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Briefings in Functional Genomics and Proteomics Advance Access originally published online on June 17, 2009
Briefings in Functional Genomics and Proteomics 2009 8(3):174-183; doi:10.1093/bfgp/elp013
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© The Author 2009. Published by Oxford University Press. For permissions, please email: journals.permissions@oxfordjournals.org

This article appears in the following Briefings in Functional Genomics and Proteomics issue: Special Issue: The Future of Microarrays in an age of high throughput sequencing [View the issue table of contents]

Special Issue Papers

Advantages of next-generation sequencing versus the microarray in epigenetic research

Paul J. Hurd * and Christopher J. Nelson *

Corresponding author. Paul J. Hurd, School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK. Tel: +44-207-882-8884; Fax: +44-208-983-0973; E-mail: p.j.hurd{at}qmul.ac.uk

Several recent studies from the field of epigenetics have combined chromatin-immunoprecipitation (ChIP) with next-generation high-throughput sequencing technologies to describe the locations of histone post-translational modifications (PTM) and DNA methylation genome-wide. While these reports begin to quench the chromatin biologists thirst for visualizing where in the genome epigenetic marks are placed, they also illustrate several advantages of sequencing based genomics compared to microarray analysis. Accordingly, next-generation sequencing (NGS) technologies are now challenging microarrays as the tool of choice for genome analysis. The increased affordability of comprehensive sequence-based genomic analysis will enable new questions to be addressed in many areas of biology. It is inevitable that massively-parallel sequencing platforms will supercede the microarray for many applications, however, there are niches for microarrays to fill and interestingly we may very well witness a symbiotic relationship between microarrays and high-throughput sequencing in the future.

Keywords: next-generation sequencing, microarray, Solexa/Illumina, Roche 454 pyrosequencing, ABI SOLiD, ChIP-Seq

*These authors contributed equally to this work.


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