PSMIX: An R package for population structure inference via maximum likelihood method

BMC Bioinformatics

Volumn 7, Issue , 2006, Pages

  Wu, Baolin ^a   Liu, Nianjun ^b   Zhao, Hongyu ^c  

^a UNIVERSITY OF MINNESOTA   (United States)

^b UNIVERSITY OF ALABAMA AT BIRMINGHAM   (United States)

^c YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATION RESOURCES; CONVERGENCE PROBLEMS; EFFICIENT COMPUTATION; EXPECTATION-MAXIMIZATION ALGORITHMS; MARKOV CHAIN MONTE-CARLO; MAXIMUM LIKELIHOOD METHODS; POPULATION STRATIFICATION; POPULATION STRUCTURES;

ALGORITHMS;

BAYESIAN NETWORKS;

ACCURACY; ALGORITHM; ARTICLE; BAYES THEOREM; BIOINFORMATICS; CALCULATION; COMPUTER PROGRAM; CONTROLLED STUDY; GENE LOCUS; GENE MAPPING; GENETIC ASSOCIATION; GENETIC MARKER; GENOTYPE; MAXIMUM LIKELIHOOD METHOD; POPULATION GENETICS; PROBABILITY; AMERICAN INDIAN; BIOLOGICAL MODEL; CAUCASIAN; CHROMOSOME MAP; COMPARATIVE STUDY; COMPUTER SIMULATION; GENETICS; HUMAN; PROCEDURES; STATISTICAL MODEL;

ALGORITHMS; AMERICAN NATIVE CONTINENTAL ANCESTRY GROUP; BAYES THEOREM; CHROMOSOME MAPPING; COMPUTER SIMULATION; EUROPEAN CONTINENTAL ANCESTRY GROUP; GENETICS, POPULATION; HUMANS; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; SOFTWARE;

EID: 33747426655     PISSN: 14712105     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-7-317     Document Type: Article

References (53)

1. Patterson N, Hattangadi N, Lane B, Lohmueller KE, Hafler DA, Oksenberg JR, Hauser SL, Smith MW, O'Brien SJ, Altshuler D, Daly M, Reich D: Methods for high-density admixture mapping of disease genes. Am J Hum Genet 2004, 74(5):979-1000.
2. Pritchard JK, Stephens M, Donnelly P: Inference of population structure using multilocus genotype data. Genetics 2000, 155(2):945-959.
3. Rosenberg NA, Burke T, Elo K, Feldman MW, Freidlin PJ, Groenen MA Hillel J, Maki-Tanila A, Tixier-Boichard M, Vignal A, Wimmersh K, Weigend S: Empirical evaluation of genetic clustering methods using multilocus genotypes from 20 chicken breeds. Genetics 2001, 159(2):699-713.
4. Rosenberg NA, Pritchard JK, Weber JL, Cann HM, Kidd KK, Zhivotovsky LA, Feldman MW: Genetic structure of human populations. Science 2002, 298(5602):2381-2385.
5. Cardon LR, Palmer LJ: Population stratification and spurious allelic association. Lancet 2003, 361(9357):598-604.
6. Freedman ML, Reich D, Penney KL, McDonald GJ, Mignault AA, Patterson N, Gabriel SB, Topol EJ, Smoller JW, Pato CN, Pato MT, Petryshen TL, Kolonel LN, Lander ES, Sklar P, Henderson B, Hirschhorn JN, Altshuler D: Assessing the impact of population stratification on genetic association studies. Nat Genet 2004, 36(4):388-393.
7. Montana G, Pritchard JK: Statistical tests for admixture mapping with case-control and cases-only data. Am J Hum Genet 2004, 75(5):771-789.
8. Reich D, Patterson N: Will admixture mapping work to find disease genes? Philos Trans R Soc Land B Biol Sci 2005, 360(1460):1605-1607.
9. Marchini J, Cardon LR, Phillips MS, Donnelly P: The effects of human population structure on large genetic association studies. Nat Genet 2004, 36(5):512-517.
10. Chen HS, Zhu X, Zhao H, Zhang S: Qualitative semi-parametric test for genetic associations in case-control designs under structured populations. Ann Hum Genet 2003, 67(Pt 3):250-264.
11. Risch NJ: Searching for genetic determinants in the new millennium. Nature 2000, 405(6788):847-856.
12. National research council: The Evaluation of Forensic DNA Evidence. 1996.
13. Kim JJ, Verdu P, Pakstis AJ, Speed WC, Kidd JR, Kidd KK: Use of autosomal loci for clustering individuals and populations of East Asian origin. Hum Genet 2005, 117(6):511-519.
14. Overall AD, Nichols RA: A method for distinguishing consanguinity and population substructure using multilocus geno-type data. Mol Biol Evol 2001, 18(11):2048-2056.
15. Evanno G, Regnaut S, Goudet J: Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 2005, 14(8):2611-2620.
16. Petit E, Balloux F, Goudet J: Sex-biased dispersal in a migratory bat: a characterization using sex-specific demographic parameters. Evolution Int J Org Evolution 2001, 55(3):635-640.
17. Corander J, Waldmann P, Marttinen P. Sillanpaa MJ: BAPS 2: enhanced possibilities for the analysis of genetic population structure. Bioinformatics 2004, 20(15):2363-2369.
18. Corander J, Waldmann P, Sillanpaa MJ: Bayesian analysis of genetic differentiation between populations. Genetics 2003, 163(1):367-374.
19. Dawson KJ, Belkhir K: A Bayesian approach to the identification of panmictic populations and the assignment of individuals. Genet Res 2001, 78(1):59-77.
20. Excoffier L, Estoup A, Cornuet JM: Bayesian analysis of an admixture model with mutations and arbitrarily linked markers. Genetics 2005, 169(3):1727-1738.
21. Falush D, Stephens M, Pritchard JK: Inference of population structure using multilocus genotype data:linked loci and correlated allele frequencies. Genetics 2003, 164(4):1567-1587.
22. Fu R, Dey DK, Holsinger KE: Bayesian models for the analysis of genetic structure when populations are correlated. Bioinformatics 2005, 21(8):1516-1529.
23. Guillot G, Estoup A, Mortier F, Cosson JF: A spatial statistical model for landscape genetics. Genetics 2005, 170(3):1261-1280.
24. Guillot G, Mortier F, Estoup A: Geneland: A computer package for landscape genetics. Molecular Ecology Notes 2005, 5(3):708-711.
25. Hoggart CJ, Parra EJ, Shriver MD, Bonilla C, Kittles RA, Clayton DG, McKelgue PM: Control of confounding of genetic associations in stratified populations. Am J Hum Genet 2003, 72(6):1492-1504.
26. Holsinger KE, Wallace LE: Bayesian approaches for the analysis of population genetic structure: an example from Platanthera leucophaea (Orchidaceae). Mol Ecol 2004, 13(4):887-894.
27. Liu N, Wu B, Zhao H: Inference of population structure using mixture model. Technical report 2005 [http://bioinformatics.med.yale.edu/psmix].
28. Purcell S, Sham P: Properties of structured association approaches to detecting population stratification. Hum Hered 2004, 58(2):93-107.
29. Satten GA, Flanders WD, Yang Q: Accounting for unmeasured population substructure in case-control studies of genetic association using a novel latent-class model. Am J Hum Genet 2001, 68(2):466-477.
30. Tang H, Peng J, Wang P, Risch NJ: Estimation of individual admixture: analytical and study design considerations. Genet Epidemiol 2005, 28(4289-301 [http://www.fhcrc.org/science/labs/tang].
31. Wang J: Maximum-likelihood estimation of admixture proportions from genetic data. Genetics 2003, 164(2):747-765.
32. Manel S, Gaggiotti OE, Waples RS: Assignment methods: matching biological questions with appropriate techniques. TRENDS in Ecology and Evolution 2005, 20(3):136-142.
33. Coulon A, Guillot G, Cosson J-F, Angibault JMA, Aulagnier S, Cargnelutti B, Galan M, Hewison AJM: Genetics structure is influenced by lansdcape features. Empirical evidence from a roe deer population. Molecular Ecology Notes in press.
34. Banks MA, Eichert W: WHICHRUN (version 3.2): a computer program for population assignment of individuals based on multilocus genotype data. J Hered 2000, 91(1):87-89.
35. Cornuet JM, Piry S, Luikart G, Estoup A, Solignac M: New methods employing multilocus genotypes to select or exclude populations as origins of individuals. Genetics 1999, 153(4):1989-2000.
36. Rannala B, Mountain JL: Detecting immigration by using multilocus genotypes. Proc Natl Acad Sci USA 1997, 94(17):9197-9201.
37. 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(Pt 2):171-186.
38. Hoggart CJ, Shriver MD, Kittles RA, Clayton DG, McKeigue PM: Design and analysis of admixture mapping studies. AmJ Hum Genet 2004, 74(5):965-978.
39. Li SL, Yamamoto T, Yoshimoto T, Uchihi R, Mizutani M, Kurimoto Y, Tokunaga K, Jin F, Katsumata Y, Saitou N: Phylogenetic relationship of the populations within and around Japan using 105 short tandem repeat polymorphic loci. Hum Genet 2006, 118(6):695-707.
40. Kuroda Y, Kaga A, Tomooka N, Vaughan DA: Population genetic structure of Japanese wild soybean (Glycine soja) based on microsatellite variation. Mol Ecol 2006, 15(4):959-974.
41. Manel S, Bellemain E, Swenson JE, Francois O: Assumed and inferred spatial structure of populations: the Scandinavian brown bears revisited. Mol Ecol 2004, 13(5):1327-1331.
42. Pearse DE, Arndt AD, Valenzuela N, Miller BA, Cantarelli V, Sites JW Jr: Estimating population structure under nonequilibrium conditions in a conservation context: continent-wide population genetics of the giant Amazon river turtle, Podocnemis expansa (Chelonia; Podocnemididae). Mol Ecol 2006, 15(4):985-1006.
43. Dempster AP, Laird NM, Rubin DB: Maximum likelihood from incomplete data via the EM algorithm. Journal of the Royal Statistical Society Series B 1977, 34:1-38.
44. Yang BZ, Zhao H, Kranzler HR, Gelernter J: Practical population group assignment with selected informative markers: characteristics and properties of Bayesian clustering via STRUCTURE. Genet Epidemiol 2005, 28(4):302-312.
45. Pritchard JK, Donnelly P: Case-control studies of association in structured or admixed populations. Theor Popul Biol 2001, 60(3):227-237.
46. Turakulov R, Easteal S: Number of SNPS loci needed to detect population structure. Hum Hered 2003, 55(1):37-45.
47. Manel S, Berthier P, Luikart G: Detecting Wildlife Poaching. Identifying the Origin of Individuals with Bayesian Assignment Tests and Multilocus Genotypes. Conservation Biology 2002, 16(3):650-659.
48. Akaike H: A new look at the statistical identification model. IEEE Trans Automatic Control 1974, 19:716-723.
49. Zhu X, Zhang S, Zhao H, Cooper RS: Association mapping, using a mixture model for complex traits. Genet Epidemiol 2002, 23(2):181-196.
50. Chen H, Chen J, Kalbfleisch JD: A modied likelihood ratio test for homogeneity in finite mixture models. Journal of Royal Statistical Society B 2001, 63:19-29.
51. Chen H, Chen J, Kalbfleisch JD: Testing for a finite mixture model with two components. Journal of Royal Statistical Society B 2004, 66:95-115.
52. Stephens M: Dealing with label-switching in mixture models. Journal of Royal Statistical Society B 2000, 62:795-809.
53. Stephens M, Smith NJ, Donnelly P: A new statistical method for haplotype reconstruction from population data. Am J Hum Genet 2001, 68(4):978-989.