NGS Expert Blog

Scarcely any biotech blog and bulletin is not reporting about Oxford Nanopore Technologies MinIon & GridIon.

Truly, the specs of the new instruments sound fantastic: read length up to 100 kbp, raw read error rate ~1%, no sample preparation necessary (at least with blood samples), RNA can be sequenced directly, costs per base comparable to competitors, only 900$ for the MinIon device and data production in the range of 20-400 bases / second / pore (GenomeWeb).

And it goes without saying that these new instruments cause a lot of fuss in the Next Generation Community: shares from competitors are down up to 6 percent, and every one discusses fictive scenarios that might now be possible.

I am also really excited about this news and it still sound unbelievable that Next Gen Sequencing devices can be so small. But I also have my doubts  and agree with the following statements:

“… If only 75% of what they claimed is true it would be impressive.” (Pathogenomics)

“…that new DNA sequencers, like everything else in life, often look better when they’re vapourware.”(Forbes)

What is definitely true is that you really have to read also the small prints at the bottom of the page. You cannot, for example, use the USB-Stick-like device “MinIon” to sequence the complete genome in 15 minutes. You would need to run 20 GridIon instruments or “nodes” in parallel to achieve this turnaround time with a coverage of 50x.

So it is definitely fascinating what might be possible with the MinIon – just think about the point-of-care market, where we would need small, disposable devices to work on site. But still you should be able to interpret the data and I look forward to learning how they will solve this issue. And furthermore I am even more curious what kind of instruments we will be using in 5 years: Smaller or faster ones or something completely different? What do you think?

Oxford Nanopore Technologies Ltd.

John Lauerman, reporter with Bloomberg News got his genome sequenced. He is part of the Human Genome Project of the harvard medical school, where 10 genomes have been sequenced and analysed so far (Bloomberg).

After receiving his result he was first relieved to find no hint to have the APOE4 gene variant that raises the risk of Alzheimer’s disease. But what he learned then is that “No news wasn’t always good news; it just wasn’t bad news”. (Bloomberg) The researchs told him that the sequencing simply didn’t reveal information about APOE4. A study update however revealed later that the APOE4 gene variant indeed is present in his genome. This variant means an approx. 3 percent increased risk of developing the disease by age 80. But what does that mean in any single individual’s genome? At least Lauerman was less worried being his parents in the late 70s and 80s and having not developed Alzheimer’s disease.

But the researches have found in addition the rare JAK2 variant in Lauerman’s genome that is linked to a cancer-like blood disorder.  Knowing the risk, he now has the chance with increased vigilance to evaluate a potential disease early and to react accordingly.

And in that context Lauerman pointed out an even more important point: as a reporter working on a story about genomics, he had access to experts and genetic counselors that many people wouldn’t. What will happen as more people get results from broad genome sequencing? (Bloomberg) The question is if people can even handle the reports.

So as a personal conclusion I suppose I would be worried to hell when I would get to know my genome disorders. But it might be also a good thing, like in John Lauerman’s case. You would have the chance to detect a potential disease in an very early stage. You never know…

In January the drug company Roche announced its intention to buy Illumina for $5.7 billion. Roche’s CEO Severin Schwan pointed out that he thinks that a fusion of Illumina and Roche would help both companies to move forward in the area of diagnostics with Next Generation Sequencing technology.

However, Illumina insisted that the bid of $5.7 billion is far too low and offered a “poison pill” to its shareholders.

Now Illumina is sued by the shareholders. They accuse Illumina for having a conflicting financial interest since Goldman Sachs could lose hundreds of millions if the Roche offer was accepted (reuters.com)

I am really curious what will happen next in the fight about Illumina. And it certainly strengthens the feeling that the MiSeq could outbeat Roche’s GS Junior.

Dear honourable reader of our NGS blog,

Actually IWF and European country leaders discuss a raise of the European secure funds to about 1.5 Trillion Euro (German = 1,5 Billiarden Euro). This is such a high number that I could not even imagine it…

This number also gave raise to the question: “How much of NGS sequencing or Whole Human Genome Sequencing (WGS) could be done with it?”

Step 1:  How many people are needed to pay 1.5 Trillion Euro of income tax?

With an average of 10,000 Euro of income tax per year 4,500,000 people would need to pay for 35 years (life time of work) to account for 1.575 Trillion Euro (1,575,000,000,000 Euro). Or more than 150 million people (150,000,000) are needed to work and pay tax money for one year – of course without any interest.

The 27 European Union countries (EU27) currently have a population of about 501 million people including babies, pensioners and all other non-tax payers (year 2011). Such about 30% of all people in EU27 need to work for one year to earn this sum of funding – of course without spending money for anything else…

Step 2: How many Human genomes would I get for this sum?

At a reasonable cost of 15,000 Euro per genome this equals 100 million (100.000.000) sequenced genomes  – that is about 1/5 of all EU27 people. At a discounted offer of 5,000 Euro per genome this equals 300 million (300,000,000) sequenced genomes – that is 2/3 of all EU 27 people. At a best price offer of about 4,000 $ (= 3,000 Euro) the money would allow to sequence about 500 million (500,000,000) genomes which is the complete population of EU 27.

Whow – this gives me the feeling we are in fact talking about a lot of money,

Best regards

Axel