Today I thought I’d give my first impressions on what HiSeq X Ten might mean, the dust has certainly not settled and yesterday there was lots of buzz about the new instruments from Illumina (see the bottom of this post for a round up of news). Iâ€™ve been reading the HiSeq X Ten datasheet and a couple of things jump out as significant changes: run speed and output per flowcell.
Obviously the biggest issue for mere mortals like myself is the need to find $10,000,000. Three companies were announced by Illumina yesterday, Macrogen, the Broad Institute, and the Garvan Institute of Medical Research. Notably absent form that list were WashU, Baylor, the Sanger and BGI. I think we can devote a whole post to what BGI might be doing if they don’t buy into HiSeq X Ten, perhaps a subject better discussed over a bottle of Tsingtao after hours at AGBT.
Iâ€™m going to continue to follow up on the other new instrument, NextSeq 500, as well as trying to find out more about the new chemistry’s and imaging technologies Illumina are using, and what we might see port over to HiSeq 2500 in the 1TB upgrade later this year. SO please keep watching Core Genomics.
Output: The new X instrument generates 50% more clusters per run than HiSeq 2000 allowing X Ten to generate 900Gb per flowcell compared to â€œjustâ€ 500Gb on a 2000. It also looks like the new nanowell flowcells might allow clustering to completion within a well using all the available “real-estate” in the well to maximise signal from each cluster. Who knows if this also means the length of fragment will be less of an issue than previously, if we can make fragment libraries of 100bp and sequence those on HiSeq X Ten physical coverage of the genome goes through the roof.
The rest of the news (well some of it anyway):
- GenomeWeb: coverage as we’ve come to expect.
- Nature news: mention 30x as the gold standard, not if you’re looking at Cancer genomes. Nature quotes Chad Nusbaum at The Broad saying X Ten is â€œlike the high-stakes poker table: if you’re playing $200 a chip, people who can’t afford those chips don’t care.â€ I’m not sure about everyone else but I certainly care. Suddenly there are a group of researchers who can do the same science as me for three fold less or more, maybe I’ve been too blind to the fact I run a lab where only a relatively small group of people can access; so being on the other side of the fence feels uncomfortable? Nature news also asks questions about what BGI might do.
- Opinionomics: Mick Watson says “Really, though, this blows the Ion Proton out of the water.”
- Dan Kobolt at MassGenomics: points out the same catch as I did, only Human Genomes!
- The Scientist
- Glenn Lockwood: A Computational Perspective, “the cost of being able to store four weeks worth of HiSeq X 10 output will run about $60,000 in capital” & “keeping up with a $10 million HiSeq X 10 system may require a compute system costing on the order of $450,000 in capital up front” are sentences to make you weep!
- NextGenSeek blog
- Matthew Herper at Forbes
- Genohub: can help you find NGS service provision, perhaps even on an X Ten?