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Waterston, Lander Confirm Importance of Whole Genome Shotgun for Mammals

COLD SPRING HARBOR, NY, May 7 - About 30 seconds after Bob Waterston presented the opening paper at Cold Spring Harbor Lab's 2002 Genome Sequencing & Biology meeting here tonight, a participant seated in the front row motioned for a microphone and spoke:


"It seems to me that you have proven that whole genome-shotgun strategy can work on mammalian genomes, and that this is a pure whole genome-shotgun strategy," the participant, still seated, said in a heavy Australian accent. He was referring to Waterston's presentation that outlined the draft mouse sequence performed by the Mouse Genome Sequencing Consortium and the Mouse Genome Analysis Group and dumped into Genbank last week.


Waterston, who two months ago was the a co-author of a letter published in PNAS charging that Celera Genomics' whole genome-shotgun methodology leaned too heavily on public data, paused for a second and smiled sheepishly.


"I think it's a fair comment that you can get a draft sequence of high quality for a mammalian genome [using whole genome shotgun], and I presume it can be done on other genomes," Waterston conceded. "But this [mouse sequence] still is a draft."


From a corner at the front of the auditorium came a booming addendum to Waterston's reply: "I think what this shows is that you can start a genome using whole shotgun and get quite far," piped up Eric Lander, whose loud voice, the butt of a mild joke earlier in the evening, defies artificial amplification. "But if you're going to finish it, I think you're going to have to do something else."


Sometime later, Waterston, the Washington University scientist, said that this sequencing project would be finished through individual BAC clones while incorporating data from the whole genome-shotgun approach. "Subclone-library construction and BAC sequencing is currently underway," according to his team's abstract.


These exchanges will likely become familiar--indeed they might already sound familiar--as the conflict between profit and scientific piety grows. Even the cover of the meeting's abstract book manages to take a shot at genomics' moneyed class. It depicts a colorful drawing of DNA's fictitious journey from a mine beneath a tropical beach above which surfers, helped along by double helixes, ride waves near a pair of black sharks whose fins are emblazoned with white dollar signs.


After a reporter showed an attendee the cover and pointed out that at least 40 corporations sponsored the meeting, one attendee who asked not to be named remarked: "Bloody typical."

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