Why did your lab purchase the Illumina GAIIx?

Up until quite recently, we were primarily a microarray lab, running a number of commercial and custom platforms and performing all the steps from nucleic acid prep, to array processing, and data analysis. I had heard about Illumina sequencing in 2007 through various meetings and publications, and was really excited by the technology, especially after seeing all the applications you can do with it, like transcriptome profiling and ChIP-Seq. We just got a GAIIx and it’s been generating a lot of excitement. It’s an instrument that I think is essential for any genomic resource - since it allows for every type of genomic and epigenetic approach already in current use, and can drive the development of novel applications to answer questions that have been beyond our reach.

How will adding the GAIIx enhance the types of services you provide?

We’re doing a lot of microRNA and gene expression work with formaldehyde-fixed paraffin-embedded (FFPE) clinical samples. Currently, we’ve been using array-based microRNA profiling, which gives relative fold changes – but that data is not the most satisfying in terms of obtaining absolute expression. Molecular profiling using GA on these samples will yield accurate counts. For gene expression, in addition to obtaining transcript counts, we’re excited about the potential for the GA platform to yield precise information about splice variants that exon arrays can’t provide and to identify novel transcripts. To improve the results from the analysis of FFPE samples, as well as enhancing the power for discovery, we’ve been utilizing the new total RNA-Seq protocol. For our researchers, the GAIIx’s multiplex capacity will keep the costs within reach so that larger studies can be undertaken. For microRNAs, we’ll be able to run at least 8-12 samples per lane, which will bring profiling costs way down.