Characterization of frequencies and distribution of single nucleotide insertions/deletions in the human genome

Gene

Volumn 376, Issue 2, 2006, Pages 268-280

  Tan, Ene Choo ^a,c   Li, Haixia ^b  

^a KK WOMEN'S AND CHILDREN'S HOSPITAL   (Singapore)

^b NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

^c NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

Author keywords

DBSNP; Density; Insertions deletions; Mononucleotide repeats; Palindromes

Indexed keywords

NUCLEOTIDE; SPACER DNA;

ARTICLE; BASE PAIRING; COMPARATIVE STUDY; EXON; GENE DELETION; GENE EXPRESSION REGULATION; GENE FREQUENCY; GENETIC VARIABILITY; GENETICS; GENOME; HUMAN; HUMAN CHROMOSOME; INTRON; NUCLEOTIDE SEQUENCE; REPRODUCIBILITY; SINGLE NUCLEOTIDE POLYMORPHISM;

BASE PAIRING; BASE SEQUENCE; CHROMOSOMES, HUMAN; DNA, INTERGENIC; EXONS; GENE FREQUENCY; GENOME, HUMAN; HUMANS; INTRONS; MUTAGENESIS, INSERTIONAL; NUCLEOTIDES; POLYMORPHISM, SINGLE NUCLEOTIDE; REPRODUCIBILITY OF RESULTS; SEQUENCE DELETION; VARIATION (GENETICS);

EID: 33748097272     PISSN: 03781119     EISSN: 18790038     Source Type: Journal    
DOI: 10.1016/j.gene.2006.04.009     Document Type: Article

References (34)

1. Astolfi, A., Bellizzi, D., Sgaramella, V., 2003. Frequency and coverage of trinucleotide repeats in eukaryotes. Gene 317, 117-125.
2. Chuzhanova, N.A., Anassis, E.J., Ball, E.V., Krawczak, M., Cooper, D.N., 2003. Meta-analysis of indels causing human genetic disease: mechanisms of mutagenesis and the role of local DNA sequence complexity. Hum. Mutat. 21, 28-44.
3. Deininger, P.L., Batzer, M.A., 1999. Alu repeats and human disease. Mol. Genet. Metab. 67, 183-193.
4. Economou, E.P., Kazazian Jr., H.H., Antonarakis, S.E., 1992. Detection of mutations in the factor VIII gene using single-stranded conformational polymorphism (SSCP). Genomics 13, 909-911.
5. Gentles, A.J., Karlin, S., 2001. Genome-scale compositional comparisons in eukaryotes. Genome Res. 11, 540-546.
6. Gu, Z.,Wang, H., Nekrutenko, A., Li,W.H., 2000. Densities, length proportions, and other distributional features of repetitive sequences in the human genome estimated from 430 megabases of genomic sequence. Gene 259, 81-88. International Human Genome Sequencing Consortium, 2001. Initial screening and analysis of the human genome. Nature 409, 860-921.
7. International Human Genome Sequencing Consortium, 2001. Initial screening and analysis of the human genome. Nature 409, 860-921.
8. Karlin, S., Ladunga, I., 1994. Comparisons of eukaryotic genomic sequences. Proc. Natl. Acad. Sci. U. S. A. 91, 12832-12836.
9. Katti, M.V., Ranjekar, P.K., Gupta, V.S., 2001. Differential distribution of simple sequence repeats in eukaryotic genome sequences. Mol. Biol. Evol. 18, 1161-1167.
10. Lander , et al., 2001. Initial sequencing and analysis of the human genome. Nature 409, 860-921 (Erratum in: Nature. 2001. 412, 565. Nature 2001. 411, 720 Szustakowki J [corrected to Szustakowski J]).
11. Lewis, S.M., Chen, S., Strathern, J.N., Rattray, A.J., 2005. New approaches to the analysis of palindromic sequences from the human genome: evolution and polymorphism of an intronic site at the NF1 locus. Nucleic Acids Res. 33, e186.
12. Lutz, S.M., Vincent, B.J., Kazazian Jr., H.H., Batzer, M.A., Moran, J.V., 2003. Allelic heterogeneity in LINE-1 retrotransposition activity. Am. J. Hum. Genet. 73, 1431-1437.
13. Marth, G., et al., 2001. Single-nucleotide polymorphisms in the public domain: how useful are they? Nat. Genet. 27, 371-372.
14. Marth, G., et al., 2003. Sequence variations in the public human genome data reflect a bottlenecked population history. Proc. Natl. Acad. Sci. U. S. A. 100, 376-381.
15. 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.
16. Mouse Genome Sequencing Consortium, 2002. Initial sequencing and comparative analysis of the mouse genome. Nature 420, 520-526.
17. Oldridge, M., et al., 1999. De novo alu-element insertions in FGFR2 identify a distinct pathological basis for Apert syndrome. Am. J. Hum. Genet. 64, 446-461.
18. Ophir, R., Graur, D., 1997. Patterns and rates of indel evolution in processed pseudogenes from humans and murids. Gene 205, 191-202.
19. Ostertag, E.M., Kazazian Jr., H.H., 2001. Biology of mammalian L1 retrotransposons. Annu. Rev. Genet. 35, 501-538.
20. Rattray, A.J., 2005. A method for cloning and sequencing long palindromic DNA junctions. Nucleic Acids Res. 32, e155.
21. Rubin, C.M., Houck, C.M., Deininger, P.L., Freidmann, T., Schmid, C.W., 1980. Partial nucleotide sequence of the 300-nucleotide interspersed repeated human DNA sequences. Nature 284, 372-374.
22. Russell, G.J., Walker, P.M., Elton, R.A., Subak-Sharpe, J.H., 1976. Doublet frequency analysis of fractionated vertebrate nuclear DNA. J. Mol. Biol. 108, 1-23.
23. Shaw, C.J., Lupski, J.R., 2004. Implications of human genome architecture for rearrangement-based disorders: the genomic basis of disease. Hum. Mol. Genet. 13, R57-R64.
24. Smit, 1996. The origin of interspersed repeats in the human genome. Curr. Opin. Genet. Dev. 6, 743-748.
25. Stankiewicz, P., Lupski, J., 2002. Molecular-evolutionary mechanisms for genomic disorders. Curr. Opin. Genet. Dev. 12, 312-319.
26. Stenger, J.E., Lobachev, K.S., Gordenin, D., Darden, T.A., Jurka, J., Resnick, M.A., 2001. Biased distribution of inverted and direct Alus in the human genome: implications for insertion, exclusion, and genome stability. Genome Res. 11, 12-27.
27. Tan, E.C., Lai, P.S., 2005. Molecular diagnosis of neurogenetic disorders involving trinucleotide repeat expansions. Expert Rev. Mol. Diagn. 5, 101-109.
28. Toth, G., Gaspari, Z., Jurka, J., 2000. Microsatellites in different eukaryotic genomes: survey and analysis. Genome Res. 10, 967-981.
29. Wallace, M.R., Andersen, L.B., Saulino, A.M., Gregory, P.E., Glover, T.W., Collins, F.S., 1991. A de novo Alu insertion results in neurofibromatosis type 1. Nature 353, 864-866.
30. Weber, J.L., David, D., Heil, J., Fan, Y., Zhao, C., Marth, G., 2002. Human diallelic insertion/deletion polymorphisms. Am. J. Hum. Genet. 71, 854-862.
31. Zhang, Z., Gerstein, M., 2003. Patterns of nucleotide substitution, insertion and deletion in the human genome inferred from pseudogenes. Nucleic Acids Res. 31, 5338-5348.
32. Zhao, Z., Boerwinkle, E., 2002. Neighboring-nucleotide effects on single nucleotide polymorphisms: a study of 2.6 million polymorphisms across the human genome. Genome Res. 12, 1679-1686.
33. Zhao, Z., Fu, Y.X., Hewett-Emett, D., Boerwinkle, E., 2003. Investigating single nucleotide polymorphism (SNP) density in the human genome and its implications for molecular evolution. Gene 312, 207-213.
34. Zielenski, J., Tsui, L.C., 1995. Cystic fibrosis: genotypic and phenotypic variations. Annu. Rev. Genet. 29, 777-807.