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Friday, September 26, 2003

It's a Dog's World

I guess by now everyone's seen the 'dog didn't eat my homework since I'm partly the dog in question' story. Well Abiola has been reading around and has a rather different take on this:

The New York Times is a great source of general news, but when it comes to science reporting, I usually find its' coverage rather lacking. In consequence, on hearing about the announcement of a draft sequence of the dog genome, I thought it best to turn elsewhere .

There are two things I feel a need to point out about this announcement. The first is that what is being announced is really only 1.5x shotgun coverage of the canine genome, which is really very little. By way of comparison, the fugu genome has been covered to a depth of 5.7x, the mouse genome achieved 7x coverage in 2002, and the finished version of the human genome achieved 8-10x coverage for each chromosome.

The minimum level of shotgun coverage usually required to call a sequence "draft quality" has been at least 3x; given that not even this much has been achieved, why the rush by The Institute for Genomic Research to publish? By their own admission, the assembled sequence so far consists of a massive 2 million fragments covering barely 80% of the canine genome, and it's safe to bet that a substantial proportion of that will be contaminated by bacterial sequences arising from the BACs* used in sequencing. Let's just say that this looks more like another Venter-inspired publicity stunt** than a truly headline-worthy milestone. I expect that once again, the really newsworthy developments will come from a non-profit organization - this time, from the Whitehead Institute, which has already completed a draft sequence of the chimpanzee genome with 4x coverage.

*Bacterial Artificial Chromosomes.
**Something similar occurred with the supposed "race" between Venter and the Human Genome Consortium to create a draft of the Human Genome; it transpired that, far from utilizing some miraculous shortcut unavailable to plodding public researchers, Venter's team was only able to assemble it's shotgun-produced sequences by leaning heavily on the detailed maps so slowly and carefully laid out by the HGC.

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