Sunday, October 23, 2016

SeqLL: Helicos van Winkle

Helicos was the first company to launch a single molecule DNA sequencing system. They never sold many systems (my estimate is fewer than 20), but some of those sites really loved their machines. One beauty of the system was a very simple sample prep: fragment your DNA, add terminal transferase and dATP and the sample was ready-to-hybridize.  Helicos demonstrated a number of interesting applications, such as direct loading of RNA onto the system and performing capture on the flowcell.  But with anemic demand and mounting losses, the company faded, finally filing for bankruptcy in November 2012.  One true believer bought up key IP and hardware and kept the torch burning as SeqLL, headquartered just down the road from me in Woburn, Massachusetts (best known for the book and movie A Civil Action, but also the birthplace of thermodynamicist Count Rumford ).  Now SeqLL is re-launching the technology in a new box, or is it similar technology? That's the big question, poorly addressed by their beta test announcement or their website, and that website seems to be positioning the new SeqLL box against the state of competing sequencing technologies of back when Helicos folded.

Friday, October 21, 2016

IGenomX Launches New Linked Read Chemistry

A hot concept in the genome world is how to capture long-range information, enabling assembly through repeats, resolving haplotypes, resolving copy number variation and many other applications in which short reads from short fragments are just not sufficient. A number of approaches have been proposed and published over the years, with some hitting commercial markets and significant use.

Wednesday, October 19, 2016

Genia Publishes Polymerase-to-pore docking scheme

Back in April, I wrote up a PNAS publication from Genia and collaborators that described the modified nucleotides they have developed for their sequencing-by-synthesis with nanopore detection sequencing scheme.  I had the opportunity to chat with George Church (who is an adviser both to my company and Genia, and a co-author on the paper) just after that and he remarked that there was a companion paper in the works describing the polymerase engineering for the system.  That paper is now out in PNAS (and Open Access) and I'll take a little walk through it.

Monday, October 17, 2016

Sequencing, not random probes, are future of microbiological diagnostics

Okay, I'll admit I take requests.  Throw a topic at me by Twitter or email, and if it piques my interest and I feel like I can say something intelligent, then I'll take it on -- but not necessarily instantly.   That's the genesis of today's item, a tweet from Kyle Serikawa directed at me, asking if a new paper  from groups at Rice and Baylor College of Medicine in Science Advances on a proposed microbial diagnostics (a paper highlighted by Eric Topol) had any legs.

I'll fully confess that I realized upfront that this paper cuts across my usual biases, so I resolved to try to read it with that in mind.  That's not really an excuse in the delay; I did read the paper right away, but the usual conflicts stretched out writing it up.  The paper, in brief, proposes a non-sequencing approach to an area which I had previously thought was going to be totally dominated by sequencing, and I inherently like sequencing.  After reading the paper, I would agree with Kyle: I'm not convinced that this method has legs.  It doesn't help that the paper has some serious issues with describing the methodology, as well as utterly failing to make its computational methods available.

Thursday, October 13, 2016

DNA: How Clean is Clean Enough?

Nick Loman has a new blog post nicely covering the current state of affairs for DNA preparation in the field.  Earlier this year I had some thoughts about DNA preparation and the degree to which our current methods reflect history rather than some ideal.  Even before Nick's post I had some new thoughts on the topic, but seeing his exposition helped me consolidate my own musings.

Thursday, October 06, 2016

Bill Gates Succumbs to Moonshot Madness

Another day, another misguided call for a moonshot in human disease.  This time, it's Bill Gates laying out four goals that he believes can be attained in the next decade, given the correct amount of dedication and determination.  Among these goals are a vaccine for HIV and a cure for neurodegenerative diseases.  I'll focus my comments on the neurodegenerative diseases with a few comments about fellow Blue Hen Joe Biden's cancer moonshot, but many of the criticisms apply to the HIV or just about any serious disease.

Wednesday, October 05, 2016

ONT's Wafer Thin Update

Oxford Nanopore's Clive Brown gave an hour-long update on their platform last week.  A busy social schedule featuring (on different nights) GMO beer and challah - plus six hours travel each way to the challah-fest. Add atop that a fast-moving upper respiratory tract infection, and I'm even more behind in blogging than usual for such events (plus I gathered another post idea away -- and had another suggested to me). Time to get working on the backlog!