Science /
Laurent Farinelli, Ph.D.
"The Genome Analyzer is enabling our clients to do things that used to be impossible, experiments that they only dreamed of doing, but can do now at a reasonable cost. "
Laurent Farinelli, Ph.D.
Co-founder and CEO, Fasteris
Fasteris is one of the first commercial service providers to offer sequencing services using the Illumina Genome Analyzer, inlcuding ChIP-Seq, large-scale genome sequencing and resequencing, Digital Gene Expression, microRNA profiling and discovery, and methylation profiling.
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Q&A with Dr. Laurent Farinelli
How has the Genome Analyzer changed your business?
It has completely changed our business. The Genome Analyzer is enabling our clients to do things that used to be impossible, experiments that they only dreamed of doing, but can do now at a reasonable cost. For example, with our capillary DNA sequencing service, we provide our clients with the sequence of one gene per sample. With the Illumina Genome Analyzer, we can provide them one genome per sample. Before installation of the Genome Analyzer, most of our clients were based in Europe, and we now have clients from worldwide locations.
How much interest are you getting from your customers in Genome Analyzer applications?
Our first partners were interested in resequencing or de novo sequencing bacteria. We carried out projects such as microRNA discovery, yeast genomes, whole transcriptome from plants with no reference sequence available, digital gene expression profiling, and ChIP-Seq. We are waiting for samples to resequence large genomic regions covering hundreds of megabases and to resequence many genes from a large number of individuals.
How has the Genome Analyzer performed in your lab?
We have been impressed by the system’s ease of use. We have been working on massively parallel DNA sequencing since 1996 and it is exciting to be able to apply the technology to novel applications. We decided to start with genomic DNA sample preparation and it worked very well the first time we tried it. Our next application required adaptation of the adaptors to introduce bar-coding bases, which permitted us to analyze several samples on one channel. We then adapted the digital gene expression profiling protocol from Illumina to fit our needs. After we received our first Gene Expression kit, in three days we prepared the cDNA samples (it worked the first time we used this protocol), and we could start the cluster generation.
After four more days (the time for the run and the software data processing), we sent our clients the gene expression profiles. For other applications such as whole transcriptome shotgun or ChIP-Seq, we simply used the protocol for genomic DNA samples. Once the DNA cluster templates are ready, the Genome Analyzer run is the same for all types of samples. We are always impressed by the amount and quality of data.
Can you tell us about your first run on the Genome Analyzer?
We have sequenced several bacterial genomes in collaboration with Professor Jacques Schrenzel’s group at the University of Geneva. The reads for the first bacterial genome we sequenced were obtained on the first run and performed at Fasteris to validate the Illumina Genome Analyzer installation. To analyze genomes for which no reference sequence is available, Dr. David Hernandez developed novel de novo assembly software. The software was first validated on a Staphylococcus aureus strain for which a whole-genome sequence was available. Without using paired reads, we demonstrated that the two million reads generated from a single channel of the Genome Analyzer permitted us to assemble 96% of this strain’s genome and its plasmid in a few minutes on a personal computer. The remaining reads that could not be assembled were from repeated regions such as 16S rDNA. We repeated this approach with similar results on other Staphylococcus strains.
Researcher Bio
Dr. Laurent Farinelli is the co-founder and CEO of Fasteris. Based in Geneva, Switzerland, Fasteris is one of the first commercial service providers to offer sequencing services using the Illumina Genome Analyzer, including ChIP-Seq, Digital Gene Expression, microRNA profiling and discovery, methylation profiling, and large-scale genome sequencing and resequencing.