{bio,medical} informatics
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CNN
Scientists question fruitfly genome accuracy"Scientists in the United States Wednesday questioned the accuracy of the fruitfly genome sequenced by Celera Genomics, saying there are numerous and significant discrepancies."
" "It turns out that more than 50 percent of the sequences that were previously known disagree substantially by more than one percent (with Celera's)."
Karlin and his colleagues' comparison showed that about 26 percent of the genes from Celera's fruitfly genome were a perfect match with the database information. Another 29 percent were nearly perfect but 45 percent had mismatches, insertions or deletions."
"Karlin claims there could be worse errors in both the public and private versions of the human genome. "Everyone was rushing," he says."
"Meanwhile, Karlin warns researchers to take care if they're studying any "new" genes revealed by Celera. "My advice is to do whatever part you're working on again," he says. His analysis reveals the perils of relying too much on computers, Karlin says. "People are trying to get away without doing experiments.""
"Gerald Rubin, the University of California at Berkeley geneticist who worked with Celera on the fruit-fly sequence, said the discrepancies are well known, and getting half of the proteins right is comparable to a baseball player hitting .500.
“I take that as a compliment. If you had said beforehand that this was the number, I would have said Celera should get a gold star,” Rubin said. He also said that nine out of 10 discrepancies found by Karlin stem from errors in the Swiss database, not in Celera’s work."
"Celera president J. Craig Venter has dismissed the criticism of his company's work.
"There's two ways to get ahead in science: One is to do something significant, and the other way is to criticize someone who has done something significant. We've chosen the former, some of our critics have chosen the latter," he said last week.
Larry Thompson, a spokesman for the National Human Genome Research Institute, which helped fund Celera's fruit fly work, said Karlin's findings were not surprising.
"They did a pretty good job if half of it is right the first time around," Thompson said."
"Karlin said he set out to indicate the dangers of rushing publication of sequenced genomes. “Since they knew about the errors, they should have spent maybe another six months resolving these differences, but they wanted to get the genome published,” he said.
Karlin added that he has spoken to a number of Drosophila researchers, “and they’re sort of split. Half of them think it’s a very good thing to have the genome as early as they have it and they’ll worry about how to use it, and the other half are saying it’s a very good thing to have these cautionary articles to make them aware they have to be more careful.”"
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