Last week, CDC director Thomas Frieden gave an interview where he asked for $40 million to set up a genomics center at the CDC, since the CDC currently has no sequencing capability (though, as you’ll will, Frieden seems confused about this). While some on the Twitterz were shocked by the price tag, that doesn’t seem so far fetched. If you were building this from scratch, including additional floor space (i.e., adding on to a building), I think that’s a pretty reasonable sum, especially if one had plans to do lots of sequencing. Remember that there’s no university that will kick in a building or faculty whose salaries are already covered. They’ll need bioinformatics expertise and computational architecture (really, they don’t have this sort of stuff despite what you see in the movies. Hollywood is really good at propaganda).
So the $40 million wouldn’t be a problem. But this is what bothered me (boldface mine):
The problem hampered the CDC’s investigation of the cholera outbreak in Haiti after the 2010 earthquake. The agency was forced to send its samples to Canada for testing.
FRIEDEN: We were able to sequence the genome, but to actually interpret it, we had to send it out of the country to be done, and I never want to have to do that again as CDC director.
This makes no sense to me. So now CDC does have sequencing capacity, but there’s no capacity in the U.S. to “interpret” genomic data? Let’s say they doneed some new facilities, more personnel, and space. But in 2010, NIAID alone funded three microbial genomics centers, plus there were many other labs in the U.S. with experience in genomic analysis. The USDA is also doing this sort of stuff. But they had to go to Canada? More disturbingly, the CDC apparently thinks, that in 2013, they still need to work outside the U.S.
While I’m not surprised that one part of the federal government is absolutely unaware what other parts are doing* (note for the non-U.S.-ians: this also explains much of our foreign policy we inflict upon you), this is ridiculous. I know for a fact that at least one NIAID microbial genomics center has now drilled (successfully) rapidly sequencing and analyzing a small number of genomes, so this capacity already exists. One would think in this funding environment that the agencies would attempt to work with each other. If CDC wants to make the argument that redundancy in our genomics-based response to disease outbreaks is a good thing, that’s fine (always good to have backups, and MOAR GENOMIKS JOBZ!). But this sounds a lot like inter-agency rivalry.
*About a year ago, I was at a meeting about international genomic surveillance with a bunch of agencies and the Danish government, and at least three (possibly four) different U.S. federal agencies (none of which were NIAID) gave self-congratulatory talks about reinventing the genomics sequencing and analysis wheel. And those wheels were kind of squarish. So of course, in 2014, the groups that NIAID are funding, and have the most experience, are seeing their budgets cut. Because that makes sense.