Tuesday, March 31, 2015

To Properly Assess Cancer Genomics, One Cannot Dismiss It

Through a happy series of professional events, I now get to have lunch very regularly with the author of the excellent blog The Curious Wavefunction.  If you haven't visited there, Ash not only delves into chemistry but the history of science.  In a most friendly way, he dropped a challenge on my Twitter-step that represents a long procrastinated blogging project, so I really couldn't turn it down.  And that challenge is: what has been the value of cancer genomics. Is it, as he asked, a very expensive exercise in looking for keys under the lamppost, or something far more valuable?

Tuesday, March 10, 2015

A Dovetail Route to Scaffolded Genomes

10X Genomics had a lot of buzz at AGBT over their approach to acquiring long range information for complex genomes via a microfluidic-assisted library preparation scheme.  Another young company, Dovetail Genomics, is starting to unveil a very different technology with similar aims.

Monday, March 09, 2015

An Impending Shakeout In Library Prep?

My ABGT teleconference-based pieces all had a theme of library preparation.  Library prep has never been as flashy as instrument performance, but is clearly critical.  A library-free sequencing technology remains a distant dream, so DNA (or RNA) must go through a series of preparative steps prior to being loaded on the sequencer.  The dominant library prep molecular biology for clonal sequencing systems consists of shearing the DNA mechanically, making flush ends with a repair mix, adding 3' runs of A and then ligating primers and finally using PCR to amplify the material.  
Mechanical shearing can be replaced with enzymatic shearing (or perhaps even chemical, though I'm unaware of chemical shearing being used in production).  For RNA of different sorts,
some upstream steps are added to convert the RNA to DNA, perhaps with a depletion at some stage of hyperabundant species such as rRNA.  This conversion may, with different levels of success, mark which strand was sense and which antisense. The transposase-based Nextera protocol represents the most drastic departure from this paradigm, enzymatically eliminating all the steps prior to PCR. 

Saturday, March 07, 2015

There's Gold in Them Thar Programs

Last night was the season five finale of the Gold Rush, which I confess is one of the few television programs that I have been watching routinely near their airing schedule (the other is The Simpsons, which is a father-son bonding experience). Now, writing in a blog mostly about science that you watch something on the Discovery Channel is a bit of a bold act, given its many panderings.  The network annually features Shark Week, that has been roundly criticized for its sensationalized portrayal of these magnificent creatures.  It also features shows which purport to show individuals routinely engaged in felonies and in one case claiming to document a violent subculture in a pacifist religious community, the Amish.  I grew up near the Amish Country of Pennsylvania; if anything like that ever existed the Philadelphia papers would have had a field day.  Gold Rush itself, and a second gold show which I've developed a fondness for, Bering Sea Gold, has shortcomings that are obvious and painful.  So why am I hooked?

Wednesday, March 04, 2015

Can BGI Really Stir Up the Sequencing Instrument Market?

I've been asked several times recently about rumors coming out from BGI.  They've started claiming they have a super sequencer which will radically beat Illumina's offerings on both cost and accuracy. The recent 10K Genomes meeting apparently had a quick talk from BGI which led to some limited Twittering, and judging from this Mendel's Pod interview at least one person believes the buzz (though the same individual quotes a price per PacBio human genome that high by at least a factor of 25). .  The claim is that this summer at ESHG BGI will release two boxes, one a benchtop model which I haven't seen any details on, and the other claimed to offer throughput superior to a HiSeq with better accuracy.  What might be backing up these claims?