Having backed off their initial business model of offering 30x human genome coverage for $30 (that’s thirty dollars, not $30k) and a social media-inspired open source database of sequence information, GnuBIO is now focused on bringing a diagnostic sequencer to the market. The GnuBIO System, with a projected list price of under $50k, generates and controls nanodrops inside which the sequencing reactions takes place using sequencing-by-hybridization (SBH) chemistry. Labeled hexamers are added (one per drop) along with polymerase and NTPs. If hybridization takes place (due to a perfect match), the polymerase will extend the strand along the length of the molecule being sequenced. When it reaches the end, the new strand displaces a quenching probe which otherwise masks a second fluorescent signal attached to the end of each molecule to be sequenced. The instrument measures both the signal from the hexamer and the presence or absence of the signal from the sequenced molecule. The process is then repeated with each of the possible hexamers and the final sequence is reconstructed based on which hexamers hybridize and which don’t. In theory this involves 4096 separate hybridizations per amplicon being sequenced, but in practice it’s a few more as some of the oligos need additional bases to create uniform melting temperatures and to cover homopolymers and repeat regions of up to 9 bases. They will launch with ~5000 probes but they have generated ~11,000 probes for internal use.
Unlike most other systems, there isn’t really the concept of a concrete “run” for the GnuBIO System. As many nanodrops as are needed can be created and analyzed in serial fashion for each sample. Therefore, a ‘run’ can be as small as low pass coverage of a single gene or as large as high pass coverage f panels of up to 100 genes of 1kb each. The system is projected to cost ~$50k and individual runs will require a $200 cartridge that will handle all of the steps starting from purified genomic DNA. Hands-on time will be under a minute and analyzed data will take around 3.5 hours.
They presented demo data from their system at CHI’s Consumer Genetics Conference in September 2013 that had accuracy rates of 99.991%. After filtering out ~4% from the ‘no call zone’, they were left with an error rate of 0%. Despite the promising results, they are still in beta testing (at a single site as of 9/2013) and said they won’t be launching until mid-2014. In April 2014 it was announced that GnuBIO has been acquired by Bio-Rad. The GnuBIO team will remain in Cambridge, MA and be incorporated into Bio-Rad’s Digital Biology Center. Bio-Rad has re-estblished the launch schedule to early 2016.
Status: Beta testing
Projected commercial availability: early 2016 (originally slated for 2Q 2012)
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