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

AUTOR(ES)

Zhao, Zhongming

FONTE

Cold Spring Harbor Laboratory Press

RESUMO

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.

Documentos Relacionados

• Slow progress on sanitation puts 2.6 billion people at risk
• The three dimensional structure of sheep liver 6-phosphogluconate dehydrogenase at 2.6 A resolution.
• The molecular structure of insecticyanin from the tobacco hornworm Manduca sexta L. at 2.6 A resolution.
• Physical Maps of the Six Smallest Chromosomes of Saccharomyces Cerevisiae at a Resolution of 2.6 Kilobase Pairs
• Serotonin transporter gene polymorphisms: a case-control study