Monday, 25 March 2013

Making NGS greener

Does your lab look like this? We get most of our deliveries on dry-ice shipped from European distribution centres. All the polystyrene and dry-ice are the tip of our energy consumption iceberg. Genomics sciences have as much environmental impact as just about everything else, and perhaps quite a bit more than other disciplines.





Our sequencers consume lots of power and are often running 24/7/365. Labs have lights and incubators left on and fridges and freezers to store all our reagents in. I'd like to hope that many of the readers of this blog are trying to reduce their impact on the environment. We're trying to do our bit, but what can the companies we use do to help? A big disincentive is the relatively low cost of shipping compared to what's in the box; dry-ice is cheap. But one company has made a significant step in the right direction.

Enzymatics room-temp NGS kits: A big advance was recently released by Enzymatics, their latest next-gen library prep kits are now room-temperature stable. This means the lyophilised reagents can be shipped and stored without expensive and energy-hungry dry-ice. The website is a little light on details for now but you can test a free 8-sample kit.

GenomeWeb carried a brief news article where Enzymatics said "the room temperature- kits feature [QC tested] lyophilized reagent mixes" and that "lyophilization enables the kits to be stored at ambient temperatures, eliminating the need for dry ice shipping, freezer storage, and lab bench ice buckets". Kits are currently available for Illumina platforms, Ion Torrent and Proton kits are coming soon. With the number of labs using library prep reagents the impact of moving over to room-temperature could be significant. Ideally we'd see more and more of the basic sequencing chemistry from Illumina, Life and Roche. 

Are enzymes stable at room-temp: There has been little change in the delivery of restriction-endonucleases for the past thirty years. Keep them cold is the mantra!

In 2000 a group from Scotland and Tanzania showed that minimal reduction in enzyme activity was seen even after 12 weeks storage at 37C. HindIII, NarI, EcoRI and a total of 23 enzymes were all stored at 4C (rather than the recommended -20) for up to 1 year showing almost no loss in activity. To demonstrate the stability of enzymes the group posted enzymes to Africa by snail-mail rather than normal cold-storage courier. All enzymes had normal activity upon arrival after three weeks in transit making the supply of enzymes to third-world markets much simpler. And having implications for the way we ship reagents in Europe or the States; normal postage and storage in a standard lab fridge. Read the paper, Extended Stability of Restriction Enzymes at Ambient Temperatures, BioTechniques 2000 29:536-542. See figure 1 from the paper below.
Figure 1: Extended Stability of Restriction Enzymes at Ambient Temperatures
BioTechniques 29:536-542 (September 2000)
In a 2003 BioTechniques paper Jim Youngblom from California State University showed similar results with T4 DNA ligase. See Extended stability of Taq DNA polymerase and T4 DNA ligase at various temperatures in Biotechniques 2003 Feb;34(2):264-6, 268. 

And in 2007 David Ng at Science Blogs posted about the issue describing molecular biology reagents that can survive difficult transit conditions.

Perhaps Enzymatics lead in this issue will spur other manufacturers to put some effort into making room-temperature or at least just wet ice shippable reagent kits. At least we'd have less to clean up after the next delivery!

4 comments:

  1. Tip of the iceberg, indeed. Considering at the full NGS workflow, you've got cell culture and/or sample storage on the frontend: incubators, refrigerators, freezers. Then post-sequencing analysis on the backend: computers eating up electricity, including the ephemeral-sounding cloud (http://www.nytimes.com/2012/09/23/technology/data-centers-waste-vast-amounts-of-energy-belying-industry-image.html).

    The good news is that economics should drive people in the right direction. Here's a case where what's cheaper is also what's more environmentally friendly. It's great when those two align.

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