bioinformatics, genomes, biology etc. "I don't mean to sound angry and cynical, but I am, so that's how it comes across"

What I know about the expansion of HiSeq X to non-human genomes

Update 15:31:

Well, it isn’t very much…..

Illumina announced that they will now allow researchers to sequence non-human genomes on the HiSeq X, and well we have HiSeq X systems, so we have a tiny bit of knowledge gleaned from our communications with them.

What they say is:

The updated rights of use will allow for market expansion and population-scale sequencing of non-human species in a variety of markets, including plants and livestock in agricultural research and model organisms in pharmaceutical research. Previously, it has been cost prohibitive to sequence non-human genomes at high coverage.

This is a bit vague, but there are a few keywords in there – “genomes” and “high coverage”.

My opinion is that this was done after pressure from the mouse and rat model-organism communities, who want to do thousands of 3Gb 30X genomes, just not human genomes.  We (as in Roslin) have also been putting on pressure to enable us to do farm animal genomes.

It’s only genomes: so not RNA-Seq, ChIP-Seq, exomes, amplicons etc – none of that.  Just genomes.

It’s only high coverage: 30X or above.  So no 10X, 5X or 1X genomes.

We asked about metagenomics (WGS): maybe (Update 08/10/2015 metagenomics is not supported)

We asked about smaller genomes (100Mb): (update 12/10/2015) small genomes are allowed, the issue is that only 12 indexes are available per lane – each lane producing around 120Gbase of data.  That’s 10Gbase per index (or 2000-fold coverage of a 5Mb bacterial genome)

We asked about medium sized genomes (1Gb): maybe (how a 30X 1Gb genome is different to a 10X 3Gb genome is anyone’s guess, but apparently, maybe, it is)

Bisulfite sequencing: my understanding is that this is supported/allowed (Update 08/10/2015)

Having said all that – my opinion is that what Illumina want to stimulate are massive, large-scale genomics projects.  Think on a scale of 1000s of 30X human genomes (90 terabases).  If you have fly, yeast, C elegans, metagenomics or small genome projects that are on that scale, I should think Illumina would be very happy to talk to you about getting them sequenced on an X somewhere.  However, if you’re smaller scale than that, well – we have the HiSeq 4000 systems at Edinburgh Genomics, which offer incredible value for money.



  1. “Only genomes”

    Is WGBS considered acceptable?

  2. My understanding is that Bisulfite sequencing is allowed

  3. Geneticist from the East

    12th October 2015 at 5:52 am

    I have always wondered whether it is possible to do WGS from human saliva sample on the HiSeq X. There should be about 11% DNA from bacteria in saliva sample. Will I then get bacteria DNA reads from HiSeq X to allow me to do a metagenomics study of mouth bacteria?

  4. Yes and yes

  5. I think the main reason for this, Mick, is cannibalisation. If they allow people to do everything at X costs, and i bet theres a fair amount of idle time on Xs, they open the future to people mostly sending off samples to X-labs. This would be *instead* of say most people going to a grant body and getting a large capex grant for a system, and a grant for facilities – and the yearly service costs and so forth. This would deprive ILMN of a ton of upfront revenues and push their dependance to consumable only revenues from X labs at a smaller number of sites at X prices. This would significantly diminish their revenue growth, and so further push their share price down. We have to wonder if Xis anywhere near as profitable as all those smaller instruments which are only used half the time.

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