Detecting highly differentiated copy-number variants from pooled population sequencing

Pacific Symposium on Biocomputing

Volumn , Issue , 2013, Pages 344-355

  Schrider, Daniel R ^a   Begun, David J ^b   Hahn, Matthew W ^a  

^a INDIANA UNIVERSITY   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA SEQUENCES; GENES; HIDDEN MARKOV MODELS;

COPY NUMBER; DROSOPHILA MELANOGASTER; LOCAL ADAPTATION; PAIRED-END READS; SEQUENCE DATA;

POPULATION STATISTICS;

ACCLIMATIZATION; ANIMAL; ARTICLE; BIOLOGY; COPY NUMBER VARIATION; DROSOPHILA MELANOGASTER; GENE FREQUENCY; GENETIC SELECTION; GENETICS; PHYSIOLOGY; POPULATION GENETICS; PROBABILITY; STATISTICS; STATISTICS AND NUMERICAL DATA;

ACCLIMATIZATION; ANIMALS; COMPUTATIONAL BIOLOGY; DNA COPY NUMBER VARIATIONS; DROSOPHILA MELANOGASTER; GENE FREQUENCY; GENETICS, POPULATION; MARKOV CHAINS; SELECTION, GENETIC;

EID: 84891469439     PISSN: 23356928     EISSN: 23356936     Source Type: Journal    
DOI: None     Document Type: Conference Paper

References (50)

1. R. Sachidanandam, et al, Nature 409, 928-933 (2001).
2. J. Sebat, et al, Science 305, 525-528 (2004).
3. D. F. Conrad, et al, Nature 464, 704-712 (2010).
4. S. Ossowski, et al, Genome Res 18, 2024-2033 (2008).
5. R. Redon, et al, Nature 444, 444-454 (2006).
6. E. Tuzun, et al, Nat Genet 37, 727-732 (2005).
7. F. Hormozdiari, et al, Genome Res 21, 2203-2212 (2011).
8. P. Medvedev, et al, Genome Res 20, 1613-1622 (2010).
9. R. E. Handsaker, et al, Nat Genet 43, 269-U126 (2011).
10. G. H. Perry, et al, Genome Res 18, 1698-1710 (2008).
11. T. A. Graubert, et al, PLoS Genet 3, e3 (2007).
12. J. J. Emerson, et al, Science 320, 1629-1631 (2008).
13. C. H. Langley, et al, Genetics, doi: 10.1534/genetics.1112.142018 (2012).
14. L. Carreto, et al, BMC Genomics 9, 524 (2008).
15. S. Girirajan, et al, PLoS Genet 7, e1002334 (2011).
16. D. Moreno-De-Luca, et al, Am J Hum Genet 87, 618-630 (2010).
17. J. R. Lupski, Nat Genet 39, S43-S47 (2007).
18. S. A. McCarroll, et al, Nat Genet 40, 1107-1112 (2008).
19. A. B. Singleton, et al, Science 302, 841 (2003).
20. D. Altshuler, et al, Nature 467, 1061-1073 (2010).
21. D. M. Altshuler, et al, Nature 467, 52-58 (2010).
22. P. C. Sabeti, et al, Nature 419, 832-837 (2002).
23. B. F. Voight, et al, PLoS Biol 4, e72 (2006).
24. L. B. Barreiro, et al, Nat Genet 40, 340-345 (2008).
25. R. C. Iskow, O. Gokcumen, C. Lee, Trends Genet 28, 245-257 (2012).
26. G. H. Perry, et al, Nat Genet 39, 1256-1260 (2007).
27. E. Gonzalez, et al, Science 307, 1434-1440 (2005).
28. B. Kolaczkowski, et al, Genetics 187, 245-260 (2011).
29. C. Cheng, et al, Genetics 190, 1417-1432 (2012).
30. A. Futschik, C. Schlotterer, Genetics 186, 207-218 (2010).
31. Y. Zhu, et al, PLoS ONE 7, e41901 (2012).
32. M. Slatkin, Genetics 99, 323-335 (1981).
33. H. Li, R. Durbin, Bioinformatics 25, 1754-1760 (2009).
34. M. D. Adams, et al, Science 287, 2185-2195 (2000).
35. G. M. Cooper, et al, Nat Genet 40, 1199-1203 (2008).
36. D. R. Schrider, M. W. Hahn, Mol Biol Evol 27, 103-111 (2010).
37. S. Wright, Genetics 28, 114-138 (1943).
38. C. Alkan, et al, Nat Genet 41, 1061-1067 (2009).
39. A. Abyzov, et al, Genome Res 21, 974-984 (2011).
40. S. Lee, et al, Nat Methods 6, 473-474 (2009).
41. S. Sindi, et al, Bioinformatics 25, I222-I230 (2009).
42. R. Kofler, A. J. Betancourt, C. Schlotterer, PLoS Genet 8, e1002487 (2012).
43. H. Ranson, et al, Science 298, 179-181 (2002).
44. P. J. Daborn, et al, Insect Bio chem Mol Biol 37, 512-519 (2007).
45. M. R. Bogwitz, et al, Proc Natl Acad Sci USA 102, 12807-12812 (2005).
46. J. Kang, J. Kim, K.-W. Choi, PLoS ONE 6, e29800 (2011).
47. P. Menozzi, et al, BMC Evol Biol 4, 4 (2004).
48. T. L. Turner, et al, Genetics 179, 455-473 (2008).
49. P. Pavlidis, et al, Mol Biol Evol, doi: 10.1093/molbev/mss1136 (2012).
50. J. D. Storey, Journal of the Royal Statistical Society Series B-Statistical Methodology 64, 479-498 (2002).