Wednesday, 15 April 2015

Should you buy a NeoPrep (or any other NGS automation)

Illumina launched NeoPrep at AGBT and Keith Robison at OmicsOmics wrote a detailed summary of what Illumina say the NeoPrep is capable of (he compared this movie of the electro-wetting technology to video games of his, and my, youth), I thought I'd write down my thoughts on how this instrument might fit into labs like mine and possibly yours too.



The main selling point of NeoPrep is that it provides a one-stop solution for NGS library prep. The price point is pretty good (around £30-35k), and speed and quality  looked great in the data presented by Illumina at AGBT (by Gary Schroth and Kevin Meldrum, Illumina have run over 5000 libraries so far); so is NeoPrep a good option for every NGS lab? There are a couple of limitations I'll return to in a bit - but broadly speaking I can see that this system really could be a good, even a sensible, fit for many many labs running NGS. In a core lab or heavy NGS research lab the NeoPrep looks like  it will take some of the worry out of NGS library prep. And even is a lab that only does a dozen or so NGS experiments per year, removing the worry that library prep will go wrong with precious samples might be enough to warrant a purchase.

Because NeoPrep can be run in such a hands-off way, and because the quality and reproducibility of data are reportedly high (although we'll have to wait for  user reports over the next six months for confirmation of this), then a lab that is spending PostDoc or PhD time making small to medium sized numbers of libraries might well buy a NeoPrep where they would never have considered purchasing a liquid handling robot due to their complexity. This means Illumina might have hit the nail squarely on the head on this instrument.

For Core Labs the ability to offer library preps with an Illumina guarantee of quality is likely to be a positive, and something customers might approve of. And as Illumina release more library prep methods for NeoPrep the instrument might be perfect for those things you rarely get asked to do.

The positives: If the hands on time claims of just 30 minutes for sequencing ready libraries are true then NeoPrep is going to save people time and that is probably our most precious commodity. Labs like mine like big projects and we tend to batch smaller ones together, this can mean a wait for users while other samples come in to fill a 96well plate. NeoPrep would allow us to run projects as small as 16 samples. Alternatively it would allow us to provide automation solutions directly to users, running NeoPrep as a bookable instrument in the core.

The price per library is attractive and Illumina are aiming for parity with manual kits (which could generate a "why bother" attitude to manual prep). The TruSeq Nano kit, comes in at around $30 per sample, and TruSeq stranded mRNA around $55. GenomeWeb quoted Illumina as saying "the "fully loaded cost per sample" using NeoPrep would be around $75 per sample, which includes the cost of amortization of the instrument...assuming 1,000 samples are run per year." Compare that to the real cost of a top-flight post-doc spending two weeks making libraries for one experiment!

Price is not everything, so also encouraging is Illumina's data on reproducibility which appears to be very good in the results presented so far; concordance of 0.97 between RNA-seq libraries of varying inputs (100ng vs 10ng, and even 100ng vs 2ng). And the NeoPrep is being touted as requiring less starting material, in fact Illumina recommends starting with 25ng to 75ng of DNA for TruSeq Nano which is several thousand genome equivalents. For TruSeq mRNA, they recommend an input of just 25ng. They also tested down to 2ng but reported some drawbacks, including a lower yield and increased numbers of duplicates. I do worry about biases in low-input experiments and we previously showed a drop in sensitivity, although not specificity, as RNA input dropped from 100ng to 10ng in Illumina HT12 arrays. I guess we should repeat this experiment with TruSeq RNA on NeoPrep!

The negatives: The most obvious problem is that you can only run Illumina reagents on the NeoPrep and whilst they are competitively priced some competitors are significantly cheaper. The range of library preps is also very limited with just DNA Nano and TruSeq stranded mRNA at the moment (GenomeWeb quoted Illumina as saying the "PCR Free kit, followed by a "steady stream of protocols" [would begin] in the second half of the year and including targeted resequencing panels"). I know I'd like to see Nextera exomes ASAP; and knowing a timescale for ChIP-seq and ribozero would be great.

There is a huge range of methods that have been developed to run on Illumina sequencer (download Jaques Retief's amazing poster with almost 150 apps), most probably only a handful of these will ever see the light of day on a NeoPrep. But many of them use steps in Illumina's core library prep technology (end-repair, adapter-ligation), so if NeoPrep could be configured by users we might be able to make it do what we want. As an example we've been making some RNaseH libraries with NEB kits for ribo-depletion, we did this by eluting the ribodepleted RNA from Agencourt RNAClean XP beads directly into the 19.5 μl of Fragment, Prime, Finish Mix in the Illumina TruSeq stranded mRNA kit, then we carried on with the protocol from "Incubate RFP" to make multiplexed RNA-seq libraries.

If it is unclear what else might come, and when, then making a purchase decision is tougher. Perhaps more important is understanding what methods Illumina can not migrate to NeoPrep, I suspect anything that needs a gel is going to be difficult.

Some of the library prep kits from other companies are way better than Illumina's for specific applications. This is not because Illumina can't make those kits (unless IP stops them), but is probably more a case of Illumina looking to see which markets are largest, and possibly which competitors they want to crush. If someone does something Illumina can't, or won't, do then we'll not be running that on NeoPrep.

My biggest concern with NeoPrep is that it is a black (and white) box so user's don't need to know what is going on under-the-hood; you could equally say my labs library prep services. I am a strong believer that you (we) need to understand the library prep technology to innovate and NeoPrep might reduce the likelihood of new users doing their homework. It could also be argued that as long as you can ask a sensible question and can validate and interpret the results, then using a black-box to go from library-prep (NeoPrep) to results (BaseSpace or similar) does not matter. However much of the innovation in NGS methods has come from tweaks to library prep methods, and I'd hate to see a slow down in this space.

Lastly 16 samples at a time could be limiting if it is not easy to run a 96plex experiment in four runs! High-plexity sequencing rocks!

How to choose if NeoPrep is for you: Illumina have data on their blog and website, they also have an unbiased buyers guide to laboratory automation that is probably worth reading if you're thinking "should I buy a NeoPrep or a Agilent/Beckman/Hamilton etc?". Ultimately you need to consider the number and type of libraries you want to make over the next couple of years. You might decide that kits like Thruplex, KAPA Hyper+ or Lexogen make library prep so simple that you don't need a robot at all.

Your needs will ultimately guide you and my thoughts in this post are very squarely for Human genomics and transcriptomics. If you are working with small genomes then other technologies to reduce costs by orders of magnitude are probably more interesting e.g. high-plexity mRNA-seq with a single library prep.

Data from my lab: I'd love to be able to share RNA-seq data from my lab with you but I can't; because there appear to be no demo units available! However I did run through the demo instrument at AGBT and the run setup wizard was a longer version of the same wizards on HiSeq, MiSeq and CBot. I could see myself starting 16 RNA-seq libraries first thing in the morning and then doing the day-job while NeoPrep makes the libraries. I could also see a lab like mine wanting three instruments so we can run 48 samples in a batch, hopefully they will rack nicely to save bench space.

7 comments:

  1. Whoever thought 16 samples at a time was a good idea when the demand for RNA-Seq is usually triplicate biological replicates?
    12 or 24 would have been ideal, especially as they sell Neoprep kits with 12 indexes (like the non-automated TruSeq RNA kits).

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  2. A great selling point for the NeoPrep over other manufacturer's is the quantified and normalized library concentrations at the end of the run. Currently, we use Kapa qPCR assays to quantify and manually normalize libraries for pooling. If the NeoPrep can do this for you, it's an additional $$$ and time savings.

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  3. A great selling point for the NeoPrep over other manufacturer's is the quantified and normalized library concentrations at the end of the run. Currently, we use Kapa qPCR assays to quantify and manually normalize libraries for pooling. If the NeoPrep can do this for you, it's an additional $$$ and time savings.

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  4. NEOprep doesn't work properly and Illumina can not deliver the reagents in time. They still have some development before this is a ready product. Don't buy yet....

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    Replies
    1. Are you using Neoprep in your lab and is your comment based on direct experience? I've certainly heard mixed reports at conferences, but I don't know anyone actively using Neoprep as their default prep method. It would be great to find out more.

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  5. It's now officially discontinued - wonder how many customers are getting paid for their 'R&D time'?

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  6. I am very happy with the NEoprep but unfortunately its going to be discontinued. Does someone know the true reason for this.
    //F

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