Lighting up the code of life

Pål Nyrén

Winner of the European Inventor Award 2013 in the category SMEs

Pål Nyrén, inventor of Pyrosequencing

The spiral-staircase-shaped double helix of DNA contains the genetic information to all biological life on earth. Genetics, or the study of genes, is leading to improved medical research and treatment. It is also revolutionising our understanding of biology, evolution and ultimately, of ourselves.

As the inventor of important DNA sequencing technology, Swedish scientist Pål Nyrén has been instrumental in furthering genetic research, making it more efficient and affordable, and its use more widespread. His patented sequencing method, known as Pyrosequencing, is one of the most common methods used today.

Pål NyrénEarly inspiration

As a post-doctoral student at the University of Cambridge, Pål Nyrén often found himself frustrated by the time-consuming and complex task of manually performing DNA sequencing. He was using the so-called Sanger method, named after Nobel Prize laureate Frederick Sanger, who had pioneered it over a decade earlier. The method remains in use today - albeit improved and automated - but in the mid-1980s it was still a rather gruelling task.

Sitting beneath a figurative Newton's apple tree - in this case cycling home from the lab on a dark, rainy evening in January 1986 - Nyrén first envisioned a new method of sequencing DNA.

As a PhD student at Stockholm University, Nyrén researched in the field of photosynthesis and developed a method capable of capturing the light emissions of a chemical reaction. Drawing on this experience, Nyrén's epiphany concerned transferring this method of measurement into the process of DNA sequencing.

Pyrosequencing’ is named for the ‘fiery’ luminescence produced during the process – similar to the luminescence a firefly displays at night.

Keeping the faith

After completing his post-doctoral work, Nyrén returned to Sweden and unsuccessfully tried to obtain financing to bring this new sequencing method to life. According to Nyrén, the grant-giving body did not, at the time, fully realise the importance of the method he was proposing.

Despite the apparent setback, he continued to work on the sequencing technique, often spending his evenings and weekends on its development. However, it wasn't until 1994 when he was fully able to dedicate himself to the task.

Aided by colleagues at the Royal Institute of Technology (KTH) in Stockholm, Nyrén finally had the time and resources necessary to develop and test his novel DNA sequencing method. He and his colleagues Mathias Uhlen and Mostafa Ronaghi filed an initial patent for a "Method of sequencing DNA", which was granted in 2001.

Shine a light

Unlike the existing DNA-sequencing procedures at the time, Nyrén's Pyrosequencing method did not resort to radioactive labelling. This technique forces scientists to handle potentially dangerous radioactive material. Nyrén's invention also allowed for much easier and faster sequencing.

‘Pyrosequencing' is named for the ‘fiery' luminescence produced during the process - similar to the luminescence a firefly displays at night. As the DNA is sequenced, a chemical reaction produces light signals that are captured by sensitive cameras, which help determine the sequence of bases in the DNA.

The Pyrosequencing method was first sold by the company founded by Nyrén, Uhlen and Ronaghi - Pyrosequencing AB - in 1999. It quickly established itself as one of the most common methods of so-called ‘next-generation sequencing', which describes technologies that help generate read-outs of DNA sequences at much greater speeds and volumes. The results have been impressive: Since 2003, the speed of sequencing a whole genome has more than doubled every two years.

“Our technological advantage, the market and our strong patent portfolio were decisive for the acquisition.”

Start-up success

In 2003, the successful start-up Pyrosequencing AB changed its name to Biotage. Five years later it was acquired for $53 million by Qiagen, a provider of sample and assay technologies. "Our technological advantage, the market and our strong patent portfolio were decisive for the acquisition," recalls Nyrén.

The Pyrosequencing method was also licensed to 454 Life Sciences, now owned by the pharmaceuticals giant Roche. The method was used to develop an array-based platform for sequencing, greatly increasing the speed and volume at which DNA can be sequenced.

Growing markets and sequencing speeds

Incidentally, it was a 454-machine that sequenced the genome of James Watson, who - along with fellow molecular biologist Francis Crick - had discovered the double-helix structure of DNA in 1953. Watson's genome was sequenced in just two months in 2007 - compared to the 13 years that it took to sequence the first ever human genome completed in 2003.

The sequencing instrument market currently generates annual revenues of around $1.6 billion, and it is expected to grow to $2.2 billion within the next four years. Due to the steep price of the individual testing units, sales of next-generation sequencing instruments are largely restricted to developed countries.

Europe accounts for just over a third of the overall market. However, increasingly affordable prices will undoubtedly make DNA sequencing accessible to a wider population.

Decreasing costs, increasing knowledge

Continued demand, improved sequencing methods and related technological advances have been driving down the cost of DNA sequencing. The cost of sequencing a genome in September 2001 was estimated at $95,263,072 whereas the cost has fallen to around $7,743 per genome in October of 2011.

This trend has contributed to a veritable revolution in the field of genetics. The greater access to, and the affordability of DNA sequencing, has spawned the creation of new fields of study. It also affords us the possibility to examine the building blocks of life in ever-closer detail. Investigating genes and their interactions help us understand hereditary diseases and feeds into research for treating them.

“The main problem is to get the research / the invention to bigger companies; Pyrosequencing AB succeeded in attracting the attention from a big player (Qiagen) and to realize the breakthrough of the technology.”

Genetic clues to fight disease

For example, genetic analyses of cancer tumours are as different from each other as one patient's genetic profile differs from the next. Cancer treatment that is effective for one patient might not work on the ‘same' type of cancer in another.

The genetic specificity of the individual, as well as the disease, suggests that for many illnesses, the most effective form of treatment is individualised, or tailored to, the patient. This form of ‘personalised medicine' will likely be the future of healthcare, and it relies heavily on genetic knowledge gleaned from DNA sequencing.

Future improvements in human health, as well as other essential applications - such as in criminal forensics - depend on continued genetic research. This research, in turn, requires sequencing technology that can process increasingly larger quantities of genetic material in shorter amounts of time.

The method of Pyrosequencing, developed by Pål Nyrén and his team, makes such vital genetic research possible and will not only contribute toward our growing theoretical body of knowledge on genetics but could likely help in combating life-threatening diseases such as cancer.

How it works

The method developed by Nyrén involves taking a single strand of DNA and synthesising its complementary strand, one base pair at a time, with a DNA-synthesising enzyme and a substrate containing a chemiluminescent enzyme - an enzyme that is emitting light as the result of a chemical reaction.

Solutions of the four nucleotide bases adenine, guanine, cytosine and thymine - are added sequentially. A successful pairing of a base pair produces a light signal through the release of a chemiluminescent enzyme that can be detected by a camera and mapped by software. The process is repeated for each of the four different nucleotide solutions, and the mapped bases combined to determine the entire DNA sequence.

A short history of DNA sequencing

The double-helix structure of DNA was discovered in 1953 by James Watson and Francis Crick. 50 years later, the first human genome to be sequenced was completed at tremendous cost over a period of thirteen years. In the short time since that milestone was reached in 2003, the speed and cost of sequencing a whole genome has changed tremendously. Today, a genome can be sequenced in weeks and at a cost of $8000 - a far cry from the approximately $95 million the first genome cost. Overall, the speed of sequencing a whole genome has more than doubled every two years.

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