TY - GEN
T1 - An integrated analysis of genome-wide DNA Methylation and genetic variants underlying etoposide-induced cytotoxicity in European and African populations
AU - Li, Ruowang
AU - Kim, Dokyoon
AU - Dudek, Scott M.
AU - Ritchie, Marylyn Deriggi
PY - 2014/1/1
Y1 - 2014/1/1
N2 - 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.
AB - 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.
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U2 - 10.1007/978-3-662-45523-4_75
DO - 10.1007/978-3-662-45523-4_75
M3 - Conference contribution
AN - SCOPUS:84915797062
T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
SP - 928
EP - 938
BT - Applications of Evolutionary Computation - 17th European Conference, EvoApplications 2014, Revised Selected Papers
A2 - Esparcia-Alcázar, Anna I.
PB - Springer Verlag
T2 - 17th European Conference on Applications of Evolutionary Computation, EvoApplications 2014
Y2 - 23 April 2014 through 25 April 2014
ER -