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

摘要: Substitution patterns at polymorphic sites and bias in nucleotides neighboring are important for understanding molecular mechanisms of mutation genome evolution. Single nucleotide polymorphism (SNP) data information about surrounding sequence motifs suitable studying mutational processes human other genomes (Zavolan Kepler 2001). However, humans previous analyses SNP variation neighboring-nucleotide effects have largely been limited to pseudogenes or a number genes with known effects, many which disease-causing (e.g., Gojobori et al. 1982; Li 1984; Cooper Krawczak 1990; 1998). In plants, extensively studied chloroplasts Morton 1995; 1997). There is considerable recent interest SNPs within every gene the regularly spaced across as tools association-mapping disease-susceptibility (Risch Merikangas 1996) identifying that associated trait may be functional (Huang There more than two one-half million available public domain. At present, most deposited by The Consortium (TSC), Sanger Genome Center, Washington University (Marth This large set provides us an opportunity investigate substitution well representative whole genome, including genic intergenic regions. also enough each type chromosome. We investigated 2,576,903 publicly through National Center Biotechnology Information (NCBI). To uncover actual extent bias, we normalized respect averaged proportion relevant Finally, transversions were reveal avoiding obvious CpG effects.