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Ron Kerkoven, Netherlands Cancer Institute Microarray Lab Leader

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AT A GLANCE : Holds a PhD in molecular biology from the Free University of Amsterdam. Did his thesis on neuropeptide systems. Conducted postdoctoral research with Rene Bernards at the Netherlands Cancer Institute. Started Netherlands Cancer Institute Microarray Facility in 1999.

QHow did you get into the microarray field?

AIn my first postdoc I worked in the Bernards lab at the Netherlands Cancer Institute in Amsterdam, studying E2F transcription factors. I tried to find target genes using differential display, Clontech filters (0.5K), Genome System filters (3.2K), and homemade filters.

Then we switched to making microarrays in 1998. We now have a fully operational facility in a brand new lab building.

QWhat role do microarrays play in research at the Netherlands Cancer Institute?

AA major role. We are very close to using microarrays for diagnostic purposes with breast cancer patients. Thousands of patient samples have been collected here over the past 15 years, and these will all be used on arrays. Our large research department is also using our mouse arrays to analyze animal models of human cancers as well as for characterization of cancer-related mouse gene knockout and transgene systems.

QHow is the microarray facility set up within the institute?

AWe have user groups that mirror the facility’s funding schemes. We train and educate these groups and provide them with free arrays. They perform their own experiments but we assist them with techniques, analysis, and data handling.

QWhat types of microarrays do you use and in what combination?

AWe make our own polylysine-coated slides, and spot human and mouse cDNA libraries. They are sequence verified, either from Research Genetics or the US National Institutes on Aging/National Institutes of Health. This is the best and most cost-efficient way of producing good quality arrays.

QHave you developed any special protocols for optimization of array performance?

AYes. Together with Frank Holstege of the University of Utrecht Academic Biomedical Center and Lance Miller of the National Cancer Institute/NIH microarray facility, we generated several purification schemes for cleaning probes and labeling RNAs. We are successfully amplifying small quantities of total RNA samples for experiments. (The protocols are on the website for the facility http://microarrays.nki.nl).

QWhat kind of arrayer do you use to make your own arrays?

AWe use a MicroGrid II from Biorobotics. QWhat methods do you use to analyze microarray data? AWe use the Imagene 4.1 and the mADB microarray software tools from NCI/NIH, plus all the freeware available. I would like to have software with the capacity of Rosetta''s Resolver, but this is not yet affordable.

QWhat is the biggest challenge you face in working with microarrays?

AThe biggest challenge is making enough arrays for all our users, and also being able to analyze hundreds of arrays from different patients simultaneously.

QHow do you tackle these challenges?

AI can rely on excellent technicians and collaborators in our own facility, but we have much support from within our institute as well as from the NCI groups that support us.

QWhat bits of advice would you give to a colleague who is setting up and running a core microarray facility?

ADo not hesitate in starting up the facility. One needs time to learn the million small steps between starting from scratch and arriving at perfection. Don’t expect microarrays to work immediately. But also work as a team in the lab. The quality of arrays you produce will be directly related to the level of organization in your facility.

QIf you could make out a wish list for microarray technology advances or improvements over the next couple of years, what would you most want or need?

AMy wish list would include international standards for comparing data, public data systems for chip data, better fluorochromes to replace Cy5, cheaper dyes, and access to better array making techniques.

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