Generalized analysis of molecular variance

PLoS Genetics

Volumn 3, Issue 4, 2007, Pages 0467-0478

  Nievergelt, Caroline M ^a,b,c   Libiger, Ondrej ^a,b   Schork, Nicholas J ^a,b,c,d  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^c San Diego   (United States)

^d SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA MARKER;

ANALYSIS OF MOLECULAR VARIANCE; ANTHROPOMETRY; ARTICLE; BLOOD PRESSURE; CLUSTER ANALYSIS; CRANIOMETRY; ETHNICITY; GENE FREQUENCY; GENERALIZED ANALYSIS OF MOLECULAR VARIANCE; GENETIC SIMILARITY; GENETIC VARIABILITY; GENOTYPE; HAPLOTYPE MAP; INFORMATION PROCESSING; MULTIPLE REGRESSION; MULTIVARIATE ANALYSIS; PHYLOGENETIC TREE; QUANTITATIVE ANALYSIS; STATISTICAL ANALYSIS; ANALYSIS OF VARIANCE; CELL LINE; CEPHALOMETRY; FEMALE; GENETIC DATABASE; GENETICS; HAPLOTYPE; HUMAN; HUMAN CHROMOSOME; MALE; PHYLOGENY;

ANALYSIS OF VARIANCE; CELL LINE; CEPHALOMETRY; CHROMOSOMES, HUMAN; DATABASES, GENETIC; FEMALE; HAPLOTYPES; HUMANS; MALE; PHYLOGENY; VARIATION (GENETICS);

EID: 34247552951     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.0030051     Document Type: Article

References (83)

1. Rosenberg NA, Pritchard JK, Weber JL, Cann HM, Kidd KK, et al. (2002) Genetic structure of human populations. Science 298: 2381-2385.
2. Bamshad M, Wooding S, Salisbury BA, Stephens JC (2004) Deconstructing the relationship between genetics and race. Nat Rev Genet 5: 598-609.
3. Serre D, Paabo S (2004) Evidence for gradients of human genetic diversity within and among continents. Genome Res 14: 1679-1685.
4. Cavalli-Sforza LL (2005) The Human Genome Diversity Project: Past, present and future. Nat Rev Genet 6: 333-340.
5. Mountain JL, Ramakrishnan U (2005) Impact of human population history on distributions of individual-level genetic distance. Hum Genomics 2: 4-19.
6. Ramachandran S, Deshpande O, Roseman CC, Rosenberg NA, Feldman MW, et al. (2005) Support from the relationship of genetic and geographic distance in human populations for a serial founder effect originating in Africa. Proc Natl Acad Sci U S A 102: 15942-15947.
7. Shriver MD, Mei R, Parra EJ, Sonpar V, Halder I, et al. (2005) Large-scale SNP analysis reveals clustered and continuous patterns of human genetic variation. Hum Genomics 2: 81-89.
8. Liu H, Prugnolle F, Manica A, Balloux F (2006) A geographically explicit genetic model of worldwide human-settlement history. Am J Hum Genet 79: 230-237.
9. Kittles RA, Chen W, Panguluri RK, Ahaghotu C, Jackson A, et al. (2002) CYP3A4-V and prostate cancer in African Americans: Causal or confounding association because of population stratification? Hum Genet 110: 553-560.
10. Cardon LR, Palmer LJ (2003) Population stratification and spurious allelic association. Lancet 361: 598-604.
11. Freedman ML, Reich D, Penney KL, McDonald GJ, Mignault AA, et al. (2004) Assessing the impact of population stratification on genetic association studies. Nat Genet 36: 388-393.
12. Marchini J, Cardon LR, Phillips MS, Donnelly P (2004) The effects of human population structure on large genetic association studies. Nat Genet 36: 512-517.
13. Campbell CD, Ogburn EL, Lunetta KL, Lyon HN, Freedman ML, et al. (2005) Demonstrating stratification in a European American population. Nat Genet 37: 868-872.
14. Helgason A, Yngvadottir B, Hrafnkelsson B, Gulcher J, Stefansson K (2005) An Icelandic example of the impact of population structure on association studies. Nat Genet 37: 90-95.
15. Reiner AP, Ziv E, Lind DL, Nievergelt CM, Schork NJ, et al. (2005) Population structure, admixture, and aging-related phenotypes in African American adults: The cardiovascular health study. Am J Hum Genet 76: 463-477.
16. Voight BF, Pritchard JK (2005) Confounding from cryptic relatedness in case-control association studies. PLoS Genet 1: e32. doi:10.1371/journal.pgen. 0010032
17. Berger M, Stassen HH, Kohler K, Krane V, Monks D, et al. (2006) Hidden population substructures in an apparently homogeneous population bias association studies. Eur J Hum Genet 14: 236-244.
18. Seldin MF, Shigeta R, Villoslada P, Selmi C, Tuomilehto J, et al. (2006) European population substructure: Clustering of northern and southern populations. PLoS Genet 2: e143. doi:10.1371/journal.pgen.0020143
19. Foll M, Gaggiotti O (2006) Identifying the environmental factors that determine the genetic structure of populations. Genetics 174: 875-891.
20. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155: 945-959.
21. Dawson KJ, Belkhir K (2001) A Bayesian approach to the identification of panmictic populations and the assignment of individuals. Genet Res 78: 59-77.
22. Satten GA, Flanders WD, Yang Q (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.
23. 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.
24. 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.
25. Stassen HH, Hoffman K, Scharfetter C (2003) Similarity by state/descent and genetic vector spaces: Analysis of a longitudinal family study. BMC Genet 4 Suppl 1: S59.
26. Kohler K, Bickeboller H (2005) Case-control association tests correcting for population stratification. Ann Hum Genet 69: 98-115.
27. Tang H, Peng J, Wang P, Risch NJ (2005) Estimation of individual admixture: Analytical and study design considerations. Genet Epidemiol 28: 289-301.
28. Tsai HJ, Choudhry S, Naqvi M, Rodriguez-Cintron W, Burchard EG, et al. (2005) Comparison of three methods to estimate genetic ancestry and control for stratification in genetic association studies among admixed populations. Hum Genet 118: 424-433.
29. Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, et al. (2006) Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet 38: 904-909.
30. Redden DT, Divers J, Vaughan LK, Tiwari HK, Beasley TM, et al. (2006) Regional admixture mapping and structured association testing: Conceptual unification and an extensible general linear model. PLoS Genet 2: e137. doi:10.1371/journal.pgen.0020137
31. Rosenberg NA, Nordborg M (2006) A general population-genetic model for the production by population structure of spurious genotype-phenotype associations in discrete, admixed, or spatially distributed populations. Genetics 173: 1665-1678.
32. Setakis E, Stirnadel H, Balding DJ (2006) Logistic regression protects against population structure in genetic association studies. Genome Res 16: 290-296.
33. Yu J, Pressoir G, Briggs WH, Vroh Bi I, Yamasaki M, et al. (2006) A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat Genet 38: 203-208.
34. 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.
35. Wu B, Liu N, Zhao H (2006) PSMIX: An R package for population structure inference via maximum likelihood method. BMC Bioinformatics 7: 317.
36. Zhang S, Zhu X, Zhao H (2003) On a semiparametric test to detect associations between quantitative traits and candidate genes using unrelated individuals. Genet Epidemiol 24: 44-56.
37. 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.
38. Bowcock AM, Ruiz-Linares A, Tomfohrde J, Minch E, Kidd JR, et al. (1994) High resolution of human evolutionary trees with polymorphic microsatellites. Nature 368: 455-457.
39. Mountain JL, Cavalli-Sforza LL (1997) Multilocus genotypes, a tree of individuals, and human evolutionary history. Am J Hum Genet 61: 705-718.
40. Shriver MD, Kennedy GC, Parra EJ, Lawson HA, Sonpar V, et al. (2004) The genomic distribution of population substructure in four populations using 8,525 autosomal SNPs. Hum Genomics 1: 274-286.
41. Li CC, Weeks DE, Chakravarti A (1993) Similarity of DNA fingerprints due to chance and relatedness. Hum Hered 43: 45-52.
42. Queller DC, Goodnight KF (1989) Estimating relatedness using genetic markers. Evolution 43: 258-275.
43. Ritland K (1996) Estimators for pairwise relatedness and individual inbreeding coefficients. Genet Res: 175-185.
44. Lynch M, Ritland K (1999) Estimation of pairwise relatedness with molecular markers. Genetics 152: 1753-1766.
45. Wang J (2002) An estimator for pairwise relatedness using molecular markers. Genetics 160: 1203-1215.
46. Rosenberg NA, Li LM, Ward R, Pritchard JK (2003) Informativeness of genetic markers for inference of ancestry. Am J Hum Genet 73: 1402-1422.
47. Collins-Schramm HE, Chima B, Morii T, Wah K, Figueroa Y, et al. (2004) Mexican American ancestry-informative markers: examination of population structure and marker characteristics in European Americans, Mexican Americans, Amerindians and Asians. Hum Genet 114: 263-271.
48. Smith MW, Patterson N, Lautenberger JA, Truelove AL, McDonald GJ, et al. (2004) A high-density admixture map for disease gene discovery in African Americans. Am J Hum Genet 74: 1001-1013.
49. Tian C, Hinds DA, Shigeta R, Kittles R, Ballinger DG, et al. (2006) A genomewide single-nucleotide-polymorphism panel with high ancestry information for African American admixture mapping. Am J Hum Genet 79: 640-649.
50. Excoffier L, Smouse PE, Quattro JM (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: Application to human mitochondrial DNA restriction data. Genetics 131: 479-491.
51. Wessel J, Schork NJ (2006) Generalized genomic distance-based regression methodology for multilocus association analysis. Am J Hum Genet 79: 792-806.
52. Zapala MA, Schork NJ (2006) Multivariate regression analysis of distance matrices for testing associations between gene expression patterns and related variables. Proc Natl Acad Sci U S A 103: 19430-19435.
53. Smouse PE, Long JC (1992) Matrix correlation analysis in anthropology and genetics. American Journal of Physical Anthropology 35: 187-213.
54. Howells WW (1973) Cranial variation in man: A study of multivariate analysis of patterns of difference among recent human populations. Cambridge (Massachusetts): Harvard University Press, Peabody Museum of Archaeology and Ethnology. 259 p.
55. Howells WW (1989) Skull shapes and the map: craniometric analyses in the dispersion of modern Homo. Cambridge (Massachusetts): Harvard University Press, Peabody Museum of Archaeology and Ethnology. 189 p.
56. Cann HM, de Toma C, Cazes L, Legrand MF, Morel V, et al. (2002) A human genome diversity cell line panel. Science 296: 261-262.
57. Manica A, Prugnolle F, Balloux F (2005) Geography is a better determinant of human genetic differentiation than ethnicity. Hum Genet 118: 366-371.
58. 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.
59. Roseman CC (2004) Detecting interregionally diversifying natural selection on modern human cranial form by using matched molecular and morphometric data. Proc Natl Acad Sci U S A 101: 12824-12829.
60. Roseman CC, Weaver TD (2004) Multivariate apportionment of global human craniometric diversity. Am J Phys Anthropol 125: 257-263.
61. Martinez-Abadias N, Gonzalez-Jose R, Gonzalez-Martin A, Van der Molen S, Talavera A, et al. (2006) Phenotypic evolution of human craniofacial morphology after admixture: a geometric morphometrics approach. Am J Phys Anthropol 129: 387-398.
62. Parra EJ, Kittles RA, Shriver MD (2004) Implications of correlations between skin color and genetic ancestry for biomedical research. Nat Genet 36: S54-S60.
63. Consortium TIH (2005) A haplotype map of the human genome. Nature 437: 1299-1320.
64. Patterson N, Price AL, Reich D (2006) Population Structure and Eigenanalysis. PLoS Genet 2: e190. doi:10.1371/journal.pgen.0020190
65. Lewontin R (1972) The apportionment of human diversity. Evolutionary Biology 6: 381-398.
66. Cavalli-Sforza LL, Feldman MW (2003) The application of molecular genetic approaches to the study of human evolution. Nat Genet 33 Suppl: 266-275.
67. Barbujani G, Goldstein DB (2004) Africans and Asians abroad: Genetic diversity in Europe. Annu Rev Genomics Hum Genet 5: 119-150.
68. Mountain JL, Risch N (2004) Assessing genetic contributions to phenotypic differences among "racial" and "ethnic" groups. Nat Genet 36: S48-S53.
69. Lander ES, Schork NJ (1994) Genetic dissection of complex traits. Science 265: 2037-2048.
70. Tishkoff SA, Kidd KK (2004) Implications of biogeography of human populations for "race" and medicine. Nat Genet 36: S21-S27.
71. Turakulov R, Easteal S (2003) Number of SNPS loci needed to detect population structure. Hum Hered 55: 37-45.
72. Yang BZ, Zhao H, Kranzler HR, Gelernter J (2005) Characterization of a likelihood based method and effects of markers informativeness in evaluation of admixture and population group assignment. BMC Genet 6: 50.
73. Nievergelt C, Kelsoe J, Shimizu C, Burns J, Schork N. (2006) Multivariate distance based methods for testing and accommodating population substructure [abstract 2203]. Annual meeting of The American Society of Human Genetics, 12 October 2006, New Orleans, Louisiana. Available: http://www.ashg.org/genetics/ ashg06s/index.shtml. Accessed 5 March 2007.
74. Van de Casteele T, Galbusera P, Matthysen E (2001) A comparison of microsatellite-based pairwise relatedness estimators. Mol Ecol 10: 1539-1549.
75. Widdig A, Nurnberg P, Krawczak M, Streich WJ, Bercovitch FB (2001) Paternal relatedness and age proximity regulate social relationships among adult female rhesus macaques. Proc Natl Acad Sci U S A 98: 13769-13773.
76. Parsons K, Durban J, Claridge D, Balcomb K, Noble L, et al. (2003) Kinship as a basis for alliance formation between male bottlenose dolphins, Tursiops truncatus, in the Bahamas. Anim Behav 66: 185-194.
77. Lobo JA, Quesada M, Stoner KE (2005) Effects of pollination by bats on the mating system of Ceiba pentandra (Bombacaceae) populations in two tropical life zones in Costa Rica. Am J Bot 92: 370-376.
78. McArdle BH, Anderson MJ (2001) Fitting multivariate models to community data: A comment on distance-based redundancy analysis. Ecology 82: 290-297.
79. Gower JC (1966) Some distance properties of latent root and vector methods used in multivariate analysis. Biometrika 53: 325-338.
80. Good P (1994) Permutation tests. New York: Springer-Verlag. 228 p.
81. Edington ES (1995) Randomization tests. New York: Marcel Dekker. 409 p.
82. Weir BS (1996) Genetic data analysis II: Methods for discrete population genetic data. Sunderland (Massachusetts): Sinauer Associates. 445 p.
83. Rosenberg NA (2007) Human genetic variation: Answers to frequently asked questions. In: Bamshad M, editor. Human genetic diversity: Implications for race, ancestry, and health. Oxford: Oxford University Press.