IN THIS MONTH'S GENOME TECHNOLOGY: New Breed of Genomics Centers Works Disease-Down, Not Genes-Up
By Meredith Salisbury, Genome Technology managing editor

NEW YORK, Aug. 13 (Genome Technology) - Sometimes it feels like there's a new one sprouting every day. You know what we mean: the Cancer Genomics Program at the MD Anderson Cancer Center, part of the University of Texas. Johns Hopkins University's Program in Applied Genomics for cardiopulmonary disease. Stanford's Asian Liver Center, using genomics to study liver cancer among Asians.

Everywhere you turn, there's a new center relying on functional genomics to study one particular disease or group of diseases. What happened to Lesson Number One in genomics history: the soup-to-nuts mega-institute shall always prevail?

As genomics matures, it looks like things at NIH are heading back to business as usual: funding allocated for specific disease research, and genomic scientists - well, really, anyone looking for grant dollars - are finding ways to apply genomics to any range of diseases, rare or common. Elias Zerhouni, NIH director, told his audience at the AAAS meeting this year that he aimed to support the growing trend toward disease-specific research.

And why not? Such specific centers seem more likely to get funding from illness-based foundations: a skim of places like Alzheimer's Association; FRAXA, the Fragile X Research Foundation; and the Cystic Fibrosis Foundation show that they're already putting money toward genomic studies in their fields. That will certainly help make NIH's dollar go a little further, and give more researchers the chance to work on these diseases.

It's too early to tell if the trend is a good one. But there are obvious concerns about having these little centers working independently on particular diseases. Duplicated efforts are costly, and small institutions often don't have the resources (large sample banks, for instance) to really come close to solving any given disease. A potential solution comes from Lesson Number Two from genomics history: the consortium model may save everything.

Time Is Right

Zerhouni may be backing the trend, but that's no indication that other types of research centers won't get funded, says Alan Guttmacher, NHGRI deputy director. "We're early in this. It makes sense to support different kinds of models," he says.

But some argue that the time is right to try out this kind of initiative. "We're starting to come into an era where a lot of what we know about genomics can be applied to disease," says David Bowtell, director of research at the Peter MacCallum Cancer Genomics and Genetics program in Australia. "It's quite reasonable to take a disease focus."

Finding Focus

Guttmacher was hardly surprised by Zerhouni's announcement this year. "NIH has always supported disease-specific centers," he says. That's encouraged, naturally, by the institutes' disease-specific identities. "In some ways, this is just applying genomics to that kind of framework."

And NIH tradition certainly has its value, points out David Altshuler of the newly formed Broad Institute, which houses the Whitehead/MIT Center for Genome Research. "Biological and medical research have done extremely well in what has become the traditional model of biomedical research," he says, adding that NIH funding history has contributed to "the most successful [scientific] enterprise in the world."

Aside from their goal of making progress toward a particular disease, research at any of these centers could prove key to myriad other health applications, Guttmacher points out. He recalls as an example a small study on familial hypercholesterolemia - designed to examine just that particular single-gene disease - which recovered so much information about the cholesterol pathway that it led to the discovery of statins, "one of the most widely used class of drugs in the country" for people at risk of various cardiovascular diseases. Even very narrowly focused biomedical research "tells us something about basic biology," Guttmacher says.

"The concept can work if it's a really integrated center," says Michael Liebman, director of computational biology at the Abramson Family Cancer Research Institute at the University of Pennsylvania. He likes the disease focus because it makes more sense from a clinical standpoint - starting from the disease and its effect in patients and stripping that down, layer by layer, to understanding "how genomics and proteomics can help differentiate between subtypes of disease" - than starting with genomics and working up from genes.

The sense of excitement about these kinds of centers doesn't hide the evident problems with the model. Like the early days of genomics, pre-HGP, lots of small centers could eat up funding and never accomplish a sweeping gesture on the order of sequencing the human genome. "We have to be very careful that we don't duplicate things," says Bruce Stillman, director of the Cold Spring Harbor Laboratory and vice chairman of a National Research Council policy board that recently released a study on how to do large-scale biomedical research. "There is not the amount of funding that is needed [already]."

There's plenty of debate over how the new breed of genomics research centers should work - including a growing community who argue in favor of the consortium model established by the HGP. Hear from the head honchos at some of these centers to check out different approaches to the problem: we look at centers including the Abramson Family Cancer Research Institute, University of Pennsylvania; Asian Liver Center, Stanford University; Cancer Genomics Core Laboratory, MD Anderson; the would-be Cardiovascular Genomics Center, Boston Heart Foundation; and Peter MacCallum Cancer Genomics and Genetics to see how they're faring. Industry leaders such as Arthur Holden, CEO of the SNP Consortium, and Muin Khoury, director of CDC's Office of Genomics and Disease Prevention, weigh in as well. The full article appears in this month's issue of Genome Technology.