Does Illlmina Also Have A Homopolymer Problem?

One of the most widely-publicized error modes with Ion Torrent and 454 sequencing has been the challenge of correctly counting the number of bases in homopolymer runs.  Because these chemistries use non-terminating nucleotides, polymerase is free to add as many as possible.  Unfortunately, the signal linearity breaks down, making it difficult to correctly count.  Ion Torrent today released a note on homopolymers, but rather than plowing this well-trod ground it goes for a less publicized problem: Illumina having a more specific challenge in this department.  The note is available on the Ion Community, free registration required.

Roche Guns For Illumina

Due to a business dinner & general exhaustion, I turned in early last night & was caught unaware this morning of the big news: Roche is making a hostile takeover bid for Illumina.  Ugh!

Sequencing Technology Fireworks

I actually awoke today expecting an exciting press release, but I sure wasn't prepared for the big announcements from Ion and Illumina.  Not that they were totally unexpected, but there's a huge difference between speculation and announced products (which, of course, are hugely different from ones you can actually buy!)

Ion Torrent Pairs: To What End?

Ion Torrent quietly released a set of paired end datasets over the holiday break.  This is a bit embarassing for me, as in my last post on Ion I stated the platform "will probably never have paired ends" and in fact Ion had already announced the protocol.  Oy!  I also missed their mate pair protocol being released, though the document itself is another victim of Ion's incredibly counterproductive security policy.  If you don't own a PGM, you can't access the document -- never mind if you are trying to plan for a potential buy or are preparing a library for a friend/collaborator to run.  

Year's End

I hoped this year to push myself to blog more frequently and regularly.  Clearly I did better than some years, but not up to the standard I had hoped for.  I've also realized that I missed noting some significant personal milestones.

Reflecting on a Year of Ion Torrent

Ion Torrent released three more datasets this morning, all generated on their 318 chip.  One's from E.coli but two are human genomic samples.  With approximately 1.2Gbp of raw data coming from these 318 chips (fron around 6 million quality filtered reads per chip), they are starting to move up the food chain in human genomics from pure amplicon sequencing to more complex small targeted resequencing efforts.

Fitting Out

One of the attractions of my new shop was the possibility to see a biotech company built from the ground up.  Each of my previous companies had been a long-standing concern by the time I got there; even Codon Devices had a year plus under its belt and some equipment already mothballed.  The new venture moved into its first lab space last week, and as you can see from the picture all we have at the moment there are bare walls.