Posted 15th May 2001

Genes + Money = Danger

The revelations below highlights the need for increased scrutiny of the NZ Dairy Board's intention to give Celera considerable money for sequencing. This intention was announced by the Dairy Board chief scientist (chemical engineer Kevin Marshall) at the NZ Dairy Workers Union annual congress, Hastings 14 June 2000. He refused to give Bob Mann anything in writing, and has just recently acted hard-done-by, posing as wounded when his announcement is bounced back at him. He now denies any intention to pay Celera lots of money, but refuses to reply to Mann's detailed questions. The time is overdue for Dr Marshall to state clearly how much money he intends to pay Celera, which is evidently a dubious investment. More generally, it should be widely known that Marshall had Dairy Board permission to pay out $30M/year for five years of gene-tampering, within which his plan to pay Celera was some unstated fraction. Any further digging will of course risk investigation for un-NZ activities and subsequent use of that information against the investigator. Something I (Alan Marston - edit) have been subject to as recently as this year when current politicians and police employees cast aspertions in print and by phone conversation, attempting to compromise me in the eyes of people cooperating over the anti-snooping Swain Bill. And this despite never having been arrested let alone convicted of any crime except free-thought. New millenium, old rules.

From New Scientist magazine,
by Andy Coghlan

Celera, the company which shared the glory for sequencing the human genome in June 2000, now faces claims that its data may be riddled with errors. As many as half the company's gene sequences for the fruit fly may contain mistakes, says Samuel Karlin, a mathematician at Stanford University in California. His work suggests there might be many errors in other genomes that have been sequenced using similar techniques, he says. But others have defended the results. "I would take 50 per cent correct as a compliment, not a criticism," says Gerry Rubin of the US's fly-sequencing programme at the Howard Hughes Medical Institute in Berkeley. An update next yearshould improve its accuracy to 75 per cent, he says. Rubin was one of the coauthors when the head of Celera, Craig Venter, published the full sequence of the fly genome in Science in March 2000. The work was hailed as a vindication of the "pure shotgun sequencing" technique the company used, where copies of a creature's DNA are broken into little pieces and sequenced. Computers then assemble the full sequence by looking for overlapping fragments.

Gone missing

But when Karlin began to use Celera's fly genome, he spotted lots of errors. "More than 60 per cent of their sequences were in substantial disagreement [with known sequences], and this got me a little bit angry," he says. So he did a fuller analysis with his colleagues. They hunted through Celera's genome for 1049 fly genes whose sequence and function had already been worked out and carefully checked in experiments. Although 26 per cent of the genes were exact matches, and a further 29 per cent accurate to within 1 per cent, the remaining 45 per cent contained a range of moderate to serious errors - or were missing altogether. "We couldn't find a lot of the genes we were working on ourselves," says Karlin. Other errors included the omission of entire protein-coding segments of genes, or exons, while other genes had been "read" from the wrong starting point. Karlin claims there could be worse errors in both the public and private versions of the human genome. "Everyone was rushing," he says. But the public project relied on a slower, more accurate version of shotgun sequencing - and Celera ended up including a substantial amount of data from the public project in its version (New Scientist, 17 February, p 4).

Decades of work

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." Celera plays down the criticisms. "We never said that the fly genome was totally and 100 per cent complete," says spokeswoman Heather Kowalski. "Annotation and analyses of genomes can go on for decades." Karlin's work appears in Nature (vol 411, p 259). He initially sent his paper to Science but the journal didn't publish it. "They sat on it for five months," he says. .