Fast and efficient estimation of individual ancestry coefficients

Genetics

Volumn 196, Issue 4, 2014, Pages 973-983

  Frichot, Eric ^a   Mathieu, François ^a   Trouillon, Théo ^a,b   Bouchard, Guillaume ^b   François, Olivier ^a  

^a UNIV GRENOBLE ALPES   (France)

^b XEROX RESEARCH CENTRE EUROPE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ADMIXTURE ALGORITHM; ALGORITHM; ANCESTRY COEFFICIENT; ARABIDOPSIS THALIANA; ARTICLE; COMPUTER PROGRAM; COMPUTER SIMULATION; CONSTANTS AND COEFFICIENTS; CROSS ENTROPY CRITERION; GENE LINKAGE DISEQUILIBRIUM; GENETIC MODEL; GENOME; GENOTYPE; HUMAN; INBRED STRAIN; NONHUMAN; NONNEGATIVE MATRIX FACTORIZATION ALGORITHM; POPULATION GENETIC STRUCTURE; PREDICTION; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; BIOLOGY; GENE FREQUENCY; GENETIC ASSOCIATION; GENETICS; PLANT; POPULATION GENETICS; POPULATION GROUP; PROCEDURES; STATISTICAL MODEL; TIME;

ALGORITHMS; COMPUTATIONAL BIOLOGY; GENE FREQUENCY; GENETIC ASSOCIATION STUDIES; GENETICS, POPULATION; GENOTYPE; HUMANS; LIKELIHOOD FUNCTIONS; PLANTS; POPULATION GROUPS; SOFTWARE; TIME FACTORS;

EID: 84901292350     PISSN: 00166731     EISSN: 19432631     Source Type: Journal    
DOI: 10.1534/genetics.113.160572     Document Type: Article

References (33)

1. Alexander, D. H., and K. Lange, 2011 Enhancements to the admixture algorithm for individual ancestry estimation. BMC Bioinformatics 12: 246.
2. Alexander, D. H., J. Novembre, and K. Lange, 2009 Fast modelbased estimation of ancestry in unrelated individuals. Genome Res. 19: 1655-1664.
3. Atwell, S., Y. S. Huang, B. J. Vilhjálmsson, G. Willems, M. Horton et al., 2010 Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines. Nature 465: 627-631.
4. Berry, M. W., M. Browne, A. N. Langville, V. P. Pauca, and R. J. Plemmons, 2007 Algorithms and applications for approximate nonnegative matrix factorization. Comput. Stat. Data Anal. 52: 155-173.
5. Brunet, J. P., P. Tamayo, T. R. Golub, and J. P. Mesirov, 2004 Metagenes and molecular pattern discovery using matrix factorization. Proc. Natl. Acad. Sci. USA 101: 4164-4169.
6. Cavalli-Sforza, L. L., and W. F. Bodmer, 1971 The Genetics of Human Populations. Dover, New York.
7. Ding, C., T. Li, and W. Peng, 2008 On the equivalence between non-negative matrix factorization and probabilistic latent semantic indexing. Comput. Stat. Data Anal. 52: 3913-3927.
8. Eastment, H. T., and W. J. Krzanowski, 1982 Cross-validatory choice of the number of components from a principal component analysis. Technometrics 24: 73-77.
9. Engelhardt, B. E., and M. Stephens, 2010 Analysis of population structure: a unifying framework and novel methods based on sparse factor analysis. PLoS Genet. 6: 12.
10. François, O., M. G. B. Blum, M. Jakobsson, and N. A. Rosenberg, 2008 Demographic history of European populations of Arabidopsis thaliana. PLoS Genet. 4: e1000075.
11. François, O., M. Currat, N. Ray, E. Han, L. Excoffier et al., 2010 Principal component analysis under population genetic models of range expansion and admixture. Mol. Biol. Evol. 27: 1257-1268.
12. Frichot, E., S. D. Schoville, G. Bouchard, and O. François, 2012 Correcting principal component maps for effects of spatial autocorrelation in population genetic data. Front. Genet. 3: 254.
13. Frichot, E., S. D. Schoville, G. Bouchard, and O. François, 2013 Testing for associations between loci and environmental gradients using latent factor mixed models. Mol. Biol. Evol. 30: 1687-1699.
14. Kim, H., and H. Park, 2007 Sparse non-negative matrix factorizations via alternating non-negativity-constrained least squares for microarray data analysis. Bioinformatics 23: 1495-1502.
15. Kim, J., and H. Park, 2011 Fast nonnegative matrix factorization: an active-set-like method and comparisons. SIAM J. Sci. Comput. 33: 3261-3281.
16. Jakobsson, M., and N. A. Rosenberg, 2007 CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics 23: 1801-1806.
17. Lawson, D. J., and D. Falush, 2012 Population identification using genetic data. Annu. Rev. Genomics Hum. Genet. 13: 337-361.
18. Lawson, D. J., G. Hellenthal, S. Myers, and D. Falush, 2012 Inference of population structure using dense haplotype data. PLoS Genet. 8: e1002453.
19. Lee, D. D., and H. S. Seung, 1999 Learning the parts of objects by non-negative matrix factorization. Nature 401(6755): 788-791.
20. Li, J. Z., D. M. Absher, H. Tang, A. M. Southwick, A. M. Casto et al., 2008 Worldwide human relationships inferred from genomewide patterns of variation. Science 319: 1100-1104.
21. Marchini, J., L. R. Cardon, M. S. Phillips, and P. Donnelly, 2004 The effects of human population structure on large genetic association studies. Nat. Genet. 36: 512-517.
22. McVean, G., 2009 A genealogical interpretation of principal components analysis. PLoS Genet. 5: 10.
23. Novembre, J., and M. Stephens, 2008 Interpreting principal component analyses of spatial population genetic variation. Nat. Genet. 40: 646-649.
24. 1000 Genomes Project Consortium, 2012 An integrated map of genetic variation from 1,092 human genomes. Nature 491: 56-65.
25. Parry, R. M., and M. D. Wang, 2013 A fast least-squares algorithm for population inference. BMC Bioinformatics 14: 28.
26. Patterson, N., A. Price, and D. Reich, 2006 Population structure and eigenanalysis. PLoS Genet. 2: e190.
27. Patterson, N. J., P. Moorjani, Y. Luo, S. Mallick, N. Rohland et al., 2012 Ancient admixture in human history. Genetics 192: 1065-1093.
28. Price, A. L., N. J. Patterson, R. M. Plenge, M. E. Weinblatt, N. A. Shadick et al., 2006 Principal components analysis corrects for stratification in genome-wide association studies. Nat. Genet. 38: 904-909.
29. Pritchard, J. K., M. Stephens, and P. Donnelly, 2000a Inference of population structure using multilocus genotype data. Genetics 155: 945-959.
30. Pritchard, J. K., M. Stephens, N. A. Rosenberg, and P. Donnelly, 2000b Association mapping in structured populations. Am. J. Hum. Genet. 67: 170.
31. Roberts, D. F., and R. W. Hiorns, 1965 Methods of analysis of the genetic composition of a hybrid population. Hum. Biol. 37: 38-43.
32. Tang, H., J. Peng, P. Wang, and N. Risch, 2005 Estimation of individual admixture: analytical and study design considerations. Genet. Epidemiol. 28: 289-301.
33. Wold, S., 1978 Cross-validatory estimation of the number of components in factor and principal components models. Technometrics 20: 397-405.