So, this piece is going to be mostly asking questions. In one of the corners of my dream world I have a scientific historian on retainer, but in the real world my substitute is to throw some questions out and hope some knowledgeable people leave comments. If someone I spark someone’s term paper or thesis topic, I ask only that I get an electronic draft!
Friday, November 15, 2013
Friday, October 25, 2013
In the movie The Spanish Prisoner, a brilliant inventor possesses a paranoia that "The Process" he has invented will be stolen by deceitful competitors, and everyone speaks with a highly distinctive cadence. The entire movie is suffused with deceit, starting with the title which is a notorious con scheme akin to the modern Nigerian scam. I spent last evening in some of the space in which the movie was filmed listening to a scientist in that mold (& distinctive speech) describe a process his group has invented (indeed, by lucky chance I helped him find the venue). But many remain unconvinced that Clive Brown and Oxford Nanopore are not themselves the puller of ocular wool.
Tuesday, October 22, 2013
I haven't talked about Ion Torrent for a while, because it was largely off my radar screen. In early 2012 the PGM had been an important contributor to my early de novo genome assemblies, as it was the only fast turnaround, low cost system I could access. But the data quality was always frustrating, with many indels, and the 200 basepair mode on the read lengths not great for assembly. Once I could access a MiSeq, that became our dominant instrument for individual genome assembly. We tried Ion once more with the 300 basepair chemistry, but were not particularly impressed.
Saturday, October 19, 2013
Roche's announcement this week that they planned to shut down the 454 sequencing business in mid-2016 was not completely unexpected, as a number of rumors of shutdown had shown up on Twitter. Most tweets on the subject fell into two categories: either just-the-facts-ma'am or jokes about the dominant error profile (which I guess you could call just the facts maaa'aaam). But, certainly I wouldn't have thought Roche on the verge of this decision when I went to AGBT 2013 in February, as 454 had a huge suite in a prime location (just by the main conference hall entrance) and many expensive events. Now, Roche's presence in the genomics space is looking like just the recently announced deal with PacBio to market human diagnostics on that platform.
Thursday, September 26, 2013
One of the two big buzzes in the genomics business world was the announcement that Roche Diagnostics has signed a major deal with Pacific Biosciences in the field of human diagnostics, which comes with a $35M upfront payment and a possible $45M in milestones, plus future sales of reagents. PacBio stock rocketed over 70% on this news. This on the same day that cancer diagnostics company Foundation Medicine went public with a similar potent climb from their offering price; a good day for those lucky enough to have the shares (which, by the way, does not include me in any way, though Foundation shares a common venture backer with Warp Drive Bio in Third Rock Ventures).
Monday, September 23, 2013
Over at Homolog.us there are two detailed blog entries on Pacific Biosciences entitled "End of Short Read Era?" (Part I and Part II). I've tweeted a number of comments on the technical aspects, but there are some more substantial thoughts reading these pieces helped me condense.