Increased gene coverage and Alu frequency in large linkage disequilibrium blocks of the human genome

Genetics and Molecular Research

Volumn 6, Issue 4, 2007, Pages 1131-1141

  Wang, Y ^a   Fong, P Y ^a   Leung, F C C ^a   Mak, W ^a   Sham, P C ^a,b  

^a UNIVERSITY OF HONG KONG   (Hong Kong)

^b KING'S COLLEGE LONDON   (United Kingdom)

Author keywords

Alu; Gene coverage; Gene density; Linkage disequilibrium blocks; Recombination

Indexed keywords

ALU SEQUENCE; AUTOSOME; CONFERENCE PAPER; DNA SEQUENCE; GENE FREQUENCY; GENE LINKAGE DISEQUILIBRIUM; GENE MAPPING; GENETIC ASSOCIATION; GENETIC CORRELATION; GENOME; GENOTYPE; HUMAN; RNA SPLICING; SIMULATION; SINGLE NUCLEOTIDE POLYMORPHISM;

ALU ELEMENTS; DATABASES, NUCLEIC ACID; GENETICS, POPULATION; GENOME, HUMAN; HUMANS; LINKAGE DISEQUILIBRIUM; MODELS, GENETIC; POLYMORPHISM, SINGLE NUCLEOTIDE; RECOMBINATION, GENETIC;

EID: 37349021398     PISSN: None     EISSN: 16765680     Source Type: Journal    
DOI: None     Document Type: Conference Paper

References (32)

1. Babcock M, Pavlicek A, Spiteri E, Kashork CD, et al. (2003). Shuffling of genes within low-copy repeats on 22q11 (LCR22) by Alu-mediated recombination events during evolution. Genome Res. 13: 2519-2532.
2. Babich V, Aksenov N, Alexeenko V, Oei SL, et al. (1999). Association of some potential hormone response elements in human genes with the Alu family repeats. Gene 239: 341-349.
3. Bailey JA, Liu G and Eichler EE (2003). An Alu transposition model for the origin and expansion of human segmental duplications. Am. J. Hum. Genet. 73: 823-834.
4. Barrett JC, Fry B, Maller J and Daly MJ (2005). Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 21: 263-265.
5. Dawson E, Abecasis GR, Bumpstead S, Chen Y, et al. (2002). A first-generation linkage disequilibrium map of human chromosome 22. Nature 418: 544-548.
6. Deininger PL and Batzer MA (1999). Alu repeats and human disease. Mol. Genet. Metab. 67: 183-193.
7. Dermitzakis ET, Reymond A, Lyle R, Scamuffa N, et al. (2002). Numerous potentially functional but non-genic conserved sequences on human chromosome 21. Nature 420: 578-582.
8. Dermitzakis ET, Kirkness E, Schwarz S, Birney E, et al. (2004). Comparison of human chromosome 21 conserved nongenic sequences (CNGs) with the mouse and dog genomes shows that their selective constraint is independent of their genic environment. Genome Res. 14: 852-859.
9. Gabriel SB, Schaffner SF, Nguyen H, Moore JM, et al. (2002). The structure of haplotype blocks in the human genome. Science 296: 2225-2229.
10. Gerton JL, DeRisi J, Shroff R, Lichten M, et al. (2000). Global mapping of meiotic recombination hotspots and coldspots in the yeast Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 97: 11383-11390.
11. Greenwood TA, Rana BK and Schork NJ (2004). Human haplotype block sizes are negatively correlated with recombination rates. Genome Res. 14: 1358-1361.
12. Harteveld KL, Losekoot M, Fodde R, Giordano PC, et al. (1997). The involvement of Alu repeats in recombination events at the alpha-globin gene cluster: characterization of two alpha-zero-thalassaemia deletion breakpoints. Hum. Genet. 99: 528-534.
13. Hinds DA, Stuve LL, Nilsen GB, Halperin E, et al. (2005). Whole-genome patterns of common DNA variation in three human populations. Science 307: 1072-1079.
14. International Human Sequencing Consortium (2001). Initial sequencing and analysis of the human genome. Nature 409: 860-921.
15. Kauppi L, Sajantila A and Jeffreys AJ (2003). Recombination hotspots rather than population history dominate linkage disequilibrium in the MHC class II region. Hum. Mol. Genet. 12: 33-40.
16. Kreahling J and Graveley BR (2004). The origins and implications of Aluternative splicing. Trends Genet. 20: 1-4.
17. Lev-Maor G, Sorek R, Shomron N and Ast G (2003). The birth of an alternatively spliced exon: 3′ splice-site selection in Alu exons. Science 300: 1288-1291.
18. Liu G, Zhao S, Bailey JA, Sahinalp SC, et al. (2003). Analysis of primate genomic variation reveals a repeat-driven expansion of the human genome. Genome Res. 13: 358-368.
19. Matthew EH, Willey D, Matthews L and Syed SH (2004). Origins of chromosomal rearrangement hotspots in the human genome: evidence from the AZFa deletion hotspots. Genome Biol. 5: 55r.
20. McVean GA, Myers SR, Hunt S, Deloukas P, et al. (2003). The finescale structure of recombination rate variation in the human genome. Science 304: 581-584.
21. Ng SK and Xue H (2006). Alu-associated enhancement of single nucleotide polymorphisms in the human genome. Gene 368: 110-116.
22. Pal C and Hurst LD (2003). Evidence for co-evolution of gene order and recombination rate. Nat. Genet. 33: 392-395.
23. Phillips MS, Lawrence R, Sachidanandam R, Morris AP, et al. (2003). Chromosome-wide distribution of haplotype blocks and the role of recombination hot spots. Nat. Genet. 33: 382-387.
24. Reich DE, Schaffner SF, Daly MJ, McVean G, et al. (2002). Human genome sequence variation and the influence of gene history, mutation and recombination. Nat. Genet. 32: 135-142.
25. Shankar R, Grover D, Brahmachari SK and Mukerji M (2004). Evolution and distribution of RNA polymerase II regulatory sites from RNA polymerase III dependant mobile Alu elements. BMC Evol. Biol. 4: 37.
26. Smith AV, Thomas DJ, Munro HM and Abecasis GR (2005). Sequence features in regions of weak and strong linkage disequilibrium. Genome Res. 15: 1519-1534.
27. Sorek R, Ast G and Graur D (2002). Alu-containing exons are alternatively spliced. Genome Res. 12: 1060-1067.
28. The International HapMap Consortium (2005). A haplotype map of the human genome. Nature 437: 1299-1320.
29. Twells RC, Mein CA, Phillips MS, Hess JF, et al. (2003). Haplotype structure, LD blocks, and uneven recombination within the LRP5 gene. Genome Res. 13: 845-855.
30. Vansant G and Reynolds WF (1995). The consensus sequence of a major Alu subfamily contains a functional retinoic acid response element. Proc. Natl. Acad. Sci. USA 92: 8229-8233.
31. Vinogradov AE (2004). Compactness of human housekeeping genes: selection for economy or genomic design? Trends Genet. 20: 248-253.
32. Wall JD and Pritchard JK (2003). Assessing the performance of the haplotype block model of linkage disequilibrium. Am. J. Hum. Genet. 73: 502-515.