Genetics, Vol. 159, 279-290, September 2001, Copyright © 2001

Alu Insertion Polymorphisms for the Study of Human Genomic Diversity

Astrid M. Roy-Engela, Marion L. Carrollb, Erika Vogela, Randall K. Garberb,c, Son V. Nguyenb, Abdel-Halim Salemb,c, Mark A. Batzerb,c, and Prescott L. Deiningera,d
a Tulane Cancer Center, Department of Environmental Health Sciences, Tulane University Health Sciences Center, New Orleans, Louisiana 70112,
b Departments of Pathology, Genetics, Biochemistry and Molecular Biology, Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, Louisiana 70112,
c Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, Baton Rouge, Louisiana 70803
d Laboratory of Molecular Genetics, Alton Ochsner Medical Foundation, New Orleans, Louisiana 70121

Corresponding author: Prescott L. Deininger, Tulane Cancer Center, SL-66, Tulane University Medical Center, 1430 Tulane Ave., New Orleans, LA 70112., pdeinin{at}tulane.edu (E-mail)

Communicating editor: Y.-X. FU

Genomic database mining has been a very useful aid in the identification and retrieval of recently integrated Alu elements from the human genome. We analyzed Alu elements retrieved from the GenBank database and identified two new Alu subfamilies, Alu Yb9 and Alu Yc2, and further characterized Yc1 subfamily members. Some members of each of the three subfamilies have inserted in the human genome so recently that about a one-third of the analyzed elements are polymorphic for the presence/absence of the Alu repeat in diverse human populations. These newly identified Alu insertion polymorphisms will serve as identical-by-descent genetic markers for the study of human evolution and forensics. Three previously classified Alu Y elements linked with disease belong to the Yc1 subfamily, supporting the retroposition potential of this subfamily and demonstrating that the Alu Y subfamily currently has a very low amplification rate in the human genome.




This article has been cited by other articles:


Home page
 J. Neurosci.Home page
B. Mosch, M. Morawski, A. Mittag, D. Lenz, A. Tarnok, and T. Arendt
Aneuploidy and DNA Replication in the Normal Human Brain and Alzheimer's Disease
J. Neurosci., June 27, 2007; 27(26): 6859 - 6867.
[Abstract] [Full Text] [PDF]

Home page
 Endocr Relat CancerHome page
A. Angelucci, G. L. Gravina, N. Rucci, D. Millimaggi, C. Festuccia, P. Muzi, A. Teti, C. Vicentini, and M. Bologna
Suppression of EGF-R signaling reduces the incidence of prostate cancer metastasis in nude mice.
Endocr. Relat. Cancer, March 1, 2006; 13(1): 197 - 210.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
L. N. van de Lagemaat, L. Gagnier, P. Medstrand, and D. L. Mager
Genomic deletions and precise removal of transposable elements mediated by short identical DNA segments in primates
Genome Res., September 1, 2005; 15(9): 1243 - 1249.
[Abstract] [Full Text] [PDF]

Home page
 Hum Mol GenetHome page
I. Sandovici, S. Kassovska-Bratinova, J. C. Loredo-Osti, M. Leppert, A. Suarez, R. Stewart, F. D. Bautista, M. Schiraldi, and C. Sapienza
Interindividual variability and parent of origin DNA methylation differences at specific human Alu elements
Hum. Mol. Genet., August 1, 2005; 14(15): 2135 - 2143.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
K. Han, J. Xing, H. Wang, D. J. Hedges, R. K. Garber, R. Cordaux, and M. A. Batzer
Under the genomic radar: The Stealth model of Alu amplification
Genome Res., May 1, 2005; 15(5): 655 - 664.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
I. Z. Mamedov, E. S. Arzumanyan, A. L. Amosova, Y. B. Lebedev, and E. D. Sverdlov
Whole-genome experimental identification of insertion/deletion polymorphisms of interspersed repeats by a new general approach
Nucleic Acids Res., January 26, 2005; 33(2): e16 - e16.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
E. A. Bennett, L. E. Coleman, C. Tsui, W. S. Pittard, and S. E. Devine
Natural Genetic Variation Caused by Transposable Elements in Humans
Genetics, October 1, 2004; 168(2): 933 - 951.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
D. J. Hedges, P. A. Callinan, R. Cordaux, J. Xing, E. Barnes, and M. A. Batzer
Differential Alu Mobilization and Polymorphism Among the Human and Chimpanzee Lineages
Genome Res., June 1, 2004; 14(6): 1068 - 1075.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
P. Jin, J. Zhang, C. Rowe-Teeter, J. Yang, L. L. Stuve, and G. K. Fu
Cloning and Characterization of a GABAA Receptor {gamma}2 Subunit Variant
J. Biol. Chem., January 9, 2004; 279(2): 1408 - 1414.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
J. Biedler and Z. Tu
Non-LTR Retrotransposons in the African Malaria Mosquito, Anopheles gambiae: Unprecedented Diversity and Evidence of Recent Activity
Mol. Biol. Evol., November 1, 2003; 20(11): 1811 - 1825.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
A.-H. Salem, D. A. Ray, J. Xing, P. A. Callinan, J. S. Myers, D. J. Hedges, R. K. Garber, D. J. Witherspoon, L. B. Jorde, and M. A. Batzer
Alu elements and hominid phylogenetics
PNAS, October 28, 2003; 100(22): 12787 - 12791.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
A.-H. Salem, G. E. Kilroy, W. S. Watkins, L. B. Jorde, and M. A. Batzer
Recently Integrated Alu Elements and Human Genomic Diversity
Mol. Biol. Evol., August 1, 2003; 20(8): 1349 - 1361.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
W. S. Watkins, A. R. Rogers, C. T. Ostler, S. Wooding, M. J. Bamshad, A.-M. E. Brassington, M. L. Carroll, S. V. Nguyen, J. A. Walker, B.V. R. Prasad, et al.
Genetic Variation Among World Populations: Inferences From 100 Alu Insertion Polymorphisms
Genome Res., July 1, 2003; 13(7): 1607 - 1618.
[Abstract] [Full Text] [PDF]

Home page
 NEJMHome page
A. Siddiqui, R. Kerb, M. E. Weale, U. Brinkmann, A. Smith, D. B. Goldstein, N. W. Wood, and S. M. Sisodiya
Association of Multidrug Resistance in Epilepsy with a Polymorphism in the Drug-Transporter Gene ABCB1
N. Engl. J. Med., April 10, 2003; 348(15): 1442 - 1448.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
Y. Fan, E. Linardopoulou, C. Friedman, E. Williams, and B. J. Trask
Genomic Structure and Evolution of the Ancestral Chromosome Fusion Site in 2q13-2q14.1 and Paralogous Regions on Other Human Chromosomes
Genome Res., November 1, 2002; 12(11): 1651 - 1662.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
A. M. Roy-Engel, A.-H. Salem, O. O. Oyeniran, L. Deininger, D. J. Hedges, G. E. Kilroy, M. A. Batzer, and P. L. Deininger
Active Alu Element "A-Tails": Size Does Matter
Genome Res., September 1, 2002; 12(9): 1333 - 1344.
[Abstract] [Full Text] [PDF]