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Towa Libermann, Director, BIDMC Genomics Center

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AT A GLANCE

Associate professor of medicine at Beth Israel-Deaconess Medical Center (BIDMC) in Boston, and director of the BIDMC Genomics Center.

Received his PhD in immunology from the Weizmann Institute of Science, Rehovot Israel in 1986.

Research interests focus on role of Ets transcriptional regulation in cancer and inflammatory diseases.

Outside interests include skiing, swimming, and tennis, classical music and opera, archeology, traveling.

QHow is the facility set up within Beth Israel Deaconess Medical Center (BIDMC)?

AThe facility is located at the Harvard Institutes of Medicine with about 2,000 square feet of space. We have a well-trained technical staff and offer project consulting, target RNA probe labeling, microarray hybridization, scanning, and bioinformatics data analysis. The Genome Center also offers a high throughput SNP analysis service. The microarrays are scanned and the results are uploaded to the research portal. We process an average of 30 to 60 RNA samples per month. Most of the activity up to now has focused on the use of Affymetrix chips.

QDo you have any other microarray systems besides Affymetrix?

AWe are right now testing various vendors of oligonucleotides including Clontech, Operon, and Compugen, and we will eventually provide human and mouse custom arrays. Affymetrix chips have worked very well so far and each generation of chips appears to become better than the previous one.

QWhich instruments do you have in the facility?

AWe have an Affymetrix GeneChip system, an Amersham generation III microarrayer, an Amersham Automatic Hybridization Station, a Nanogen Microelectronic Chip System, a Qiagen Masscode System, a Ciphergen Mass Spec Proteomics system, as well as data storage and analysis facilities.

QWhich researchers use your facility?

AAlthough priority is given to investigators from the BIDMC and other Harvard associated institutions, the BIDMC Genomics Center is open to other academic institutions as well. The center has been involved in more than 30 different highly productive collaborations with investigators within the BIDMC as well as other Harvard associated institutes, Harvard Medical School, Boston University, Brazil, and Bahrain.

QHow do you work with the researchers who use your facility?

AInvestigators are continuously consulting with us prior to as well as after the experiment on experimental design and data analysis. They are routinely in our lab observing the technical aspects, learning how to isolate RNA and to label probes, as well as training for bioinformatic analysis of microarray data.

QHow have you gone about educating the BIDMC community about microarray technology?

AWe have established a web-accessible BIDMC Genomics Research Portal for data entry, annotation, and analysis, www.bidmcgenomics.org. It also provides a user-friendly portal for online ordering and registration of experiments, choosing the specific microarray chips, tracking the status and progress of orders, and managing of the samples.

We are also in the process of establishing an educational core that conducts training courses and weekly seminars in functional genomics and bioinformatics.

QWhat methods do you use to analyze microarray data?

AFor Affymetrix data, we use the Affymetrix software. We also use GeneSpring to perform some clustering analysis. Most other bioinformatics tools are provided by our collaboration with Isaac Kohane and his group at Children’s Hospital, and include Relevance Networks, an approach that creates networks of hypothetical associations from data sets such as generalized linear modeling.

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?

AI would like to have the whole human and mouse genome on a single chip, higher sensitivity for low abundance genes, be able to use nanograms rather than micrograms of total RNA for hybridization, and have access to high throughput microarrays. Preferably, prices should also drop further.

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