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Agnes Viale, Director, Memorial Sloan-Kettering Genomics Core Lab

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AT A GLANCE

Received a PhD in biochemistry from University of Nice, France, in 1997.

In 1998, studied neuropeptides in the regulation of obesity at Jeffrey Friedman’s Rockefeller University laboratory. Developed mouse hypothalamic cDNA microarrays, or Hypochips.

Outside interests include: running, cooking, and learning languages.

QHow is the facility set up within Memorial Sloan-Kettering Cancer Center (MSKCC)?

AThere are six people working in the lab, including four technicians, one computer scientist, and myself. We provide services to the entire MSKCC scientific community. Our services include experimental design, labeling, hybridization, and basic data analysis for cDNA- and Affymetrix-based experiments. We also perform P53 genotyping on the Affymetrix platform. Upon completion of the experiment, the users are presented with an Excel spreadsheet containing the raw data. Affymetrix data (around 1,500 arrays so far) is archived in an Affymetrix LIMS system. We also maintain a database for different parameters of an array experiment, including tissue type, starting amount of RNA, and outputs; percent of genes expressed, scaling factor, background noise, etc.

QDo you make your own arrays or do you just use the pre-fabricated Affymetrix arrays?

AWe make human and mouse spotted arrays, both cDNA- and oligonucleotide-based, but 90 percent of our users employ the Affymetrix platform. Given the uncertain state of amplification protocols, the main advantage of an Affymetrix experiment is the relatively small amount of RNA required per experiment. It uses 5 to 10 micrograms of total RNA, in comparison with the cDNA platform, which uses 40 to 50 micrograms of total RNA. This is an important consideration for an institution specializing in cancer research, where the majority of the investigators are monitoring gene expression in human biopsies. Ten micrograms of total RNA is often beyond what they can purify. Still, the flexibility and affordability offered by a cDNA platform is unique, so we offer custom-made cDNA arrays.

QHow do you charge for arrays?

AWe only have a charge back system to recover the cost of the reagents used during the labeling and the purchase of the arrays. We do not charge for services provided, either technician time or time necessary to complete additional data analyses.

QWhat’s the biggest bottleneck in the array experimentation process?

ADefinitely data analysis. Many different analytical tools are available, but these tools can give conflicting outputs that are difficult to reconcile. This often leads to confusion as to which is the best method. This is an unanswered question. But, by being methodical and trying different analytical tools, we attempt to find a solution that helps the experimentalist extract the most relevant biological information.

We are developing in-house data analysis tools that integrate our statistical analysis software and commercially available data visualization packages such as GeneSpring. We are also developing a user interactive web interface, in collaboration with Terry Gaasterland at Rockefeller University.

QIf a colleague at another institution were setting up a microarray facility, what advice would you give that colleague?

ADon’t rush. Take time to evaluate the performance of several pieces of equipment. You and your staff are going to spend a lot of time working with this equipment. So you’d better feel comfortable working with it.

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?

AIt seems that presently, microrrray data requires validation by conventional techniques in order to be accepted by the scientific community. So, more than a technological improvement, what the field needs is a change in mindset.

I think we are presently exploiting only three to five percent of the results provided by a DNA array experiment. In a place like MSKCC where medical and basic research are so intimately linked, the creation of a “gigantic” database that gathers epidemiological data, clinical observations, genotyping results, gene expression profiling, protein array data, cytogenetic analysis, pathology examinations, and any other relevant information would tremendously and synergistically increase the value of a microarray experiment.

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