Modeling genetic imprinting effects of DNA sequences with multilocus polymorphism data

Sheron Wen, Chenguang Wang, Arthur Berg, Yao Li, Myron M. Chang, Roger B. Fillingim, Margaret R. Wallace, Roland Staud, Lee Kaplan, Rongling Wu

Research output: Contribution to journalArticle

Abstract

Single nucleotide polymorphisms (SNPs) represent the most widespread type of DNA sequence variation in the human genome and they have recently emerged as valuable genetic markers for revealing the genetic architecture of complex traits in terms of nucleotide combination and sequence. Here, we extend an algorithmic model for the haplotype analysis of SNPs to estimate the effects of genetic imprinting expressed at the DNA sequence level. The model provides a general procedure for identifying the number and types of optimal DNA sequence variants that are expressed differently due to their parental origin. The model is used to analyze a genetic data set collected from a pain genetics project. We find that DNA haplotype GAC from three SNPs, OPRKG36T (with two alleles G and T), OPRKA843G (with alleles A and G), and OPRKC846T (with alleles C and T), at the kappa-opioid receptor, triggers a significant effect on pain sensitivity, but with expression significantly depending on the parent from which it is inherited p = 0.008). With a tremendous advance in SNP identification and automated screening, the model founded on haplotype discovery and statistical inference may provide a useful tool for genetic analysis of any quantitative trait with complex inheritance.

Original languageEnglish (US)
Article number1748
Number of pages1
JournalAlgorithms for Molecular Biology
Volume4
Issue number1
DOIs
StatePublished - Aug 11 2009

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ASJC Scopus subject areas

  • Structural Biology
  • Molecular Biology
  • Computational Theory and Mathematics
  • Applied Mathematics

Cite this

Wen, S., Wang, C., Berg, A., Li, Y., Chang, M. M., Fillingim, R. B., Wallace, M. R., Staud, R., Kaplan, L., & Wu, R. (2009). Modeling genetic imprinting effects of DNA sequences with multilocus polymorphism data. Algorithms for Molecular Biology, 4(1), [1748]. https://doi.org/10.1186/1748-7188-4-11