Friday, 29 April 2016

SPRI alternatives for NGS

SPRI beads, generally in the form of AMPureXP beads, are almost ubiquitous in genomics applications such as library prep for NGS. The most popular thing I've ever written was a post on this blog four years ago: "How do SPRI beads work?" with almost 100,000 readers - people obviously want to understand how this wonderful technology can be used. They'd also like it to be cheaper as the Agencourt AMPureXP product (now Beckman) is somewhat expensive - so I've taken a look at some of the alternatives on the market, including DIY SPRI!


Alternatives to AMPure XP: There are several companies making products that work in the same way as AMPure XP. How good they are I do not know; although we've considered testing them in the past, we are generally happy with the AmPure XP product, also a lot of our beads come packaged in Illumina's library prep kits anyway. As most labs only use a relatively small amount we've bought in the big bottles and aliquot them out to make things more cost-effective. Maybe we'll get round to making our own one day?
  • It would be unfair to start discussing alternatives without listing the AMPure XP from Beckman. It is the most widely used and often appears as an OEM component in NGS library prep kits.  The workflow is efficient and easily automated which can be a real boon to labs doing lots of cleanup.
  • AlineBiosciences has the PCRclean-dx kit and say it is a "superior Ampure XP alternative...with a fraction of cost."
  • Promega's DNA-IQ system is designed for forensic and paternity laboratories, but uses paramagnetic beads to isolate clean DNA for use in STR analysis.

DIY SPRI anyone: OpenWetWare has a very well written method to make your own beads by Joseph Foley (McGill University) and Philippe Jolivet (Université de Montréal). They recommend the carboxylated Sera-Mag Magnetic SpeedBeads from GE Healthcare LifeSci. They point out that you must adhere to the mixing instructions very carefully, and describe why addition of Tween 20 helps - it stops DNA sticking to your Eppendorf (but I'd also recommend the use of low-bind tubes where possible). They also list instructions for the binding buffers (DNA & RNA) on a separate page so users can make these to adjust the conditions of reactions without adding more beads.

The MolecularEcologst points SPRI users to the Genome Research paper that describes a home-brew SPRI-clean-up (also using SeraMag Speed Beads). He very helpfully posted a gel image comparing his home-brew mix and AMPure XP.


From: http://www.molecularecologist.com


Lastly the Just-a-Plate PCR purification tech from CharmBiotech dispenses with magnetic beads entirely. There Solid Surface Reversible Binding (SSRB) technology uses  96 well plates coated with SSRB chemistry to bind amplified DNA directly from PCR reactions.

Hopefully you took the pop up poll that appeared when you came to this page...if not please do let me know which SPRI technology you are using by answering the poll now?

4 comments:

  1. What about NucleoMag NGS Clean-up and Size Select from MACHEREY-NAGEL ?

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  2. Added...thanks for the feedback.

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  3. HighPrep PCR form Magbio is another alternative

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    Replies
    1. We use HighPrep PCR form Magbio too

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