak JKT, Mangel M (1990) Ranking loci for genetic stock identification by curvature methods. Can J Fish Aquat Sci 47:611-619
23. Guinand B, Topchy A, Page KS, Burnham-Curtis MK, Punch WF, Scribner KT (2002) Comparisons of likelihood and machine learning methods of individual classification. J Hered 93:260-269
24. Hoggart CJ, Parra EJ, Shriver MD, Bonilla C, Kittles RA, Clayton DG, McKeigue PM (2003) Control of confounding of genetic associations in stratified populations. Am J Hum Genet 72:1492-1504
25. Kullback S (1959) Information theory and statistics. Dover, Mineola, New York
26. Lowe AL, Urquhart A, Foreman LA, Evett IW (2001) Inferring ethnic origin by means of an STR profile. Forensic Sci Int 119:17-22
27. Manel S, Berthier P, Luikart G (2002) Detecting wildlife poaching: identifying the origin of individuals with Bayesian assignment tests and multilocus genotypes. Conserv Biol 16:650-659
28. 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
29. Millar RB (1991) Selecting loci for genetic stock identification using maximum likelihood, and the connection with curvature methods. Can J Fish Aquat Sci 48:2173-2179
30. Molokhia M, Hoggart C, Patrick AL, Shriver M, Parra E, Ye J, Silman AJ, et al (2003) Relation of risk of systemic lupus erythematosus to west African admixture in a Caribbean population. Hum Genet 112:310-318
31. Paetkau D, Calvert W, Stirling I, Strobeck C (1995) Microsatellite analysis of population structure in Canadian polar bears. Mol Ecol 4:347-354
32. Primmer CR, Koskinen MT, Piironen J (2000) The one that did not get away: individual assignment using microsatellite data detects a case of fishing competition fraud. Proc R Soc Lond B 267:1699-1704
33. Pritchard JK, Donnelly P (2001) Case-control studies of association in structured or admixed populations. Theor Popul Biol 60:227-237
34. Pritchard JK, Rosenberg NA (1999) Use of unlinked genetic markers to detect population stratification in association studies. Am J Hum Genet 65:220-228
35. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945-959
36. Ramachandran S, Rosenberg NA, Zhivotovsky LA, Feldman MW. Robustness of the inference of human population structure: a comparison of X-chromosomal and autosomal microsatellites. Hum Genomics (in press)
37. Rannala B, Mountain JL (1997) Detecting immigration by using multilocus genotypes. Proc Natl Acad Sci USA 94:9197-9201
38. Risch N, Burchard E, Ziv E, Tang H (2002) Categorization of humans in biomedical research: genes, race and disease. Genome Biol 3:comment2007
39. Rosenberg N, Stong R (2003) Problem 11039. Amer Math Monthly 110:743
40. Rosenberg NA, Burke T, Elo K, Feldman MW, Freidlin PJ, Groenen MAM, Hillel J, et al (2001) Empirical evaluation of genetic clustering methods using multilocus genotypes from 20 chicken breeds. Genetics 159:699-713
41. Rosenberg NA, Pritchard JK, Weber JL, Cann HM, Kidd KK, Zhivotovsky LA, Feldman MW (2002) Genetic structure of human populations. Science 298:2381-2385
42. _ (2003) Response to comment on "Genetic structure of human populations." Science 300:1877
43. Ruiz Linares A (1999) Microsatellites and the reconstruction of the history of human populations. In: Goldstein DB, Schlötterer C (eds) Microsatellites: evolution and applications. Oxford University Press, Oxford, pp 183-197
44. Shriver MD, Smith MW, Jin L, Marcini A, Akey JM, Deka R, Ferrell RE (1997) Ethnic-affiliation estimation by use of population-specific DNA markers. Am J Hum Genet 60:957-964
45. Smith MW, Lautenberger JA, Shin HD, Chretien J-P, Shrestha S, Gilbert DA, O'Brien SJ (2001) Markers for mapping by admixture linkage disequilibrium in African American and Hispanic populations. Am J Hum Genet 69:1080-1094
46. Smouse PE, Spielman RS, Park MH (1982) Multiple-locus allocation of individuals to groups as a function of the genetic variation within and differences among human populations. Am Nat 119:445-463
47. Sokal RR, Rohlf FJ (1995) Biometry. 3rd ed. Freeman, New York
48. Stephens JC, Smith MW, Shin HD, O'Brien SJ (1999) Tracking linkage disequilibrium in admixed populations with MALD using microsatellite loci. In: Goldstein DB, Schlötterer C (eds) Microsatellites: evolution and applications. Oxford University Press, Oxford, pp 211-224
49. Weir BS (1996) Genetic data analysis II. Sinauer, Sunderland, MA
50. Weiss L (1961) Statistical decision theory. McGraw-Hill, New York
51. Zhivotovsky LA, Rosenberg NA, Feldman MW (2003) Features of evolution and expansion of modern humans, inferred from genomewide microsatellite markers. Am J Hum Genet 72:1171-1186
52. Ziv E, Burchard EG (2003) Human population structure and genetic association studies. Pharmacogenomics 4:431-441