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13 October 2008
ROLEXA paper accepted
The article submitted by Jacques Rougemont et al. describing the base-calling software ROLEXA has been accepted for publication in BMC Bioinformatics.
This work is the result of a collaboration between the Ecole Polytechnique Fédérale de Lausanne (EPFL); the Ludwig Institute for Cancer Research (LICR) in Lausanne; the Swiss Institute of Bioinformatics (SIB); Vital-IT and Fasteris.
20 June 2008
Partnership with ImaGenes GmbH in Austria and Germany
imaGenes GmbH and Fasteris SA announced that they will partner in Next Generation Sequencing in Germany and Austria to offer their customers the widest range of applications, including challenging upstream and downstream processes.
NB: This partnership ended in December 2009.
4-6 June 2008
Presentations at illumina Genome Analyzer seminars
We presented our experience in Barcelona and Paris, as well as during the 2nd DECHEMA Status Workshop "Microbial Genome Research in the Age of Ultrafast Sequencing Technologies" Frankfurt, June, 5-6th, 2008.
15 May 2008
Offices and lab space expansion
With an increasing number of collaborators and expanding business, we moved into new offices in the same building, doubling the surface, while conserving the existing facility.
29 April 2008
New 96-capillaries DNA sequencer installed
A 96-capillaries ABI3730xl instrument has been installed in our laboratories to increase the throughput of our "classical" DNA sequencing service.
18 April 2008
2nd Genome Analyzer (GA II) installed
We are pleased to announce that a second deep-sequencing instrument of the latest generation GAII, has been installed in our facilities.
The GA II has 40% more throughput and will complement our existing instrument.
10 March 2008
De novo assembly EDENA software published in Genome Research
We are pleased to announce that the article
"De novo bacterial genome sequencing: millions of very short reads assembled on a desktop
computer" written by David Hernandez as part of a collaboration between Fasteris and the group
of Prof. Jacques Schrenzel at the Geneva University Hospitals is available as
advanced publication in Genome Research.
19 & 21 February 2008
Presentations at illumina Genome Analyzer seminars in Berlin and Paris
We presented our experience with the Genome Analyzer system and described the various applications developped at Fasteris, e.g. whole genome or transcriptome, digital-gene expression profiling, ChIP-SEQ, array-capture.
8 February 2008
Poster at USGEB 2008 on accuracy of Solexa Sequencing
In collaboration with the group of Prof. Schrenzel at the Geneva University Hospitals, we studied the accuracy of Genome Analyzer data using Staphylococcus aureus MW2 as a model, with a combination of re-sequencing and de novo sequencing.
10 November 2007
Bar-coded samples to reduce costs
We developed a bar-coding procedure enabling to analyze several samples in the same channel,
thus reducing the cost per sample of the Illumina Genome Analyzer analysis.
20 August 2007
de novo Assembly of a Whole Transcriptome
One of our clients, Dr Michel Schalk from Firmenich SA (Geneva), a world
leading company in development and production of fragrances and flavors, is
interested in identifying genes involved in specific metabolic pathways.
One of the difficulties of such projects is that there is no reference
sequence information available for the plant species of interest, and that
genes homologous to the target genes are available only for distantly
related species. Using classical approaches of library hybridization or PCR
amplification, such projects are time consuming and the chances of success
are conditioned by the choice of the sequences selected to design the probes
and primers. We attempted to sequence the whole transcriptome of a plant
tissue using the Illumina Genome Analyzer system with a shotgun approach
followed by de novo assembly. Our first try was successful without using
paired reads. The large contigs were shown to match with plants genes known
to be highly expressed, such as RUBISCO. We were able to find candidate
sequences for the target genes among the smaller contigs and the reads.
These sequences were used to design specific PCR primers and permitted to
recover the full-length transcripts by 5' and 3' RACE. The whole project was
carried out in a few weeks.
17 August 2007
Comparison of Difficult-to-Sequence Bacteria
In collaboration with the team of Prof. Joachim Frey of the University of
Berne, we re-sequenced the genome of a pathogenic strain and a vaccine
strain of the bacterium Mycoplasma mycoides subs. mycoides SC. This
bacterial species is the agent of contagious bovine pleuropneumonia, a
severe, highly contagious respiratory disease of cattle and buffalo.
Genomic DNA is difficult to obtain as the bacteria are expensive to grow. Using a
shotgun approach, genomic DNA was fragmented and DNA colony templates were
prepared for sequencing on the Illumina Genome Analyzer. For each strain, we
obtained enough reads on one channel to achieve coverage of 30-60x and align
the reads on a reference sequence. We identified several genetic variants
that are being analyzed for confirmation of their role in the phenotypic differences observed between the strains.
15 August 2007
de novo Assembly from 100 ng of genomic DNA
A customer, Prof. Dieter Ebert from the University of Basel, came to
Fasteris to help sequencing a notoriously difficult genome from an
intracellular parasite.
The inability to extract large amounts of DNA from Microsporidia and the
lack of any sequence knowledge had stymied the customer's earlier efforts to
sequence this organism. Dr Farinelli, Fasteris co-founder, says, "With the Genome Analyzer we were
able to generate the first draft sequence for this small eukaryote using
less than 100ng of DNA." Prof. Ebert and his group are using this data to mine for candidate genes for host parasite
interactions and for genetic markers (VNTRs).
28 June 2007
de novo Assembly of 96% of a Bacterial Genome
We sequenced several bacterial genomes in collaboration with the group of
Prof. Jacques Schrenzel, our partner at the University of Geneva. The reads
for the first bacterial genome were obtained on the first run performed at
Fasteris, to validate the Illumina Genome Analyzer installation. The genomic
DNA shotgun sample preparation was performed at Fasteris before system
installation, using only the Illumina protocol and adapters as the sample
preparation kits were not available yet.
In order to analyze genomes for which no reference sequence is available,
Dr. David Hernandez developped a 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 2 mio reads generated from a single channel of the
Genome Analyzer permitted to assemble 96% of the genome and its plasmid in a
few minutes on a personal computer. The remaining reads that could not be
assembled are from repeated regions such as 16S rDNA.
The approach was performed with similar results on other Staphylococcus
strains.
7 June 2007
Bar-coded small RNAs
We adapted the sample preparation protocols to permit analysis of 2 miRNA samples in the same channel.
With the Genome Analyzer, it is possible to count the miRNA species present in a sample.
We provided our client a profile for each sample, which will help finding the sequences correlated with the phenotypic differences observed.
20 April 2007
First Bacterial Genome sequenced
The reads for the first bacterial genome we sequenced were obtained on the first run performed at Fasteris to validate the Illumina Genome Analyzer installation.
11 April 2007
2006 Illumina Genome Analyzer installed
Fasteris is pleased to announce the installation of an Illumina
Genome Analyzer, at its Geneva services facility. The Genome Analyzer is a next-generation gene sequencing system that can generate more than one billion finished bases of high quality data in a single run. This level of performance, which is equivalent to sequencing one third of an entire human genome in a single run, will enable work at speeds 100 times greater than with previous sequencing instruments and at a fraction of the cost.
Fasteris intends to provide next-generation sequencing services starting in June 2007, becoming the first commercial services provider in the world to use the Illumina Genome Analyzer System.
Among the first planned applications, re-sequencing of bacterial genomes in partnership with local researchers will help resolve questions that were too difficult or expensive to tackle with previous DNA sequencing technologies. However, the wide range of expected applications includes whole genome re-sequencing, gene expression analysis, and small RNA discovery and analysis.
(see press release, InSequence, Le Temps)
19 December 2005
2006 IMD Start-up Competition
Fasteris is among the 4 winners of 2006
IMD Start-up Competition for the Executive MBA (EMBA) Program, one of
the most selective business programs in the world.
20 June 2005
Plasmid preparation
Introducing additional services for custom preparation of milligrams of
plasmid DNA at competitive costs.
1 September 2004
Moving to New Offices
While remaining in Plan-les-Ouates, near Geneva, we moved into new offices
and laboratories. We are located in the ANTES building, within the Industrial Area.
The move was carried out without interruption of our services.
15 November 2003
Online DNA sequencing service
With the launch of its improved website, FASTERIS provides customers with
additional information and even better service.
3 November 2003
Next Day DNA Sequencing Service
FASTERIS' customers can count on very fast turnover time. Sequencing reads
can generally be completed overnight, provided that the samples are
received by 2 p.m. Customers will receive their sequencing data by the
next day without any extra cost. Manual editing of the sequence may
require more time. However, as we may need to repeat analysis, we
guarantee delivery within 48 hours of receipt.
17 October 2003
Fasteris SA incorporated
Fasteris Life Sciences was incorporated as Fasteris SA at the Geneva trade registry.
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