Single Nucleotide Polymorphisms and DNA Methylation Analysis Using Pyrosequencing Methods

2008 ◽  
pp. 119-140 ◽  
Author(s):  
Jinsheng Yu ◽  
Sharon Marsh
Keyword(s):  
Dna Methylation ◽  
Single Nucleotide Polymorphisms ◽  
Nucleotide Polymorphisms ◽  
Methylation Analysis ◽  
Single Nucleotide ◽  
Dna Methylation Analysis

scholarly journals DNA Methylation Analysis of the Macrosatellite Repeat Associated with FSHD Muscular Dystrophy at Single Nucleotide Level

PLoS ONE ◽  
2014 ◽  
Vol 9 (12) ◽  
pp. e115278 ◽  
Author(s):  
Claudia Huichalaf ◽  
Stefano Micheloni ◽  
Giulia Ferri ◽  
Roberta Caccia ◽  
Davide Gabellini
Keyword(s):  
Dna Methylation ◽  
Muscular Dystrophy ◽  
Methylation Analysis ◽  
Nucleotide Level ◽  
Single Nucleotide ◽  
Dna Methylation Analysis

scholarly journals Unified variable selection in semi-parametric models

2015 ◽  
Vol 26 (6) ◽  
pp. 2821-2831 ◽  
Author(s):  
William Terry ◽  
Hongmei Zhang ◽  
Arnab Maity ◽  
Hasan Arshad ◽  
Wilfried Karmaus
Keyword(s):  
Dna Methylation ◽  
Single Nucleotide Polymorphisms ◽  
Variable Selection ◽  
Reproducing Kernel ◽  
Allergic Sensitization ◽  
Joint Effect ◽  
Bayesian Variable Selection ◽  
Parametric Models ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide

We propose a Bayesian variable selection method in semi-parametric models with applications to genetic and epigenetic data (e.g., single nucleotide polymorphisms and DNA methylation, respectively). The data are individually standardized to reduce heterogeneity and facilitate simultaneous selection of categorical (single nucleotide polymorphisms) and continuous (DNA methylation) variables. The Gaussian reproducing kernel is applied to the transformed data to evaluate joint effect of the variables, which may include complex interactions between, e.g., single nucleotide polymorphisms and DNA methylation. Indicator variables are introduced to the model for the purpose of variable selection. The method is demonstrated and evaluated using simulations under different scenarios. We apply the method to identify informative DNA methylation sites and single nucleotide polymorphisms in a set of genes based on their joint effect on allergic sensitization. The selected single nucleotide polymorphisms and methylation sites have the potential to serve as early markers for allergy prediction, and consequently benefit medical and clinical research to prevent allergy before its manifestation.

scholarly journals COHCAP: an integrative genomic pipeline for single-nucleotide resolution DNA methylation analysis

2013 ◽  
Vol 41 (11) ◽  
pp. e117-e117 ◽  
Author(s):  
Charles D. Warden ◽  
Heehyoung Lee ◽  
Joshua D. Tompkins ◽  
Xiaojin Li ◽  
Charles Wang ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Methylation Analysis ◽  
Single Nucleotide ◽  
Nucleotide Resolution ◽  
Dna Methylation Analysis ◽  
Single Nucleotide Resolution
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