2002
DOI: 10.1101/gr.287302
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Neighboring-Nucleotide Effects on Single Nucleotide Polymorphisms: A Study of 2.6 Million Polymorphisms Across the Human Genome

Abstract: 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… Show more

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Cited by 138 publications
(140 citation statements)
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“…This was significantly lower than previously reported values, such as the 1.91 determined in a large-scale, genome-wide study [Zhao and Boerwinkle, 2002]. The reduced ratio in our study may be explained by the nature of the target regions that are enriched with CpG islands, where CpG dinucleotides are abundant but are undermethylated [Majewski and Ott, 2002].…”
Section: Nucleotide Diversity and Positional E¡ectscontrasting
confidence: 55%
“…This was significantly lower than previously reported values, such as the 1.91 determined in a large-scale, genome-wide study [Zhao and Boerwinkle, 2002]. The reduced ratio in our study may be explained by the nature of the target regions that are enriched with CpG islands, where CpG dinucleotides are abundant but are undermethylated [Majewski and Ott, 2002].…”
Section: Nucleotide Diversity and Positional E¡ectscontrasting
confidence: 55%
“…Many coalescent statistics couple the uniform-mutation model with the infinite-sites model that assumes that each mutation occurs at a different nucleotide site, thereby making it impossible for the same site to experience multiple mutational hits. Such a mutational model is unrealistic for much human DNA (Templeton et al, 2000a;Bacon et al, 2001;Lercher and Hurst, 2002;Zhao and Boerwinkle, 2002;Tomso and Bell, 2003;Tomatsu et al, 2004;Buzin et al, 2005;Fryxell and Moon, 2005), and can lead to incorrect conclusions (Templeton et al, 2000a).…”
Section: Mutationmentioning
confidence: 99%
“…Transition mutations, which are the most common mutational process (65.6% of mutations) in the human genome, do not compromise the ability of B-box elements to base pair with the U2 snRNA ( Fig. 5A; Zhao and Boerwinkle 2002).…”
Section: Human Genetic Variation At Branchpointsmentioning
confidence: 99%