A Third GridION X5 Pricing Plan

When Oxford Nanopore announced their GridION X5 instrument in March, I and others attempted to parse the difference between the two pricing plans  -- and I made a bit of a hash of it.  The X5 runs 5 MinION flowcells independently in parallel from a single desktop instrument, which also includes FPGA-based acceleration of basecalling plus a license to perform sequencing-for-hire.  Indeed, Matt Loose tweeted out an image of an "X6" and then mention of an "X7"; the X6 had a MinION plugged into the USB port and apparently the FPGA unit can keep up with seven flowcells all running simultaneously.  Now Oxford has launched an interesting third "Starter Pack" plan that offers an even lower price point for the system.

STAT Proves Not Resistant To Antibiotic Tropes

Tuesday's Boston Globe carried a piece originating from STAT news on an interesting natural product antibiotic, pleuromutilin.  A research group recently published a new total synthesis of this fungal terpene, an advance which promises to enable greater medicinal chemistry around the molecule.  That part is cool.  Unfortunately, when it gets to the biology of pleuromutilin the piece by Eric Boodman completely spits the bit, trotting out some horribly inaccurate tropes.

New Life in the Sanger Market

In my bit on "I'm not dead yet" technologies recently, I included large scale Sanger sequencing. That reflects to a large degree my personal experiences and biases.  Targeted Sanger is great for spot checking the occasional junction or misbehaving clone or strain, but I forget that many clinicians still see it as a gold standard.  Apparently there are others who disagree with me, as Thermo Fisher recently launched a new Sanger instrument targeted at small labs, and according to GenomeWeb Promega plans an instrument offering in the same space as well.

Ice Ghosts:A Shortage of Maps

I'm going to step outside the usual topic space here and cover an interesting but frustrating book I read partly on the flight to London Calling (which is about the only connection it has to genomics).  Ice Ghosts, by Paul Watson, covers the searches for the lost Franklin Expedition, a mid-1800s British Navy attempt to find the Northwest Passage.  It's a pretty good book, after all it did win a Pulitzer Prize,  The topic is thrilling: explorers under difficult conditions and a mystery that lasted over a century.  There are lessons for science in general, such as the value in carefully evaluating oral histories that some would discard as unreliable. But what is maddening for me is that in a book for which a central theme is poorly understood geographies and their interpretations, the set of supplied maps fail miserably at assisting in the telling of the story.

What Is (and Is Not) Sequence Assembly?

In the closing talk of the pre-London Calling workshop, Hans Jansen had closed his presentation with a question whether at some future date sequence assembly would become obsolete.  This was meant to be an aspirational vision for a distance timepoint, but one correspondent on Twitter saw it as hype.  I got in a bit of a discussion, constrained by the dreaded 140 character limit, which ended up largely illustrating that I have a somewhat more restricted definition of assembly than some people.  I'm going to explore this and you can judge for yourself

London Calling 2017: Plant & Animal de novo Genomes

Okay, I'm desperately behind on writing up the external science from London Calling.  Not helpful that I claimed I would not only do so, but in multiple installments.  A number of the plenaries focused on large genome assembly, so that's what I'll tackle now -- plus a few other bits.   See also my Storify summaries, which include other reports on the conference.  Also check out my storifies on the SMRT Leiden conference, which ran at the beginning of the same week and discusses many similar topics.

SFAF & I'm Not Dead Yet Technologies

Jonathan Jacobs posted his annual reminder that the Sequencing, Finishing and Analysis in the Future Meeting (SFAF) will be this week.  Alas, that meeting hasn't had many more tweeters in the past than Jonathan, but perhaps this year there will be more.  There's a glut of genomics conferences to track, compile tweets and opine on -- besides London Calling, there's been SMRT Leiden and Biology of Genomes, all in the span of two weeks!  This post is going to be a bit short on actual writing and more to just flag some talks at SFAF that grabbed my attention.  What I realized is that the talks at SFAF illustrate that a number of technologies I consider effectively dead retain significant attention.

#ImBiased, but… Best conf. of 2017: #SFAF2017 #infectiousdisease #inherited #disease #agrigenomics #human #genomics https://t.co/yTu2MxKc41 pic.twitter.com/FCoSmTp6an

— Jonathan Jacobs (@bioinformer) May 10, 2017

London Calling 2017: A Theme of Consolidation

London Calling 2017 came to a close last Friday.  Any excuses of jet lag or nights running up ONT's bar tab won't hold up much longer, so time to finish this post (I really did start the night after Clive's talk!) I'm going to largely divide coverage on the dividing line of who presented: today's piece on Oxford Nanopore presentations, particularly Clive Brown's, and in the near future at least one focusing on the science users presented.  For other summaries of the action, I've created a storify of just blog posts and similar summaries of the meeting, as there were a great number (and I am on the hunt for additional ones I've missed)

Nanopore Workshop Notes

I attended on Wednesday the London Calling pre-conference workshop, an add-on for those wishing for help getting started with MinION sequencing.  Judging from who I spoke to, many participants were utterly new to nanopore sequencing and more than a few were like me in that they had tried the platform and wanted to do better.  My colleague has gotten some very good results recently, which has re-fired my determination to get good at that myself.  Below are some limited notes I took that may be of general interest. Large portions of the workshop will go largely uncovered, as I focused on what was surprising or new.

London Calling 2017: A Preview

Oxford Nanopore's London Calling confab runs Thursday and Friday, with a training workshop on Wednesday.  I'll be there -- who can resist a conference nearly at the Tower of London? -- and will also be testing whether my personal "field of nanopore sequencing suppression" can defeat ONT's best trainers.  Here's some preview of what I'll be particularly looking for, though being surprised will be lots of fun too. Much more fun that reading (the wrong) patents!

Oxford Nanopore's Enigmatic Patent Litigation

Oxford Nanopore has launched lawsuits in the UK and Germany against Pacific Biosciences, alleging infringement of a European patent licensed from Daniel Branton's lab at Harvard, EP1192453, which is apparently exclusively licensed to Oxford.  When I wrote about Pacific Biosciences first lawsuit against Oxford Nanopore late last year I titled it "PacBio's Quixotic Patent Litigation", as it appeared the Oxford could easily dodge the lawsuit by abandoning the 2D sequencing technology, which Oxford is in the process of doing.  I've swapped in "enigmatic" for this title, as I'm not even sure what aspect of PacBio is allegedly infringing the patent.

Exercise: A Sequence Signature for Transcription-Translation Coupling in Bacteria?

A pretty common question over on Quora is something along the lines of "how do I learn bioinformatics".  Great question!  Tonight I'm going to outline a project which I think would make a good first bioinformatics project.  It is rich in content and keys off an interesting new non-computational result.  And since I've left graffiti on multiple Quora threads that I would write something like this in the immediate future, here it is!

Pinniped Karyotypes & N50 Statistics

In my recent piece on long read assembly, I laid out part of the case against the N50 statistic.  Historically, the issues with the statistic have been around the fact it can be gamed at the expense of assembly correctness or assembly coverage. These are concerns for the typical sort of short read assemblies we've grown used to: lots of contigs and the temptation (perhaps justified) to try to go for higher N50s by more aggressive merging or by filtering out the short contigs.  Elin Videvall over at The Molecular Ecologist has a nice ongoing series of posts illustrating the statistic and these commonplace issues:

• What’s N50?
• The N50 filtering problem
• The N50 misassembly problem
• A solution to the N50 filtering problem

I'm going to come at the problem from the other end, as a new preprint from 10x Genomics illustrates the problem of using an N50 statistic (or any related Nxx statistic) with good long-read / linked read assemblies -- but doesn't demonstrate this point quite as strongly as I thought when I first started drafting this.

Time to Retire HeLa?

A TV movie produced by and starring American culture mogul Oprah Winfrey is about to hit screens which dramatizes Rebecca Skloot's The Immortal Life of Henrietta Lacks.  If you haven't read this remarkable book, you really should.  It should certainly be required reading for anyone entering biomedical fields.  That's not to claim it is perfect; one of Lacks' sons has objected to the way his family is portrayed.  But it is a searing human story of how the most famous cell line in the world came to be.  Even if you excuse some of the injustices done as compatible with then contemporary ethical standards, it is a thought-provoking piece on the topic of what our biomedical ethics should be.

Alexandria Jumps Into Shuttle Business

A restaurant I frequented during my grad school days had a map on the wall showing Boston area transit routes from roughly the 1940s.  Remarkably, most of those streetcar routes are found largely unchanged in the MBTA's current bus routes.  Yes, routes have been altered to account for expansion of the Red Line and shifting of the Orange Line, but most of the routes are little changed and very, very few new ones have been added.  Some of that reflects the canalization of routes by the street patterns; there are only so many large streets suitable for buses and Somerville's hills and the various rivers impose further constraints.  Much of it lies in the always tight purses at the T and the political difficulty of ever closing an old route to enable moving resources to a new one.  Unfortunately, the commuting patterns in Boston are not conserved from the 1940s, with far more workers commuting from distant suburbs and dense developments springing up.

10x Launches Mass T-Cell Receptor Decoding

Adaptive immunity is an endlessly fascinating topic which I have not explored very deeply, which is particularly unfortunate given the many parallels to computing.  Combinatorial logic is used to construct a vast array of possible antigen readers, expression logic ensures that only one such reader is expressed in a given cell and hypermutation and evolution are used to optimize these readers to match specific antigens.  All this not only creates weapons to deploy against foreign invaders, but also a memory which effectively records an individual's history of environmental exposures.  Just before I started writing this two tweets highlighted using adaptive immunity profiling to reveal exposure to tuberculosis and cytomegalovirus.  Adaptive immunity is responsible for transplant rejection, with new companies looking to more selectively modulate immunity to enable transplants without shutting the immune system down.  Adaptive immunity also ties into the white hot field of immunotherapy for oncology, exploring whether differences in antigen response underlay variation in immunotherapy success.  To enable profiling adaptive immunity on a mass scale, 10x Genomics has now introduced a single-cell kit for targeted profiling of T-cell receptor variable regions.

SageHLS: Automated uHMW DNA Preparation

Advances in optical mapping, linked reads, PacBio and nanopore sequencing are enabling generating highly contiguous large genome sequences routinely and inexpensively.  However, this in turn is creating intense demand for efficiently and reliably preparing ultra-high molecular weight (uHMW) DNA.  By this term,  I mean DNA approaching or exceeding a megabase in size.  Methods for preparing HMW and uHMW DNA tend to be very old-school, reaching back at least back to the 1970s, 80s and 90s for approaches used in the early days.  Phenol-chloroform preps with the DNA spooled out onto a glass hook or rod are one popular approach; another is to embed cells in agarose blocks, extract the DNA within the block and then degrade the agarose to retrieve the DNA.  Nuclei preps are yet another approach. Any liquid handling must be performed gently and with wide bore pipettes.  These techniques tend to be tedious and slow affairs, requiring many manual steps.  As an alternative, Sage Sciences has launched an instrument which automates a process with no hazardous chemicals, the SageHLS.

Chromosome-Scale Scaffolds And The State of Genome Assembly

A new paper on using Hi-C sequencing appeared in Science recently, demonstrating the generation of chromosome-length scaffolds for human as well as several insect genomes.  The authors even provide a cost model, proposing that by processing multiple genomes in parallel the sequencing reagent cost (but not labor) of this approach should be about $10K per human genome. In the case of the insect genomes, the paper enables a look at chromosome evolution which is simply impossible with lower resolution.  These findings resonate with a number of pieces I've written over the years, but particularly with my recent criticism of the proposal Earth BioGenome project and a spirited defense of that concept made in the comments of my piece by a member of the steering committee.

Differential Mammalian Toxicity: Why Do Some Human Foods Kill Dogs?

I've been contemplating this post for a while, but it can be seen as another angle on my recent post on the challenges of drug discovery, so it finally left the mental queue.  We often use other mammalian species in drug development to predict human toxicity.  We know animals aren't the same as people, but lacking a better alternative that's what we do.  Now, as regular readers know I keep company with a dog, and that sometimes has me wondering: how well do we understand the cases of things we can eat but which are dangerous for our canines?

Targets: Drugability Revisited

My correspondent @datarade shot a tweet my way on his quest to understand drug discovery. He does this despite the fact I've promised posts on previous tweets that are submerged in my mental queue.  But the best part of teaching is forcing yourself to rethink what you think you know, so I'm going to actually take this one on in the space of "what is a target, how do we pick them and how do we drug them".  Which I've found to be enlightening and frustrating.  It's a messy space because so much is empirical, and I keep devising and then discarding taxonomies and explanatory approaches because they all seem unsatisfactory.