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Holly Dressman, Director Duke Medical Center Genome Core



PhD in Genetics from Penn State, 1994.

Postdoctoral fellow at NIHS.

Started core microarray facility at Duke in 1999.

Outside interests: Swimming and biking, spending time with her two sons.


QHow is the microarray facility set up at Duke Medical Center?


AIn the beginning we were just processing Affymetrix chips. Right now we’re a core facility that any investigator can use, and we have about 60 investigators using our services. We average about 90 to 100 samples per month for Affymetrix chips and have four people total in our lab now. Within a few weeks, we are moving to a larger facility where we will also be able to do spotted arrays.

QHow do you work with the researchers on individual projects?


AI discuss with investigators the experimental setup and design. We look at the questions they want to answer, because they’re going to get all this data and in the end, they are going to have to make sense of it. We also figure out how many replicates they need to do. Then we take the RNA or poly-aRNA and make the probe, hybridize it to the Affymetrix chip, process it, give them back their data, and also try to help them with analysis.


QHow do you cover the cost of the arrays and the facility?


AWe charge the investigators for the cost of supplies, then we add on the cost of labor. We are part of the Duke Comprehensive Cancer Center, so they give us some support. Also we get grant support of for technicians to help subsidize some costs.


QWith Affy arrays what kinds do you use?


AWe’ve got human, mouse rat, yeast, rat, Arabidopsis, and p53 chips.


QHow have you found the Affymetrix equipment and products?


AIt’s a very nice, straightforward platform. Its reproducibility is pretty good. We do find tissues tend to be a little more difficult to work with than cell lines. We have to increase the amount of the RNA to get better signals. Overall I think it is a very good system, but it is a very costly system for a university setting. Also, the Affymetrix software for data analysis is quite limiting. It doesn’t really account for replicates. But the NetAffx website they introduced has been wonderful as far as getting functional information about these genes, because that’s the next big thing that researchers want to know.


QWith your new foray into spotted arrays, what kind of arrayer did you buy and what are you planning to do with that?


AWe have a GeneMachines OmniGrid arrayer and Telechem pins. We have an Axon GenePix 4000A scanner. We have done small scale spotting for a Cryptococcus project where we’re looking at PCR products and oligos together. When we move into our new facility, we’re going to be focusing on oligonucleotides. We’ll have the human, mouse, rat, and yeast oligo sets from Operon.


QThese offerings seem to duplicate the Affy chips you offer, don’t they?


AIt is offering people another platform at a lower cost. The cost would come down to less than $100 per array, depending on how many slides you can get out of an oligo batch, and depending on consistency of spotting. The labeling and reaction costs are much cheaper than with Affymetrix. Except then you weigh in more variability in experimental design. It has its plusses and minuses, but it’s very cost-driven.

Also, researchers are not just interested in looking at 13,000 genes on a chip, but once they identify genes of interest, want to conduct large-scale screening on a small number of genes of interest. They could do this with tissue-specific spotted arrays, which we are developing.


QWhat methods do you use to analyze microarray data?


AWe have several packages other than Affymetrix. We have GeneSpring and Partek. We’ve also been beta testing a product called Arrayex, made by a company based here (in Durham, NC) called Incellico. The software is very good. It’s not a lot different from the others out there, but it allows you to say ëhere’s my list of genes’ and find out all of the functional information about it. Pulling together all of the other known pathways and functions, saying ëhow we tie these genes together’ is very useful. We also have worked in collaboration with (Duke statistician) Mike West, who uses Bayesian statistics and does more predictive modeling.

Another area we are working on is building a database. Right now we are saving everything on CDs, and rely on the investigators to copy their data. But we are trying to develop a database where we can put this information in and query everything out. I wish when we first started this facility that we had developed a database, with a naming system for each file.


QWhat type of new tools for microarray facility would you most like to see developed in the near future?

AFor spotted arrays, it would be nice to have one universal system, and one universal reference array. A major problem is comparing data from your lab and another lab. It would be nice to know what the reference points were, and whether they were the same in different experiments so you can compare them. I would also like to see someone bridge the gap between platforms for spotted arrays and Affymetrix array data that would enable you to analyze the data together.

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