dbRIP: A highly integrated database of retrotransposon insertion polymorphisms in humans

Human Mutation

Volumn 27, Issue 4, 2006, Pages 323-329

  Wang, Jianxin ^a,c   Song, Lei ^a   Grover, Deepak ^b   Azrak, Sami ^a   Batzer, Mark A ^b   Liang, Ping ^a  

^a ROSWELL PARK CANCER INSTITUTE   (United States)

^b LOUISIANA STATE UNIVERSITY   (United States)

^c Znomics Inc   (United States)

Author keywords

Alu; Database; L1; Mutation; Polymorphism; Retrotransposition; SVA

Indexed keywords

ALU SEQUENCE; DATA BASE; EVOLUTION; GENE INSERTION; GENE MUTATION; GENETIC DISORDER; GENETIC POLYMORPHISM; GENETIC VARIABILITY; GENOTYPE; HUMAN; HUMAN GENETICS; HUMAN GENOME; LONG INTERSPERSED REPEAT; MULTIGENE FAMILY; PRIORITY JOURNAL; RETROPOSON; REVIEW;

DATABASES, GENETIC; GENOME, HUMAN; HUMANS; MUTAGENESIS, INSERTIONAL; POLYMORPHISM, GENETIC; RETROELEMENTS;

EID: 33645786590     PISSN: 10597794     EISSN: None     Source Type: Journal    
DOI: 10.1002/humu.20307     Document Type: Review

References (56)

1. Arcot SS, Fontius JJ, Deininger PL, Batzer MA. 1995. Identification and analysis of a "young" polymorphic Alu element. Biochim Biophys Acta 1263:99-102.
2. Badge RM, Alisch RS, Moran JV. 2003. ATLAS: a system to selectively identify human-specific L1 insertions. Am J Hum Genet 72:823-838.
3. Bamshad MJ, Wooding S, Watkins WS, Ostler CT, Batzer MA, Jorde LB. 2003. Human population genetic structure and inference of group membership. Am J Hum Genet 72:578-589.
4. Batzer MA, Deininger PL. 1991. A human-specific subfamily of Alu sequences. Genomics 9:481-487.
5. Batzer MA, Gudi VA, Mena JC, Foltz DW, Herrera RJ, Deininger PL. 1991. Amplification dynamics of human-specific (HS) Alu family members. Nucleic Acids Res 19:3619-3623.
6. Batzer MA, Rubin CM, Hellmann-Blumberg U, Alegria-Hartman M, Leeflang EP, Stern JD, Bazan HA, Shaikh TH, Deininger PL, Schmid CW. 1995. Dispersion and insertion polymorphism in two small subfamilies of recently amplified human Alu repeats. J Mol Biol 247:418-427.
7. Batzer MA, Deininger PL, Hellmann-Blumberg U, Jurka J, Labuda D, Rubin CM, Schmid CW, Zietkiewicz E, Zuckerkandl E. 1996. Standardized nomenclature for Alu repeats. J Mol Evol 42:3-6.
8. Batzer MA, Deininger PL. 2002. Alu repeats and human genomic diversity. Nat Rev Genet 3:370-379.
9. Bennett EA, Coleman LE, Tsui C, Pittard WS, Devine SE. 2004. Natural genetic variation caused by transposable elements in humans. Genetics 168:933-951.
10. Boeke JD. 1997. LINEs and Alus-the polyA connection, Nat Genet 16:6-7.
11. Boeke JD, Chapman KB. 1991. Retrotransposition mechanisms. Curr Opin Cell Biol 3:502-507.
12. Boissinot S, Chevret P, Furano AV. 2000. L1 (LINE-1) retrotransposon evolution and amplification in recent human history. Mol Biol Evol 17:915-928.
13. Boissinot S, Entezam A, Young L, Munson PJ, Furano AV. 2004. The insertional history of an active family of L1 retrotransposons in humans. Genome Res 14:1221-1231.
14. Brouha B, Schustak J, Badge RM, Lutz-Prigge S, Farley AH, Moran JV, Kazazian HH Jr. 2003. Hot L1s account for the bulk of retrotransposition in the human population. Proc Natl Acad Sci USA 100:5280-5285.
15. Buzdin A, Ustyugova S, Gogvadze E, Lebedev Y, Hunsmann G, Sverdlov E. 2003. Genome-wide targeted search for human specific and polymorphic L1 integrations. Hum Genet 112:527-533.
16. Buzdin A, Vinogradova T, Lebedev Y, Sverdlov E. 2005. Genome-wide experimental identification and functional analysis of human specific retroelements. Cytogenet Genome Res 110:468-474.
17. Callinan PA, Hedges DJ, Salem AH, Xing J, Walker JA, Garber RK, Watkins WS, Bamshad MJ, Jorde LB, Batzer MA. 2003. Comprehensive analysis of Alu-associated diversity on the human sex chromosomes. Gene 317:103-110.
18. Carroll ML, Roy-Engel AM, Nguyen SV, Salem AH, Vogel E, Vincent B, Myers J, Ahmad Z, Nguyen L, Sammarco M, Watkins WS, Henke J, Makalowski M, Jorde LB, Deininger PL, Batzer MA. 2001. Large-scale analysis of the Alu Ya5 and Yb8 subfamilies and their contribution to human genomic diversity. J Mol Biol 311:17-40.
19. Carter AB, Salem AH, Hedges DJ, Keegan CN, Kimball B, Walker JA, Watkins WS, Jorde LB, Batzer MA. 2004. Genome-wide analysis of the human Alu Yb-lineage. Hum Genomics 1:167-178.
20. Deininger PL, Batzer MA. 1999. Alu repeats and human disease. Mol Genet Metab 67:183-193.
21. Deininger PL, Batzer MA. 2002. Mammalian retroelements. Genome Res 12:1455-1465.
22. Dewannieux M, Esnault C, Heidmann T. 2003. LINE-mediated retrotransposition of marked Alu sequences. Nat Genet 35:41-48.
23. Holmes SE, Dombroski BA, Krebs CM, Boehm CD, Kazazian HH Jr. 1994. A new retrotransposable human L1 element from the LRE2 locus on chromosome 1q produces a chimaeric insertion. Nat Genet 7:143-148.
24. Hsu F, Pringle TH, Kuhn RM, Karolchik D, Dickhans M, Haussler D, Kent WJ. 2004. The UCSC Proteome Browser. Nuc Acids Res 33(Suppl 1):D454-D458.
25. Kazazian HH Jr, Wong C, Youssoufian H, Scott AF, Phillips DG, Antonarakis SE. 1988. Haemophilia A resulting from de novo insertion of L1 sequences represents a novel mechanism for mutation in man. Nature 332:164-166.
26. Kent WJ. 2002. BLAT-the BLAST-like alignment tool. Genome Res 12:656-664.
27. Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D. 2002. The human genome browser at UCSC. Genome Res 12:996-1006.
28. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, 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 JP, 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 JC, Mungall A, Plumb R, Ross M, Shownkeen R, Sims S, Waterston RH, Wilson RK, Hillier LW, McPherson JD, Marra MA, Mardis ER, Fulton LA, Chinwalla AT, Pepin KH, Gish WR, Chissoe SL, Wendl MC, Delehaunty KD, Miner TL, Delehaunty A, Kramer JB, Cook LL, Fulton RS, Johnson DL, Minx PJ, Clifton SW, Hawkins T, Branscomb E, Predki P, Richardson P, Wenning S, Slezak T, Doggett N, Cheng JF, Olsen A, Lucas S, Elkin C, Uberbacher E, Frazier M, Gibbs RA, Muzny DM, Scherer SE, Bouck JB, Sodergren EJ, Worley KC, Rives CM, Gorrell JH, Metzker ML, Naylor SL, Kucherlapati RS, Nelson DL, Weinstock GM, 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, Bruis T, Pelletier E, Robert C, Wincker P, Smith DR, Doucette-Stamm L, Rubenfield M, Weinstock K, Lee HM, 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 RW, Federspiel NA, Abola AP, Proctor MJ, Myers RM, Schmutz J, Dickson M, Grimwood J, Cox DR, Olson MV, Kaul R, Raymond C, Shimizu N, Kawasaki K, Minoshima S, Evans GA, Athanasiou M, Schultz R, Roe BA, Chen F, Pan H, Ramser J, Lehrach H, Reinhardt R, McCombie WR, de la BM, Dedhia N, Blocker H, Hornischer K, Nordsiek G, Agarwala R, Aravind L, Bailey JA, Bateman A, Batzoglou S, Birney E, Bork P, Brown DG, Burge CB, Cerutti L, Chen HC, Church D, Clamp M, Copley RR, Doerks T, Eddy SR, Eichler EE, Furey TS, Galagan J, Gilbert JG, Harmon C, Hayashizaki Y, Haussier D, Hermjakob H, Hokamp K, Jang W, Johnson LS, Jones TA, Kasif S, Kaspryzk A, Kennedy S, Kent WJ, Kitts P, Koonin EV, Korf I, Kulp D, Lancet D, Lowe TM, McLysaght A, Mikkelsen T, Moran JV, Mulder N, Pollara VJ, Ponting CP, Schuler G, Schultz J, Slater G, Smit AF, Stupka E, Szustakowski J, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Wallis J, Wheeler R, Williams A, Wolf YI, Wolfe KH, Yang SP, Yeh RF, Collins F, Guyer MS, Peterson J, Felsenfeld A, Wetterstrand KA, Patrinos A, Morgan MJ, Szustakowki J, De Jong P, Catanese JJ, Osoegawa K, Shizuya H, Choi S. 2001. Initial sequencing and analysis of the human genome. Nature 409:860-921.
29. Mamedov IZ, Arzumanyan ES, Amosova AL, Lebedev YB, Sverdlov ED. 2005. Whole-genome experimental identification of insertion/deletion polymorphisms of interspersed repeats by a new general approach. Nucleic Acids Res 33:e16.
30. Miki Y, Nishisho I, Horii A, Miyoshi Y, Utsunomiya J, Kinzler KW, Vogelstein B, Nakamura Y. 1992. Disruption of the APC gene by a retrotransposal insertion of L1 sequence in a colon cancer. Cancer Res 52:643-645.
31. Miki Y, Katagiri T, Kasumi F, Yoshimoto T, Nakamura Y. 1996. Mutation analysis in the BRCA2 gene in primary breast cancers. Nat Genet 13:245-247.
32. Miki Y. 1998. Retrotransposal integration of mobile genetic elements in human diseases. J Hum Genet 43:77-84.
33. Myers JS, Vincent BJ, Udall H, Watkins WS, Morrish TA, Kilroy GE, Swergold GD, Henke J, Henke L, Moran JV, Jorde LB, Batzer MA. 2002. A comprehensive analysis of recently integrated human Ta L1 elements. Am J Hum Genet 71:312-326.
34. Narita N, Nishio H, Kitoh Y, Ishikawa Y, Ishikawa Y, Minami R, Nakamura H, Matsuo M. 1993. Insertion of a 5′ truncated L1 element into the 3′ end of exon 44 of the dystrophin gene resulted in skipping of the exon during splicing in a case of Duchenne muscular dystrophy. J Clin Invest 91:1862-1867.
35. Ostertag EM, Prak ET, DeBerardinis RJ, Moran JV, Kazazian HH Jr. 2000. Determination of L1 retrotransposition kinetics in cultured cells. Nucleic Acids Res 28:1418-1423.
36. Ostertag EM, Kazazian HH Jr. 2001. Biology of mammalian L1 retrotransposons. Annu Rev Genet 35:501-538.
37. Ostertag EM, DeBerardinis RJ, Goodier JL, Zhang Y, Yang N, Gerton GL, Kazazian HH Jr. 2002. A mouse model of human L1 retrotransposition. Nat Genet 32:655-660.
38. Ostertag EM, Goodier JL, Zhang Y, Kazazian HH Jr. 2003. SVA elements are nonautonomous retrotransposons that cause disease in humans. Am J Hum Genet 73:1444-1451.
39. Otieno AC, Carter AB, Hedges DJ, Walker JA, Ray DA, Garber RK, Anders BA, Stoilova N, Laborde ME, Fowlkes JD, and others. 2004. Analysis of the human Alu Ya-lineage. J Mol Biol 342:109-118.
40. Perna NT, Batzer MA, Deininger PL, Stoneking M. 1992. Alu insertion polymorphism: a new type of marker for human population studies. Hum Biol 64:641-648.
41. Roy AM, Carroll ML, Kass DH, Nguyen SV, Salem AH, Batzer MA, Deininger PL. 1999. Recently integrated human Alu repeats: finding needles in the haystack. Genetica 107:149-161.
42. Salem AH, Myers JS, Otieno AC, Watkins WS, Jorde LB, Batzer MA. 2003. LINE-1 preTa elements in the human genome. J Mol Biol 326:1127-1146.
43. Salem AH, Ray DA, Batzer MA. 2005a. Identity by descent and DNA sequence variation of human SINE and LINE elements. Cytogenet Genome Res 108:63-72.
44. Salem AH, Ray DA, Hedges DJ, Jurka J, Batzer MA. 2005b. Analysis of the human Alu Ye lineage. BMC Evol Biol 5:18.
45. Sassaman DM, Dombroski BA, Moran JV, Kimberland ML, Naas TP, DeBerardinis RJ, Gabriel A, Swergold GD, Kazazian HH Jr. 1997. Many human L1 elements are capable of retrotransposition. Nat Genet 16:37-43.
46. Schwahn U, Lenzner S, Dong J, Feil S, Hinzmann B, van Duijnhoven G, Kirschner R, Hemberger M, Bergen AA, Rosenberg T, Pinckers AJ, Fundele R, Rosenthal A, Cremers FP, Ropers HH, Berger W. 1998. Positional cloning of the gene for X-linked retinitis pigmentosa 2. Nat Genet 19:327-332.
47. Sheen FM, Sherry ST, Risch GM, Robichaux M, Nasidze I, Stoneking M, Batzer MA, Swergold GD. 2000. Reading between the LINEs: human genomic variation induced by LINE-1 retrotransposition. Genome Res 10:1496-1508.
48. Shen L, Wu LC, Sanlioglu S, Chen R, Mendoza AR, Dangel AW, Carroll MC, Zipf WB, Yu CY. 1994. Structure and genetics of the partially duplicated gene RP located immediately upstream of the complement C4A and the C4B genes in the HLA class III region. Molecular cloning, exon-intron structure, composite retroposon, and breakpoint of gene duplication. J Biol Chem 269:8466-8476.
49. Stoneking M, Fontius JJ, Clifford SL, Soodyall H, Arcot SS, Saha N, Jenkins T, Tahir MA, Deininger PL, Batzer MA. 1997. Alu insertion polymorphisms and human evolution: evidence for a larger population size in Africa. Genome Res 7:1061-1071.
50. Vincent BJ, Myers JS, Ho HJ, Kilroy GE, Walker JA, Watkins WS, Jorde LB, Batzer MA. 2003. Following the LINEs: an analysis of primate genomic variation at human-specific LINE-1 insertion sites. Mol Biol Evol 20:1338-1348.
51. Wallace MR, Andersen LB, Saulino AM, Gregory PE, Glover TW, Collins FS. 1991. A de novo Alu insertion results in neurofibromatosis type 1. Nature 353:864-866.
52. Wang H, Xing J, Grover D, Hedges DJ, Han K, Walker JA, Batzer MA. 2005. SVA elements: a hominid-specific retroposon family. J Mol Biol 354:994-1007.
53. Wang J, Song L, Gonder MK, Azrak S, Ray D. A., Batzer MA, Tishkoff SA, Liang P. 2006. Whole genome computational comparative genomics: a fruitful approach for ascertaining Alu insertion polymorphisms. Gene 365:11-20.
54. Watkins WS, Ricker CE, Bamshad MJ, Carroll ML, Nguyen SV, Batzer MA, Harpending HC, Rogers AR, Jorde LB. 2001. Patterns of ancestral human diversity: an analysis of Alu-insertion and restriction-site polymorphisms. Am J Hum Genet 68:738-752.
55. Watkins WS, Rogers AR, Ostler CT, Wooding S, Bamshad MJ, Brassington AM, Carroll ML, Nguyen SV, Walker JA, Prasad BV, Reddy PG, Das PK, Batzer MA, Jorde LB. 2003. Genetic variation among world populations: inferences from 100 Alu insertion polymorphisms. Genome Res 13:1607-1618.
56. Xing J, Salem AH, Hedges DJ, Kilroy GE, Watkins WS, Schienman JE, Stewart CB, Jurka J, Jorde LB, Batzer MA. 2003. Comprehensive analysis of two Alu Yd subfamilies. J Mol Evol 57(Suppl 1):S76-S89.