Monday, 16 May 2016

How many genomes can the world sequence per year on X Ten?

Illumina's X Ten was a major announcement. It arguably delivered the "$1000 genome", kickstarted national population genomics as a science, and delivered the final blow to Complete Genomics. It is debatable as to whether Illumina needed to release X Ten at $1000, or with such huge capacity; and it is unclear what the X Ten economics really look like for customers or Illumina themselves, but the world can now sequence an unprecedented number of genomes: about 576,000 per year!


Where are all the X Tens: There look to be about 320 X Ten instruments, I searched online and at AllSeq (great) and Genohub (not so great). Installations include - Baylor College of Medicine (10), Broad Institute (14), CEN4GEN (5), Centre National de GeŽnotypage (5), Core Genetics (?), DKFZ (10), Garvan Institute of Medical Research (10), GENEWIZ (10), Genome Quebec (5), GRAIL (?), HudsonAlpha (10), Human Longevity Inc (20), Macrogen (10), McDonnell Genome Institute (10), New York Genome Center (10), Novogene (10), SciLifeLab (10), Sidra Medical and Research Center (10), SNP&SEQ (?), Theragen Etex Bio (10), Wellcome Trust Sanger Institute (10), WuXi AppTec (10), Genomics England (Illumina) (30), Scottish Genomes Partnership (15), DeCode.

How genomes are actually being sequenced: While each X Ten box can generate one thousand eight hundred $1000 genomes per year it is unclear how heavily they being used. There are very few reports of X Tens being used at capacity and even 80% capacity seems to be optimistic so a large number of those boxes may be sitting idle. The reasons for this are likely to vary from lab to lab but three main factors need to be considered:
  1. Sample collection: getting enough patients recruited
  2. The cost of sequencing: finding the cash
  3. Analysis and interpretation: hiring enough Bioinformaticians
We're just about to send off our first X Ten project for 1000 genomes...tough to do on two HiSeq 4000's!

12 comments:

  1. GeneWiz just announced acquiring an X10

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  2. James, I'm glad you found our list at AllSeq.com helpful! We try to keep it as up to date as possible, but remember that it’s a list of HiSeq X Service Providers. There are X owners out there (like deCODE Genetics) who seem to use all of the capacity for internal samples. Another way to getting at this estimate is just to look at the total # of machines out there (which Illumina usually let’s us know during their earnings calls) and ignoring where they’re placed. The current estimate is ~320 HiSeq X’s. The official # of genomes per machine is 1800/yr (not sure where you got the 1000/yr number from). That gives us 576,000 samples per year as a theoretical maximum. However, as you’ve noted, it’s not reasonable to assume all machines are operating 100% of the time. A more realistic ‘maximum’ would be 80-90%. But we can take another shortcut (again from info Illumina shares during their earnings calls) – the stated reagent revenue pull through from each HiSeq X is in the range of $650k-$700k. That means on average the HiSeq’s are operating at ~50% capacity. That brings the real-world samples/yr number to 288k!

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    Replies
    1. Thanks Sawn...a font of knowledge as usual. Uniformed Services University of the Health Sciences also have an X Ten for internal work. Finding all these sites is tough...if only someone put them all on a map!

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    2. Somewhat confused, are we talking HiSeq X Ten? Don't we only count the whole big box as 1 and not ten?

      "This automation is essential for laboratories scaling to 18,000 genomes per year."
      http://www.illumina.com/systems/hiseq-x-sequencing-system/illumina-seqlab.html

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    3. An X Ten is 10 HiSeq X instruments. Each X instrument is essentially an upgraded HiSeq 2500, running the new patterned flowcells.

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  3. Met with the Broad last week. They have 28 HiSeq X now and have sequenced 40,000 since early 2014.

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  4. I updated this post to use Shawn's numbers - not sure where my 1000 genomes per year came from. I guess this shows how important it is to double check numbers before pressing "post"!

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