The complementary neighborhood patterns and methylation-to-mutation likelihood structures of 15,110 single-nucleotide polymorphisms in the bovine genome.

Genetics
Zhihua JiangRaymond W Wright

Abstract

Bayesian analysis was performed to examine the single-nucleotide polymorphism (SNPs) neighborhood patterns in cattle using 15,110 SNPs, each with a flanking sequence of 500 bp. Our analysis confirmed three well-known features reported in plants and/or other animals: (1) the transition is the most abundant type of SNPs, accounting for 69.8% in cattle; (2) the transversion occurs most frequently (38.56%) in cattle when the A + T content equals two at their immediate adjacent sites; and (3) C <--> T and A <--> G transitions have reverse complementary neighborhood patterns and so do A <--> C and G <--> T transversions. Our study also revealed several novel SNP neighborhood patterns that have not been reported previously. First, cattle and humans share an overall SNP pattern, indicating a common mutation system in mammals. Second, unlike C <--> T/A <--> G and A <--> C/G <--> T, the true neighborhood patterns for A <--> T and C <--> G might remain mysterious because the sense and antisense sequences flanking these mutations are not actually recognizable. Third, among the reclassified four types of SNPs, the neighborhood ratio between A + T and G + C was quite different. The ratio was lowest for C <--> G, but increased for C <--> T/A ...Continue Reading

References

Oct 9, 1980·Nature·B K Duncan, J H Miller
Oct 10, 1995·Proceedings of the National Academy of Sciences of the United States of America·B R Morton
Jun 26, 1999·Annals of Internal Medicine·S N Goodman
Feb 22, 2002·Current Opinion in Plant Biology·Antoni Rafalski
Dec 2, 2004·European Journal of Cancer : Official Journal for European Organization for Research and Treatment of Cancer (EORTC) [and] European Association for Cancer Research (EACR)·A HarderA von Deimling
Sep 6, 2005·Pharmacogenetics and Genomics·Danxin WangWolfgang Sadée
Mar 27, 2007·International Journal of Biological Sciences·Feng-Xing DuMichael M Lohuis
Mar 30, 2007·Annual Review of Biomedical Engineering·Sobin Kim, Ashish Misra
Oct 19, 2007·Cancer Research·Zuben E SaunaMichael M Gottesman
Nov 13, 2007·Bulletin of Mathematical Biology·Michel E Beleza Yamagishi, Alex Itiro Shimabukuro

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