Life Science Tools of the Trade

I’ve spent considerable amounts of time here, elsewhere on the Science Advisory Board, and in a few other places, writing about so-called “next-generation” sequencing. While some vendors are already shying away from this “next-generation” moniker, it’s a good enough catch-all phrase for now, I think. Anyway, most people seem to know what it means.

The currently available technologies include the Illumina (née Solexa) Genome Analyzer II (replacing the flaky Genome Analyzer), the Roche (née 454) GS-FLX (replacing the original GS20), and the Applied Biosystems SOLiD (still in its initial release). There’s also the Helicos HeliScope, which as far as I can tell is kind of like the mythical white elephant, or the Loch Ness Monster – many agree that it exists, but nobody’s ever seen one.*

Jumping in to this game rather cautiously, we ran a very unreliable GA for a while, and after considerable beating up on it have obtained some very nice data (in particular, for some ChIP-seq experiments, where the miniscule 30-ish base reads from this instrument are ideal). It’s now in the process of being replaced by the GAII, and for the time being both are co-existing on the same bench.

Spot the difference.

But, not to fall prey to the single technology trap, we’ve also added an Applied Biosystems SOLiD, which is currently being installed. Here it is with its doors open (look away, children).

This sequencer photo is rated PG-13 for partial nudity.

And, just to make sure that our bases are completely covered, we’re also ordering a GS-FLX, since it seems there will be quite a lot of genome-sequence backfilling in our future, and the long reads (with reliable paired-end capability) should do the trick.

Fun and games. Our old 3730xl capillary sequencers would be feeling sad, if they weren’t so darned busy screening for mutations and making sure everybody’s plasmids are what they’re supposed to be.

A few years ago, this NGS stuff all seemed like voodoo. Now it’s here, and, like any good scientists, we’re itching to play with it. Good times.

*I have shamelessly stolen this analogy from a colleague. It can equally well be applied to the results of certain experiments that are supposed to have been done around here.

The lab budget and the books are my boss’s job. I just try to keep the lab stocked and the supplies ordered for the lab. That said, I shop around a bit and buy when items are on sale. Most of our lab supplies have stayed pretty constant through the years. Restriction enzymes, tissue culture supplies, chemicals, the prices on these *old* lab items haven’t changed much and they’re not that expensive.

What I am noticing is the expensive price of all the *new* supplies. The RT-PCR reagents, the deep sequencing supplies, the modified oligos, FACS analysis… those items are pricey! The control for the RT is a couple hundred. The oligos a few hundred. Is it the new technology or the times dictating the prices? I’m not sure. It does make me wonder though how some labs can afford to do these experiments. I’m assuming the price will eventually come down on these items. In the mean time, I wonder how many experiments aren’t performed because the cost of doing them is just too high for the lab.