Paper Info
Title
An integrated analysis of genome-wide DNA methylation and genetic variants underlying etoposide-induced cytotoxicity in European and African populations.
Abstract
Genetic variations among individuals account for a large portion of variability in drug response. The underlying mechanism of the variability is still not known, but it is expected to comprise of a wide range of genetic factors that interact and communicate with each other. Here, we present an integrated genome-wide approach to uncover the interactions among genetic factors that can explain some of the inter-individual variation in drug response. The International HapMap consortium generated genotyping data on human lymphoblastoid cell lines of (Center d'Etude du Polymorphisme Humain population - CEU) European descent and (Yoruba population - YRI) African descent. Using genome-wide analysis, Huang et al. identified SNPs that are associated with etoposide, a chemotherapeutic drug, response on the cell lines. Using the same lymphoblastoid cell lines, Fraser et al. generated genome-wide methylation profiles for gene promoter regions. We evaluated associations between candidate SNPs generated by Huang et al and genome-wide methylation sites. The analysis identified a set of methylation sites that are associated with etoposide related SNPs. Using the set of methylation sites and the candidate SNPs, we built an integrated model to explain etoposide response observed in CEU and YRI cell lines. This integrated method can be extended to combine any number of genomics data types to explain many phenotypes of interest.
Year
DOI
Venue
2014
10.1007/978-3-662-45523-4_75
Lecture Notes in Computer Science
Field
DocType
Volume
Population,Genotyping,Biology,International HapMap Project,Genetic variation,Methylation Site,Genomics,DNA methylation,Single-nucleotide polymorphism,Bioinformatics,Genetics
Conference
8602
ISSN
Citations 
PageRank 
0302-9743
0
0.34
References 
Authors
2
4
Name
Order
Citations
PageRank
Ruowang Li1184.15
Do Kyoon Kim211.05
Scott M. Dudek320626.27
Marylyn D. Ritchie469286.79