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Q&A with Dr. Rickard Sandberg
- How has the Genome Analyzer changed the scope of your research?
- You have a lot of experience with exon and tiling arrays, what advantages does the Genome Analyzer offer for your research?
How has the Genome Analyzer changed the scope and focus of your research?
As a pilot experiment, we sequenced mRNA isolated from a panel of nine normal human tissues and five cell lines using the Genome Analyzer. We analyzed more than 300 million 32-base pair reads and mapped them to the genome and transcriptome. The data generated in this single study greatly exceeds the total sample of EST data that's been accumulating in the database for the last two decades.
With such sequencing depth, we could see for the first time that the vast majority of human genes are alternatively spliced. We could also see that there is a high level of tissue-bias in the expression of mRNA isoforms. It seems like some single-exon genes are clearly not alternatively spliced, but almost all of the multi-exon genes are transpliced. For us this study has shifted the focus from how many genes are alternatively spliced to how many exons, or what exons, are involved in this kind of regulation.
We believe that the Genome Analyzer is a powerful technology capable of detecting alternative mRNA isoforms with unprecedented coverage and resolution. Now, in a single experiment we can study alternative promoters, alternative splicing, and all types of mRNA-isoform regulation. The questions we are asking are old, but given the resolution of Genome Analyzer data and how clean the data come out, for the first time we can really see many of the mRNA-isoform changes we've been interested in.
You have a lot of experience with exon and tiling arrays, what advantages does the Genome Analyzer offer for your research?
Some of the biggest advantages we found are the high signal-to-noise ratio and the disappearance of background noise. Sequencing-based data is much cleaner, essentially taking care of the two main limitations in tiling and exon array data: background noise and cross hybridization. Because the data are digital you can use very simple statistics and the resolution improves. If you have enough depth, and if you do an mRNA-seq experiment, you can generate a good picture of a transcriptome that's not going to change.
I like the idea that with the Genome Analyzer I can take a global approach and see what type of regulation seems to be the most important, rather than having to assume one type of regulation that will be most important and zoom in on that one modality. The Genome Analyzer lets me be open-minded. For my projects I'm definitely going to continue with sequencing mRNA; I'm not going back to exon or tiling arrays.
Back to Dr. Rickard Sandberg’s Profiles.