Commentary: ChIP-chip vs ChIP-seq and $$

Ok, so with the rush to ChIP-seq and all the hype (much of it deserved) around “next-generation” sequencing generally, you might think that arrays are dead as used for ChIP (i.e. ChIP-chip).

I don’t think this is going to happen for simple cost reasons. For the near future, there will be lots of genome-scale ChIP studies and, for these, I strongly support ChIP-seq. It is a lot cheaper for better data. But I see a strong trend toward ChIP studies targeted toward specific biological questions and often questions requiring large sample numbers (e.g. epigenetic changes is cancer).

The financial math really isn’t that hard; with ChIP-seq running ~$5000 for external users and ChIP-chip running at $660 for external users (NimbleGen single arrays), it seems pretty clear that if a fair number of samples are involved, ChIP-chip is the way to go. That is, unless high-res whole genome coverage is absolutely necessary (usually not).

Furthermore, for taking chances on experiments, $660/sample is a lot more appealing on a lab budget than $5000/sample, particularly when you consider that, in the real world, even poor testing of a speculative idea is going to take 2 or 3 samples at minimum (=~$15,000 for ChIP-seq vs $1980 for ChIP-chip). A lot of labs can blow $2000; blowing $15,000 really hurts.

Given this analysis, it seems to me that NimbleGen should really push the low end of the market – in other words, try to get the cost even lower on a per sample basis (for fewer spots). I think they are on the right track with their multiplex arrays, but development of these has been disappointingly slow, and last time I looked, the cost structure around the 4plex with 70K/quadrant really wasn’t very attractive.

I may revisit this topic another time, but that is it for now.

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2 Responses

  1. Hi Mark, enjoy your blog. But just to clarify, you would not run a whole flow cell on the Illumina system, just a lane would suffice. Also multiplexing samples is relatively trivial so the actual cost even without multiplexing is about $5k/7, that is, about $700. Other advantages, in addition to the information quality is that the amount of DNA reqd is substantially lower than for Chip:Chip, and no prior assumptions about target sequences is required.

    • For ChIP-seq in human/mouse/most other mammals, I think it is pretty clear that you need five lanes or so – maybe even more if you are running control lanes. One lane just isn’t enough reads, esp considering that many reads may be lost in some ChIP-seq experiments due to repeats.
      As to pricing, I indicated in the post – but perhaps not clearly enough – that I was looking at pricing as an “external user.” That means that I have to send samples to another university. The lowest quotes that I received were $1000 (US dollars)/lane. Commercial quotes were significantly higher, as were quotes from most core facilities.

      So 5 lanes x $1000/lane = $5000. You will note that The Scientist published the same numbers for ChIP-seq in the last few months.

      Mark

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