An integrated analysis of genome-wide DNA Methylation and genetic variants underlying etoposide-induced cytotoxicity in European and African populations

Ruowang Li, Dokyoon Kim, Scott M. Dudek, Marylyn Deriggi Ritchie

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Scopus citations

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.

Original languageEnglish (US)
Title of host publicationApplications of Evolutionary Computation - 17th European Conference, EvoApplications 2014, Revised Selected Papers
EditorsAnna I. Esparcia-Alcázar
PublisherSpringer Verlag
Pages928-938
Number of pages11
ISBN (Electronic)9783662455227
DOIs
StatePublished - Jan 1 2014
Event17th European Conference on Applications of Evolutionary Computation, EvoApplications 2014 - Granada, Spain
Duration: Apr 23 2014Apr 25 2014

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume8602
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Other

Other17th European Conference on Applications of Evolutionary Computation, EvoApplications 2014
CountrySpain
CityGranada
Period4/23/144/25/14

All Science Journal Classification (ASJC) codes

  • Theoretical Computer Science
  • Computer Science(all)

Fingerprint Dive into the research topics of 'An integrated analysis of genome-wide DNA Methylation and genetic variants underlying etoposide-induced cytotoxicity in European and African populations'. Together they form a unique fingerprint.

Cite this