Answers to all possible questions about genomes

Published on
June 1, 2012

CAT-AgroFood’s purchase of so-called second- and third-generation DNA sequencers (with accompanying ICT and bioinformatics infrastructure) has indisputably strengthened Wageningen UR’s top position in the field of bioinformatics. “Having these machines is very important.” states dr. Gabino Sanchez Perez of Plant Research International (PRI), part of Wageningen UR. “However, much more important is the knowledge to extract biology out of the gigabytes of data that these machines provide. We have that expertise.”

“We provide tailor-made services.” The group leader of PRI Bioscience can’t stretch his point enough: “The first step is always the same: listening to what the client wants.” What the final step is, depends on the client. “We can do the entire process, from preparation of the samples to the analysis, or we can just assist in running the samples and provide the client with the raw data”, Sanchez Perez says.

CAT-AgroFood’s two new DNA sequencers were installed recently, in October 2011 and January 2012. An Illumina HiSeq 2000 was placed at PRI on Wageningen Campus; a PacBio RS is hosted by the biotechnology company KeyGene in Wageningen. “But we also have other equipment, such as the somewhat older but still very useful 454 technique”, says Sanchez Perez. “Sometimes you need to use a combination of techniques, the so-called hybrid approach, but sometimes you need only one. We can help clients to set up the experimental design that is required to answer their specific biological questions.”

Zooming in on details…

Every technique has its advantages. The second generation sequencer Illumina HiSeq 2000 delivers a high throughput of DNA reads up to a maximum of one hundred base pairs. An excellent machine to use if you want to investigate the smallest details of organisms, even if no previous genomic data is available of that species. Wageningen researchers are now, for instance, sequencing the genomes of 150 tomato types.

…and getting a better understanding of the bigger picture

The third generation sequencer PacBio RS can produce DNA fragments of several thousand base pairs. Reading ‘kilobases’ gives more information about the order in which base pairs are placed on a DNA string. Research using this type of sequencer is still in an early stage.

The new DNA sequencing platform also constitutes an enormous boost in terms of the speed of analyses. To illustrate: scanning base pairs using this facility is 5,000 times faster than in 2007 and 25,000 times faster than in 1997.

Increasing demand

Wageningen UR and KeyGene are currently the primary users of these facilities, enabling them to execute genomics research for a broad array of samples of microbial, plant, animal, and human origin. Other organisations and companies are also showing an increased demand for CAT-AgroFood’s DNA sequencers, Sanchez Perez has noticed. “Not surprisingly”, he adds. “There are not many of these machines in the Netherlands. Yes, you can send your samples somewhere else, but if there is not enough material or not enough quality for sequencing, they will just send your samples back or send you a check for failed runs. If we get samples that cannot be read, we will offer assistance to prepare the samples properly. And we’ll make sure that we know what questions you want to have answered. That’s the difference. We can simply decode the DNA and send clients a whole lot of data, but it’s not about quantity, it’s about quality; interpreting the data and providing insight into the genomes the client is interested in.”

Sanchez Perez’ group is specialised in plants, but they can as easily assist in designing ways to decode the DNA of animals or microbes. They can also prepare the samples and do the first steps of the analysis. “And if clients want more details, we can rely on the expertise of other groups within Wageningen UR to give assistance.”