New software for the fast estimation of population recombination rates (FastEPRR) in the genomic era

G3: Genes, Genomes, Genetics

Volumn 6, Issue 6, 2016, Pages 1563-1571

  Gao, Feng ^a,b   Ming, Chen ^a,b   Hu, Wangjie ^a,b   Li, Haipeng ^a  

^a INSTITUTE OF GEOLOGY AND GEOPHYSICS   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

Author keywords

Boosting; Fast estimation; Genetic map; Genomic era; Population recombination rates

Indexed keywords

AVERAGING; COMB; COMPUTER PROGRAM; CORRELATION COEFFICIENT; DEMOGRAPHY; DIPLOIDY; GENE MAPPING; GENE MUTATION; HUMAN; HUMAN EXPERIMENT; HUMAN TISSUE; MACHINE LEARNING; NEXT GENERATION SEQUENCING; POPULATION MODEL; SAMPLE SIZE; ALGORITHM; GENETIC POLYMORPHISM; GENETIC RECOMBINATION; GENOME; GENOMICS; HAPLOTYPE; POPULATION GENETICS; PROCEDURES; REPRODUCIBILITY; SOFTWARE;

ALGORITHMS; GENETICS, POPULATION; GENOME; GENOMICS; HAPLOTYPES; HUMANS; POLYMORPHISM, GENETIC; RECOMBINATION, GENETIC; REPRODUCIBILITY OF RESULTS; SOFTWARE;

EID: 84973124298     PISSN: None     EISSN: 21601836     Source Type: Journal    
DOI: 10.1534/g3.116.028233     Document Type: Article

References (48)

1. Altshuler, D., R. M. Durbin, G. R. Abecasis, D. R. Bentley, A. Chakravarti et al., 2010 A map of human genome variation from population-scale sequencing. Nature 467(7319): 1061-1073.
2. Altshuler, D. M., R. M. Durbin, G. R. Abecasis, D. R. Bentley, A. Chakravarti et al., 2012 An integrated map of genetic variation from 1,092 human genomes. Nature 491(7422): 56-65.
3. Auton, A., and G. McVean, 2007 Recombination rate estimation in the presence of hotspots. Genome Res. 17(8): 1219-1227.
4. Auton, A., Y. Rui Li, J. Kidd, K. Oliveira, J. Nadel et al., 2013 Genetic recombination is targeted towards gene promoter regions in dogs. PLoS Genet. 9(12): e1003984.
5. Baudat, F., J. Buard, C. Grey, A. Fledel-Alon, C. Ober et al., 2010 PRDM9 is a major determinant of meiotic recombination hotspots in humans and mice. Science 327(5967): 836-840.
6. Cao, J., K. Schneeberger, S. Ossowski, T. Gunther, S. Bender et al., 2011 Whole-genome sequencing of multiple Arabidopsis thaliana populations. Nat. Genet. 43(10): 956-963.
7. Coop, G., and M. Przeworski, 2007 An evolutionary view of human recombination. Nat. Rev. Genet. 8(1): 23-34.
8. Ewing, G., and J. Hermisson, 2010 MSMS: a coalescent simulation program including recombination, demographic structure and selection at a single locus. Bioinformatics 26(16): 2064-2065.
9. Fearnhead, P., and P. Donnelly, 2001 Estimating recombination rates from population genetic data. Genetics 159(3): 1299-1318.
10. Fearnhead, P., and P. Donnelly, 2002 Approximate likelihood methods for estimating local recombination rates. J. R. Stat. Soc. Series B Stat. Methodol. 64: 657-680.
11. Fu, Y. X., and W. H. Li, 1993 Statistical tests of neutrality of mutations. Genetics 133(3): 693-709.
12. Griffiths, R. C., and P. Marjoram, 1996 Ancestral inference from samples of DNA sequences with recombination. J. Comput. Biol. 3(4): 479-502.
13. Gutenkunst, R. N., R. D. Hernandez, S. H. Williamson, and C. D. Bustamante, 2009 Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data. PLoS Genet. 5(10): e1000695.
14. Hernandez, R. D., J. L. Kelley, E. Elyashiv, S. C. Melton, A. Auton et al., 2011 Classic selective sweeps were rare in recent human evolution. Science 331(6019): 920-924.
15. Hill, W. G., and A. Robertson, 1968 Linkage disequilibrium in finite populations. Theor. Appl. Genet. 38(6): 226-231.
16. Hothorn, T., P. Buehlmann, T. Kneib, M. Schmid, and B. Hofner, 2015 mboost: model-based boosting. Available at: http://CRAN.Rproject.org/package=mboost. Accessed: February 25, 2015.
17. Hudson, R. R., 1985 The sampling distribution of linkage disequilibrium under an infinite allele model without selection. Genetics 109(3): 611-631.
18. Hudson, R. R., 1987 Estimating the recombination parameter of a finite population-model without selection. Genet. Res. 50(3): 245-250.
19. Hudson, R. R., 2001 Two-locus sampling distributions and their application. Genetics 159(4): 1805-1817.
20. Hudson, R. R., 2002 Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 18(2): 337-338.
21. Hudson, R. R., and N. L. Kaplan, 1985 Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Genetics 111(1): 147-164.
22. Johnston, H. R., and D. J. Cutler, 2012 Population demographic history can cause the appearance of recombination hotspots. Am. J. Hum. Genet. 90 (5): 774-783.
23. Kamm, J.A., J.P. Spence, J. Chan, and Y.S. Song, 2015 An exact algorithm and efficient importance sampling for computing two-locus likelihoods under variable population size. arXiv:1510.06017. Available at: http://adsabs.harvard.edu/abs/2015arXiv151006017K. Accessed: October 20, 2015.
24. Kong, A., G. Masson, M. L. Frigge, A. Gylfason, P. Zusmanovich et al., 2008 Detection of sharing by descent, long-range phasing and haplotype imputation. Nat. Genet. 40(9): 1068-1075.
25. Kong, A., G. Thorleifsson, D. F. Gudbjartsson, G. Masson, A. Sigurdsson et al., 2010 Fine-scale recombination rate differences between sexes, populations and individuals. Nature 467(7319): 1099-1103.
26. Kuhner, M. K., J. Yamato, and J. Felsenstein, 2000 Maximum likelihood estimation of recombination rates from population data. Genetics 156(3): 1393-1401.
27. Li, H., and R. Durbin, 2011 Inference of human population history from individual whole-genome sequences. Nature 475(7357): 493-496.
28. Li, H. P., and W. Stephan, 2005 Maximum-likelihood methods for detecting recent positive selection and localizing the selected site in the genome. Genetics 171(1): 377-384.
29. Li, H. P., and W. Stephan, 2006 Inferring the demographic history and rate of adaptive substitution in Drosophila. PLoS Genet. 2(10): 1580-1589.
30. Li, N., and M. Stephens, 2003 Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data. Genetics 165(4): 2213-2233.
31. Lin, K., A. Futschik, and H. Li, 2013 A fast estimate for the population recombination rate based on regression. Genetics 194(2): 473-484.
32. Lu, S. J., C. H. Zong, W. Fan, M. Y. Yang, J. S. Li et al., 2012 Probing meiotic recombination and aneuploidy of single sperm cells by wholegenome sequencing. Science 338(6114): 1627-1630.
33. McVean, G., P. Awadalla, and P. Fearnhead, 2002 A coalescent-based method for detecting and estimating recombination from gene sequences. Genetics 160(3): 1231-1241.
34. Myers, S. R., and R. C. Griffiths, 2003 Bounds on the minimum number of recombination events in a sample history. Genetics 163(1): 375-394.
35. Nielsen, R., 2000 Estimation of population parameters and recombination rates from single nucleotide polymorphisms. Genetics 154(2): 931-942.
36. Ohta, T., and M. Kimura, 1971 Linkage disequilibrium between two segregating nucleotide sites under the steady flux of mutations in a finite population. Genetics 68(4): 571-580.
37. Price, A. L., A. Tandon, N. Patterson, K. C. Barnes, N. Rafaels et al., 2009 Sensitive detection of chromosomal segments of distinct ancestry in admixed populations. PLoS Genet. 5(6): e1000519.
38. Pugach, I., R. Matveyev, A. Wollstein, M. Kayser, and M. Stoneking, 2011 Dating the age of admixture via wavelet transform analysis of genome-wide data. Genome Biol. 12(2): R19.
39. Reed, F. A., and S. A. Tishkoff, 2006 Positive selection can create false hotspots of recombination. Genetics 172(3): 2011-2014.
40. Sattath, S., E. Elyashiv, O. Kolodny, Y. Rinott, and G. Sella, 2011 Pervasive adaptive protein evolution apparent in diversity patterns around amino acid substitutions in Drosophila simulans. PLoS Genet. 7(2): e1001302.
41. Shannon, C. E., 1948 A mathematical theory of communication. Bell Syst. Tech. J. 27(4): 623-656.
42. Stephens, M., and P. Scheet, 2005 Accounting for decay of linkage disequilibrium in haplotype inference and missing-data imputation. Am. J. Hum. Genet. 76(3): 449-462.
43. Stephens, M., N. J. Smith, and P. Donnelly, 2001 A new statistical method for haplotype reconstruction from population data. Am. J. Hum. Genet. 68(4): 978-989.
44. Wall, J. D., 2000 A comparison of estimators of the population recombination rate. Mol. Biol. Evol. 17(1): 156-163.
45. Walter, K., J. L. Min, J. Huang, L. Crooks, Y. Memari et al., 2015 The UK10K project identifies rare variants in health and disease. Nature 526(7571): 82.
46. Wang, Y., and B. Rannala, 2008 Bayesian inference of fine-scale recombination rates using population genomic data. Philos. Trans. R. Soc. Lond. B Biol. Sci. 363(1512): 3921-3930.
47. Wang, Y., and B. Rannala, 2009 Population genomic inference of recombination rates and hotspots. Proc. Natl. Acad. Sci. USA 106(15): 6215-6219.
48. Weiss, K. M., and A. G. Clark, 2002 Linkage disequilibrium and the mapping of complex human traits. Trends Genet. 18: 19-24.