Differential Evolution approach to detect recent admixture

BMC Genomics

Volumn 16, Issue 8, 2015, Pages

  Kozlov, Konstantin ^a   Chebotarev, Dmitri ^b   Hassan, Mehedi ^c   Triska, Martin ^c,e   Triska, Petr ^d   Flegontov, Pavel ^e   Tatarinova, Tatiana V ^f  

^a PETER THE GREAT ST PETERSBURG POLYTECHNIC UNIVERSITY   (Russian Federation)

^b International Rice Research Institute   (United States)

^c UNIVERSITY OF GLAMORGAN   (United Kingdom)

^d UNIVERSITY OF PORTO   (Portugal)

^e UNIVERSITY OF OSTRAVA   (Czech Republic)

^f UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

Author keywords

Admixture; Ancestry prediction; Differential evolution; Geographical origin

Indexed keywords

ADMIXTURE; ANCESTRY GROUP; ARTICLE; BIOGEOGRAPHY; COMPARATIVE STUDY; COMPUTER ANALYSIS; COMPUTER INTERFACE; COMPUTER PREDICTION; COMPUTER PROGRAM; COMPUTER SIMULATION; CONTROLLED STUDY; ETHNICITY; GENE FREQUENCY; GENETIC ALGORITHM; GENETIC DATABASE; GEOGRAPHIC ORIGIN; HUMAN; HUMAN GENOME; ONLINE ANALYSIS; POPULATION GENETIC PARAMETERS; POPULATION GENETICS; ANIMAL; BIOLOGY; ETHNIC GROUP; EVOLUTION; GENETICS; MEDICAL GENETICS; PROCEDURES; SOFTWARE;

ANIMALS; BIOLOGICAL EVOLUTION; COMPUTATIONAL BIOLOGY; ETHNIC GROUPS; GENETICS, MEDICAL; HUMANS; SOFTWARE;

EID: 84969584485     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-16-S8-S9     Document Type: Article

References (38)

1. Tishkoff SA, Kidd KK: Implications of biogeography of human populations for "race" and medicine. Nature Genetics. 2004, 21-27. doi:10.1038/ng1438
2. Takeda J-i, Yamasaki C, Murakami K, Nagai Y, Sera M, Hara Y, Obi N, Habara T, Gojobori T, Imanishi T: H-invdb in 2013: an omics study platform for human functional gene and transcript discovery. Nucleic Acids Research. 2013, 41 (D1): 915-919. 10.1093/nar/gks1245. doi:10.1093/nar/gks1245, [ http://nar.oxfordjournals.org/content/41/D1/D915.full.pdf+html ]
3. Novembre J, Johnson T, Bryc K, Kutalik Z, Boyko AR, Auton A, Indap A, King KS, Bergmann S, Nelson MR, Stephens M, Bustamante CD: Genes mirror geography within europe. Nature. 2008, 456: doi:10.1038/nature07331
4. Yang W-Y, Novembre J, Eskin E, Halperin E: A model-based approach for analysis of spatial structure in genetic data. Nature Genetics. 2012, 44: doi:10.1038/ng.2285
5. François O, Currat M, Ray N, Han E, Excoffier L, Novembre J: Principal component analysis under population genetic models of range expansion and admixture. Molecular Biology and Evolution. 2010, 27 (6): 1257-1268. 10.1093/molbev/msq010. doi:10.1093/molbev/msq010, [ http://mbe.oxfordjournals.org/content/27/6/1257.full.pdf+html ]
6. Rannala B, Mountain JL: Detecting immigration by using multilocus genotypes. Proceedings of the National Academy of Sciences. 1997, 94 (17): 9197-9201. 10.1073/pnas.94.17.9197. [ http://www.pnas.org/content/94/17/9197.full.pdf+html ]
7. Brown R, Pasaniuc B: Enhanced methods for local ancestry assignment in sequenced admixed individuals. PLoS Comput Biol. 2014, 10 (4): 1003555-10.1371/journal.pcbi.1003555. doi:10.1371/journal.pcbi.1003555
8. Sankararaman S, Sridhar S, Halperin E: Estimating local ancestry in admixed populations. The American Journal of Human Genetics. 2014, 82 (2): 290-303. doi:10.1016/j.ajhg.2007.09.022
9. Churchhouse C, Marchini J: Multiway admixture deconvolution using phased or unphased ancestral panels. Genetic Epidemiology. 2013, 37 (1): 1-12. 10.1002/gepi.21692. doi:10.1002/gepi.21692
10. Alexander DH, Lange K: Enhancements to the admixture algorithm for individual ancestry estimation. BMC Bioinformatics. 2011, 12 (246): doi:10.1186/1471-2105-12-246
11. Pritchard JK, Stephens M, Donnelly P: Inference of population structure using multilocus genotype data. Genetics. 2000, 155 (2): 945-959. [ http://www.genetics.org/content/155/2/945.full.pdf+html ]
12. 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. [ http://www.genetics.org/content/164/4/1567.full.pdf+html ]
13. Price AL, Tandon A, Patterson N, Barnes KC, Rafaels N, Ruczinski I, Beaty TH, Mathias R, Reich D, Myers S: Sensitive detection of chromosomal segments of distinct ancestry in admixed populations. PLoS Genet. 2009, 5 (6): 1000519-10.1371/journal.pgen.1000519. doi:10.1371/journal.pgen.1000519
14. Liu Y, Nyunoya T, Leng S, Belinsky SA, Tesfaigzi Y, Bruse S: Softwares and methods for estimating genetic ancestry in human populations. Human Genomics. 2013, 7 (1): 1-10.1186/1479-7364-7-1. doi:10.1186/1479-7364-7-1
15. Frichot E, Schoville SD, Bouchard G, Francois O: Correcting principal component maps for effects of spatial autocorrelation in population genetic data. Frontiers in Genetics. 2012, 3 (254): doi:10.3389/fgene.2012.00254
16. Elhaik E: The missing link of jewish european ancestry: Contrasting the rhineland and the khazarian hypotheses. Genome Biology and Evolution. 2012, doi:10.1093/gbe/evs119, [ http://gbe.oxfordjournals.org/content/early/2012/12/14/gbe.evs119.full.pdf+html ]
17. Yang W-Y, Platt A, Chiang CW-K, Eskin E, Novembre J, Pasaniuc B: Spatial localization of recent ancestors for admixed individuals. bioRxiv. 2014, doi:10.1101/004713
18. Sohn K-A, Ghahramani Z, Xing EP: Robust estimation of local genetic ancestry in admixed populations using a nonparametric bayesian approach. Genetics. 2012, 191 (4): 1295-1308. 10.1534/genetics.112.140228. doi:10.1534/genetics.112.140228, [ http://www.genetics.org/content/191/4/1295.full.pdf+html ]
19. Drummond AJ, Rambaut A: Beast: Bayesian evolutionary analysis by sampling trees. BMC Evolutionary Biology. 2007, 7 (24): doi:10.1186/1471-2148-7-214
20. Ree RH, Smith SA: Maximum likelihood inference of geographic range evolution by dispersal, local extinction, and cladogenesis. Systematic Biology. 2008, 57 (1): 4-14. 10.1080/10635150701883881. doi:10.1080/10635150701883881, [ http://sysbio.oxfordjournals.org/content/57/1/4.full.pdf+html ]
21. Elhaik E, Tatarinova T, Chebotarev D, Piras IS, Maria Calò C, De Montis A, Atzori M, Marini M, Tofanelli S, Francalacci P, Pagani L, Tyler-Smith C, Xue Y, Cucca F, Schurr TG, Gaieski JB, Melendez C, Vilar MG, Owings AC, Gómez R, Fujita R, Santos FR, Comas D, Balanovsky O, Balanovska E, Zalloua P, Soodyall H, Pitchappan R, GaneshPrasad A, Hammer M, Matisoo-Smith L, Wells RS, Consortium TG: Geographic population structure analysis of worldwide human populations infers their biogeographical origins. Nature Communications. 2014, 5: doi:10.1038/ncomms4513
22. Wang W: The rise of intermarriage: Rates, characteristics vary by race and gender. Technical report. 2012, Pew Social & Demographic Trends, Washington, D.C
23. Elhaik E, Tatarinova T, Klyosov A, Graur D: The "extremely ancient" chromosome that isn't: A forensic bioinformatics investigation of albert perry's x-degenerate portion of the y chromosome. European Journal of Human Genetics. 2014, 22: 1111-1116. 10.1038/ejhg.2013.303. doi:10.1038/ejhg.2013.303
24. Elhaik E, Greenspan E, Staats S, Krahn T, Tyler-Smith C, Xue Y, Tofanelli S, Francalacci P, Cucca F, Pagani L, Jin L, Li H, Schurr T, Greenspan B, Spencer WR, Consortium G: The genochip: a new tool for genetic anthropology. Genome Biol Evol. 2013, 5: 1021-31. 10.1093/gbe/evt066. doi:10.1093/gbe/evt066
25. Alexander DH, Novembre J, Lange K: Fast model-based estimation of ancestry in unrelated individuals. Genome Research. 2009, doi:10.1101/gr.094052.109, [ http://genome.cshlp.org/content/early/2009/07/31/gr.094052.109.full.pdf+html ]
26. Jakobsson M, Rosenberg NA: Clumpp: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics. 2007, 23: 1801-1806. 10.1093/bioinformatics/btm233.
27. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira M, Bender D, Maller J, Sklar P, de Bakker P, Daly M, Sham P: Plink: a tool set for whole-genome association and population-based linkage analyses. The American Journal of Human Genetics. 2007, 81: 559-575. 10.1086/519795.
28. Berkelaar M, Eikland K, Notebaert P: Package "lpsolve". CRAN. 2004, 1-11.
29. Storn R, Price K: Differential evolution - a simple and efficient heuristic for global optimization over continuous spaces. Technical Report Technical Report TR-95-012, ICSI. 1995
30. Storn R, Price K: Differential Evolution - a simple and efficient heuristic for global optimization over continuous spaces. Journal of Global Optimization. 1997, 11 (4): 341-359. 10.1023/A:1008202821328.
31. Kozlov K, Samsonov A: Deep - differential evolution entirely parallel method for gene regulatory networks. Journal of Supercomputing. 2013, 57: 172-178.
32. Fan H-Y, Lampinen J: A trigonometric mutation operation to differential evolution. Journal of Global Optimization. 2003, 27: 105-129. 10.1023/A:1024653025686.
33. Zaharie D: Parameter adaptation in differential evolution by controlling the population diversity. Proc. of 4th InternationalWorkshop on Symbolic and Numeric Algorithms for Scientific Computing. Edited by: Petcu D. 2002, Timisoara, Romania, 385-397.
34. Nuriddinov MA, Kazantsev FV, Rozanov AS, Kozlov KN, Peltek SE, Akberdin IR, Kolchanov NA: Mathematical modeling of ethanol and lactic acid biosynthesis by theromphilic geobacillus bacteria. Russian Journal of Genetics: Applied Research. 2013, 17 (4/1): 686-704.
35. Ivanisenko NV, Mishchenko EL, Akberdin IR, Demenkov PS, Likhoshvai VA, Kozlov KN, Todorov DI, Gursky VV, Samsonova MG, Samsonov AM, Clausznitzer D, Kaderali L, Kolchanov NA, Ivanisenko VA: A new stochastic model for subgenomic hepatitis c virus replication considers drug resistant mutants. PLoS ONE. 2014, 9 (3): 91502-10.1371/journal.pone.0091502. doi:10.1371/journal.pone.0091502
36. Kozlov K, Surkova S, Myasnikova E, Reinitz J, Samsonova M: Modeling of gap gene expression in Drosophila Kruppel mutants. PLoS Comput Biol. 2012, 8 (8): 1002635-10.1371/journal.pcbi.1002635. doi:10.1371/journal.pcbi.1002635
37. Tatarinova T, Neely M, Bartroff J, van Guilder M, Yamada W, Bayard D, Jelliffe R, Leary R, Chubatiuk A, Schumitzky A: Two general methods for population pharmacokinetic modeling: non-parametric adaptive grid and non-parametric Bayesian. Journal of Pharmacokinetics and Pharmacodynamics. 2013, 40 (1): 189-199.
38. Tatarinova T, Kryshchenko A, Triska M, Hassan M, Murphy D, Neely M, Schumitzky A: NPEST: a nonparametric method and a database for Transcription Start Site prediction. Quantitative Biology. 2013, 1 (4): 261-271. 10.1007/s40484-013-0022-2.