Rate and directionality of mutations and effects of allele size constraints at anonymous, gene-associated, and disease-causing trinucleotide loci

Molecular Biology and Evolution

Volumn 16, Issue 9, 1999, Pages 1166-1177

  Deka, Ranjan ^c   Guangyun, Sun ^c   Smelser, Diane ^c   Zhong, Yixi ^a   Kimmel, Marek ^c   Chakraborty, Ranajit ^a,b  

^a UNIVERSITY OF TEXAS   (United States)

^b UNIVERSITY OF TEXAS SCHOOL OF PUBLIC HEALTH   (United States)

^c NONE

Author keywords

Allele size constraint; Coalescence; Genome location; Stepwise mutation; Trinucleotide diseases

Indexed keywords

ALLELE; ARTICLE; GENE LOCUS; GENE MUTATION; GENETIC VARIABILITY; HETEROZYGOSITY; HUMAN; MUTATION RATE; RACE DIFFERENCE; TRINUCLEOTIDE REPEAT;

EID: 0032840798     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/oxfordjournals.molbev.a026207     Document Type: Article

References (36)

1. BOWCOCK, A. M., A. RUIZ-LINARES, J. TOMFOHRDE, E. MINCH, J. R. KIDD, and L. L. CAVALLI-SFORZA. 1994. High resolution of human evolutionary trees with polymorphic microsatellites. Nature 368:455-457.
2. CANN, R. L., M. STONEKING, and A. C. WILSON. 1987. Mitochondrial DNA and human evolution. Nature 325:31-36.
3. CHAKRABORTY, R., and L. JIN. 1992. Heterozygote deficiency, population substructure and their implications in DNA fingerprinting. Hum. Genet. 88:267-272.
4. CHAKRABORTY, R., M. KIMMEL, D. N. STIVERS, L. J. DAVISON, and R. DEKA. 1997. Relative mutation rates at di-, tri, and tetranucleotide microsatellite loci. Proc. Natl. Acad. Sci. USA 94:1041-1046.
5. CHAKRABORTY, R., and D. N. STIVERS. 1996. Paternity exclusions by DNA markers: effects of paternal mutations. J. Forensic Sci. 41:667-673.
6. CHAKRABORTY, R., D. N. STIVERS, and Y. ZHONG. 1997. Estimation of mutation rates from parentage testing data: applications to STR and VNTR loci. Mutat. Res. 354:41-48.
7. DAVID, G., N. ABBAS, G. STEVANIN et al. (19 co-authors). 1997. Cloning of the SCA7 gene reveals a highly unstable CAG repeat expansion. Nat. Genet. 17:65-70.
8. DEKA, R., L. JIN, M. D. SHRIVER, L. M. YU, S. DECROO, J. HUNDRIESER, C. H. BUNKER, R. E. FERRELL, and R. CHAKRABORTY. 1995. Population genetics of dinucleotide (dC-dA)n.(dG-dT)n polymorphisms in world populations. Am. J. Hum. Genet. 56:461-474.
9. DI RIENZO, A., A. C. PETERSON, J. C. GARZA, A. M. VALDES, M. SLATKIN, and N. B. FREIMER. 1994. Mutational processes of simple-sequence repeat loci in human populations. Proc. Natl. Acad. Sci. USA 91:3166-3170.
10. EWENS, W. J. 1979. Mathematical population genetics. Springer-Verlag, Berlin.
11. FU, Y.-H., A. PIZZUTI, R G. FENWICK JR. et al. (15 co-authors). 1992. An unstable triplet repeat in a gene related to myotonic muscular dystrophy. Science 255:1256-1258.
12. HAMMOND, H. A., L. JIN, Y. ZHONG, C. T. CASKEY, and R. CHAKRABORTY. 1994. Evaluation of 13 short tandem repeat loci for use in personal identification applications. Am. J. Hum. Genet. 55:175-189.
13. JIN, L., and R. CHAKRABORTY. 1995. Population substructure, stepwise mutations, heterozygote deficiency and their implications in DNA forensics. Heredity 74:274-285.
14. JODICE, C., B. GIOVANNONE, V. CALABRESI, M. BELLOCCHI, L. TERRENATO, and A. NOVELLETTO. 1997. Population variation analysis at nine loci containing expressed trinucleotide repeats. Ann. Hum. Genet. 61:425-438.
15. KAWAGUCHI, Y., T. OKAMOTA, M. TANIWAKI et al. (13 co-authors). 1994. CAG expansions in a novel gene for Machado-Joseph disease at chromosome 14q32.1. Nat. Genet. 8:221-228.
16. KENDALL, M. G. 1947. The advanced theory of statistics. Vol. 1. Charles Griffin, London.
17. KIMMEL, M., and R. CHAKRABORTY. 1996. Measures of variation at DNA repeat loci under a general stepwise mutation model. Theor. Popul. Biol. 50:345-367.
18. KIMMEL, M., R. CHAKRABORTY, J. P. KING, M. BAMSHAD, W. S. WATKINS, and L. B. JORDE. 1998. Signatures of population expansion in microsatellite data. Genetics 148:1921-1930.
19. KIMMEL, M., R. CHAKRABORTY, D. N. STIVERS, and R. DEKA. 1996. Dynamics of repeat polymorphisms under a forward-backward mutation model: within-and between-population variability at microsatellite loci. Genetics 143:549-555.
20. KOIDE, R., T. IKEUCHI, O. ONODERA et al. (13 co-authors). 1994. Unstable expansion of CAG repeat in hereditary dentatorubral-pallidoluysiari atrophy (DRPLA). Nat. Genet. 6: 9-13.
21. LI, S.-H., M. G. MCINNIS, R. L. MARGOLIS, S. E. ANTONARAKIS, and C. A. ROSS. 1993. Novel triplet repeat containing genes in human brain: cloning, expression, and length polymorphisms. Genomics 16:572-579.
22. MCKUSICK, V. A. 1997. Mendelian inheritance in man. 12th edition. Johns Hopkins, Baltimore.
23. MARGOLIS, R. L., T. S. BRESCHEL, S.-H. LI, A. S. KIDWAI, M. G. MCINNIS, and C. A. Ross. 1995. Polymorphic (AAT)n trinucleotide repeats derived from a human brain cDNA library. Hum. Genet. 96:495-496.
24. NEI, M. 1978. Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89:583-590.
25. OHTA, T., and M. KIMURA. 1973. A model of mutation appropriate to estimate the number of electrophoretically detectable alleles in a finite population. Genet. Res. 22:201-204.
26. ORR, H. T., M. CHUNG, S. BANFI, T. J. KWIATKOWSKI JR., A. SERVADIO, A. L. BEAUDET, A. E. MCCALL, L. A. DUVICK, L. P. W. RANUM, and H. Y. ZOGHBI. 1993. Expansion of an unstable trinucleotide CAG repeat in spinocerebellar ataxia type 1. Nat. Genet. 4:221-226.
27. PRITCHARD, J. K., and M. W. FELDMAN. 1996. Statistics for microsatellite variation based on coalescence. Theor. Popul. Biol. 50:325-344.
28. RIGGINS, G. J., L. K. LOCKEY, J. L. CHASTAIN, H. A. LEINER, S. L. SHERMAN, K. D. WILKINSON, and S. T. WARREN. 1992. Human genes containing polymorphic trinucleotide repeats. Nat. Genet. 2:186-191.
29. ROGERS, A. R., and H. HARPENDING. 1992. Population growth makes waves in the distribution of pairwise genetic differences. Mol. Biol. Evol. 9:552-569.
30. RUBINSZTEIN, D. C., W. AMOS, J. LEGGO, S. GOODBURN, R. S. RAMESAR, J. OLD, R. BONTROP, R. MCMAHON, D. E. BARTON, and M. A. FERGUSON-SMITH. 1994. Mutational bias provides a model for the evolution of Huntington's disease and predicts a general increase in disease prevalence. Nat. Genet. 7:525-530.
31. SHRIVER, M. D., L. JIN, R. CHAKRABORTY, and E. BOERWINKLE. 1993. VNTR allele frequency distributions under the stepwise mutation model: a computer simulation approach. Genetics 134:186-191.
32. SUTHERLAND, G. R., and R. I. RICHARDS. 1995. Simple tandem DNA repeats and human genetic disease. Proc. Natl. Acad. Sci. USA 92:3636-3641.
33. WARNER, J. P., L. H. BARRON, and D. J. H. BROCK. 1993. A new polymerase chain reaction (PCR) assay for the trinucleotide repeat that is unstable and expanded on Huntington's disease chromosomes. Mol. Cell. Probes 7: 235-239.
34. WAVE, J. S., B. ENG, H. Y. NI, M. A. BLAJCHMAN, and G. CARMODY. 1994. Trinucleotide repeat polymorphism within the human antithrombin gene (AT3): allele frequency data for three population groups. Mol. Cell. Probes 8:149-154.
35. WEBBER, J. L., and C. WONG. 1993. Mutation of human short tandem repeats. Hum. Mol. Genet. 2:1123-1128.
36. ZHUCHENKO, O., J. BAILEY, P. BONNEN, T. ASHIZAWA, D. W. STOCKTON, C. AMOS, W. B. DOBYNS, S. H. SUBRAMONY, H. Y. ZOGHBI, and C. C. LEE. 1997. Autosomal dominant cerebellar ataxia (SCA6) associated with small polyglutamine expansions in the a1A-voltage-dependent calcium channel. Nat. Genet. 15:62-69.