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Ranjan Perera Says Stowers Institute is Taj Mahal of the MidWest

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AT A GLANCE

Director of Genomics, Stowers Institute for Medical Research in Kansas City, Mo., a new privately-funded institute focusing on basic genomic and proteomic research that can enable improved prevention and control of disease.

Received his PhD in molecular genetics from Moscow University, 1988.

Posdoctoral fellowship at MIT with Ethan Siegal in DNA recombination and repair.

Set up a genomics facility in Auckland, New Zealand.

Early employee at Akkadix in San Diego.

QLast August, you moved from the sunny and biotech-rich land of San Diego to Kansas City, which is not exactly known for its genomics. What motivated you to do that?

AThat’s a good question, and it’s the same question I struggle with when I recruit people. For me, it was the challenge of setting everything up from scratch. The institute is also amazing. People call it the Taj Mahal of the Midwest. The vision of the founders, Virginia and Jim Stowers, is that if they give scientists the right set up and conditions, then they can expect more from these people. It’s a unique setup not seen anywhere else.

QWhat kinds of research are going on at Stowers, and about how many people do you have?

AWe have 10 groups and are expecting to grow to 50 to 54 groups. The groups consist of fly, mouse, and human research, and also sea urchins. They are the cream of the crop.

QIn your new position as director of genomics at Stowers, I understand you have some grand opportunities to set up first-class facilities, given that Stowers has a $1.6 billion endowment and a new $200 million state-of-the art facility. How are you setting up the department?

AUnder my operation, there are three major projects, high-throughput sequencing, cDNA microarrays, and Affymetrix arrays. With cDNA microarrays I am particularly interested in setting up new protocols in technology development areas and testing new materials. I am very keen on coming up with proprietary new biochips.

QWhat kind of equipment are you using to do cDNA arrays?

AWe use a Molecular Dynamics Amersham system. We also have an Axon b4000 scanner, and have a special bioinformatics team working with us very closely. One of the major drawbacks in most microarray groups is that the bioinformatics group is somewhere else. One of my major conditions at the very beginning was to have a strong bioinformatics team. They are looking to recruit almost 18 people for the group, including a statistician, and now we have four people.

QWhat kinds of microarray analysis tools are you using?

AWe use Affymetrix tools, Eisen [clustering] software [from Stanford], and GeneSpring. We are also planning to get the X-Mine software. My strategy is not to do everything in house, but if we identify someone outside the institute who is good in genomic analysis, I would talk to them. I am also pushing very hard to set up databases. If someone wants to do genomics and microarrays, they have to have a good genomics interface, and the proper documentation from beginning to end. We are getting into LIMS systems and have people who are creating databases according to our requirements.

QWhy did you go with Affymetrix as well as cDNA arrays?

AWe went with Affymetrix because I am keen on oligo arrays, and I think they are going to be revolutionary in the future. But with Affymetrix you can’t do everything. If you study specific genes and pathways, you want to bring these genes to one chip, and study the variations and synergy. Also we are interested in cell cycle, meiosis, and gene repair. Eventually we are going to go after these genes using our bioinformatics strength to identify the genes, then PCR the genes and put them on a chip.

QWhat’s your wish list for future genomics tools you’d like to see come onto the market?

AMy wish list would be to be able to use a tiny amount of RNA for detection of gene expression down to a low abundance of transcripts. We have a method we are developing, and if it works, we will be able to talk about it at the next [Northwest Microarray Conference] in Seattle.