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If you’re a regular reader of this site, there are some times when my university doesn’t come through for me, such as its reluctance to subscribe to Nature and Science. But there are other times when my university really shines, such as on Friday afternoon, when I visited the Joint Genome Institute’s Production Genomics Facility Joint Genome Institute - Production Genomics Facilityin Walnut Creek, California because one of my classes arranged a tour.

Aside from being one of the largest dedicated DNA sequencing operations in the world, the JGI’s Production Genomics Facility is remarkable because it is helping sequence the Neandertal genome. The specific JGI scientists, James Noonan, Doug Smith, Joe Alessi, Feng Chen, Darren Platt, and Edward Rubin along with others, published the first 65,000 or base pairs of the Neandertal genome last year in this publication, “Sequencing and Analysis of Neanderthal Genomic DNA,” and they continue to make some headway.

I didn’t get to meet Noonan and Rubin, unfortunately. But I did get to see their facilities and the methodology they use to sequence any genome. They use a tried and true method of sequencing DNA which involves shearing all the genomic DNA first. Then, they insert the fragments of DNA into vectors of various sizes. This creates libraries that are important for scaffolding which is a way of rearranging fragments into a genome once sequencing is done. The vectors are shocked into bacteria, who, after platting and incubating, replicate with the vectors inside. The bacteria grow into colonies which are picked and the vectors are removed. Another round, or 30, of amplification is done with PCR and the samplesare labeled with florescent dyes and cleaned up to be sequenced.

The DNA is loaded into machines to be sequenced via capillary electrophoresis. This is called the Sanger method which reads the florescently labeled DNA fragments. These fragments, of varying size, are reassembled like a puzzle. The overlapping pieces help piece together the puzzle just as one uses the edges of a puzzle to create a framework. Once that’s done, the genome is finished and annotated.

This is all done at the JGI’s facility in Walnut Creek. It’s a really breathtaking operation, not only because it’s all done in house but because it is almost fully automated. Once the genome is sheared up and inserted into vectors, machines basically take over. I was in the room full of the sequencers, the Sanger machines, and I was nearly floored with how amazing it was. Even the platting of bacteria is automated. The coolest thing was the machines that pick off the bacteria. The robots take a photo of the plate and determine the ‘right’ colony to be plucked. Then an arm with a bunch of needles delicately picks up the bacteria.

I did get to see the 454 sequencing machines, which they currently have two of. I’ve introduced 454 before, because they are playing a vital role in sequencing the Neandertal genome. 454 is really good at sequencing small fragments of DNA, something which the Sanger machines can’t do well. An experiment was being loaded up while I was there. I was shocked to hear each usage of the machine requires over $5,000 worth of reagents to complete.

Also in their new technologies department was a Solexa/Illumina sequencer, which is kinda of a competitor to 454. They both use massive parallel sequencing of millions of fragments, but the Solexa is more or less continuous. Each experiment with Solexa instrument creates over 1 terabyte of data. That’s a crazy amount! The informatics there must be inundated.

Anyways, I was completely enamored. The US Department of Energy really has a gold mine of an institute there. If you live in the area, or ever visit the East Bay area, definitely check them out. They give tours to the public and educate you thoroughly. They also send you off with a lot of schwag, which is always nice.

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