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Laboratory Methods for the Analysis of Primate Mobile Elements

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Book cover Genetic Variation

Part of the book series: Methods in Molecular Biology ((MIMB,volume 628))

Abstract

Mobile elements represent a unique and powerful set of tools for understanding the variation in a genome. Methods exist not only to utilize the polymorphisms among and within taxa to various ends but also to investigate the mechanism through which mobilization occurs. The number of methods to accomplish these ends is ever growing. Here, we present several protocols designed to assay mobile element-based variation within and among individual genomes.

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References

  1. Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C., Zody, M. C., Baldwin, J., et al. (2001). Initial sequencing and anal­ysis of the human genome. Nature 409, 860–921.

    Article  PubMed  CAS  Google Scholar 

  2. Waterston, R. H., Lindblad-Toh, K., Birney, E., Rogers, J., Abril, J. F., Agarwal, P., et al. (2002). Initial sequencing and comparative analysis of the mouse genome. Nature 420, 520–62.

    Article  PubMed  CAS  Google Scholar 

  3. Berg, D. E. & Howe, M. M., Eds. (1989). Mobile DNA. Washington, DC: American Society for Microbiology.

    Google Scholar 

  4. Pace, J. K., 2nd & Feschotte, C. (2007). The evolutionary history of human DNA transposons: evidence for intense activity in the primate lineage. Genome Research 17, 422–32.

    Article  PubMed  CAS  Google Scholar 

  5. Deininger, P. L., Batzer, M. A. (1993). Evolution of retroposons. Evolutionary Biology 27, 157–196.

    Article  Google Scholar 

  6. Batzer, M. A., Deininger, P. L. (2002). Alu repeats and human genomic diversity. Nature Reviews Genetics 3, 370–9.

    Article  PubMed  CAS  Google Scholar 

  7. Deininger, P. L, Batzer, M. A. (1999). Alu repeats and human disease. Mol Genet Metab 67, 183–93.

    Article  PubMed  CAS  Google Scholar 

  8. Kajikawa, M., Okada, N. (2002). LINEs mobilize SINEs in the eel through a shared 3′ sequence. Cell 111, 433–44.

    Article  PubMed  CAS  Google Scholar 

  9. Kazazian, H. H., Jr., Moran, J. V. (1998). The impact of L1 retrotransposons on the human genome. Nature Genetics 19, 19–24.

    Article  PubMed  CAS  Google Scholar 

  10. Luan, D. D., Korman, M. H., Jakubczak, J. L. & Eickbush, T. H. (1993). Reverse transcription of R2Bm RNA is primed by a nick at the chromosomal target site: a mechanism for non-LTR retrotransposition. Cell 72, 595–605.

    Article  PubMed  CAS  Google Scholar 

  11. Wang, W., Kirkness, E. F. (2005). Short interspersed elements (SINEs) are a major source of canine genomic diversity. Genome Research 15, 1798–808.

    Article  PubMed  CAS  Google Scholar 

  12. Sinnett, D., Richer, C., Deragon, J. M. & Labuda, D. (1992). Alu RNA transcripts in human embryonal carcinoma cells. Model of post-transcriptional selection of master sequences. Journal of Molecular Biology 226, 689–706.

    Article  PubMed  CAS  Google Scholar 

  13. Ostertag, E. M., Goodier, J. L., Zhang, Y. & Kazazian, H. H., Jr. (2003). SVA elements are nonautonomous retrotransposons that cause disease in humans. American Journal of Human Genetics 73, 1444–51.

    Article  PubMed  CAS  Google Scholar 

  14. Dewannieux, M., Esnault, C. & Heidmann, T. (2003). LINE-mediated retrotransposition of marked Alu sequences. Nature Genetics 35, 41–8.

    Article  PubMed  CAS  Google Scholar 

  15. Boeke, J. D. (1997). LINEs and Alus-the polyA connection. Nature Genetics 16, 6–7.

    Article  PubMed  CAS  Google Scholar 

  16. Feng, Q., Moran, J. V., Kazazian, H. H., Jr. & Boeke, J. D. (1996). Human L1 retrotransposon encodes a conserved endonuclease required for retrotransposition. Cell 87, 905–16.

    Article  PubMed  CAS  Google Scholar 

  17. Jurka, J. (1997). Sequence patterns indicate an enzymatic involvement in integration of mammalian retroposons. Proceedings of the National Academy of Sciences of the United States of America 94, 1872–7.

    Article  PubMed  CAS  Google Scholar 

  18. Deininger, P. L., Batzer, M. A., Hutchison, C. A., 3rd, Edgell, M. H. (1992). Master genes in mammalian repetitive DNA amplification. Trends in Genetics 8, 307–11.

    PubMed  CAS  Google Scholar 

  19. Cordaux, R., Hedges, D. J. & Batzer, M. A. (2004). Retrotransposition of Alu elements: how many sources? Trends in Genetics 20, 464–7.

    Article  PubMed  CAS  Google Scholar 

  20. Matera, A. G., Hellmann, U., Hintz, M. F., Schmid, C. W. (1990). Recently transposed Alu repeats result from multiple source genes. Nucleic Acids Research 18, 6019–23.

    Article  PubMed  CAS  Google Scholar 

  21. Shen, M. R., Batzer, M. A. & Deininger, P. L. (1991). Evolution of the master Alu gene(s). Journal of Molecular Evolution 33, 311–20.

    Article  PubMed  CAS  Google Scholar 

  22. Batzer, M. A., Arcot, S. S., Phinney, J. W., Alegria-Hartman, M., Kass, D. H., Milligan, S. M., et al. (1996). Genetic variation of recent Alu insertions in human populations. Journal of Molecular Evolution 42, 22–9.

    Article  PubMed  CAS  Google Scholar 

  23. Kapitonov, V. & Jurka, J. (1996). The age of Alu subfamilies. Journal of Molecular Evolution 42, 59–65.

    Article  PubMed  CAS  Google Scholar 

  24. Carroll, M. L., Roy-Engel, A. M., Nguyen, S. V., Salem, A. H., Vogel, E., Vincent, B., et al. (2001). Large-scale analysis of the Alu Ya5 and Yb8 subfamilies and their contribution to human genomic diversity. Journal of Molecular Biology 311, 17–40.

    Article  PubMed  CAS  Google Scholar 

  25. Carter, A. B., Salem, A. H., Hedges, D. J., Keegan, C. N., Kimball, B., Walker, J. A., et al. (2004). Genome-wide analysis of the human Alu Yb-lineage. Human Genomics 1, 167–78.

    PubMed  CAS  Google Scholar 

  26. Han, K., Xing, J., Wang, H., Hedges, D. J., Garber, R. K., Cordaux, R. & Batzer, M. A. (2005). Under the genomic radar: the stealth model of Alu amplification. Genome Research 15, 655–64.

    Article  PubMed  CAS  Google Scholar 

  27. Otieno, A. C., Carter, A. B., Hedges, D. J., Walker, J. A., Ray, D. A., Garber, R. K., et al. (2004). Analysis of the human Alu Ya-lineage. Journal of Molecular Biology 342, 109–18.

    Article  PubMed  CAS  Google Scholar 

  28. Okada, N., Shedlock, A. M. & Nikaido, M. (2004). Retroposon mapping in molecular systematics. In: Mobile Genetic Elements: Protocols and Genomic Applications, Vol. 260, pp. 189–226. Humana Press, Totowa, NJ.

    Chapter  Google Scholar 

  29. Ray, D. A. (2007). SINEs of progress: Mobile element applications to molecular ecology. Molecular Ecology 16, 19–33.

    Article  PubMed  CAS  Google Scholar 

  30. Ray, D. A., Xing, J., Salem, A.-H., Batzer, M. A. (2006). SINEs of a nearly perfect character. Systematic Biology 55, 928–935.

    Article  PubMed  Google Scholar 

  31. Shedlock, A. M., Okada, N. (2000). SINE insertions: powerful tools for molecular systematics. Bioessays 22, 148–60.

    Article  PubMed  CAS  Google Scholar 

  32. Shedlock, A. M., Takahashi, K., Okada, N. (2004). SINEs of speciation: tracking lineages with retroposons. Trends in Ecology and Evolution 19, 545–553.

    Article  PubMed  Google Scholar 

  33. Zietkiewicz, E., Richer, C., Labuda, D. (1999). Phylogenetic affinities of tarsier in the context of primate Alu repeats. Molecular Phylogenetics and Evolution 11, 77–83.

    Article  PubMed  CAS  Google Scholar 

  34. Watanabe, M., Nikaido, M., Tsuda, T. T., Inoko, H., Mindell, D. P., Murata, K. & Okada, N. (2006). The rise and fall of the CR1 subfamily in the lineage leading to penguins. Gene 365, 57–66.

    Article  PubMed  CAS  Google Scholar 

  35. Takahashi, K., Terai, Y., Nishida, M., Okada, N. (2001). Phylogenetic relationships and ancient incomplete lineage sorting among cichlid fishes in Lake Tanganyika as revealed by analysis of the insertion of retroposons. Molecular Biology and Evolution 18, 2057–66.

    Article  PubMed  CAS  Google Scholar 

  36. Sasaki, T., Takahashi, K., Nikaido, M., Miura, S., Yasukawa, Y. & Okada, N. (2004). First application of the SINE (short interspersed repetitive element) method to infer phylogenetic relationships in reptiles: an example from the turtle superfamily Testudinoidea. Molecular Biology and Evolution 21, 705–15.

    Article  PubMed  CAS  Google Scholar 

  37. Salem, A. H., Ray, D. A., Xing, J., Callinan, P. A., Myers, J. S., Hedges, D. J., et al. (2003). Alu elements and hominid phylogenetics. Proceedings of the National Academy of Sciences of the United States of America 100, 12787–91.

    Article  PubMed  Google Scholar 

  38. Ray, D. A., Xing, J., Hedges, D. J., Hall, M. A., Laborde, M. E., Anders, B. A., et al. (2005). Alu insertion loci and platyrrhine primate phylogeny. Molecular Phylogenetics and Evolution 35, 117–26.

    Article  PubMed  CAS  Google Scholar 

  39. Murata, S., Takasaki, N., Saitoh, M., Okada, N. (1993). Determination of the phylogenetic relationships among Pacific salmonids by using short interspersed elements (SINEs) as temporal landmarks of evolution. Proceedings of the National Academy of Sciences of the United States of America 90, 6995–9.

    Article  PubMed  CAS  Google Scholar 

  40. Cordaux, R., Lee, J., Dinoso, L., Batzer, M. A. (2006). Recently integrated Alu retrotransposons are essentially neutral residents of the human genome. Gene 373, 138–44.

    Article  PubMed  CAS  Google Scholar 

  41. Kass, D. H. (2003). Generation of human DNA profiles by Alu-based multiplex polymerase chain reaction. Analytical Biochemistry 321, 146–9.

    Article  PubMed  CAS  Google Scholar 

  42. Thomas, E., Herrera, R. J. (1998). Multiplex polymerase chain reaction of Alu polymorphic insertions. Electrophoresis 19, 2373–9.

    Article  PubMed  CAS  Google Scholar 

  43. Flavell, A. J., Knox, M. R., Pearce, S. R. & Ellis, T. H. (1998). Retrotransposon-based insertion polymorphisms (RBIP) for high throughput marker analysis. Plant J 16, 643–50.

    Article  PubMed  CAS  Google Scholar 

  44. Salem, A. H., Ray, D. A., Hedges, D. J., Jurka, J. & Batzer, M. A. (2005). Analysis of the human Alu Ye lineage. BMC Evolutionary Biology 5, 18.

    Article  PubMed  Google Scholar 

  45. Xing, J., Salem, A. H., Hedges, D. J., Kilroy, G. E., Watkins, W. S., Schienman, J. E., et al. (2003). Comprehensive analysis of two Alu Yd subfamilies. Journal of Molecular Evolution 57, S76-S89.

    Article  PubMed  CAS  Google Scholar 

  46. Shewale, J. G., Schneida, E., Wilson, J., Walker, J. A., Batzer, M. A. & Sinha, S. K. (2007). Human genomic DNA quantitation system, H-Quant: development and validation for use in forensic casework. Journal of Forensic Science 52, 364–70.

    Article  CAS  Google Scholar 

  47. Nicklas, J. A. & Buel, E. (2003). Development of an Alu-based, real-time PCR method for quantitation of human DNA in forensic samples. Journal of Forensic Science 48, 936–44.

    PubMed  CAS  Google Scholar 

  48. Nicklas, J. A., Buel, E. (2003). Quantification of DNA in forensic samples. Anal Bioanal Chem 376, 1160–7.

    Article  PubMed  CAS  Google Scholar 

  49. Nicklas, J. A., Buel, E. (2005). An Alu-based, MGB Eclipse real-time PCR method for quantitation of human DNA in forensic samples. Journal of Forensic Science 50, 1081–90.

    Article  CAS  Google Scholar 

  50. Nicklas, J. A., Buel, E. (2006). Simultaneous determination of total human and male DNA using a duplex real-time PCR assay. Journal of Forensic Science 51, 1005–15.

    Article  CAS  Google Scholar 

  51. Sifis, M. E., Both, K., Burgoyne, L. A. (2002). A more sensitive method for the quantitation of genomic DNA by Alu amplification. Journal of Forensic Sciences 47, 589–92.

    PubMed  CAS  Google Scholar 

  52. Walker, J. A., Kilroy, G. E., Xing, J., Shewale, J., Sinha, S. K. & Batzer, M. A. (2003). Human DNA quantitation using Alu element-based polymerase chain reaction. Analytical Biochemistry 315, 122–8.

    Article  PubMed  CAS  Google Scholar 

  53. Walker, J. A., Hedges, D. J., Perodeau, B. P., Landry, K. E., Stoilova, N., Laborde, M. E., et al. (2005). Multiplex polymerase chain reaction for simultaneous quantitation of human nuclear, mitochondrial, and male Y-chromosome DNA: application in human identification. Analytical Biochemistry 337, 89–97.

    Article  PubMed  CAS  Google Scholar 

  54. Hedges, D. J., Walker, J. A., Callinan, P. A., Shewale, J. G., Sinha, S. K., Batzer, M. A. (2003). Mobile element-based assay for human gender determination. Analytical Biochemistry 312, 77–9.

    Article  PubMed  CAS  Google Scholar 

  55. Ray, D. A., Walker, J. A., Hall, A., Llewellyn, B., Ballantyne, J., Christian, A. T., et al. (2005). Inference of human geographic origins using Alu insertion polymorphisms. Forensic Science International 153, 117–24.

    Article  PubMed  CAS  Google Scholar 

  56. Bamshad, M. J., Wooding, S., Watkins, W. S., Ostler, C. T., Batzer, M. A. & Jorde, L. B. (2003). Human population genetic structure and inference of group membership. American Journal of Human Genetics 72, 578–89.

    Article  PubMed  CAS  Google Scholar 

  57. Jorde, L. B., Watkins, W. S., Bamshad, M. J., Dixon, M. E., Ricker, C. E., Seielstad, M. T. & Batzer, M. A. (2000). The distribution of human genetic diversity: a comparison of mitochondrial, autosomal, and Y-chromosome data. American Journal of Human Genetics 66, 979–88.

    Article  PubMed  CAS  Google Scholar 

  58. Roy-Engel, A. M., Carroll, M. L., Vogel, E., Garber, R. K., Nguyen, S. V., Salem, A. H., et al. (2001). Alu insertion polymorphisms for the study of human genomic diversity. Genetics 159, 279–90.

    PubMed  CAS  Google Scholar 

  59. Salem, A. H., Kilroy, G. E., Watkins, W. S., Jorde, L. B., Batzer, M. A. (2003). Recently integrated Alu elements and human genomic diversity. Molecular Biology and Evolution 20, 1349–61.

    Article  PubMed  CAS  Google Scholar 

  60. Watkins, W. S., Rogers, A. R., Ostler, C. T., Wooding, S., Bamshad, M. J., Brassington, A. M., et al. (2003). Genetic variation among world populations: inferences from 100 Alu insertion polymorphisms. Genome Research 13, 1607–18.

    Article  PubMed  CAS  Google Scholar 

  61. CSAC. (2005). Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437, 69–87.

    Article  Google Scholar 

  62. Gibbs, R. A., Rogers, J., Katze, M. G., Bumgarner, R., Weinstock, G. M., Mardis, E. R., et al. (2007). Evolutionary and biomedical insights from the rhesus macaque genome. Science 316, 222–34.

    Article  PubMed  CAS  Google Scholar 

  63. Kohn, M., Knauer, F., Stoffella, A., Schroder, W., Paabo, S. (1995). Conservation genetics of the European brown bear-a study using excremental PCR of nuclear and mitochondrial sequences. Mol Ecol 4, 95–103.

    Article  PubMed  CAS  Google Scholar 

  64. Matsubara, M., Basabose, A. K., Omari, I., Kaleme, K., Kizungu, B., Sikubwabo, K., et al. (2005). Species and sex identification of western lowland gorillas (Gorilla gorilla gorilla), eastern lowland gorillas (Gorilla beringei graueri) and humans. Primates 46, 199–202.

    Article  PubMed  Google Scholar 

  65. Taberlet, P., Camarra, J. J., Griffin, S., Uhres, E., Hanotte, O., Waits, L. P., et al. (1997). Noninvasive genetic tracking of the endangered Pyrenean brown bear population. Molecular Ecology 6, 869–76.

    Article  PubMed  CAS  Google Scholar 

  66. Yan, P., Wu, X. B., Shi, Y., Gu, C. M., Wang, R. P., Wang, C. L. (2005). Identification of Chinese alligators (Alligator sinensis) meat by diagnostic PCR of the mitochondrial cytochrome b gene. Biological Conservation 121, 45–51.

    Article  Google Scholar 

  67. Domingo-Roura, X., Marmi, J., Ferrando, A., Lopez-Giraldez, F., Macdonald, D. W. & Jansman, H. A. H. (2006). Badger hair in shaving brushes comes from protected Eurasian badgers. Biological Conservation 128, 425–430.

    Article  Google Scholar 

  68. Han, K., Lee, J., Meyer, T. J., Wang, J., Sen, S. K., Srikanta, D., Liang, P. & Batzer, M. A. (2007). Alu recombination-mediated structural deletions in the chimpanzee genome. PLoS Genet 3, 1939–49.

    Article  PubMed  CAS  Google Scholar 

  69. Khan, H., Smit, A., Boissinot, S. (2006). Molecular evolution and tempo of amplification of human LINE-1 retrotransposons since the origin of primates. Genome Res 16, 78–87.

    Article  PubMed  CAS  Google Scholar 

  70. Lee, J., Cordaux, R., Han, K., Wang, J., Hedges, D. J., Liang, P., Batzer, M. A. (2007). Different evolutionary fates of recently integrated human and chimpanzee LINE-1 retrotransposons. Gene 390, 18–27.

    Article  PubMed  CAS  Google Scholar 

  71. Callinan, P. A., Wang, J., Herke, S. W., Garber, R. K., Liang, P., Batzer, M. A. (2005). Alu retrotransposition-mediated deletion. Journal of Molecular Biology 348, 791–800.

    Article  PubMed  CAS  Google Scholar 

  72. Han, K., Sen, S. K., Wang, J., Callinan, P. A., Lee, J., Cordaux, R., Liang, P. & Batzer, M. A. (2005). Genomic rearrangements by LINE-1 insertion-mediated deletion in the human and chimpanzee lineages. Nucleic Acids Res 33, 4040–52.

    Article  PubMed  CAS  Google Scholar 

  73. Sen, S. K., Han, K., Wang, J., Lee, J., Wang, H., Callinan, P. A., et al. (2006). Human Genomic Deletions Mediated by Recombination between Alu Elements. American Journal of Human Genetics 79, 41–53.

    Article  PubMed  CAS  Google Scholar 

  74. Moran, J. V., Holmes, S. E., Naas, T. P., DeBerardinis, R. J., Boeke, J. D. & Kazazian, H. H., Jr. (1996). High frequency retrotransposition in cultured mammalian cells. Cell 87, 917–27.

    Article  PubMed  CAS  Google Scholar 

  75. Wei, W., Morrish, T. A., Alisch, R. S., Moran, J. V. (2000). A transient assay reveals that cultured human cells can accommodate multiple LINE-1 retrotransposition events. Analytical Biochemistry 284, 435–8.

    Article  PubMed  CAS  Google Scholar 

  76. Dombroski, B. A., Mathias, S. L., Nanthakumar, E., Scott, A. F., Kazazian, H. H., Jr. (1991). Isolation of an active human transposable element. Science 254, 1805–8.

    Article  PubMed  CAS  Google Scholar 

  77. Brouha, B., Schustak, J., Badge, R. M., Lutz-Prigge, S., Farley, A. H., Moran, J. V., Kazazian, H. H., Jr. (2003). Hot L1s account for the bulk of retrotransposition in the human population. Proceedings of the National Academy of Sciences of the United States of America 100, 5280–5.

    Article  PubMed  CAS  Google Scholar 

  78. Gilbert, N., Lutz, S., Morrish, T. A. & Moran, J. V. (2005). Multiple fates of L1 retrotransposition intermediates in cultured human cells. Molecular and Cellular Biology 25, 7780–95.

    Article  PubMed  CAS  Google Scholar 

  79. Gilbert, N., Lutz-Prigge, S., Moran, J. V. (2002). Genomic deletions created upon LINE-1 retrotransposition. Cell 110, 315–25.

    Article  PubMed  CAS  Google Scholar 

  80. Symer, D. E., Connelly, C., Szak, S. T., Caputo, E. M., Cost, G. J., Parmigiani, G., Boeke, J. D. (2002). Human l1 retrotransposition is associated with genetic instability in vivo. Cell 110, 327–38.

    Article  PubMed  CAS  Google Scholar 

  81. Moran, J. V., DeBerardinis, R. J., Kazazian, H. H., Jr. (1999). Exon shuffling by L1 retrotransposition. Science 283, 1530–4.

    Article  PubMed  CAS  Google Scholar 

  82. Cost, G. J., Boeke, J. D. (1998). Targeting of human retrotransposon integration is directed by the specificity of the L1 endonuclease for regions of unusual DNA structure. Biochemistry 37, 18081–93.

    Article  PubMed  CAS  Google Scholar 

  83. Watkins, W. S., Rogers, A. R., Ostler, C. T., Wooding, S., Bamshad, M. J., Brassington, A. M., et al. (2003). Genetic variation among world populations: inferences from 100 Alu insertion polymorphisms. Genome Research 13, 1607–18.

    Article  PubMed  CAS  Google Scholar 

  84. Pritchard, J. K., Stephens, M., Donnelly, P. (2000). Inference of population structure using multilocus genotype data. Genetics 155, 945–59.

    PubMed  CAS  Google Scholar 

  85. Falush, D., Stephens, M., Pritchard, J. K. (2003). Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164, 1567–87.

    PubMed  CAS  Google Scholar 

  86. Herke, S. W., Xing, J., Ray, D. A., Zimmerman, J. W., Cordaux, R., Batzer, M. A. (2007). A SINE-based dichotomous key for primate identification. Gene 390.

    Google Scholar 

  87. Holmes, S. E., Dombroski, B. A., Krebs, C. M., Boehm, C. D. & Kazazian, H. H., Jr. (1994). A new retrotransposable human L1 element from the LRE2 locus on chromosome 1q produces a chimaeric insertion. Nature Genetics 7, 143–8.

    Article  PubMed  CAS  Google Scholar 

  88. Wallace, M. R., Andersen, L. B., Saulino, A. M., Gregory, P. E., Glover, T. W., Collins, F. S. (1991). A de novo Alu insertion results in neurofibromatosis type 1. Nature 353, 864–6.

    Article  PubMed  CAS  Google Scholar 

  89. Ullu, E. & Tschudi, C. (1984). Alu sequences are processed 7SL RNA genes. Nature 312, 171–2.

    Article  PubMed  CAS  Google Scholar 

  90. Dhellin, O., Maestre, J., Heidmann, T. (1997). Functional differences between the human LINE retrotransposon and retro­viral reverse transcriptases for in vivo mRNA reverse transcription. Embo J 16, 6590–602.

    Article  PubMed  CAS  Google Scholar 

  91. Kimberland, M. L., Divoky, V., Prchal, J., Schwahn, U., Berger, W. & Kazazian, H. H., Jr. (1999). Full-length human L1 insertions retain the capacity for high frequency retrotransposition in cultured cells. Human Molecular Genetics 8, 1557–60.

    Article  PubMed  CAS  Google Scholar 

  92. Morrish, T. A., Gilbert, N., Myers, J. S., Vincent, B. J., Stamato, T. D., Taccioli, G. E., et al. (2002). DNA repair mediated by endonuclease-independent LINE-1 retrotransposition. Nature Genetics 31, 159–65.

    Article  PubMed  CAS  Google Scholar 

  93. Munroe, D. J., Haas, M., Bric, E., Whitton, T., Aburatani, H., Hunter, K., Ward, D., Housman, D. E. (1994). IRE-bubble PCR: a rapid method for efficient and representative amplification of human genomic DNA sequences from complex sources. Genomics 19, 506–14.

    Article  PubMed  CAS  Google Scholar 

  94. Roy, A. M., Carroll, M. L., Kass, D. H., Nguyen, S. V., Salem, A. H., Batzer, M. A., Deininger, P. L. (1999). Recently integrated human Alu repeats: finding needles in the haystack. Genetica 107, 149–61.

    Article  PubMed  CAS  Google Scholar 

  95. Swofford, D. L. (2002). PAUP: Phylogenetic analysis using parsimony (*and Other Methods) 4.0b10 edit. Sinauer Associates, Sunderland, Massachusetts.

    Google Scholar 

  96. Felsenstein, J. (1989). PHYLIP - Phylogeny Inference Package (Version 3.2). Cladistics 5, 164–166.

    Google Scholar 

  97. Rozen, S. & Skaletsky, H. (2000). Primer3 on the WWW for general users and for biologist programmers. Methods in Molecular Biology 132, 365–86.

    PubMed  CAS  Google Scholar 

  98. Kibbe, W. A. (2007). OligoCalc: an online oligonucleotide properties calculator. Nucleic Acids Research 35, W43–6.

    Article  PubMed  Google Scholar 

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Acknowledgments

Our research is supported by National Science Foundation BCS-0218338 (MAB) and EPS-0346411 (MAB), National Institutes of Health RO1 GM59290 (MAB) and PO1 AG022064 (MAB), and the State of Louisiana Board of Regents Support Fund (MAB). DAR is supported by the Eberly College of Arts and Sciences at West Virginia State University.

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Authors and Affiliations

  1. Department of Biology, West Virginia University, Morgantown, WV, USA

    David A. Ray

  2. Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, Baton Rouge, LA, USA

    Kyudong Han & Jerilyn A. Walker

  3. Department of Biological Sciences, Biological Computation and Visualization Center, Center for BioModular Multi-Scale Systems, Louisiana State University, Baton Rouge, LA, USA

    Mark A. Batzer

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  1. David A. Ray
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Correspondence to Mark A. Batzer .

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  1. Medicines Research Centre, GlaxoSmithKline R&D Limited, Gunnels Wood Road, Stevenage, Hertfordshire, SG12NY, United Kingdom

    Michael R. Barnes

  2. Institute of Psychiatry, Social, Genetic & Developmental, King's College, Denmark Hill 111, London, SE58AF, United Kingdom

    Gerome Breen

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Ray, D.A., Han, K., Walker, J.A., Batzer, M.A. (2010). Laboratory Methods for the Analysis of Primate Mobile Elements. In: Barnes, M., Breen, G. (eds) Genetic Variation. Methods in Molecular Biology, vol 628. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-60327-367-1_9

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  • DOI: https://doi.org/10.1007/978-1-60327-367-1_9

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-60327-366-4

  • Online ISBN: 978-1-60327-367-1

  • eBook Packages: Springer Protocols

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