Tag Archives: Roche

Do You Still Remember Which NGS Sequencer Was The First On The Market?

gs-20It was 2005, when Roche launched the first NGS sequencer called the Genome Sequencer 20 (GS 20). This device was able to achieve read length of approx. 100 bp, with a total data output of approx. 20 Mbp per run.
As a consequence, sequencing of a bacterial genome of 5 Mbp (e.g. E. coli) with 20-fold coverage required 5 individual runs on the GS 20. Sequencing costs were in the range of several tens of thousands Euros, bringing the cost compared to Sanger sequencing down 10-fold.

Looking back it’s also difficult to imagine for me, that the GS 20 software at that time could handle genomes of a max size of 50 Mbp only.

Since then, 5 major leaps in the Roche/454 sequencer’s development took place:

  • GS 20 to GS FLX
  • GS FLX to GS FLX with Titanium chemistry
  • Launch of the desktop sequencer GS Junior
  • GS FLX Titanium to FLX+
  • FLX + to FLX++ sequencing (new GS FLX software v2.8)

This all happened in only 7 years.

The current Roche/454 FLX++ chemistry enables read length up to 1100 bp and read outputs of up to 1.2 Gbp per run. As a consequence, today, 8 years later, sequencing of a 5 Mbp bacterial strain can be done on a ¼ plate of a full run. The 9-10-fold longer reads make a great difference in respect to contig length and contig number of the genome assembly.

Meanwhile other NGS sequencers dominate the market. Nevertheless the Roche /454 technology is still of superior quality for de-novo sequencing of genomes of any size and for amplicon sequencing.

High-Throughput Sequencing Machines By Platform

The High-Throughput Sequencing map by James Hadfield (Cancer Research UK, Cambridge) gives us a very interesting overview about sequencing activities around the world. We ran a survey to find out if your favourite machines correspond with the platforms listed by James in his overview.

Here are the results: Your personal favourites are nearly a perfect match with platforms in the genome centers worldwide. Great match!

survey

 

New Bid From Roche For Illumina?

The analyst and sequencing community is currently divided on whether to believe the rumors of a new bid from Roche to buy Illumina. The source of the controversial discussions is an article from the Swiss Newspaper L’Agefi that reported end of December that Roche and Illumina might have agreed to a deal for Roche to acquire Illumina. Since Illumina turned down Roche’s original bid in January, continuous interest from Roche has been reported several times, but the report from L’Agefi is also mentioning concrete amounts of the bid. According to them, the acquisition might take place for $66 per share, valuing the deal at about $8.14 billion in total.

The offer is $15 per share higher than the previous offer of $51 in April last year. According to the analyst Devia Ferreiro of Oppenheimer the new bid is definitely at a level that might lead to a final deal.

With Roche having only about 9% of the NGS market and next generation sequencing becoming most likely an important clinical diagnostic tool in the next years, the strategy focus of Roche must be to get better access to the NGS market and to take NGS to clinical practice. The acquisition of the NGS market leader Illumina represents an optimal starting point.

We’ll see if the rumors are built on a solid foundation within the next two weeks: The Swiss newspaper L’Agefi reported that the announcement might come during the first half of January.

Survey Result:
Applications Using Roche GS Technology Providing Read Length <700 bp

We asked, for which kind of application do you use the Roche GS FLX+, the GS FLX Titanium or GS Junior sequencing technology providing read length of up to 700 bp? 36 people answered the poll:

 

 

 

 

 

 

 

 

 

Please find on the right hand side our new poll and add your voice!

A Never Ending Story?

Every now and then I think about writing again about the proposal from Roche to Illumina; but everytime I have the feeling that something fundamental could happen tomorrow. And to be honest – I never expected that this hostile takeover would take so long. It is anyhow fascinating that such huge acquisition plans are discussed in public.

Anyhow the latest news I can share is that Illumina compares itself with the giant “Apple” now. Quite funny is the comment of David Benoit from the WSJ Blogs about that:  “That’s some high talk for a company with a market capitalization of about $6.3 billion, roughly 1/100th the size of Apple.”

But nevertheless I have to endorse the statement of Illumina, since Apple also started as a really small company and due to the enthusiasm of its founders it grew to this giant company. Imagine Microsoft would have bought Apple in their early days? We might still use a normal mobile phone to connect with each other. No iPod, no iPad? So it seems totally clear to me that also the founders of Illumina should fight for their company and the freedom to be self-sustaining.

What do you think – how long will it take until Roche takes over Illumina, or is Illumina strong enough to defense itself?

Genome-Wide Studies to Identify Rare Variants in BAG3

The June webinar of the free NimbleGen webinar series is talking about
Genome-wide studies of copy number variation and exome sequencing identify rare variants in BAG3 as a cause of dilated cardiomyopathy >

For further information and registration, please visit the NimbleGen website.

Roche Versus Illumina: Where is it Going?

Six and five years after the commercial launch of their first next generation sequencers, the companies Roche and Illumina are still at the forefront of the next generation sequencing market. By today, Roche technology has enabled 1209 peer-reviewed publications while Illumina technology has even enabled 1631 publications (from both companies’ websites).

The current sequencer of both companies are the Roche GS FLX with an average read length of 350-450 bp and 400 Mbp data output per run and the Illumina HiSeq 2000 with read length of up to 100 bp and up to 320 Gbp data output per run.

Both companies’ focus on technological improvements is mainly on enhancing read number and read length. Illumina has recently launched the 150 bp read length (for GAIIx only) and has further announced doubling of yield for Q2 in 2011. Roche is planning to launch the extended average read length of 750 bp sometimes before the end of June according to GenomeWeb News on April 19th, 2011.
In my point of view third generation sequencing will not replace these technologies but enable additional applications as well as combining third generation and second generation technologies for specific project layouts.