While it could previously take up to three weeks to analyse a few selected genes, the new instruments can sequence all of the significant gene sequences in an entire genome in a third of the time.
“It took 14 years for a huge number of researchers in several countries to map the human genome as part of the Human Genome Project,” says Christofer Flood, one of the researchers behind the new investments at Genomics. “With our new instruments we could map all of a person’s genes in just ten days.”
This is next-generation sequencing, and uses two instruments: the larger Illumina HiScanSQ and the smaller MiSeq.
“Although these instruments pave the way for all kinds of opportunities in genetic studies, we’ll still be using our existing equipment,” says researcher Annica Wilzén, who is also responsible for next-generation sequencing at Genomics. “By way of example, it’s good to be able to replicate and verify the results from the new machines using established technology.”
The instruments have already been brought into use: recently a group of researchers completed a run where they compared the DNA from a cancer tumour with that from the same patient’s blood.
“Different tumours can have lots of different genetic changes, which can play a crucial role in the prognosis and decisions on the best possible treatment,” says Wilzén.
The larger instrument is of particular interest to basic researchers who can now more readily analyse large numbers of genes. The smaller instrument can be used to run a patient sample during the course of a day, and can therefore be of enormous benefit to clinical research.
Genomics’ investment in next-generation sequencing has run to many millions of kronor. The centre has also invested in the recruitment of an additional bioinformatics data analyst to interpret and manage the data generated by the instruments.
“A single run of the larger instrument generates many terabytes of data which are analysed and scaled down to just a few gigabytes,” says Flood. “This makes considerable demands of both the hardware and the network. We’re working with Chalmers University of Technology to cope with the technical management of all the data.”