Some probabilistic results on the nonrandomness of simple sequence repeats in DNA sequences

Bulletin of Mathematical Biology

Volumn 68, Issue 7, 2006, Pages 1747-1759

  Ndifon, Wilfred ^a,b   Nkwanta, Asamoah ^a   Hill, Dwayne ^a  

^a MORGAN STATE UNIVERSITY   (United States)

^b PRINCETON UNIVERSITY   (United States)

Author keywords

DNA sequence evolution; Microsatellites; Neurological disorders; Sequence analysis; Simple sequence repeats

Indexed keywords

ANDROGEN RECEPTOR; AR PROTEIN, HUMAN; HD PROTEIN, HUMAN; MICROSATELLITE DNA; NERVE PROTEIN; NUCLEAR PROTEIN;

ALGORITHM; ARTICLE; BIOLOGICAL MODEL; GENETICS; HUMAN; MUTATION; NUCLEOTIDE SEQUENCE; PROBABILITY; SPINOCEREBELLAR DEGENERATION; STATISTICAL MODEL; TANDEM REPEAT;

ALGORITHMS; BASE SEQUENCE; HUMANS; MICROSATELLITE REPEATS; MODELS, GENETIC; MODELS, STATISTICAL; MUTATION; NERVE TISSUE PROTEINS; NUCLEAR PROTEINS; PROBABILITY; RECEPTORS, ANDROGEN; SPINOCEREBELLAR ATAXIAS; TANDEM REPEAT SEQUENCES;

EID: 33748702894     PISSN: 00928240     EISSN: 15229602     Source Type: Journal    
DOI: 10.1007/s11538-005-9029-9     Document Type: Article

References (44)

1. Arzimanoglou, I.I., Gilbert, F., Barber, H.R., 1998. Microsatellite instability in human solid tumors. Cancer 82, 1808-1820.
2. Baldi, P., Baisnee, P.F., 2000. Sequence analysis by additive scales: DNA structure for sequences and repeats of all lengths. Bioinformatics 16, 865-889.
3. Baldi, P., Brunak, S., 1999. Structural basis for triplet repeat disorders: a computational analysis. Bioinformatics 15, 919-929.
4. Bell, G.I., 1996. Evolution of simple sequence repeats. Comput. Chem. 20, 41-48.
5. Bell, G.I., Jurka, J., 1997. The length distribution of perfect dimer repetitive DNA is consistent with its evolution by an unbiased single-step mutation process. J. Mol. Evol. 44, 414-421.
6. Butler, J.M., 2001. Forensic DNA Typing: Biology and Technology Behind STR Markers. Academic Press, London.
7. Calabrese, P.P., Durrett, R.T., Aquadro, C.F., 2001. Dynamics of microsatellite divergence under stepwise mutation and proportional slippage/point mutation models. Genetics 159, 839-852.
8. Chrysaphinou, O., Papstavridis, S., 1988. A limit theorem on the number of overlapping appearances of a pattern in a sequence of independent fields. Probab. Theory Relat. Fields 79, 129-143.
9. Cox, R., Mirkin, M.S., 1997. Characteristic enrichment of DNA repeats in different genomes. Proc. Natl. Acad. Sci. U.S.A. 94, 5237-5242.
10. De Vrij, F.M.S., Sluijs, J.A., Gregori, L., Fischer, D.F., Hermens, W.T.J., Goldgaber, D., Verhaagen, J., van Leeuwen, F.W., Hol, E.M., 2001. Mutant ubiquitin expressed in Alzheimer's disease causes neuronal death. FASEB J. 15, 2680-2688.
11. Ellegren, H., 2000. Heterogeneous mutation processes in human microsatellite DNA sequences. Nat. Genet. 24, 400-402.
12. Grimaldi, R., 1998. Discrete and Combinatorial Mathematics: An Applied Introduction. Pearson Education, Upper Saddle River, NJ.
13. Gusev, V.D., Nemytikova, L.A., Chuzhanova, N.A., 1999. On the complexity measures of genetic sequences. Bioinformatics 15, 994-999.
14. Jurka, J., Pethiyagoda, C., 1995. Simple repetitive DNA sequences from primates: compilation and analysis. J. Mol. Evol. 40, 120-126.
15. Karlin, S., Brocchieri, L., Bergman, A., Mŕazek, J., Gentles, J., 2002. Amino acid runs in eukaryotic proteomes and disease associations. Proc. Natl. Acad. Sci. U.S.A. 99, 333-338.
16. Kolchin, V.F., Sevast'yanov, B.A., Chistyakov, V.P., 1978. Random Allocations. V.H. Winston, Washington, DC.
17. Kruglyak, S., Durret, R.T., Schug, M., Aquadro, C.F., 1998. Equilibrium distributions of microsatellite repeat length resulting from a balance between slippage events and point mutations. Proc. Natl. Acad. Sci. U.S.A. 95, 10774-10778.
18. Kruglyak, S., Durrett, R.T., Schug, M.D., Aquadro, C.F., 2000. Distribution and abundance of microsatellites in the yeast genome can be explained by a balance between slippage events and point mutations. Mol. Biol. Evol. 17, 1210-1219.
19. Kuraoda, J., Kimura, S., Kobayashi, Y., Wada, K., Uoshima, N., Yoshikawa, T., 2002. Unusual myelodysplastic syndrome with the initial presentation mimicking idiopathic thrombocytopenic purpura. Acta Hematol. 108, 139-143.
20. Landles, C., Bates, G.P., 2004. Huntingtin and the molecular pathogenesis of Huntington's disease. Fourth in molecular medicine review series. EMBO Rep. 5, 958-963.
21. Lindsten, K., De Vrij, F.M., Verhoef, L.G., Fischer, D.F., van Leeuwen, F.W., Hol, E.M., Masucci, M.G., Dantuma, N.P., 2002. Mutant ubiquitin found in neurodegenerative disorders is a ubiquitin fusion degradation substrate that blocks proteasomal degradation. J. Cell Biol. 157, 417-427.
22. Lippert, R.A., Huang, H., Waterman, M.S., 2002. Distributional regimes for the number of k-word matches between two random sequences. Proc. Natl. Acad. Sci. U.S.A. 99, 13980-13989.
23. Margolis, R.L., McInnis, M.G., Rosenblatt, A., Ross, C.A., 1999. Trinucleotide repeat expansion and neuropsychiatric disease. Arch. Gen. Psychiatry 56, 1019-1031.
24. McInnis, M.G., Margolis, R.L., 1998. Anticipation, triplet repeats, and psychiatric disorders. In: Rubinsztein, D.C., Heyden, M.R. (Eds.), Analysis of Triplet Repeat Disorders. Bios Scientific Press, Oxford, pp. 401-411.
25. Milenkovic, O., Compton, K., 2004. On probabilistic transforms and classical urn models. Comb. Probab. Comput. 13, 645-675.
26. Nakamura, Y., Leppert, M., O'Connell, P., Wolff, R., Holm, T., Culver, M., Martin, C., Fujimoto, E., Hoff, M., Kumlin, E., 1987. Variable number of tandem repeat (VNTR) markers for human gene mapping. Science 235, 1616-1622.
27. Nicode'me, P., 2003. Q-gram analysis and urn models. Discrete Math. Theor. Comput. Sci., AC, 243-258.
28. Nicode'me, P., Salvy, B., Flajolet, P., 2002. Motif statistics. Theor. Comput. Sci. 287, 593-618.
29. Percus, J.K., 2002. Mathematics of Genome Analysis. Cambridge University Press, Cambridge, UK.
30. Rahman, S., Rivals, E., 2000. Exact and efficient computation of the expected number of missing and common words in random texts. In: Proceedings of the 11th Symposium on Combinatorial Pattern Matching. Springer Verlag, Berlin.
31. Regnier, M., 2000. A unified approach to word occurrence probabilities. Discrete Appl. Math. 104, 259-280.
32. Reinert, G., Schbath, S., 1998. Compound Poisson and Poisson process approximations for occurrences of multiple words in Markov chains. J. Comput. Biol. 5, 223-253.
33. Sashida, G., Ohyashiki, J.H., Ito, Y., Ohyashiki, K., 2002. Monoclonal constitution of neutrophils detected by PCR-based human androgen receptor gene assay in a subset of idiopathic thrombocytopenic purpura patients. Leuk. Res. 26, 825-830.
34. Schbath, S., 1997. An efficient statistic to detect over- and under-represented words in DNA sequences. J. Comput. Biol. 4, 189-192.
35. Schlötterer, C., 2000. Evolutionary dynamics of microsatellite DNA. Chromosoma 109, 365-371.
36. Takeuchi, F., Futamura, Y., Yoshikura, H., Yamamoto, K., 2003. Statistics of trinucleotides in coding sequences and evolution. J. Theor. Biol. 222, 139-149.
37. Tanaka, F., Doyu, M., Ito, Y., Matsumoto, M., Mitsuma, T., Abe, K., Aoki, M., Itoyama, Y., Fischbeck, K.H., Sobue, G., 1996. Founder effect in spinal bulbarmuscular atrophy (SBMA). Hum. Mol. Genet. 5, 1253-1257.
38. Toth, G., Gaspari, Z., Jurka, J., 2000. Microsatellites in different eukaryotic genomes: survey and analysis. Genome Res. 10, 967-981.
39. Troyanskaya, O.G., Arbell, O., Koren, Y., Landau, G., Bolshoy, A., 2002. Sequence complexity profiles of prokaryotic genomic sequences: a fast algorithm for calculating linguistic complexity. Bioinformatics 18, 679-688.
40. van Dijk, R., Fischer, D.F., Sluijs, J.A., Sonnemans, M.A., Hobo, B., Mercken, L., Mann, D.M., Hol, E.M., van Leeuwen, F.W., 2004. Frame-shifted amyloid precursor protein found in Alzheimer's disease and Down's syndrome increases levels of secreted amyloid beta 40. J. Neurochem. 90, 712-723.
41. van denHurk, W.H., Willems, H.J., Bloemen, M., Martens, G.J., 2001. Novel frameshift mutations near short simple repeats. J. Biol. Chem. 276, 11496-11498.
42. van Leeuwen, F.W., De Kleijn, D.P.V., Van den Hurk, H.H., Neubauer, A., Sonnemans, M.A.F., Sluijs, J.A., Koycu, S., Ramdjielal, R.D.J., Salehi, A., Martens, G.J.M., Grosveld, F.G., Burbach, J.P.H., Hol, E.M., 1998. Frameshift mutants of beta Amyloid precursor protein and Ubiquitin-B in Alzheimer's and Down patients. Science 279, 242-247.
43. van Leeuwen, F.W., Fischer, D.F., Benne, R., Hol, E.M., 2004. Molecular misreading. A new type of transcript mutation in gerontology. Ann. N.Y. Acad. Sci. 98, 267-281.
44. Wooster, R., Cleton-Jansen, A.M., Collins, N., Mangion, J., Cornelis, R.S., Cooper, C.S., Gusterson, B.A., Ponder, B.A., von Deimling, A., Wiestler, O.D., 1994. Instability of short tandem repeats (microsatellites) in human cancer. Nat. Genet. 6, 152-156.