Illumina/McDonald’s dollar menu
Researchers are thrifty. We’re always looking for ways to make our expensive supplies and reagents go the extra mile. This shit has been going on for decades – hell, probably even centuries: I remember when I was a kid and my dad paid me $0.10 for every box of pipette tips that I re-filled by hand (attn: Child Services – this is way below minimum wage).
Well, hold onto your britches bargain-whole-genome-sequencers, because there’s a new preprint that’s just for you!
“tagmentation” using Illumina’s Nextera library prep kit (from: illumina.com)
Nextera library
Illumina’s Nextera sample prep kits are my kind of protocol. You basically skip all of the foreplay (shearing, end-repair, A-tailing, and extra cleanups) and get right down to the good stuff: adaptor ligation, PCR, and sequencing. In order to do this, the Nextera kits use what is called “tagmentation”, which is where a transposon simultaneously fragments and “tags” your DNA with sequencing primers (and then you do a few PCRs to add the adaptors). Because of the reduced number of steps and reaction cleanups, there are two major benefits of the Nextera kits: 1) You can start with a much smaller amount of template DNA – as low as 1ng!!! 2) The whole prep takes about 90 minutes – which saves you on the most expensive of all expenses: SALARY! There is, however, one major downside: Cost…. Until now
The $8/sample Nextera ‘hack’
Baym et al published a modified Nextera protocol that brings the cost per reaction down from ~$50 to ~$8 per sample. The gist of it is that they use about 1/10 of the recommended amount of Nextera enzyme (the expensive stuff) per reaction. Importantly, they found that this economical approach does not negatively impact the diversity of the sequencing library. In other words, you get the same breadth of coverage across the genome as you would as if you used more input material and reagents.
So far, this bare-bones protocol has only been tested out on smaller genomes – those ranging up to ~5 Mb. So if you study an organism with a small genome, then this is the protocol for you! On the other hand, if you, like I, study organisms with larger genomes, then you might need to tinker with the protocol to get it to sing quite as nicely as the authors did here.
Until then… happy sequencing!
REFERENCES
Baym M, Kryazhimskiy S, Lieberman TD, Chung H, Desai MM & Kishony R (2015) Inexpensive Multiplexed Library Preparation for Megabase-Sized Genomes, Cold Spring Harbor Labs Journals. doi: http://dx.doi.org/10.1101/013771