What role did the Genome Analyzer have in your groundbreaking research?

Our group was first interested in looking at the methylome at single base pair resolution. Unlike other next-gen sequencing systems, the Genome Analyzer works really well for sequencing a three base pair genome, which is essentially what you get after bisulfite conversion. Then we decided that because there’s so much small RNA-directed DNA methylation we should layer that type of regulation onto the study as well.

So we sequenced the small RNAome. And then we wanted to answer the ultimate question: how does DNA methylation affect gene expression? So we sequenced the full-length mRNA component of the transcriptome as well. With all this data we could really start to look at functionality of these epigenetic marks and how they lead to differences in regulation of actual gene expression. We could really get to the heart of how these pathways affect the biology of the organism. Without the Genome Analyzer, we couldn’t have data sets with this much depth.

This system is making sequencing available to biologists that never could have done this type of genomic study before. Because we can inexpensively sequence a genome with a couple of runs in a couple of days, we can ask deeper and more genome-wide type of questions.

Are you planning on sequencing more "omes"?

It’s safe to say that at this point we haven’t found anything that we can’t sequence with the Genome Analyzer. Wherever the biology leads us, that’s where we’ll go and with this system we can go there at single-base resolution. We’re not limited anymore with asking if the resolution is going to be good enough to make this study worthwhile because we can go down to single base resolution.