NGS Expert Blog

In the last weeks we were continuously following the hostile bid from Roche for Illumina. Now, after the shareholder meeting, Roche didn’t extend the offer and let Illumina from the hook – for the moment?
However, this could also be good news. From my point of view there is a wide range of applications that work best with the FLX technology. In order to be competitive with all other NGS technologies Roche needs to invest more in FLX+. After launching the upgrade last year they faced continuously problems with the performance of the technique as highlighted for example in an article in InSequence last week.

I think, because the NGS future of Roche is again more focussed on FLX+, they will work even harder to get the long reads up an running on every GS FLX site – maybe a FLX+ upgrade for the GS Junior might be possible soon.

Of course it also might be that they are looking for an alternative for Illumina as highlighted by Julia Karow and Monica Heger. However, all possiblities discussed in this article – a cooperation with Life (Ion Torrent), an acquisition of Oxford Nanopore technologies or the development of a brand new technique might not be as scary for the FLX technology as Illumina because all technologies are “very early in the commercialization”.

A documentary titled “Cracking Your Genetic Code” was recently released, and it offers a glimpse on how genomics is transforming medicine. Prominent scientists are featured, including Francis Collins from the National Institute of Health and Eric Lander from the Massachusetts Institute of Technology. In the documentary we are introduced to technologies for sequencing the entire genome; Illumina is being mentioned as one of the companies with such technology. We hear real-life stories where genome sequencing and genotyping led to diagnoses and successful treatments that would not happen otherwise.

The documentary does not only present the promises that personalized medicine is bringing, it also raises important questions concerning the readiness of the society in adopting this new form of medicine. There are always pros and cons with introducing new technologies to our daily lives. It is a matter of engaging and educating the public so the society as a whole can make some informed decisions during this healthcare revolution. Cracking your Genetic Code is a great introduction to the new role of sequencing in medicine, and I hope you will share it with your colleagues and friends!

Recently the Hollywood filmmaker James Cameron (director of “Titanic”) reached in a custom made submarine the deepest point of the Mariana Trench, breaking a world record for the deepest solo dive. Deep-sea trenches have lured explorers for decades, tantalizing them with glimpses of an ecosystem shrouded in darkness.

Although Cameron’s journey to the abyss yielded little new scientific data, it whetted the public appetite for information about life in the otherworldly environments of deep-sea trenches.

An international group of marine scientists may soon provide a feast of such data, from the first major systematic study of a deep-sea trench. If all goes well the team will start exploring the South sea of New Zealand in a depth between 6.000 and 11.000 meters. A team around Timothy Shank from the Woods Hole Institution (WHI) inMassachusetts will systematically explore this complete unknown biotope with robots. An article about this program is published in the recent issue of Science.

New forms of life and deep insight into evolution are to be expected.

As a scuba diver I am excited to learn more about this fascinating biotope and I am sure that Next Generation sequencing technologies will significantly contribute to new chapters of the book of life.

Just after posting my last update about the fight between Roche and Illumina I read two more interesting news which I would like to share with you.

1. Three important shareholder advisors aid Illumina’s board. Glass Lewis, ISS and Egan-Jones recommend that all shareholders shall support the board by not voting for any of Roche’s candidates to extend the Illumina board. From my point of view this is a clear announcement towards Roche.
2. The current behaviour of Roche is not new. They acquired already two companies in the same way: Genentech & Ventana. Roche always needed to increase the offer per share once and in both cases it took more than 6 months until the deal was signed. Since the discussion about the takeover is public since January I won’t expect a solution now before autumn this year.

On the annual Illumina shareholder meeting this week we will definitely learn how the shareholders react on the recommendations of all advisors and on the offer from Roche.  Will they adopt a clear position? We will know that soon.

Since 2010 several studies have been published that analyze microbial community composition by amplicon sequencing on the Illumina Genome Analyzer (GA). However, direct adaption of these protocols for sequencing on the HiSeq 2000 – the currently predominant Illumina sequencer – is not possible as both systems use different basecalling pipelines. Therefore amplicon sequencing on Illumina HiSeq 2000 is still left to the very experienced users and only a few publications can be studied on this.

In the meanwhile Illumina has introduced the MiSeq as the optimal platform for this kind of projects. In this context they have published an application note presenting sequencing of the V4 region of 16S rRNA genes on the MiSeq system.

And I totally agree that the MiSeq is a very good tool for these studies. For me, the most important advantages of the MiSeq layout in comparison to the sequencing on Illumina HiSeq 2000 are as follows:

• Shorter turnaround time: The sequencing run itself takes a bit more than one full day, while a HiSeq 2000 run takes up to 12 days.
• More informational content: By overlapping two paired end reads of 150 bp, full-length reads of about 250 bp can be generated
• Potential for even longer reads: Illumina has announced read length of 250 bp for the end of the year. Then reads of up to 450 bp should be possible.

Nevertheless Roche GS FLX+ sequencing is still able to generate much longer reads with an average of up to 500-600 bp. And the long read length will provide a deeper insight into the microbiome of interest or more precisely higher classification efficiency down to species level. However Roche sequencing goes along with higher costs per base, so it will always be a decision based on the individual experiment, whether read length or sequencing depth is the most important factor.

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?