Linked Life Data

12421754

Source:http://linkedlifedata.com/resource/pubmed/id/12421754

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
11
pubmed:dateCreated
2002-11-7
pubmed:abstractText
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.
pubmed:commentsCorrections
http://linkedlifedata.com/resource/pubmed/commentcorrection/12421754-11005839, http://linkedlifedata.com/resource/pubmed/commentcorrection/12421754-11279516, http://linkedlifedata.com/resource/pubmed/commentcorrection/12421754-11682302, http://linkedlifedata.com/resource/pubmed/commentcorrection/12421754-11793750, http://linkedlifedata.com/resource/pubmed/commentcorrection/12421754-1588594, http://linkedlifedata.com/resource/pubmed/commentcorrection/12421754-2192981, http://linkedlifedata.com/resource/pubmed/commentcorrection/12421754-2423876, http://linkedlifedata.com/resource/pubmed/commentcorrection/12421754-6442359, http://linkedlifedata.com/resource/pubmed/commentcorrection/12421754-7120431, http://linkedlifedata.com/resource/pubmed/commentcorrection/12421754-7568204, http://linkedlifedata.com/resource/pubmed/commentcorrection/12421754-8801636, http://linkedlifedata.com/resource/pubmed/commentcorrection/12421754-9302315, http://linkedlifedata.com/resource/pubmed/commentcorrection/12421754-9683596
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Nov
pubmed:issn
1088-9051
pubmed:author
pubmed:issnType
Print
pubmed:volume
12
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
1679-86
pubmed:dateRevised
2009-11-18
pubmed:meshHeading
pubmed:year
2002
pubmed:articleTitle
Neighboring-nucleotide effects on single nucleotide polymorphisms: a study of 2.6 million polymorphisms across the human genome.
pubmed:affiliation
Human Genetics Center and Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, Texas 77030, USA.
pubmed:publicationType
Journal Article, Research Support, U.S. Gov't, P.H.S., Research Support, Non-U.S. Gov't