Large-scale analysis of the Alu Ya5 and Yb8 subfamilies and their contribution to human genomic diversity

被引:123
作者
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, W
Jorde, LB
Deininger, PL
Batzer, MA
机构
[1] Louisiana State Univ, Dept Biol Sci, Biol Computat & Visualizat Ctr, Baton Rouge, LA 70803 USA
[2] Louisiana State Univ, Hlth Sci Ctr, Stanley S Scott Canc Ctr, Dept Pathol,Neurosci Ctr Excellence, New Orleans, LA 70112 USA
[3] Louisiana State Univ, Hlth Sci Ctr, Stanley S Scott Canc Ctr, Dept Genet Biochem & Mol Biol,Neurosci Ctr Excell, New Orleans, LA 70112 USA
[4] Tulane Univ, Hlth Sci Ctr, Dept Environm Hlth Sci, Tulane Canc Ctr, New Orleans, LA 70112 USA
[5] Univ Utah, Hlth Sci Ctr, Dept Human Genet, Salt Lake City, UT 84112 USA
[6] Inst Blutgrp Forsch, D-50501 Cologne, Germany
[7] NIH, Natl Ctr Biotechnol Informat, Natl Lib Med, Bethesda, MD 20894 USA
[8] Alton Ochsner Med Fdn & Ochsner Clin, Mol Genet Lab, New Orleans, LA 70121 USA
关键词
Alu insertion polymorphism; gene conversion; computational biology;
D O I
10.1006/jmbi.2001.4847
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
We have utilized computational biology to screen GenBank for the presence of recently integrated Ya5 and Yb8 Alu family members. Our analysis identified 2640 Ya5 Alu family members and 1852 Yb8 Alu family members from the draft sequence of the human genome. We selected a set of 475 of these elements for detailed analyses. Analysis of the DNA sequences from the individual Alu elements revealed a low level of random mutations within both subfamilies consistent with the recent origin of these elements within the human genome. Polymerase chain reaction assays were used to determine the phylogenetic distribution and human genomic variation associated with each Alu repeat. Over 99 % of the Ya5 and Yb8 Alu family members were restricted to the human genome and absent from orthologous positions within the genomes of several non-human primates, confirming the recent origin of these Alu subfamilies in the human genome. Approximately 1 % of the analyzed Ya5 and Yb8 Alu family members had integrated into previously undefined repeated regions of the human genome. Analysis of mosaic Yb8 elements suggests gene conversion played an important role in generating sequence diversity among these elements. Of the 475 evaluated elements, a total of 106 of the Ya5 and Yb8 Alu family members were polymorphic for insertion presence/absence within the genomes of a diverse array of human populations. The newly identified Alu insertion polymorphisms will be useful tools for the study of human genomic diversity. (C) 2001 Academic Press.
引用
收藏
页码:17 / 40
页数:24
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