Mobile element-based forensic genomics

Mutation Research - Fundamental and Molecular Mechanisms of Mutagenesis

Volumn 616, Issue 1-2, 2007, Pages 24-33

  Ray, David A ^a   Walker, Jerilyn A ^a   Batzer, Mark A ^a  

^a LOUISIANA STATE UNIVERSITY   (United States)

Author keywords

Forensic genomics; Mobile element; SINEs

Indexed keywords

BIOMATERIAL; MOLECULAR MARKER;

ALU SEQUENCE; ARTICLE; DNA DETERMINATION; DNA SEQUENCE; FORENSIC MEDICINE; GENE INSERTION; GENETIC POLYMORPHISM; GENOMICS; GEOGRAPHIC ORIGIN; HOMOPLASY; HUMAN; NONHUMAN; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; RETROPOSON; SHORT INTERSPERSED REPEAT; SPECIES DIFFERENCE;

ALU ELEMENTS; ANIMALS; CATTLE; CHICKENS; DNA; FORENSIC GENETICS; GENETIC MARKERS; HUMANS; INTERSPERSED REPETITIVE SEQUENCES; MEAT; POLYMORPHISM, GENETIC; RETROELEMENTS; SEQUENCE ANALYSIS, DNA; SEX CHARACTERISTICS; SHORT INTERSPERSED NUCLEOTIDE ELEMENTS; SPECIES SPECIFICITY;

EID: 33846704655     PISSN: 00275107     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mrfmmm.2006.11.019     Document Type: Article

References (110)

1. Lander E.S., Linton L.M., Birren B., Nusbaum C., Zody M.C., Baldwin J., Devon K., Dewar K., Doyle M., FitzHugh W., Funke R., Gage D., Harris K., Heaford A., Howland J., Kann L., Lehoczky J., LeVine R., McEwan P., McKernan K., Meldrim J., Mesirov J.P., Miranda C., Morris W., Naylor J., Raymond C., Rosetti M., Santos R., Sheridan A., Sougnez C., Stange-Thomann N., Stojanovic N., Subramanian A., Wyman D., Rogers J., Sulston J., Ainscough R., Beck S., Bentley D., Burton J., Clee C., Carter N., Coulson A., Deadman R., Deloukas P., Dunham A., Dunham I., Durbin R., French L., Grafham D., Gregory S., Hubbard T., Humphray S., Hunt A., Jones M., Lloyd C., McMurray A., Matthews L., Mercer S., Milne S., Mullikin J.C., Mungall A., Plumb R., Ross M., Shownkeen R., Sims S., Waterston R.H., Wilson R.K., Hillier L.W., McPherson J.D., Marra M.A., Mardis E.R., Fulton L.A., Chinwalla A.T., Pepin K.H., Gish W.R., Chissoe S.L., Wendl M.C., Delehaunty K.D., Miner T.L., Delehaunty A., Kramer J.B., Cook L.L., Fulton R.S., Johnson D.L., Minx P.J., Clifton S.W., Hawkins T., Branscomb E., Predki P., Richardson P., Wenning S., Slezak T., Doggett N., Cheng J.F., Olsen A., Lucas S., Elkin C., Uberbacher E., Frazier M., Gibbs R.A., Muzny D.M., Scherer S.E., Bouck J.B., Sodergren E.J., Worley K.C., Rives C.M., Gorrell J.H., Metzker M.L., Naylor S.L., Kucherlapati R.S., Nelson D.L., Weinstock G.M., Sakaki Y., Fujiyama A., Hattori M., Yada T., Toyoda A., Itoh T., Kawagoe C., Watanabe H., Totoki Y., Taylor T., Weissenbach J., Heilig R., Saurin W., Artiguenave F., Brottier P., Bruls T., Pelletier E., Robert C., Wincker P., Smith D.R., Doucette-Stamm L., Rubenfield M., Weinstock K., Lee H.M., Dubois J., Rosenthal A., Platzer M., Nyakatura G., Taudien S., Rump A., Yang H., Yu J., Wang J., Huang G., Gu J., Hood L., Rowen L., Madan A., Qin S., Davis R.W., Federspiel N.A., Abola A.P., Proctor M.J., Myers R.M., Schmutz J., Dickson M., Grimwood J., Cox D.R., Olson M.V., Kaul R., Shimizu N., Kawasaki K., Minoshima S., Evans G.A., Athanasiou M., Schultz R., Roe B.A., Chen F., Pan H., Ramser J., Lehrach H., Reinhardt R., McCombie W.R., de la Bastide M., Dedhia N., Blocker H., Hornischer K., Nordsiek G., Agarwala R., Aravind L., Bailey J.A., Bateman A., Batzoglou S., Birney E., Bork P., Brown D.G., Burge C.B., Cerutti L., Chen H.C., Church D., Clamp M., Copley R.R., Doerks T., Eddy S.R., Eichler E.E., Furey T.S., Galagan J., Gilbert J.G., Harmon C., Hayashizaki Y., Haussler D., Hermjakob H., Hokamp K., Jang W., Johnson L.S., Jones T.A., Kasif S., Kaspryzk A., Kennedy S., Kent W.J., Kitts P., Koonin E.V., Korf I., Kulp D., Lancet D., Lowe T.M., McLysaght A., Mikkelsen T., Moran J.V., Mulder N., Pollara V.J., Ponting C.P., Schuler G., Schultz J., Slater G., Smit A.F., Stupka E., Szustakowski J., Thierry-Mieg D., Thierry-Mieg J., Wagner L., Wallis J., Wheeler R., Williams A., Wolf Y.I., Wolfe K.H., Yang S.P., Yeh R.F., Collins F., Guyer M.S., Peterson J., Felsenfeld A., Wetterstrand K.A., Patrinos A., Morgan M.J., Szustakowki J., de Jong P., Catanese J.J., Osoegawa K., Shizuya H., Choi S., and Chen Y.J. Initial sequencing and analysis of the human genome. Nature 409 (2001) 860-921
2. Waterston R.H., Lindblad-Toh K., Birney E., Rogers J., Abril J.F., Agarwal P., Agarwala R., Ainscough R., Alexandersson M., An P., Antonarakis S.E., Attwood J., Baertsch R., Bailey J., Barlow K., Beck S., Berry E., Birren B., Bloom T., Bork P., Botcherby M., Bray N., Brent M.R., Brown D.G., Brown S.D., Bult C., Burton J., Butler J., Campbell R.D., Carninci P., Cawley S., Chiaromonte F., Chinwalla A.T., Church D.M., Clamp M., Clee C., Collins F.S., Cook L.L., Copley R.R., Coulson A., Couronne O., Cuff J., Curwen V., Cutts T., Daly M., David R., Davies J., Delehaunty K.D., Deri J., Dermitzakis E.T., Dewey C., Dickens N.J., Diekhans M., Dodge S., Dubchak I., Dunn D.M., Eddy S.R., Elnitski L., Emes R.D., Eswara P., Eyras E., Felsenfeld A., Fewell G.A., Flicek P., Foley K., Frankel W.N., Fulton L.A., Fulton R.S., Furey T.S., Gage D., Gibbs R.A., Glusman G., Gnerre S., Goldman N., Goodstadt L., Grafham D., Graves T.A., Green E.D., Gregory S., Guigo R., Guyer M., Hardison R.C., Haussler D., Hayashizaki Y., Hillier L.W., Hinrichs A., Hlavina W., Holzer T., Hsu F., Hua A., Hubbard T., Hunt A., Jackson I., Jaffe D.B., Johnson L.S., Jones M., Jones T.A., Joy A., Kamal M., Karlsson E.K., Karolchik D., Kasprzyk A., Kawai J., Keibler E., Kells C., Kent W.J., Kirby A., Kolbe D.L., Korf I., Kucherlapati R.S., Kulbokas E.J., Kulp D., Landers T., Leger J.P., Leonard S., Letunic I., Levine R., Li J., Li M., Lloyd C., Lucas S., Ma B., Maglott D.R., Mardis E.R., Matthews L., Mauceli E., Mayer J.H., McCarthy M., McCombie W.R., McLaren S., McLay K., McPherson J.D., Meldrim J., Meredith B., Mesirov J.P., Miller W., Miner T.L., Mongin E., Montgomery K.T., Morgan M., Mott R., Mullikin J.C., Muzny D.M., Nash W.E., Nelson J.O., Nhan M.N., Nicol R., Ning Z., Nusbaum C., O'Connor M.J., Okazaki Y., Oliver K., Overton-Larty E., Pachter L., Parra G., Pepin K.H., Peterson J., Pevzner P., Plumb R., Pohl C.S., Poliakov A., Ponce T.C., Ponting C.P., Potter S., Quail M., Reymond A., Roe B.A., Roskin K.M., Rubin E.M., Rust A.G., Santos R., Sapojnikov V., Schultz B., Schultz J., Schwartz M.S., Schwartz S., Scott C., Seaman S., Searle S., Sharpe T., Sheridan A., Shownkeen R., Sims S., Singer J.B., Slater G., Smit A., Smith D.R., Spencer B., Stabenau A., Stange-Thomann N., Sugnet C., Suyama M., Tesler G., Thompson J., Torrents D., Trevaskis E., Tromp J., Ucla C., Ureta-Vidal A., Vinson J.P., Von Niederhausern A.C., Wade C.M., Wall M., Weber R.J., Weiss R.B., Wendl M.C., West A.P., Wetterstrand K., Wheeler R., Whelan S., Wierzbowski J., Willey D., Williams S., Wilson R.K., Winter E., Worley K.C., Wyman D., Yang S., Yang S.P., Zdobnov E.M., Zody M.C., and Lander E.S. Initial sequencing and comparative analysis of the mouse genome. Nature 420 (2002) 520-562
3. Bennetzen J.L. Transposable element contributions to plant gene and genome evolution. Plant Mol. Biol. 42 (2000) 251-269
4. Deininger P.L., and Roy-Engel A.M. Mobile elements in animal and plant genomes. In: Craig N.L., Craigie R., Gellert M., and Lambowitz A.M. (Eds). Mobile DNA II (2002), ASM Press, Washington, DC
5. Labrador M., and Corces V.G. Interactions between transposable elements and the host genome. In: Craig N.L., Craigie R., Gellert M., and Lambowitz A.M. (Eds). Mobile DNA II (2002), ASM Press, Washington, DC
6. Nouaud D., Quesneville H., and Anxolabehere D. Recurrent exon shuffling between distant P-element families. Mol. Biol. Evol. 20 (2003) 190-199
7. Hamdi H.K., Nishio H., Tavis J., Zielinski R., and Dugaiczyk A. Alu-mediated phylogenetic novelties in gene regulation and development. J. Mol. Biol. 299 (2000) 931-939
8. Vidal F., Mougneau E., Glaichenhaus N., Vaigot P., Darmon M., and Cuzin F. Coordinated posttranscriptional control of gene expression by modular elements including Alu-like repetitive sequences. Proc. Natl. Acad. Sci. U.S.A. 90 (1993) 208-212
9. Deininger P.L., and Batzer M.A. Alu repeats and human disease. Mol. Genet. Metab. 67 (1999) 183-193
10. Deininger P.L., and Batzer M.A. Evolution of retroposons. Evol. Biol. 27 (1993) 157-196
11. Kazazian Jr. H.H. Mobile elements: drivers of genome evolution. Science 303 (2004) 1626-1632
12. Ostertag E.M., Goodier J.L., Zhang Y., and Kazazian Jr. H.H. SVA elements are nonautonomous retrotransposons that cause disease in humans. Am. J. Hum. Genet. 73 (2003) 1444-1451
13. Baust C., Baillie G.J., and Mager D.L. Insertional polymorphisms of ETn retrotransposons include a disruption of the wiz gene in C57BL/6 mice. Mammal. Genome 13 (2002) 423-428
14. Batzer M.A., and Deininger P.L. Alu repeats and human genomic diversity. Nat. Rev. Genet. 3 (2002) 370-379
15. Kidwell M.G., and Lisch D.R. Perspective: transposable elements, parasitic DNA, and genome evolution. Evolution 55 (2001) 1-24
16. Brouha B., Schustak J., Badge R.M., Lutz-Prigge S., Farley A.H., Moran J.V., and Kazazian Jr. H.H. Hot L1s account for the bulk of retrotransposition in the human population. Proc. Natl. Acad. Sci. U.S.A. 100 (2003) 5280-5285
17. Gilbert N., Lutz-Prigge S., and Moran J.V. Genomic deletions created upon LINE-1 retrotransposition. Cell 110 (2002) 315-325
18. Symer D.E., Connelly C., Szak S.T., Caputo E.M., Cost G.J., Parmigiani G., and Boeke J.D. Human 11 retrotransposition is associated with genetic instability in vivo. Cell 110 (2002) 327-338
19. Callinan P.A., Wang J., Herke S.W., Garber R.K., Liang P., and Batzer M.A. Alu retrotransposition-mediated deletion. J. Mol. Biol. 348 (2005) 791-800
20. Han K., Sen S.K., Wang J., Callinan P.A., Lee J., Cordaux R., Liang P., and Batzer M.A. Genomic rearrangements by LINE-1 insertion-mediated deletion in the human and chimpanzee lineages. Nucleic Acids Res. 33 (2005) 4040-4052
21. Pickeral O.K., Makalowski W., Boguski M.S., and Boeke J.D. Frequent human genomic DNA transduction driven by LINE-1 retrotransposition. Genome Res. 10 (2000) 411-415
22. Goodier J.L., Ostertag E.M., and Kazazian Jr. H.H. Transduction of 3′-flanking sequences is common in L1 retrotransposition. Hum. Mol. Genet. 9 (2000) 653-657
23. Jiang N., Bao Z., Zhang X., Eddy S.R., and Wessler S.R. Pack-MULE transposable elements mediate gene evolution in plants. Nature 431 (2004) 569-573
24. Xing J., Wang H., Belancio V.P., Cordaux R., Deininger P.L., and Batzer M.A. Emergence of new primate genes by retrotransposon-mediated transduction. Proc. Natl. Acad. Sci. U.S.A. 103 (2006) 17608-17613
25. Gebow D., Miselis N., and Liber H.L. Homologous and nonhomologous recombination resulting in deletion: effects of p53 status, microhomology, and repetitive DNA length and orientation. Mol. Cell. Biol. 20 (2000) 4028-4035
26. Sen S.K., Han K., Wang J., Lee J., Wang H., Callinan P.A., Dyer M., Cordaux R., Liang P., and Batzer M.A. Human genomic deletions mediated by recombination between Alu elements. Am. J. Hum. Genet. 79 (2006) 41-53
27. Bailey J.A., Liu G., and Eichler E.E. An Alu transposition model for the origin and expansion of human segmental duplications. Am. J. Hum. Genet. 73 (2003) 823-834
28. Roy-Engel A.M., Carroll M.L., El-Sawy M., Salem A.H., Garber R.K., Nguyen S.V., Deininger P.L., and Batzer M.A. Non-traditional Alu evolution and primate genomic diversity. J. Mol. Biol. 316 (2002) 1033-1040
29. Fischer S.E., Wienholds E., and Plasterk R.H. Continuous exchange of sequence information between dispersed Tc1 transposons in the Caenorhabditis elegans genome. Genetics 164 (2003) 127-134
30. Kass D.H., Batzer M.A., and Deininger P.L. Gene conversion as a secondary mechanism of short interspersed element (SINE) evolution. Mol. Cell. Biol. 15 (1995) 19-25
31. Ejima Y., and Yang L. Trans mobilization of genomic DNA as a mechanism for retrotransposon-mediated exon shuffling. Hum. Mol. Genet. 12 (2003) 1321-1328
32. Gray Y.H. It takes two transposons to tango: transposable-element-mediated chromosomal rearrangements. Trends Genet. 16 (2000) 461-468
33. In: Berg D.E., and Howe M.M. (Eds). Mobile DNA (1989), American Society for Microbiology, Washington, DC
34. Luan D.D., Korman M.H., Jakubczak J.L., and Eickbush T.H. Reverse transcription of R2Bm RNA is primed by a nick at the chromosomal target site: a mechanism for non-LTR retrotransposition. Cell 72 (1993) 595-605
35. Voytas D.F., and Boeke J.D. Ty1 and Ty5 of Saccharomyces cerevisiae. In: Lambowitz A.M. (Ed). Mobile DNAII (2002), American Society for Microbiology, Washington, DC 631-662
36. Kolosha V.O., and Martin S.L. High-affinity, non-sequence-specific RNA binding by the open reading frame 1 (ORF1) protein from long interspersed nuclear element 1 (LINE-1). J. Biol. Chem. 278 (2003) 8112-8117
37. Kolosha V.O., and Martin S.L. In vitro properties of the first ORF protein from mouse LINE-1 support its role in ribonucleoprotein particle formation during retrotransposition. Proc. Natl. Acad. Sci. U.S.A. 94 (1997) 10155-10160
38. Martin S.L., Cruceanu M., Branciforte D., Wai-Lun Li P., Kwok S.C., Hodges R.S., and Williams M.C. LINE-1 retrotransposition requires the nucleic acid chaperone activity of the ORF1 protein. J. Mol. Biol. 348 (2005) 549-561
39. Martin S.L., and Bushman F.D. Nucleic acid chaperone activity of the ORF1 protein from the mouse LINE-1 retrotransposon. Mol. Cell. Biol. 21 (2001) 467-475
40. Feng Q., Moran J.V., Kazazian Jr. H.H., and Boeke J.D. Human L1 retrotransposon encodes a conserved endonuclease required for retrotransposition. Cell 87 (1996) 905-916
41. Hattori M., Kuhara S., Takenaka O., and Sakaki Y. L1 family of repetitive DNA sequences in primates may be derived from a sequence encoding a reverse transcriptase-related protein. Nature 321 (1986) 625-628
42. Moran J.V., and Gilbert N. Mammalian LINE-1 retrotransposons and related elements. In: Lambowitz A.M. (Ed). Mobile DNA II (2002), American Society for Microbiology Press, Washington, DC 836-869
43. Jurka J. Sequence patterns indicate an enzymatic involvement in integration of mammalian retroposons. Proc. Natl. Acad. Sci. U.S.A. 94 (1997) 1872-1877
44. Cost G.J., and Boeke J.D. Targeting of human retrotransposon integration is directed by the specificity of the L1 endonuclease for regions of unusual DNA structure. Biochemistry 37 (1998) 18081-18093
45. McClintock B. The Discovery and Characterization of Transposable Elements: The Collected Papers of B. McClintock (1987), Garland, New York
46. Kajikawa M., and Okada N. LINEs mobilize SINEs in the eel through a shared 3′ sequence. Cell 111 (2002) 433-444
47. Dewannieux M., Esnault C., and Heidmann T. LINE-mediated retrotransposition of marked Alu sequences. Nat. Genet. 35 (2003) 41-48
48. Kalendar R., Vicient C.M., Peleg O., Anamthawat-Jonsson K., Bolshoy A., and Schulman A.H. Large retrotransposon derivatives: abundant, conserved but nonautonomous retroelements of barley and related genomes. Genetics 166 (2004) 1437-1450
49. Witte C.P., Le Q.H., Bureau T., and Kumar A. Terminal-repeat retrotransposons in miniature (TRIM) are involved in restructuring plant genomes. Proc. Natl. Acad. Sci. U.S.A. 98 (2001) 13778-13783
50. Deininger P.L., Moran J.V., Batzer M.A., and Kazazian Jr. H.H. Mobile elements and mammalian genome evolution. Curr. Opin. Genet. Dev. 13 (2003) 651-658
51. Okada N. SINEs. Curr. Opin. Genet. Dev. 1 (1991) 498-504
52. Ohshima K., Hamada M., Terai Y., and Okada N. The 3′ ends of tRNA-derived short interspersed repetitive elements are derived from the 3′ ends of long interspersed repetitive elements. Mol. Cell. Biol. 16 (1996) 3756-3764
53. Ohshima K., and Okada N. SINEs and LINEs: symbionts of eukaryotic genomes with a common tail. Cytogenet. Genome Res. 110 (2005) 475-490
54. Kapitonov V.V., and Jurka J. ACROBAT1, a nonautonomous DNA transposon from zebrafish. Repbase Rep. 2 (2002) 1
55. Jurka J. Novel families of repetitive elements from the human genome. Nucleic Acids Res. 18 (1990) 137-141
56. Smit A.F., and Riggs A.D. Tiggers and DNA transposon fossils in the human genome. Proc. Natl. Acad. Sci. U.S.A. 93 (1996) 1443-1448
57. D.A. Ray, J. Xing, A.-H. Salem, M.A. Batzer, SINEs of a nearly perfect character, Syst. Biol., in press.
58. D.A. Ray, SINEs of progress: mobile element applications to molecular ecology, Mol. Ecol., in press.
59. Tajima K., Enishi O., Amari M., Mitsumori M., Kajikawa H., Kurihara M., Yanai S., Matsue H., Yasue H., Mitsuhashi T., Kawashima T., and Matsumoto M. PCR Detection of DNAs of animal origin in feed by primers based on sequences of short and long interspersed repetitive elements. Biosci. Biotechnol. Biochem. 66 (2002) 2247-2250
60. Walker J.A., Hughes D.A., Anders B.A., Shewale J., Sinha S.K., and Batzer M.A. Quantitative intra-short interspersed element PCR for species-specific DNA identification. Anal. Biochem. 316 (2003) 259-269
61. Streeck R.E. A multicopy insertion sequence in the bovine genome with structural homology to the long terminal repeats of retroviruses. Nature 298 (1982) 767-769
62. Yasue H., and Wada Y. A swine SINE (PRE-1 sequence) distribution in swine-related animal species and its phylogenetic analysis in swine genome. Anim. Genet. 27 (1996) 95-98
63. Walker J.A., Hughes D.A., Hedges D.J., Anders B.A., Laborde M.E., Shewale J., Sinha S.K., and Batzer M.A. Quantitative PCR for DNA identification based on genome-specific interspersed repetitive elements. Genomics 83 (2004) 518-527
64. Carroll M.L., Roy-Engel A.M., Nguyen S.V., Salem A.H., Vogel E., Vincent B., Myers J., Ahmad Z., Nguyen L., Sammarco M., Watkins W.S., Henke J., Makalowski W., Jorde L.B., Deininger P.L., and Batzer M.A. Large-scale analysis of the Alu Ya5 and Yb8 subfamilies and their contribution to human genomic diversity. J. Mol. Biol. 311 (2001) 17-40
65. Carter A.B., Salem A.H., Hedges D.J.N.K., Kimball C.B., Walker J.A., Watkins W.S., Jorde L.B., and Batzer M.A. Genome wide analysis of the human Alu Yb lineage. Hum. Genomics 1 (2004) 167-178
66. Roy-Engel A.M., Carroll M.L., Vogel E., Garber R.K., Nguyen S.V., Salem A.H., Batzer M.A., and Deininger P.L. Alu insertion polymorphisms for the study of human genomic diversity. Genetics 159 (2001) 279-290
67. Callinan P.A., Hedges D.J., Salem A.H., Xing J., Walker J.A., Garber R.K., Watkins W.S., Bamshad M.J., Jorde L.B., and Batzer M.A. Comprehensive analysis of Alu-associated diversity on the human sex chromosomes. Gene 317 (2003) 103-110
68. Arcot S.S., Fontius J.J., Deininger P.L., and Batzer M.A. Identification and analysis of a 'young' polymorphic Alu element. Biochim. Biophys. Acta 1263 (1995) 99-102
69. Walker J.A., Kilroy G.E., Xing J., Shewale J., Sinha S.K., and Batzer M.A. Human DNA quantitation using Alu element-based polymerase chain reaction. Anal. Biochem. 315 (2003) 122-128
70. Hedges D.J., Walker J.A., Callinan P.A., Shewale J.G., Sinha S.K., and Batzer M.A. Mobile element-based assay for human gender determination. Anal. Biochem. 312 (2003) 77-79
71. Sullivan K.M., Mannucci A., Kimpton C.P., and Gill P. A rapid and quantitative DNA sex test: fluorescence-based PCR analysis of X-Y homologous gene amelogenin. Biotechniques 15 (1993) 636-638 640-631
72. Santos F.R., Pandya A., and Tyler-Smith C. Reliability of DNA-based sex tests. Nat. Genet. 18 (1998) 103
73. Steinlechner M., Berger B., Niederstatter H., and Parson W. Rare failures in the amelogenin sex test. Int. J. Legal Med. 116 (2002) 117-120
74. Thangaraj K., Reddy A.G., and Singh L. Is the amelogenin gene reliable for gender identification in forensic casework and prenatal diagnosis?. Int. J. Legal Med. 116 (2002) 121-123
75. Brinkmann B. Is the amelogenin sex test valid?. Int. J. Legal Med. 116 (2002) 63
76. Chakraborty R., Stivers D.N., Su B., Zhong Y., and Budowle B. The utility of short tandem repeat loci beyond human identification: implications for development of new DNA typing systems. Electrophoresis 20 (1999) 1682-1696
77. Sifis M.E., Both K., and Burgoyne L.A. A more sensitive method for the quantitation of genomic DNA by Alu amplification. J. Forensic Sci. 47 (2002) 589-592
78. Nicklas J.A., and Buel E. Development of an Alu-based QSY 7-labeled primer PCR method for quantitation of human DNA in forensic samples. J. Forensic Sci. 48 (2003) 1-10
79. Nicklas J.A., and Buel E. Development of an Alu-based, real-time PCR method for quantitation of human DNA in forensic samples. J. Forensic Sci. 48 (2003) 936-944
80. Nicklas J.A., and Buel E. Quantification of DNA in forensic samples. Anal. Bioanal. Chem. 376 (2003) 1160-1167
81. Nicklas J.A., and Buel E. An Alu-based, MGB Eclipse real-time PCR method for quantitation of human DNA in forensic samples. J. Forensic Sci. 50 (2005) 1081-1090
82. Batzer M.A., Arcot S.S., Phinney J.W., Alegria-Hartman M., Kass D.H., Milligan S.M., Kimpton C., Gill P., Hochmeister M., Ioannou P.A., Herrera R.J., Boudreau D.A., Scheer W.D., Keats B.J., Deininger P.L., and Stoneking M. Genetic variation of recent Alu insertions in human populations. J. Mol. Evol. 42 (1996) 22-29
83. Stoneking M., Fontius J.J., Clifford S.L., Soodyall H., Arcot S.S., Saha N., Jenkins T., Tahir M.A., Deininger P.L., and Batzer M.A. Alu insertion polymorphisms and human evolution: evidence for a larger population size in Africa. Genome Res. 7 (1997) 1061-1071
84. Romualdi C., Balding D., Nasidze I.S., Risch G., Robichaux M., Sherry S.T., Stoneking M., Batzer M.A., and Barbujani G. Patterns of human diversity, within and among continents, inferred from biallelic DNA polymorphisms. Genome Res. 12 (2002) 602-612
85. Watkins W.S., Rogers A.R., Ostler C.T., Wooding S., Bamshad M.J., Brassington A.M., Carroll M.L., Nguyen S.V., Walker J.A., Prasad B.V., Reddy P.G., Das P.K., Batzer M.A., and Jorde L.B. Genetic variation among world populations: inferences from 100 Alu insertion polymorphisms. Genome Res. 13 (2003) 1607-1618
86. Bamshad M., Kivisild T., Watkins W.S., Dixon M.E., Ricker C.E., Rao B.B., Naidu J.M., Prasad B.V., Reddy P.G., Rasanayagam A., Papiha S.S., Villems R., Redd A.J., Hammer M.F., Nguyen S.V., Carroll M.L., Batzer M.A., and Jorde L.B. Genetic evidence on the origins of Indian caste populations. Genome Res. 11 (2001) 994-1004
87. Bamshad M.J., Wooding S., Watkins W.S., Ostler C.T., Batzer M.A., and Jorde L.B. Human population genetic structure and inference of group membership. Am. J. Hum. Genet. 72 (2003) 578-589
88. Barbalic M., Pericic M., Skaric-Juric T., and Narancic N.S. Ace Alu insertion polymorphism in Croatia and its isolates. Collegium Antropol. 28 (2004) 603-610
89. Bulayeva K., Jorde L.B., Ostler C., Watkins S., Bulayev O., and Harpending H. Genetics and population history of Caucasus populations. Hum. Biol. 75 (2003) 837-853
90. Comas D., Calafell F., Benchemsi N., Helal A., Lefranc G., Stoneking M., Batzer M.A., Bertranpetit J., and Sajantila A. Alu insertion polymorphisms in NW Africa and the Iberian Peninsula: evidence for a strong genetic boundary through the Gibraltar Straits. Hum. Genet. 107 (2000) 312-319
91. Comas D., Schmid H., Braeuer S., Flaiz C., Busquets A., Calafell F., Bertranpetit J., Scheil H.G., Huckenbeck W., Efremovska L., and Schmidt H. Alu insertion polymorphisms in the Balkans and the origins of the Aromuns. Ann. Hum. Genet. 68 (2004) 120-127
92. Cotrim N.H., Auricchio M.T., Vicente J.P., Otto P.A., and Mingroni-Netto R.C. Polymorphic Alu insertions in six Brazilian African-derived populations. Am. J. Hum. Genet. 16 (2004) 264-277
93. Dornelles C.L., Battilana J., Fagundes N.J., Freitas L.B., Bonatto S.L., and Salzano F.M. Mitochondrial DNA and Alu insertions in a genetically peculiar population: the Ayoreo Indians of Bolivia and Paraguay. Am. J. Hum. Biol. 16 (2004) 479-488
94. Dunn D.S., Romphruk A.V., Leelayuwat C., Bellgard M., and Kulski J.K. Polymorphic Alu insertions and their associations with MHC class I alleles and haplotypes in the northeastern Thais. Ann. Hum. Genet. 69 (2005) 364-372
95. Gonzalez-Perez E., Via M., Esteban E., Lopez-Alomar A., Mazieres S., Harich N., Kandil M., Dugoujon J.M., and Moral P. Alu insertions in the Iberian Peninsula and north west Africa-genetic boundaries or melting pot?. Collegium Antropol. 27 (2003) 491-500
96. Maca-Meyer N., Villar J., Perez-Mendez L., Cabrera de Leon A., and Flores C. A tale of aborigines, conquerors and slaves: Alu insertion polymorphisms and the peopling of Canary Islands. Ann. Hum. Genet. 68 (2004) 600-605
97. Majumder P.P., Roy B., Banerjee S., Chakraborty M., Dey B., Mukherjee N., Roy M., Thakurta P.G., and Sil S.K. Human-specific insertion/deletion polymorphisms in Indian populations and their possible evolutionary implications. Eur. J. Hum. Genet. 7 (1999) 435-446
98. Mansoor A., Mazhar K., Khaliq S., Hameed A., Rehman S., Siddiqi S., Papaioannou M., Cavalli-Sforza L.L., Mehdi S.Q., and Ayub Q. Investigation of the Greek ancestry of populations from northern Pakistan. Hum. Genet. 114 (2004) 484-490
99. Mastana S., Lee D., Singh P.P., and Singh M. Molecular genetic variation in the East Midlands, England: analysis of VNTR, STR and Alu insertion/deletion polymorphisms. Ann. Hum. Biol. 30 (2003) 538-550
100. Nasidze I., Risch G.M., Robichaux M., Sherry S.T., Batzer M.A., and Stoneking M. Alu insertion polymorphisms and the genetic structure of human populations from the Caucasus. Eur. J. Hum. Genet. 9 (2001) 267-272
101. Novick G.E., Novick C.C., Yunis J., Yunis E., Antunez de Mayolo P., Scheer W.D., Deininger P.L., Stoneking M., York D.S., Batzer M.A., and Herrera R.J. Polymorphic Alu insertions and the Asian origin of Native American populations. Hum. Biol. 70 (1998) 23-39
102. Vishwanathan H., Edwin D., Usharani M.V., and Majumder P.P. Insertion/deletion polymorphisms in tribal populations of southern India and their possible evolutionary implications. Hum. Biol. 75 (2003) 873-887
103. Xiao F.X., Yang J.F., Cassiman J.J., and Decorte R. Diversity at eight polymorphic Alu insertion loci in Chinese populations shows evidence for European admixture in an ethnic minority population from northwest China. Hum. Biol. 74 (2002) 555-568
104. Vincent B.J., Myers J.S., Ho H.J., Kilroy G.E., Walker J.A., Watkins W.S., Jorde L.B., and Batzer M.A. Following the LINEs: an analysis of primate genomic variation at human-specific LINE-1 insertion sites. Mol. Biol. Evol. 20 (2003) 1338-1348
105. Salem A.H., Ray D.A., and Batzer M.A. Identity by descent and DNA sequence variation of human SINE and LINE elements. Cytogenet. Genome Res. 108 (2005) 63-72
106. Bamshad M.J., Wooding S., Watkins W.S., Ostler C.T., Batzer M.A., and Jorde L.B. Human population genetic structure and inference of group membership. Am. J. Hum. Genet. 72 (2003) 578-589
107. Falush D., Stephens M., and Pritchard J.K. Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164 (2003) 1567-1587
108. Pritchard J.K., Stephens M., and Donnelly P. Inference of population structure using multilocus genotype data. Genetics 155 (2000) 945-959
109. Ray D.A., Walker J.A., Hall A., Llewellyn B., Ballantyne J., Christian A.T., Turteltaub K., and Batzer M.A. Inference of human geographic origins using Alu insertion polymorphisms. Forensic Sci. Int. 153 (2005) 117-124
110. Sorensen K.J., Turteltaub K., Vrankovich G., Williams J., and Christian A.T. Whole-genome amplification of DNA from residual cells left by incidental contact. Anal. Biochem. 324 (2004) 312-314