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In Time for the Spring Semester, Schena Debuts Microarray Textbook

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At A Glance

  • Received his PhD in biochemistry from the University of California, San Francisco in 1990.
  • Postdoctoral Research Fellow with Ron Davis, Beckman Center for Genetic and Molecular Medicine, Stanford University, 1990-1999.
  • Currently serves as visiting scholar with TeleChem/Arrayit, Sunnyvale, Calif. He is also a consultant to no less than 20 firms.
  • With the publication of Microarray Analysis, he has published three books including Microarray BioChip Technology (2000) and DNA Microarrays, A Practical Approach (1999).
  • Research interests include: microarray analysis, gene expression, genomics, diagnostics, genetic, screening, neonatal testing, transcription factors, nucleic acids, biochemistry, human genetics, surface chemistry, and model organisms.
  • His most recent speaking engagement was at Beijing University, Beijing.
  • Co-author of “Quantitative monitoring of gene expression patterns with a complementary DNA microarray,” Science 1995, regarded as the first paper on microarray analysis.

Mark, some call you the father of microarray analysis. What do you think of that title?

It’s better than being the mother of microarrays.

I’m holding in my hand, a hefty 630-page hardback, the textbook, Microarray Analysis, hot off the press from the publishing house, John Wiley & Sons. This would appear to be the first textbook for a class on microarray analysis. When did you finish writing it, how long did it take, and how did this come about?

I finished the editing process about six weeks ago. It took a year and a half to write it. The senior life sciences editor contacted Paul Haje (TeleChem/Arrayit.com) and they put things together. They felt that the field was evolving so rapidly, and they were getting requests for a textbook, that they wanted someone to do it quickly.

We had a deadline to finish by the beginning of September and it took some terribly intensive editing steps. I won’t write another textbook again. I’ll do updates and future editions for sure. I’m committed to Microarray Analysis as a project, but the amount of energy required to do a book de novo, it was just a completely overpowering force in my life. I won’t have the time to devote to this in the future. To take a year or two off to focus on a book, logistically, it just won’t happen.

Is this book a document or a snapshot? What kind of an approach did you take to do this?

The content is foundational, most of the book is going to be as relevant a hundred years from now as it is today. The concept of a textbook has acquired a little more meaning for me, just because there is a huge amount of information out there and it was not clear how to organize it or place it into context at the beginning.

I took a methodological approach rather than a technological approach. I tried to build the foundation based on the fundamentals and concepts rather than building on the flavor of the day.

Who is the book designed for? What level course would be taught with this?

I suspect 201, maybe for juniorlevel undergraduates and then beginning graduate students. I took a number of graduate-level courses as a junior. The book was written for undergraduates. It has an undergraduate-level focus, and the difficulty factor is undergrad, early graduate level. I’m hoping that it will be broadly used, and, hopefully it will have broad appeal to students, clinical people, and folks from other areas, business or law or IT or whatever. We would love to have the book used to teach a course in this area. In writing it, I tried to be as even-handed as possible.

So, now that you are done, are you going to retire to a ranch in Arizona?

I don’t think so. But, believe it or not, I think over the next five years, I’m going to make a million bucks on the book. But, remember, in California or New York, that’s not that much. It will buy some niceties.

Can you ‘crystal ball’ about the field of microarrays for me? Let’s talk about standards.

Developing reasonable standards is an issue as the technology begins moving into the medical and clinical area, in conjunction with regulatory agencies like the FDA. They are also important for trying to establish the platform as a widely-used one that is worth the people’s investment of time and money, in terms of developing technologies for the field. We are trying to do those things, getting together with the FDA and discussing the technology, which is something I’m doing every few weeks. They are genuinely interested in microarrays, but they are not certain what the technical issues are and what the standards should be in terms of approval of these products for use in genetic screening, testing and diagnostics, and that’s what they are trying to assess by meeting with various luminaries. They are trying to understand the technology, its strengths and limitations, and figure out what the approval process should be for the use of the technology in diagnostics and the assessment of the safety of drugs and other things. [These are] two really key areas they are interested in.

This is a market that is expected to double, or triple, in the next five years or so. Do you think the influx of big money will change things?

What is going to happen is that the size of the field is going to increase by an order of magnitude. What is happening is that the technology is making a transition from a research tool to a diagnostics tool. When that happens, the size of the market is 10 to 100 times the size of the current research market. So, if you look at just the CLIA clinical testing labs that’s 170,000 labs in the US, so it’s easy to see that if the technology moves into the clinical realm, the size of the field will increase dramatically. Because of that, it is attracting companies that wouldn’t look at the life sciences otherwise. Agilent is looking at the life sciences and making products for this field. IBM is thinking about bioinformatics and computational issues, Texas Instruments is contributing technology. Large corporations are taking a look at this field and microarrays are just one focal point of that, so we think the involvement of major players is going to be key to insuring the viability of the technology for widespread use. That’s not going to be at the expense of researchers, it’s going to be just the opposite. The better the tools, the more robust the research and the more powerful the questions that can be asked of basic researchers. It’s going to increase the quality of basic research in small laboratories.

Can you see a division between the US and Europe and markets like Asia?

Over the year, we have done some workshops internationally. What has been impressive has been the rapid proliferation of the technology internationally, in western Europe and Asia, China, Taiwan, and Australia as well. The vast majority of publications are from labs in the US But nine other countries have contributed at least 1 percent of the publications in microarrays. [These] include the UK, Japan, Germany, France, Finland, and China. So, there have been contributions from a lot of different geographical areas, an indicator of the general recognition of the technology that can be used to address a bunch of different problems. Specific technologies that already exist, semiconductor or otherwise, can be brought to bear on the life sciences. If you visit the People’s Republic of China, you can be impressed by the technology, which is quite advanced. They are taking micro- and nanotechnology very seriously. You see a lot of labs in Beijing and Shanghai working pretty inten sively in this area.

Do you think this technology will converge on one platform?

I think that what we are seeing right now is kind of interesting. We are trying to find a two-part emphasis in terms of the technology platform. There are proprietary or closed platforms from people like Affymetrix and a proliferation of open platforms, nominally, in the microscope slide format. Companies and researchers are publishing and inventing in each of those two categories. We have seen very little consolidation and dramatic expansion in terms of different technologies, surfaces, assays — DNA, proteins, antibodies, carbohydrates, small molecules. We have also seen a rapid proliferation of instruments to read the devices. In five to 10 years, I’m not sure I have an idea of what that landscape would look like. It could become increasingly complex, or a really large player like a Microsoft, an Oracle, or an Agilent would purchase the technologies and develop a universal use platform. An exponential expansion in terms of tools is likely to continue for a number of years.

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