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Collins Says Bioinformatics Is Key Support For the House that Genomics Built

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Flashing an architect’s watercolor rendering of a Frank Lloyd Wright-style home, Francis Collins last week offered an early look at the National Human Genome Research Institute’s future role following the completion of the Human Genome Project in April.

The image represented a metaphorical three-story building that rests upon the foundation of the Human Genome Project. The first floor consisted of “genomics to biology” (basic research), the second “genomics to health” (medical applications), and the top floor “genomics to society” (non-medical applications and ethical and social issues) — each one of the broad goals the institute has set out for itself in the coming years. In addition, the building contains six vertical supports that cut across each floor, representing their importance as enabling elements, Collins said. Computational biology is one of these key pillars, Collins noted, along with ELSI (ethical, legal, and social isues), education, training, technical development, and resources.

This blueprint, which Collins laid out during his keynote address at the Bio-IT World Conference and Expo in Boston, amounted to a plan for “the next phase of genome research,” first hammered out in November during a meeting of 180 scientists hosted by the NHGRI at Airlie House in Warrenton, Va.

A peer-reviewed paper describing the NHGRI plan in detail is scheduled for publication in mid-April, Collins said, but in the meantime, he was able to share some of the “grand challenges” that each of the three segments will tackle over the coming years. Computational biology will certainly play a major role in the first two areas, he said, noting that newly launched initiatives such as the international haplotype mapping project and the Encode (Encyclopedia of DNA Elements) project already provide prime opportunities for bioinformatics innovation.

In the case of the HapMap project, he pointed out that there is still “no computational way to know where the boundaries of haplotype blocks are,” extending a challenge to the “computational types” in the audience to develop such a method.

Collins was particularly enthusiastic about the computational aspects of the Encode initiative, which will soon begin evaluating a number of functional genomics technologies against a 30-megabase region of the human genome to determine their effectiveness in detecting protein-coding genes as well as non-protein-coding genes, regulatory regions, and other functional elements.

In terms of other IT challenges, Collins noted that it will be crucial to find new and better ways of storing and manipulating data sets of a terabyte or more. More importantly, he said, new developments in hardware and software will be required to handle cross-comparisons of hundreds of vertebrate sequences. “I’m a little bit worried about that one,” he confessed.

The “genomics to society” level of the NHGRI house won’t rely so heavily on technological innovation or science and, perhaps for that very reason, promises to be a bit more challenging than the first two areas. Collins noted that many of the issues that must be addressed before genomics research can proceed are out of NHGRI’s hands. For example, he noted with obvious frustration, a genetic discrimination bill has been languishing in Congress for six years. While the scientific community is able and willing to determine an ethical course of action, “we don’t have the ability to sit a member of Congress down and tell them what’s good for the American public,” he said.

— BT

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