Neighboring-nucleotide effects on single nucleotide polymorphisms: A study of 2.6 million polymorphisms across the human genome

Genome Research

Volumn 12, Issue 11, 2002, Pages 1679-1686

  Zhao, Zhongming ^a   Boerwinkle, Eric ^a  

^a UNIVERSITY OF TEXAS MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENINE; CYTOSINE; DINUCLEOTIDE; GUANINE; NUCLEOTIDE; THYMINE;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ARTICLE; CHROMOSOME 19; CHROMOSOME 22; CONTROLLED STUDY; GENBANK; GENE MUTATION; HUMAN; HUMAN GENOME; MOLECULAR EVOLUTION; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM;

BASE COMPOSITION; CHROMOSOMES, HUMAN, PAIR 19; CHROMOSOMES, HUMAN, PAIR 22; GENOME, HUMAN; HUMANS; NUCLEOTIDES; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA;

EID: 0036852246     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.287302     Document Type: Article

References (13)

1. Bird, A.P. 1986. CpG-rich islands and the function of DNA methylation. Nature 321: 209-213.
2. Blake, R.D., Hess, S.T., and Nicholson-Tuell, J. 1992. The influence of nearest neighbors on the rate and pattern of spontaneous point mutations. J. Mol. Evol. 34: 189-200.
3. Cooper, D.N. and Krawczak, M. 1990. The mutational spectrum of single base-pair substitutions causing human genetic disease: Patterns and predictions. Hum. Genet. 85: 55-74.
4. Gojobori, T., Li, W.-H., and Graur, D. 1982. Patterns of nucleotide substitution in pseudogenes and functional genes. J. Mol. Evol. 18: 360-369.
5. Huang, Q., Morrison, A.C., and Boerwinkle, E. 2001. Linkage disequilibrium structure and its impact on the localization of a candidate functional mutation. Genet. Epidemiol. 21: S620-S625.
6. Krawczak, M., Ball, E.V., and Cooper, D.N. 1998. Neighboring-nucleotide effects on the rates of germ-line single-base-pair substitution in human genes. Am. J. Hum. Genet. 63: 474-488.
7. Li, W.-H., Wu, C.-I., and Luo, C.-C. 1984. Nonrandomness of point mutation as reflected in nucleotide substitutions in pseudogenes and its evolutionary implications. J. Mol. Evol. 21: 58-71.
8. Marth, G., Yeh, R., Minton, M., Donaldson, R., Li, Q., Duan, S., Davenport, R., Miller, R.D., and Kwok, P.-Y. 2001. Single-nucleotide polymorphisms in the public domain: How useful are they? Nat. Genet. 27: 371-372.
9. Morton, B.R. 1995. Neighboring base composition and transversion/transition bias in a comparison of rice and maize chloroplast noncoding regions. Proc. Natl. Acad. Sci. 92: 9717-9721.
10. Morton, B.R., Oberholzer, V.M., and Clegg, M.T. 1997. The influence of specific neighboring bases on substitution bias in noncoding regions of the plant chloroplast genome. J. Mol. Evol. 45: 227-231.
11. Risch, N. and Merikangas, K. 1996. The future of genetic studies of complex human diseases. Science 273: 1516-1517.
12. Zavolan, M. and Kepler, T.B. 2001. Statistical inference of sequence-dependent mutation rates. Curr. Opin. Genet. Dev. 11: 612-615.
13. Zhao, Z., Li, J., Fu, Y.-X., Ramsay, M., Jenkins, T., Leskinen, E., Pamilo, P., Trexler, M., Patthy, L., Jorde, L.B., et al. 2000. Worldwide DNA sequence variation in a 10-kilobase noncoding region on human Chromosome 22. Proc. Natl. Acad. Sci. 97: 11354-11358.