Next-gen sequencing is a revolution. San Diego-based Illumina owns most of the market but German giant Qiagen is prepared to disrupt this fact by stepping in massively by the end of the year. The fight has only begun.

Imagine you could sequence your genome to discover the disease you may have in the future.

What if I told you, that this is now becoming a reality thanks to the the next-gen sequencing revolution. The first human genome has been sequenced thanks to the Human Genome Project for a total cost of 100 million dollars. Now, sequencing an entire genome costs a mere 1,000$, as the graph bellow perfectly illustrates.


Data from NHGRI, Credit to Ben Moore

This opens plenty of new possibilities. Times have indeed changed… Back in the day, sequencing may have been a rarely used academic method or only reserved to rich people desiring a personalized diagnostic, yet this era is now outdated. The technique has become a standardized method to detect genetic diseases or to better understand cancers. This leads and drives the currently undergoing personalized healthcare revolution. McKinsey even listed Next-gen sequencing (NGS) as one of the 12 technologies that will transform our lives! The consultancy firm also stated that next-gen sequencing could have an impact of 1.6 trillion dollars on the global economy by 2025.

But how does the technology work? Here is a figure from Illumina.


The basic concept is to split DNA in many small fragments, sequence them individually, align the obtained sequences and reconstitute the whole DNA sequence. Sounds easy but it gets challenging when you know the human genome has over 3 billion genome base pairs (A,T,C, or G).

Many improvements have been made to genome sequencing since the 90s. The first method widely introduced to labs was the Sanger method. This methods worked well with small fragments, but was way too expensive and not reliable for big sequences. The next-gen sequencing has completely changed the field. Each fragment is marked with a “barcode”, allowing to sequence many fragments at the same time and to recognize each of them afterwards in the data analysis step.

Two main technologies are fighting today: pH-changes and light emission (click for an explanatory video). The first one entitled ‘Ion Torrent’ by the company Life Technologies and the second one being used by Illumina. Life Technologies is facing many issues with the pH-changes technology, which allowed Illumina to capture over 60% of the worldwide market shares. This success led the company to acquire $1.4B in annual revenues in 2014 and now counts over 4000 employees in its ranks.

But keeping a leading position in a very fast evolving market is no walk in the park.

German giant Qiagen could be Illumina’s main competitor. I was impressed when I visited the company a month ago during our North-Germany documentary (watch video here). This lab-equipment leader plans to launch a complete product line in the NGS field by the end of the year. Qiagen already has the automation expertise thanks to other products they developed. Back in early 2015, the firm took over the world leading producer of next-gen sequencing enzymes Enzymatics. It has an extensive bioinformatic expertise in the field and uses a similar technology to Illumina’s. In a nutshell, a strong challenger for Illumina.


Qiagen’s operational headquarters next to Düsseldorf, Germany

Illumina’s first move to counteract Qiagen was to open its European headquarters in Cambridge’s superbiocluster. Last week, it just signed a lease for a 155,000 square feet building that could be extended to 225,000 square feet. Several reasons make Cambridge a good destination for Illumina. The UK is investing massively in genome sequencing, as the 100,000 genome project shows. The Cambridge cluster is definitely one of the most dynamic life science clusters throughout Europe with many talents every square meter.

But the main reason behind this strategy seems to be the will of Illumina to increase its presence in Europe. Why? To grow on Qiagen’s domestic market! Qiagen may be selling worldwide, but Europe still remains its main market. Machines are produced in Switzerland, the fiscal headquarters are in Netherlands and the operational headquarters lie next to Düsseldorf, Germany.

6 months ago, on January 17th, I wrote an article called Qiagen, the new giant in next-gen sequencing tools? following the acquisition of Enzymatics. At that time, I believed Qiagen would only provide tools for leading manufacturers such as Illumina or Life Technologies, but it is finally going on the battlefront. And I truly believe Qiagen has several advantages to catch a big part of the next-gen sequencing’s market.

Let the fight really begin.

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  • Dan

    The author suggests that Qiagen will disrupt the market but makes no mention of what products or technology they might use. A tiny bit of homework would have at least uncovered that the sequencing is based on IBS’ technology.

    • Hi Dan,

      Thanks for your interesting comment. Indeed, Qiagen will probably use part of Intelligent Bio-Systems’ acquisition in 2012. But I don’t think Qiagen will make the difference with Illumina on the pure sequencing technology but on all the rest around it, as described above.


      • Dan

        Philip, the only other Qiagen-specific detail mentioned was that they purchased Enzymatics. Indirectly this is an advantage because they control the enzymes that NEB and Illumina use in their kits. To me the real advantage to Qiagen is the Gene Reader DNA panels both custom, off-the-shelf and mix-n-match. The Ingenuity acquisition is also a differentiator to Illumina who doesn’t own a LIMS company. If Qiagen can launch their sequencer – a key “if” – then they should fare well. Cheers. -Dan

        • Thanks Dan for the additional infos. Let’s see in the coming months how it goes!

  • Pastel BioScience

    Just to note that the generally recognised number of bases for the human genome is usually quoted as 3 billion, not the 3 trillion you have in the article.

    • Hi,

      Thank you for your comment. You’re right, it’s billion. It’s corrected.


  • Frank

    actually, there are 12 billion bases in the human genome.

  • Frank

    …and illumina sequencing is not 99%+ accurate. That’s spin. Just like they claim the $1000 genome with the Hiseq 10X. Sure it might be $1000 if you sequence tens of thousands in four years and don’t include overheads and informatics but raw information is useless without interpretation.

    Illumina is that accurate for the small portion of the genome that It can sequence due to its short read capability. There is a vast amount of information It can never access hence is not anywhere near that accurate if we really want to fully understand genomes and beyond.

    This is supposed to be about better understanding of our world.

    • Frank, thanks for your second comment. Concerning the price, of course, you have to calculate the prize of the machine, the reagents and the number of sequencing you can do.

      Concerning the accuracy, do you have any source showing it is not 99% accurate?


  • Frank

    There are about 3 billion base pairs in the human genome so 6 billion bases. Better to think of it this way because of the epigenetic changes that could be different on each strand, template and the compliment. Besides at this early stage in our understanding of genomics it’s an assumption that sequencing one strand provides the answer to the other strand. Science isn’t about assumption.

    Human beings are diploid meaning we have two copies of our genome per cell, hence, about 12 billion bases. There are different alleles etc on each copy one being inherited from the mother and the from the father. It’s well known that epigenetics changes the function of one copy from the other in many many ways.

    So to understand the human genome both copies have to be sequenced.

  • Frank

    I don’t think there is a reference needed, it’s quite obvious that short read sequencing cannot do repeat regions homopolymers at the very least. There are kits that produce synthetic long reads but they don’t seem to catch on with the researchers because the sample preparation is time-consuming and I’m not sure there are many reports on their accuracy.

    Conversely then, I would challenge anyone to say that any genome has been fully sequenced to 99.9% accuracy other than with Sanger sequencing.

    • Thanks for the additional informations on the accuracy.

  • Richard

    Hi Philip. You seem to limit the Market to two big competitors but some small competitors are probably emerging, following a niche strategy. What is your opinion on this subject ? What are for you the challengers of this Market, those who catch some Market Shares in the next 10 years ? thanks

    • Hi Richard,
      Very good questions which would require a review to fully answer them. Of course, the Next-gen sequencing market is huge and many actors are active within the space. I think the sector may change a lot within the new years and we will keep you posted here on 😉