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.

Obviousness: Rarely Obvious

Pacific Biosciences has made new thrusts in their ongoing intellectual property action against Oxford Nanopore, adding two recently issued patents to the fray.  Oxford has publicly brushed these off as "another pore excuse for a lawsuit", but certainly the battle is not over.  One of these patents, 9,542,527 "Compositions and methods for nucleic acid sequencing", appears to concern using hairpin linkages to read both strands, much like the 9,404,146 "Compositions and methods for nucleic acid sequencing"  patent that PacBio led with.  Since Oxford has announced they will abandon their "2D" methods that use such hairpins, this angle would seem to be soon irrelevant (as I predicted back when PacBio originally attacked).  But the other, US 9,546,400 "Nanopore sequencing using n-mers" covers basecalling methods, which is a new twist.  A route to challenge any patent is to identify "prior art", information which was publicly available at the time of the patent filing which impinges on the claims in the patent application.  Not only can exact matches to prior art be an issue, but also anything which would be "obvious" to a skilled practitioner.  And that can certainly be a can of worms

plexWell: Illumina Libraries by the Plateload

The advent of so-called next generation sequencers, particularly those from Illumina, have brought the price of sequence data down dramatically.  However, there is a catch: the cost of preparing DNA to go into the sequencer, the process known as library preparation, has glided downwards on a much shallower trajectory.  This means that for projects wishing to sequence very large numbers of small genomes or large constructs the cost of library preparation can be similar to or even exceed the cost of data generation.  A small company north of Boston called seqWell Inc™ has a new approach to Illumina library generation which they are on the cusp of making widely available, and not only does this bring the cost per well down but it is designed to yield normalized libraries from relatively unnormalized samples.

ONT Updates: GridION X5, PromethION, 1D^2, Scrappie, FPGAs and More

Clive Brown gave a webcast today with updates on a number of Oxford Nanopore topics, but clearly the flagship announcement was a new instrument, GridION X5.  Due to the raging snowstorm in the Boston area I was home with my teammate and we've been doggedly going through the tweets (now storified) and my notes (plus David Eccles' nice set) to retrieve the juiciest bones therein.

Blog team member intently watching @Clive_G_Brown webcast - now must confer & write-up impressions pic.twitter.com/jPGpw1w0lg

— Keith Robison (@OmicsOmicsBlog) March 14, 2017

MinION Leviathan Reads: An Update

Last week I posted a piece on some amazing new nanopore data, only to be red-faced to discover the next morning that I had misread the axes.  So I re-posted the piece with the offending data and subsequent analysis in strike-thru font.  After I did that, I was informed that the same dataset actually did have leviathan reads, bigger than my misinterpretation.

Catching Up On Oxford Nanopore News: More, Better, Meth & Huge

Oxford Nanopore and its collaborators have shown at least three interesting advances in the last few months which I haven't yet covered; the most astounding of which was announced this week.  I'll take these three in an order which works logically for me, though it isn't strictly chronological plus I'll touch on some parts of their platform which have not made advances which were perhaps expected.

(Morning after: Ugh, ugh, ugh -- I misread an axis, inserting an extra 0 -- so major crossouts in one section; why I shouldn't post late at night during pauses in day job stuff)

Earth BioGenome Project: Ill-Conceived Megaproject Du Jour

There's been a bit of buzz recently about an unfunded proposal to ultimately sequence every living species on Earth, warming up by sequencing every eukaryotic species, with a targeted cost of $4.8B.  It pains me a bit to write this, but I'm with those who think this is not a wise way to spend money and certainly not likely to work for anywhere near that budget.

#AGBT17 Tweet Archive is Up!

I've used my scheme for collecting and organizing tweets to capture most of the feed from this week's AGBT17 conference.  I still need to pore over these in detail, so I won't try to distill out much thoughts (other than single-cell sequencing is clearly in exponential growth phase!).

Bagging Novel Enzymes Via Mass Spec Metabolomics

Obtaining a complete genome sequence for a bacterium or archean is essentially a solved problem, if you can culture the bug.  Grow up biomass, purify the DNA and then use PacBio alone or a combination of long reads (PacBio or Oxford Nanopore) and short reads.  These should yield a closed genome with a very low error rate.  A few bugs spit at you by repeated failing PacBio sequencing or having some monster prophage or other repeat that is longer than the read lengths, but these are very rare.  With advances in metagenomics techniques, the solving of uncultured genomes is becoming increasingly easy and many of these remarks also apply to fungi and other eukaryotic microorganisms. Once you have the sequence, then the lack of introns in bacteria and archea makes gene prediction almost trivial, and you now have a parts list for the organism.  But is that a useful parts list?  A new paper in Nature Methods makes some progress in improving the utility of those parts lists, though we are still far from actually fully understanding an organism given its genome.

Could Hermione Tackle MinION Yield Variability?

A bit of a foray into Oxford Nanopore land again.  By replacing a bench bumbler with someone competent, we've seen some success with our MinION at Starbase.  Highly variable yields though.  I've done some looking and discovered this isn't a unique experience.  And now Oxford is suggesting that software upgrades alone will give MinION about another 50% boost in yield; it will be interesting to see what this does for variability.  Finally, I have a notion of some of the sources of variability and an idea for a troubleshooting tool

Illumina Drops NeoPrep

At the 2015 AGBT meeting, Illumina launched the NeoPrep, a ~$40K instrument to automate the preparation of up to 16 sequencing libraries at a time, using a technology called electrowetting microfludics. Now news comes that Illumina is dropping the NeoPrep, halting sales immediately and allowing existing users about a year of reagents.  What happened and how does it impact genomics?

On The International Nature of American Biotech

I'll spend two hours in project meetings tomorrow. Around the table will be a group of scientists who are all at the top of the game and among the best in the world at what they do. We will be trying to push forward new antibiotics to save lives. Yes, we are also trying to be rewarded monetarily with it, but we all share a mission to improve humanity by finding new drugs for important medical needs.

Perl: The Bad Habit I Can't Quite Kick

TULIP is a new assembler for long, error-rich reads such as from nanopore. I was a bit stunned to see that TULIP is written in Perl; I was starting to wonder how many holdouts like me there were. Which led to this exchange on Twitter

@hans_j_jansen @github as someone who can't quite kick the habit, I both applaud&grimace with your use of Perl for leading edge bfx

— Keith Robison (@OmicsOmicsBlog) January 23, 2017

@hans_j_jansen @OmicsOmicsBlog @github if it ain't broken... #perlforever

— Roger Pettett (@zerojinx) January 24, 2017

Notes on a Conversation with 10X

I've been remiss in writing up a piece on 10X Genomics based on a phone discussion last week with Michael Schnall-Levin (VP Computational Biology and Applications) and Anup Parikh (Director, Product Marketing).  I always appreciate companies reaching out to me and spending time to educate me on their products and plans, and this was a very interesting and enjoyable conversation.

Gen9 Vanishes

Earlier this week one of my colleagues had gotten a somewhat ominous email  from the CEO of Gen9 titled "Special Gen9 Announcement", which led off by saying that their holiday shutdown would be followed with a "corporate restructuring period" during which "Gen9 will not be accepting orders". The next day came an article from Scott Kirsner detailing the effective shutdown of Gen9 and sale of its assets to Ginkgo Bioworks for an undisclosed amount of cash and stock.  Interestingly, Kirsner reports that only 10 Gen9 employees will make the transition and that most of the Gen9 staff was laid off in mid-December.  It is surprising that no gossip of the cutbacks seemed to enter my radar, given a number of personal connections to the company (CEO Kevin Munnelly was a colleague at Millennium; several members of the Gen9 business group were ex-Codon or ex-Infinity and we had done limited business with Gen9)

Bio-Rad Sips Up RainDance

Monday evening brought news that Bio-Rad has further consolidated its grip on the droplet microfluidics space by acquiring RainDance Technologies for an undisclosed price.  Bio-Rad had previously acquired droplet digital PCR company QuantaLife back in October of 2011 and targeted sequencing company GnuBio in April of 2014.  While the droplet digital PCR has been marketed for many years now, the GnuBio effort had gone relatively quiet since the acquisition.  However, Bio-Rad announced the JP Morgan conference that this technology will be launched as OncoDrop late this year.

Illumina Unveils HiSeq Successor NovaSeq

At today's J.P. Morgan Healthcare Conference Illumina made a number of small announcements -- some new partnerships, Firefly on track for launch later this year, launch of the single cell workflow partnered with Bio-Rad.  Then CEO Francis deSouza dropped the big news: a new high-end sequencer architecture to ultimately replace all of the HiSeq instruments.  It sounds like an interesting evolution of the Illumina product line, but unfortunately too many headlines and tweets have focused on a distant goal of $100 human genomes.  Worse, not only did some commentators misconstrue the announcement as delivering on $100 genomes, but some also touted a sequencing speed of one hour for a genome which isn't remotely true.

Pondering What Is Lost In Teaching Translation

I'm good at acquiring distractions, and a relatively new one is Quora.  This site allows users to ask questions which are then answered by members of the community.  I lurk in a number of fields, but have answered a few questions related to genomics and related fields of biology.  Tackling a question last night required re-learning some details I was disappointed I had forgotten.  In researching to regain that knowledge, I skimmed a number of study guides online, which leads to this post.