Tuesday, 17 January 2012

$1000 genomes need $1 sample prep

The recent announcements from Life Tech and Illumina, and the expected announcements from the competing technologies are giving us a hint of what it will be like to live in the $1000 genome world. From a genomics perspective the reduction in sequencing costs is very welcome and is likely to be reflected in significantly larger projects (from groups already sequencing), in more projects (from groups not yet sequencing) or from both.

All of these people are going to have to make sequenceable libraries and many will find there are challenges to be faced in generating something that gives high quality data for analysis. There are many methods for making libraries, kits can be bought from sequencing instrument providers (e.g. Illumina), from third party vendors (e.g. NEB, Agilent, Beckman) or by making home-brew versions (e.g. Enzymatics). We have used all of these at some point over the past four years in my lab and all have been successful. It used to be that the cost was usually lowest with home-brew, higher with 3rd party suppliers and highest from the instrument vendor, competition has seen that shift so there is very little in it for most small to medium sized labs. The costs today are around $50 for a DNA sequencing library and compared to 18 months ago this price is great.

However the increases in sequencing capacity and corresponding drop in costs mean we can run many more samples than before. When a genome cost $250,000 or even $20,000 then $500 or even $100 for a library prep was fine. As we are able to process multiple genomes per sequencer run the sample-prep cost starts to be something we can no longer ignore.

As soon as we move away from whole Human genome sequencing then library prep cost can be a significant factor in total project costs. Anyone sequencing bacterial or model organism genomes that wants to sequence 100-1000 genomes in a single run is confronted with a large sample prep bill with $50+ prep costs. Sometimes the sample-prep costs more than the actual sequencing.

The same issues faces projects using differential RNA-seq where only around 5-10M reads and as few as 1M may be comparable to microarrays. At this read depth 30-300 samples can be processed in a single lane using $1000 of sequencing reagents. At $50 per samples, $1500-15,000 for library prep is not going to be maintained long term.

Hopefully this issue will push labs to develop new methods, similar to Epicentre/Illumina’s Nextera transposome technology, or microfluidic methods that use vanishingly small amounts of reagent and sample. A $1 bacterial genome prep or a $10 transcriptome prep are likely to be well received.

If there is anyone working on this yet please do get in touch!

7 comments:

  1. Sounds like multiplexed sample prep is in order. Just like multiplexed sequencing, but introducing the tag much earlier in the process.

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  2. Did you ever demo the Advanced Analytical fragment analyser for quantifying your libraries? If so, what was the verdict?
    Cheers,
    Richard

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  3. The Drosophila Genetic Reference Panel publication was covered on GenomeWeb today..!!

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  4. We have 1-2$ RNAseq library prep protocol here at Cambridge. It is correct, 2$/RNA sample for reagents to make RNAseq library. 1 ng of fragmented RNA is enough and protocol is 5 hours long.

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  5. Can you tell me more? Drop me an email if you prefer.
    Thanks.
    James.

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  6. Hi Dear!! I like your blog post. It contains awesome information. It helps me a lot. Thanks for sharing it.

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  7. Thanks for this posting.
    Your blog is very knowledgeable!! Keep it always updated.
    Sample Preparation

    ReplyDelete

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