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Experts Assess Progress and Challenges After a Decade of Human Genomics

By Andrea Anderson

NEW YORK (GenomeWeb News) – A decade after first sequencing the human genome, researchers are taking stock of the progress made in genomics and the challenges that remain.

"There were a lot of pretty wild statements in 2000 about how this was going to revolutionize medicine overnight," National Institutes of Health Director Francis Collins told GenomeWeb Daily News.

Ten years on, Collins said, the human genome sequencing effort still promises to be one of humanity's most significant scientific achievements. Even so, he explained, the full potential of the accomplishment may not be realized for years or even decades.

In a series of opinion articles appearing online today in Nature, Collins, Craig Venter, and others described the race to sequence the human genome, developments in the field over the past 10 years, and the approaches needed to understand and apply information in the human genome down the road.

In the first of these articles, Collins, who led the public human genome sequencing effort, outlined what he sees as five main lessons from the last decade.

In particular, he emphasized a need for open access to genome data, technological developments to facilitate continued genomics progress, studies aimed at finding genetic and environmental risk factors for disease, public-private partnerships for developing targeted treatments based on genomic data, and appropriate policies to support genomics research.

While some clinical applications of genomics have been slow, Collins noted, progress has been made in finding genetic variants tied to disease. In addition, steps have been taken towards using genomic and genetic information to develop drugs and target existing treatments.

He also highlighted the dramatic drop in DNA sequencing costs and subsequent rise in genome sequence data for a host vertebrates, invertebrates, plants, fungi, and microorganisms as well as the advent of large projects to explore population genetics and genomics (such as the International HapMap and 1000 Genomes projects) and regulation of the human genome (such as the Encyclopedia of DNA Elements and the NIH's Roadmap Program in Epigenomics).

Although there's a way to go before the genome revolution lives up to its clinical promise and improves health care for the general population, Collins explained, researchers now have a better appreciation for the complexity of the human genome, the importance of non-protein coding regions, and more.

Touching on his own experiences with direct-to-consumer genetic testing, Collins called it "rather riveting" to be able to explore his own genotype data, "despite the limited clinical validity and utility of many of these predictions."

"The promise of a revolution in human health remains quite real," Collins wrote. "Those who somehow expected dramatic results overnight may be disappointed, but should remember that genomics obeys the First Law of Technology: we invariably overestimate the short-term impacts of new technologies and underestimate their longer-term effects."

Researchers now have an opportunity to begin capitalizing on genomic information, Collins said, especially in terms of "targeted, rational drug development" based on genes and pathways identified through discovery-based studies. He predicts improved individual disease risk prediction within the next three to five years as sequencing costs continue to decrease and researchers parse out the roles of common and rare genetic variants.

"Genomics has had an exceptionally powerful enabling role in biomedical advances over the past decade," Collins concluded. "Only time will tell how deep and how far that power will take us. I'm wiling to bet that the best is yet to come."

In his own opinion article, Venter touted the public-private race to sequence the first human genome as a driving force behind some of the technological improvements used in genomics research today.

"Today, thanks to innovation inspired in part by the race for the first draft between my company Celera Genomics, then in Rockville, Maryland, and the public effort led by Collins, it is possible to sequence a human genome in a day on a single machine for just a few thousand dollars," Venter wrote.

Nevertheless, he cautioned, a great deal needs to be done before researchers will fully understand the human genome and routinely apply genomic information in a clinical setting.

"The challenges facing researchers today are at least as daunting as those my colleagues and I faced a decade ago," Venter noted, arguing that more research is needed in a range of areas — from linking genomic information to phenotype to unraveling the extent and consequences of human genetic variation.

"The experiments that will change medicine, revealing the relationship between human genetic variation and biological outcomes such as physiology and disease, will require the complete genomes of tens of thousands of humans together with comprehensive digitized phenotype data," he wrote, noting that such an effort would require improvements in computational infrastructure.

Meanwhile, in another pair of opinion articles in Nature, Todd Golub, director of the Broad Institute's cancer program, and Robert Weinberg, a biology researcher at the Massachusetts Institute of Technology and founding member of the Whitehead Institute for Biomedical Research, discussed the role of genomics in cancer research.

While Golub focused on the use of genomic information for understanding pathways involved in cancer, finding new drug targets, and using existing treatments more judiciously, Weinberg cautioned against neglecting hypothesis-driven research in favor of large-scale genomics projects.

For his part, Collins agreed with the need to balance hypothesis-based studies by individual researchers with community level genomics studies. But, he said, such studies can co-exist and complement one another, with large-scale community resource studies providing tools that can aid individual researchers.

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