Document Detail


Neighboring-nucleotide effects on single nucleotide polymorphisms: a study of 2.6 million polymorphisms across the human genome.
MedLine Citation:
PMID:  12421754     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
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.
Authors:
Zhongming Zhao; Eric Boerwinkle
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Publication Detail:
Type:  Journal Article; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, P.H.S.    
Journal Detail:
Title:  Genome research     Volume:  12     ISSN:  1088-9051     ISO Abbreviation:  Genome Res.     Publication Date:  2002 Nov 
Date Detail:
Created Date:  2002-11-07     Completed Date:  2003-01-14     Revised Date:  2009-11-18    
Medline Journal Info:
Nlm Unique ID:  9518021     Medline TA:  Genome Res     Country:  United States    
Other Details:
Languages:  eng     Pagination:  1679-86     Citation Subset:  IM    
Affiliation:
Human Genetics Center and Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, Texas 77030, USA.
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MeSH Terms
Descriptor/Qualifier:
Base Composition / genetics
Chromosomes, Human, Pair 19 / genetics
Chromosomes, Human, Pair 22 / genetics
Genome, Human
Humans
Nucleotides / chemistry*,  genetics*
Polymorphism, Single Nucleotide / genetics*
Sequence Analysis, DNA / statistics & numerical data
Chemical
Reg. No./Substance:
0/Nucleotides
Comments/Corrections

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