Genome Research cityscape

Home Help [Feedback] [For Subscribers] [Archive] [Search] [Contents]
QUICK SEARCH:   [advanced]


     

This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Right arrow Citation Map
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrow reprints & permissions
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Zhao, Z.
Right arrow Articles by Boerwinkle, E.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Zhao, Z.
Right arrow Articles by Boerwinkle, E.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us   Add to Digg   Add to Reddit   Add to Technorati  
What's this?

Vol. 12, Issue 11, 1679-1686, November 2002

LETTER
Neighboring-Nucleotide Effects on Single Nucleotide Polymorphisms: A Study of 2.6 Million Polymorphisms Across the Human Genome

Zhongming Zhao, and Eric Boerwinkle1

Human Genetics Center and Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, Texas 77030, USA

We investigated substitution patterns and neighboring-nucleotide effects for 2,576,903 single nucleotide polymorphisms (SNPs) publicly available through the National Center for Biotechnology Information (NCBI). The proportions of substitutions were A/G, 32.77%; C/T, 32.81%; A/C, 8.98%; G/T, 9.06%; A/T, 7.46%; and C/G, 8.92%. The two nucleotides immediately neighboring the variable site showed major deviation from genome-wide and chromosome-specific expectations, although lesser biases extended as far as 200 bp. On the 5' side, the biases for A, C, G, and T were 1.43%, 4.91%, -1.70%, and -4.62%, respectively. These biases were -4.44%, -1.59%, 5.05%, and 0.99%, respectively, on the 3' side. The neighboring-nucleotide patterns for transitions were dominated by the hypermutability effects of CpG dinucleotides. Transitions were more common than transversions, and the probability of a transversion increased with increasing A + T content at the two adjacent sites. Neighboring-nucleotide biases were not consistent among chromosomes, with Chromosomes 19 and 22 standing out as different from the others. These data provide genome-wide information about the effects of neighboring nucleotides on mutational and evolutionary processes giving rise to contemporary patterns of nucleotide occurrence surrounding SNPs.

1 Corresponding author.

12:1679-1686 ©2002 by Cold Spring Harbor Laboratory Press  ISSN 1088-9051/02 $5.00
Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us   Add to Digg Digg   Add to Reddit Reddit   Add to Technorati Technorati    What's this?


This article has been cited by other articles:


Home page
 Mol Biol EvolHome page
Z. Zhao and C. Jiang
Methylation-Dependent Transition Rates Are Dependent on Local Sequence Lengths and Genomic Regions
Mol. Biol. Evol., January 1, 2007; 24(1): 23 - 25.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
X. Tian, J. Zheng, S. Hu, and J. Yu
The Rice Mitochondrial Genomes and Their Variations
Plant Physiology, February 1, 2006; 140(2): 401 - 410.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
B. R. Morton, I. V. Bi, M. D. McMullen, and B. S. Gaut
Variation in Mutation Dynamics Across the Maize Genome as a Function of Regional and Flanking Base Composition
Genetics, January 1, 2006; 172(1): 569 - 577.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
N. Backstrom, H. Ceplitis, S. Berlin, and H. Ellegren
Gene Conversion Drives the Evolution of HINTW, an Ampliconic Gene on the Female-Specific Avian W Chromosome
Mol. Biol. Evol., October 1, 2005; 22(10): 1992 - 1999.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
K. K. Alharbi, M. A. Aldahmesh, E. Spanakis, L. Haddad, R. A. Whittall, X.-h. Chen, H. Rassoulian, M. J. Smith, J. Sillibourne, N. J. Ball, et al.
Mutation scanning by meltMADGE: Validations using BRCA1 and LDLR, and demonstration of the potential to identify severe, moderate, silent, rare, and paucimorphic mutations in the general population
Genome Res., July 1, 2005; 15(7): 967 - 977.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
F. Zhang and Z. Zhao
SNPNB: analyzing neighboring-nucleotide biases on single nucleotide polymorphisms (SNPs)
Bioinformatics, May 15, 2005; 21(10): 2517 - 2519.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
E. Axelsson, M. T. Webster, N. G.C. Smith, D. W. Burt, and H. Ellegren
Comparison of the chicken and turkey genomes reveals a higher rate of nucleotide divergence on microchromosomes than macrochromosomes
Genome Res., January 1, 2005; 15(1): 120 - 125.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
D. G. Hwang and P. Green
Inaugural Article: Bayesian Markov chain Monte Carlo sequence analysis reveals varying neutral substitution patterns in mammalian evolution
PNAS, September 28, 2004; 101(39): 13994 - 14001.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
E. Axelsson, N. G.C. Smith, H. Sundstrom, S. Berlin, and H. Ellegren
Male-Biased Mutation Rate and Divergence in Autosomal, Z-Linked and W-Linked Introns of Chicken and Turkey
Mol. Biol. Evol., August 1, 2004; 21(8): 1538 - 1547.
[Abstract] [Full Text] [PDF]

Home page
 Clin. Chem.Home page
M. Liew, R. Pryor, R. Palais, C. Meadows, M. Erali, E. Lyon, and C. Wittwer
Genotyping of Single-Nucleotide Polymorphisms by High-Resolution Melting of Small Amplicons
Clin. Chem., July 1, 2004; 50(7): 1156 - 1164.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
A. Siepel and D. Haussler
Phylogenetic Estimation of Context-Dependent Substitution Rates by Maximum Likelihood
Mol. Biol. Evol., March 1, 2004; 21(3): 468 - 488.
[Abstract] [Full Text] [PDF]


Home Help [Feedback] [For Subscribers] [Archive] [Search] [Contents]
Genes Dev. Learn. Mem.
Protein Science RNA Genome Res.