Closing the books on 2015

The last line of Perl has been written, the last SQL select executed. As 2015 draws to a close, I want to extend a thank you to everyone who has read this blog, commented on it here or over on Twitter, followed me on Twitter, engaged me on Twitter, or any of the other myriad of ways that suggest that what I write and tweet is of interest to others. It is very rewarding to know that others find this space engaging, and I hope to continue to earn your attention and time.

So long 2015.  I mustered a bit more resolve this year than previous years, hitting the 5th most number of posts for a full year (which should make it the median). 2016 promises to be an exciting year in the sequencing and genomics arena and I will try to both up the frequency and reduce the variance in the frequency of these posts -- ideally while improving the quality.  Will I succeed -- only you, the reader, can score the quality aspect.

Loose 2015 Threads #2: Thanks for the help with bootstrap values

I owe a belated thank you to everyone who responded to my post on my muddled thinking around phylogenetic tree bootstrap values.  I think I'm straightened out now and even dare to think I can explain this to someone else. 

Loose 2015 threads #1: MiSeq 2x300 Issues

Before 2015 ends, I'd like to tie up two loose threads.  In doing so, I'll deviate slightly from my usual pattern and publish two posts in a day; I could have lumped them together but instead I'll split.  First up, a belated explanation, prompted by a comment, of my mention of issues with the MiSeq 2x300 reagents and a bit more on my confusion with regard to bootstrap values.

Thoughts on the Synthetic Biology of Seveneves

Neal Stephenson's Seveneves is a sprawling space novel of truly epic ambition and scope, which I enjoyed thoroughly.  I'm not going to review it or give a detailed plot summary, but there are aspects related to the biology angles which interest me enough to scribble -- which means I must reveal some key plot points.  I've grown increasingly sensitive to spoilers and (yo Charles Schulz's ghost: thanks for wrecking Citizen Kane for me at a young age!) for myself prefer to go into a major book or movie as cold as possible.  So, if you haven't read the book and were planning to do so, please don't jump beyond the jump break.  If you do, don't blame me for any reveals!

MinION and Time-to-Result

Peripatetic blogger Dale Yuzuki posed a question on my last piece which I'll answer with a separate post because it crystallizes for me what makes the Oxford Nanopore platform so different for a large number of counting-type assays.  Dale's question was on Zev William's talk on pre-implantation screening and the number of reads required.

MinION Community Meeting 2015: Reflections & Wrap-Up

I spent the end of last week at the New York Genome Center for Oxford Nanopore's MinION Community Meeting 2015.  Since the family joined me for the weekend, I let my thoughts simmer for a wrap-up.  Plus I've been spending time scrutinizing the complementary "pen" for a USB connection and sample port, with no luck.  Wisely, I've given up on that -- so I can start the same process with the "notepad".  I've also finally stopped looking over my shoulder for a pitchfork-and-torch crowd after my numerous Twitter miscues, ranging from omitting speakers' names and affiliations to various mutations of the official hashtag (when I remembered any hashtag).  For a slightly better synthesis of the Twitter stream, see my Storify.

Admitting to Ignorance on Interpreting Bootstrap Values

Okay, one of the points of this space has always been to crowdsource the project of educating myself, which also means on of the underlying principles is that I sometimes need to admit ignorance in a very public manner.  After staring at a lot of phylogenetic trees, I've sufficiently unglued my confidence in my deep understanding of the principals (beyond coming just plain unglued) of confidence / bootstrap values.  Despite trying a number of sites and reviews and threads on the Net, I can't quite find a detangling of the particular mental knot I've tied, so I'm throwing out the problem for group help.

Well, that was brief!

BGI news today is that they are jettisoning the Revolocity large sequencing system, announced all the way back in June.  Along with the product abandonment, 40% of the ex-Complete Genomics group in the Bay Area is being laid off, with remaining staff focusing on the desktop BGISEQ-500 sequencer.

Do Demons Dream of Phylogeny Packages?

Miserable day today  - spent my entire day wrestling with bad formats and flaky tools and trying to bull my way past them, leading to many a mad expostulation. The whole day down in the pit, with the pendulum of multiple deadlines swinging just over my head. The MBTA released new schedules that muck with my routines.  And the then to top it off, Mick Watson writes a piece titled "The Five Habits of Bad Bioinformaticians" that cuts far too close to home.  So I arrived home in a foul mood, my senses unpleasantly heightened to every sound.

Comments on "The use and misuse of supplementary material in science publications"

Mihai Pop and Steven Salzberg have an opinion piece in BMC Bioinformatics titled "Use and mis-use of supplementary material in science publications", examining issues arising from the ever growing data supplements accompanying papers, particularly in high-profile journals with strict article length limits.  Pop & Salzberg make a number of important points, but there are some topics they didn't cover that I think are also worth treatment.

HelicosTech Back on the Dance Floor?

It's Halloween, and as is my habit I fired up Saint-Saëns, As death tunes up his violin in a graveyard, the dead residents live again and dance with abandon, until the rooster (oboe) crows in the dawn. In a similar vein, a pre-print on bioRxiv has demonstrated new life in the Helicos single molecule sequencing platform, though while the platform stopped being commercially distributed (and Helicos went bankrupt just under 3 years ago), a scrappy little company called SeqLL has kept up a service business.  A new Chinese company called Direct Genomics, with two Helicos founders onboard, plans to commercialize the new version of the technology.

BGI Launches the BGISEQ-500

This weekend brought the formal launch of the BGISEQ-500 desktop sequencing instrument from BGI (though deliveries won't begin until early next year).  Utilizing the ex-Complete Genomics ligation technology also used in the Revolocity system, the instrument appears to sport a price similar to the Illumina NextSeq but offers throughput somewhere running from a NextSeq up to the low end of a HiSeq. Two flowcells can be run at a time (apparently in sync with each other, unlike QIAGEN's long-delayed machine), with a small and large versions of the flowcells.  There's some ambiguity on questions such as the precise read length, though it is very short compared the the typical Illumina offerings.  Dale Yuzuki has a nice write-up (complete with a picture next to the box) based on attending the International Congress of Genomics 100 where it was unveiled.  One of these days I should wangle my way to that conference -- not only would the genomics be fascinating, but China holds a special allure -- or more specifically, Ailuropoda, for our household.

Concepts for Better Sequencer Calibration

Last week's release of the MARC data for the Oxford Nanopore MinION rebooted a train of thought I've had around DNA samples used as standards.  Ideally, standards would meet a number of criteria, though some of these may be inherently in conflict and there are issues of practicality. But as a whole, the standards used for molecular technologies are often short of ideals in ways which could be addressed, as I will attempt to argue here.  While many of my comments will be placed directly around MinION, many apply to other platforms -- as would solutions I have been contemplating.

Dovetail Takes Flight

Back in March I covered the unveiling of Dovetail Genomics' approach to scaffolding genomes via deriving long distance constraints from reconstituted chromatin.  This morning the company announced full access to their genome sequencing and scaffolding service.   Founder Ed Green and CEO Todd Dickinson chatted with me by phone last night about this launch.

Dovetail's offering is a complete service for sequencing or scaffolding large animal or plant genomes.  Users can choose from a menu of service components, which can range from scaffolding an existing short read assembly for around $10K to a complete genome sequencing and scaffolding for around $40K, with a turnaround in either case of 6-8 weeks and scaffold sizes on the order of chromosome arms.  

Since the beta program opened in the spring, Dovetail has worked to streamline both their wet lab and informatics protocols as they completed over 45 different customer projects.  Of particular note is that the input DNA requirements are down from 5-10 10ug to 1-2ug.  However, the Dovetail team agreed with my comment from before that with their current markets, de novo sequencing and structural variant calling on known genomes, input DNA has not been a serious constraint.  They do believe they can substantially reduce the requirements further, perhaps to a few hundred nanograms.

While the service offerings can include users supplying their own high molecular weight DNA, Dovetail prefers to perform the extractions in house.  The logic here is simpler: results are critically dependent on the size of the input DNA.  As a result, Dovetail has spent great effort becoming expert in extracting DNA from a wide variety of different species and sample types, as well as using pulsed-field gel electrophoresis for DNA quality control  

Dovetail is currently offering their Chicago technology only as a service, which has obvious advantages.  Anyone who has attempted technology transfer will know how difficult it can be to make a process consistently repeatable at multiple sites, not to mention the variances that can easily creep in due to the vagaries of shipping.  Aspects of this can be seen in the recently released MARC data for Oxford Nanopore.  For users, a pure service offering means no learning curve and no equipment purchases; just turn over some biomass to Dovetail and wait for a high quality genome to be returned.

That doesn't mean kits aren't in on the horizon; Dovetail does plan to offer them at some future point.  Also in future plans is expanding the service offerings to include metagenomes and haplotype calling. In the nearer term, a publication describing the scaffolding of a human sample (NA12878) and the American Alligator genome, which Dovetail has discussed in the past, is "well along" the publication pipeline.  While the current offering is based on Illumina sequencing technology, Dovetail emphasizes that the technology itself is platform-agnostic.  In a similar vein, when asked about how Dovetail differentiates themselves from the growing swarm of long range technologies, including Oxford Nanopore, PacBio Sequel, BioNano Genomics, and the now-launched 10X GemCode, their team praised the field  as full of exciting technologies, but emphasized that they offer the ability to scaffold complex genomes very fast with no specialized equipment and no new techniques to learn..

Personally, a pure service offering is very attractive, since that means not having to find internal resources to learn the new technology and then execute on it. I checked with Dovetail, and while I don't have $40K burning a hole in my pocket, if I did I could grab something out of the garden or from the local seafood market, I really could have a complex genome scaffold of my very own in about two months.  That's an exciting vision, and perhaps will be a major force in the sunsetting of science's tolerance for highly fragmented draft genomes.

MARC spots the Ox(ford)

Last week's end brought the initial report from MARC, the MinION Analysis and Reference Consortium, detailing a body of experiments intended to benchmark the performance and consistency of the Oxford Nanopore MinION sequencing device.   The MARC paper is also the inaugural research article in F1000's new channel for nanopore papers.

PacBio Sequel: Smaller Box, Bigger Bang

Boy, am I regretting taking a vacation from online due to being engrossed in A Canticle for Leibowitz.  Between last night and this morning, my neglect of my Twitter feed meant a colleague tipped me to the new PacBio machine with "what's this Sequel I keep hearing about from PacBio".  So a lot of folks had a huge jump and covered it pretty well, including Keith Bradnam, Mick Watson, and James Hadfield.  Long rumored, the new instrument costs about half as much (but that's still $350K), takes up much less floor space (and doesn't need any reinforced floors) yet the new flowcells deliver about 6 7 times as many reads than the older ones.  WOW!

Farewell Nabsys

A bit over a week ago brought news that mapping instrument hopeful Nabsys had ceased operations.  As a veteran of one failed biotech, I have a lot of sympathy for the team there. Plus, I knew a bunch of folks at the Providence RI firm.  Nabsys's signle molecule mapping technology was a wonder -- what single molecule technology isn't? Already stories are emerging of a disgruntled founder who wants to buy up the intellectual property and give it another go. It is easy to admire that stick-to-it spirit; it's a lot harder to find a rational reason to believe that such a revival will be any more successful.

How Do You Differentiate Archea and Bacteria in the First Week of High School Biology???

I have a long standing interest in biology education -- I seriously considered it as at least a career to explore -- but now I really have skin in the game.  TNG just executed a schedule move that will defer his biology this year to the second half of the term, but I also have a niece who is taking AP Biology at her STEM high school.  Even in his short time in biology class, TNG has succeeded in asking for homework help that has me scratching my head.

Freely & Unrepentantly Confessing to Heresy

Keith Bradnam reported a huge influx of traffic for a recent post -- not surprising, since he labeled it NSFW (Not Safe For WorK).  And yes, despite my skepticism that it would be truly offensive, I'll confess I checked it with phone, not my work laptop.

Ion's S5

The Ion Torrent team rolled out a new sequencer line this morning, the S5.  The S5, whose impending release had been tipped on the internet by the leak of a manual, arrives in two models, the standard and the XL, which differ only by on-board computing power and not sequencing metrics.   As has been the trend, Ion's focus is entirely on focused sequencing, and the new lineup emphasizes making targeted sequencing with AmpliSeq and other approaches fast and simple.

The Road to Hell is Paved with Bioinformatics Formats

If you really want to raise a bioinformaticist's blood pressure, loudly declare your new tool generates output in brand new data formats.  This leads to the frequent observation that a large fraction of bioinformatics work is simply converting formats. It is probably consensus that the field is awash in too many formats, though it is equally clear that we can't agree on which should survive.  Between some recent news and a Twitter thread on the subject that erupted last night, there was a bunch of fodder for me to collect in a Storify -- and to lay out my own idiosyncratic views.

Do Helix's Numbers Work?

A number of efforts in the consumer genomics space have been attempted in the past, with 23andMe appearing to make limited headway and Knome not much at all.  I haven't been able to get any investment interest in my own concept, though perhaps that's because it was tongue-in-cheek (or tongue held out while panting).  Last week brought a big splash, with a new company Helix launching with $100M and three major players as backers: Illumina, LabCorp and the Mayo Clinic

Clinical Metagenomics Pipelines: Revisiting & Reflecting

When I set out to start this blog nearly over eight years ago, I set myself a number of goals.  One goal was to take some risks -- not crazy risks but to not just play it safe.  But counterbalancing that goal was one to be open, accurate and honest. My piece last week on clinical metagenomics pipelines had a fair amount of attention, and resulted in an ongoing electronic conversation with one of the key parties.  In the course of this, there are now parts of that piece I wish I had handled differently. Some other important topics have been raised, and I would like to cover here.

Leaky clinical metagenomics pipelines are a very serious issue

Update: Some significant issues with the tone of this post are discussed in a follow-up.

I am a firm believer that the practice of science is the result of contingency; we do not necessarily have the best scientific culture possible but rather one which has evolved over time driven by chance, necessity and human nature.  We should never hesitate to re-examine the way science is actually practiced, and that particularly holds true for how we analyze data and publish results.  A re-analysis of a prominent Lancet paper has just come out in F1000, and this work by Steven Salzberg and colleagues illustrates a number of significant issues that slipped past the conventional peer review publishing practice

June 2015: Busting Out All Over with Genomics Technology

This month I again entered the prime of my life, though next year my programming brother points out that next year I (and the first Apollo manned missions) hit the big 30.  Beyond my personal milestone, it's been a busy last couple of weeks on the genomics technology front. Despite a lack of conferences or other traditional venues, big news has poured out from Pacific Biosciences, BioNano Genomics, Genapsys, BGI (which had another announcement earlier in the month), 10X Genomics and a pair from Oxford Nanopore.

BGI Unveils a Sequencing Factory to Go

When I was in George Church's lab, he submitted a grant proposal (which, alas, was not funded) for a sequencing factory to generate one megabase of data per day.  In those days that was an ambitious goal, and the plan would have truly been on a factory scale, with a large workforce and an assembly line of stages to yield the final product of data.

Is Illumina Serious About an Alternate Chemistry for the Rapid Amplicon Market?

Back in January, at the end of my post on Illumina's new machine lineup I speculated whether Illumina might see a niche for a lower cost, lower throughput sequencing system that would slot below the MiSeq in their lineup.  Such an instrument, I posited, might go after applications in biosurveilance and diagnostics where relatively small amounts of data are needed quickly. I speculated that perhaps a smaller instrument with less expensive optics could compete in this arena, which is heating up due to Oxford Nanopore and the growing acceptance of DNA-based diagnostics.  As luck would have it, a few days later Molly He, Mostafa Ronaghi and colleagues at Illumina actually published a proof-of-concept paper for just such an instrument.  Unlike many sequencing technology PoC papers, this one demonstrates feasibility of reading actual templates (phiX rides again!). 

London Calling Wrap-Up

The second, and final, day of Oxford Nanopore's London Calling conference concluded last Friday -- and I'm behind on writing it up.  Some of that was due to travel (and the wrong power supply going on the trip) and post-trip exhaustion, but failing to finish this last night was pure slacking. That route was shut down when one reader asked when I'd get things done.  Anyway, I again organized the activity into a storify story as I did for the first day of the conference. I'm going to go into less detail on individual presentations below and instead engage in the vice of far-ranging speculation.

London Calling Day 1: Highlights

Oxford Nanopore's London Calling conference kicked off today; I've Storified a large collection of Tweets from it, covering today up through about dinner.  I'll summarize some highlights below

Oxford Nanopore's London Calling: Pre-meeting speculation

Oxford Nanopore's London Calling confab starts up in a matter of hours.  Alas, several issues scotched my plans to attend (not only does it promise to be an exciting conference, but I simply love exploring London on foot).  It is worth emphasizing that the MinION devices and consumbables have been out in the wild for not quite 11 months at this time.  In that time, Oxford has dealt with a wide variety of technical and logistical headaches. While performance is still variable, many MAP participants are forging forward and the available tools for nanopore data continue to grow.  London Calling will likely bring a burst of new announcements; Oxford's Clive Brown has been giving talks recently but has promised that exciting stuff has been reserved for the confab.  Below is a set of semi-informed speculations calling out likely happenings, mostly based on Clive's recent presentations and tweets.

PacBio's New Sample Prep Plan: Too Late to the Dance?

Pacific Biosciences had a string of announcements around its earnings release last week.  Of particular interest is a collaboration with RainDance to develop a new sample preparation system for generating long synthetic reads from minuscule inputs.  If some of that sounds familiar, the loose outline in the press release suggests an approach similar to that of 10X.  But is this proposed system arriving too late to the party?

Revisiting the RNA Tie Club

As mentioned previously, by wonderful luck I now have regular contact with Ash from the Curious Wavefunction, and he has stimulated a new burst of scientific history interest in me.  I've ripped through a bunch of scientific memoirs -- by Crick, Djerassi and Dyson -- and have learned how to summon the biographies of Wilkins and Chargaff, as well as trying to dive again into The Eighth Day of Creation.  One topic I keep stumbling across is an interesting little bit of genetic history called the RNA Tie Club, which is a story worth re-telling and re-examining

Interested in the History of Biotech Companies? Don't start with Wikipedia.

I'm generally a big fan of Wikipedia and use it often for background research.  I've gotten more active this year in editing it, particularly around biographies of scientists.  For example, this year I've made major additions or edits to the entries for Walter Gilbert and Arthur Pardee and the , created entries for Martinas Ycas, Benno Müller-Hill, Monica Riley and Helen Donis-Keller. I also stumbled my way into a campaign of major revisions to the entry on Marie Antoinette, getting sometimes into a revision war with one other editor (which we resolved with a truce).  Along the way I've gotten almost adept at writing Wikipedia references and discovered a bizarre recurrent vandalism of Wally's page in which the vandal changes his name and personal details.  Recently, I've discovered a whole category of flawed entries: those on companies in the biotechnology industry.

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?

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.

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. 

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?

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?

What's Been Cooking for Ion At AGBT15

Rounding out my remote coverage of platform news from AGBT, the Ion Torrent team also lent me some of their time (and at risk of sounding obsequious, I do greatly appreciate this -- vendors have almost no down time at these events) to touch on some of the topics I I wrote about in my Ion history and speculation piece.

10X Reveals Its Facets

Perhaps the heavily anticipated launch at AGBT this year is the library prep instrument for 10X Genomics.  This Bay Area startup made a huge splash at the beginning of the year by announcing a monster ($55.5M) financing.  A member of my professional network had been part of the early team and had given me very minimal hints at last year's AGBT, so I've been eagerly awaiting details for a long time. Several members of 10X's team were kind enough to chat with me by phone yesterday with the proviso that I hold off on launching this piece after their talk today at the conference (interestingly, I had crossed paths with all of them in some previous setting).  Also, they sent me some promotional materials and permitted me to post some clips from them. Now, the GemCode system is officially launched, with orders being taken now and devices planned to be delivered in early Q2.

Illumina Launches NeoPrep (#agbt15)

The 2015 AGBT conference started out today.  A few hardware makers have let me chat by phone with members of their team, since they're there and I'm not.  Tonight's dispatch is from a chat with Illumina focused on their now launched NeoPrep library preparation instrument

Can Ion Torrent Buzz Again?

In my AGBT 2015 Preview / Speculation at one point had a tightly packed (and overly long) paragraph on Ion Torrent, but I realized that this was a symptom of trying to to cram too much in too little a space -- plus I really had a lot more thoughts worth unpacking.  So here's a long form look at Ion Torrent -- with plenty of references to past AGBTs to make writing this now apropos.  One advance bit of excuse making: the historical background that follows is not intended to be a comprehensive history of Ion Torrent technology, but more of an impressionistic sketch (but as always, my worst excesses and omissions are fair game for comments!).

#AGBT2015 Preview

The annual genomics party on Gulf of Mexico beaches named AGBT runs next week, and already there have been some speculations flying.  I'd better dash something off before I'm any later to the preshow -- or more importantly before I get contaminated with embargoed information.

The MBTA Must Embrace Data!

As you may have heard, we’ve had a bit of snow in the Boston area recently.  Two storms, one the beginning of last week and one which just ended yesterday, each dumped close to a meter of snow in the area.  The two storms each had different profiles: last week’s storm featured rapid snowfall and furious winds, with the snow falling over a 24-36 hour period.  The more recent storm started on Friday afternoon, ended on Tuesday morning, with a steady fall of lazy snowflakes.  Last week a hare, this week a tortoise.  But both weeks, a paralyzed Boston from a transportation standpoint, with the MBTA mass transit system performing dismally.

Unfortunately, the main response to that failure has been a lot of political theater. GM Beverly Scott gave a press conference yesterdaythat featured the usual refrain: the system features antiquated equipment, our crews are working hard, nobody could deal with this.  In other words, a string of unquantifiable and unactionable clichés.  There's already an unhelpful murmur in the press that Scott might be fired, which would seem little fix but mostly fodder for more column inches of newspaper opinion (such as this and this)

How not to write a sequence assembly comparison paper

Lex Nederbragt flagged, via Twitter, a preprint on the F1000 site with a questionable table comparing sequencing systems.  Alas, once I looked at the paper I've gotten myself in a state where only writing up its numerous deficiencies will free my mind of it.  I've even volunteered to F1000 to review the paper, but I haven't heard anything and so I will use this space.  I'm afraid this paper fall into the small category of manuscripts that I would recommend rejection.

The preprint is titled "Advantages of distributed and parallel algorithms that leverage Cloud Computing platforms for large-scale genome assembly".  Alas, the paper doesn't attempt to deliver anything of the scope promised by that, and the abstract isn't much better.  Most papers have a certain amount of preamble and then deliver some new finding; the preamble to the paper is overlong and badly executed, and the work in the paper is far too minimal and also badly executed.

Cargo Cult Networking & Other LinkedIn Laments

LinkedIn is a social media tool I find greatly flawed, but useful.  Part of the devil's pact one makes with LinkedIn is to receive great amounts of requests from individuals who wish to grow their networks.  I have a personal guideline for such which help me weed through the requests, but last year I got a request that had me laughing -- and slightly revising that guideline.

JPM Wrap-Up:

In this final installment of a series of reactions to news coming from the J.P. Morgan Conference, I'll cover an interesting complementary technology that was announced.  But first, it might appear my prediction of no radical sequencer announcements may have been invalidated, with an announcement from BGI of plans to launch two sequencers based on Complete Genomic's technology.  Unfortunately, the only outlet that seems to have covered this is GenomeWeb, and it is in their premium (paywalled) section, so I know nothing beyond that.  It appears this was only announced around JPM and not at JPM, so I have a Clintonesque out as well.

Illumina's Expanded Lineup

In my JP Morgan predictions for sequencing platforms, I didn't do badly.  The only major player to make a platform announcement was Illumina, and they did indeed announce instruments that are not radical departures from the prior platforms.  I am kicking myself for not making more specific predictions, as the nature of the new boxes was really unsurprising and it would have been nice to nail that.

2015: Another Year of Sequencing Evolution (not Revolution)?

The J.P. Morgan Conference is firing up, and for the past few years that has meant big sequencing platform announcements -- HiSeq or Ion Proton or such.  This has stolen some of the thunder from AGBT in terms of major announcements (sadly, I won't be attending this year -- and will try not to land my self into surgery the way I did the last time I didn't attend AGBT).  I figured I'd better write this tonight before any more JPM-related sequencing instrument announcements show up, or more to my prediction, before the conference ends without any.

Druggability: An Underappreciated Issue in Translating the Human Genome Into Therapeutics

I'm sorely guilty of neglecting this space, but a recent (and now storified) Twitter conversation from Jonathan Eisen (@phylogenomics) has improbably fired me up enough to scribble something.

Reanalysis Lays Bare MinION Review's Spectacular Flaws

I will confess that when our first MinION burn-in data for lambda came in & I threw a few aligners at it (after first getting my data extractor in Julia shaken out), I was disappointed at the results.  Very few 2D reads, very few aligned reads and the alignments all short.  At this point, I sat back to wait to see what others had experienced and to think of additional bioinformatics approaches.  It never occurred to me to dash off a glorified  blog post and submit it to a journal.

Oxford Takes Some Flak, Fires Back

A huge event in the genomics community this summer has been the Oxford Nanopore MinION Access Program (MAP), which has enabled a sizable but select group of researchers to try out ONT's novel nanopore-based sequencing technology.  While results and rumors have periodically drifted out over the summer, this week saw three disclosures, one of which resulted in fireworks and action

The good, bad & missing from Bio* libraries?

As I mentioned recently, I've been exploring how I might use the emerging Julia language to solve problems.  While that requires a large amount of mental work, I see some potential gains, both in having more readable code than Perl as well as to potentially leverage a lot of high-level concepts for parallel execution that are built into the language.  But beyond the challenge of elderly canine pedagogy that I present, there is the issue that the BioJulia library is quite embryonic, with serious consideration of treating much of the existing code base as a first draft (or, that is the impression I get from skimming the Google group).  So I'm going to try to pitch in, despite my multiple handicaps.

After the New Yorker piece, what of disruptive innovation?

I don't read a lot of books aimed at the MBA crowd, but one set I have liked, and sometimes cite here, are Clayton Christensen's on inovation and disruption.  As you may have heard, a recent article in the New Yorker by Jill Lepore took a gimlet-eye view to the whole concept and raised serious questions about Christensen's methods.  This was then summarized by another author in Slate and since then Christensen has responded in part via a Business Week interview.  He's also scheduled to be interviewed on PBS this weekend, so likely there will be further developments.  Indeed, after sketching this out on the commute home I discovered a Financial Times article whose tone is very similar to what I have written below.

Dabbling with Julia

As I've remarked before, I've done significant coding in a large number of languages over the last 35-or-so years.  I don't consider myself a computer language savant; I've known folks who can pick up new languages quickly and switch between them facilely, but for me it is more difficult.  I haven't tried learning a new language in perhaps 5 years, but this week I backed into one

NGS Saves A Young Life

One of the most electrifying talks at AGBT this year was given by Joe DeRisi of UCSF, who gave a brief intro on the difficulty of diagnosing the root cause of encephalitis (as it can be autoimmune, viral, protozoal, bacterial and probably a few other causes) and then ran down a gripping case history which seemed straight out of House.

A Sunset for Draft Genomes?

The sun set during AGBT 2014 for a final time over a week ago.  The posters have long been down, and perhaps the liver enzyme levels of the attendees are now down to normal as well.  This year’s conference underscored a possibility that was suggested last year: that the era of the poorly connected, low quality draft genome is headed for the sunset as well

How will you deal with GRCh38?

I was foolishly attempting to catch up with Twitter last night during Valerie Schneider's AGBT talk last night on the new human reference, GRCh38. After all, my personal answer to my title is nothing, because this isn't a field I work in.  But Dr. Schneider is a very good speaker and I could not help but have my attention pulled in.  While clearly not the final word on a human reference, this new edition fixes many gaps, expands the coverage of highly polymorphic regions, and even models the difficult to assemble centromeres.  Better assembly, combined with emerging tools to better handle those complex regions via graph representations, means better mapping send better variant calls.

So, a significant advance, but a bit unpleasant one if you are in the space.  You now have several ugly options before you with regard to your prior data mapped to an earlier reference.

The do nothing option must appeal to some. Forgo the advantages of the new reference and just stick to the old. Perhaps start new projects on the new one, leading to a cacophony of internal tools dealing with different versions, with an ongoing risk of mismatched results. Also, cross your fingers that none of changes might be revised if analyzed against the new reference.  Perhaps this route will be rationalized as healthy procrastination until a well-vetted set of graph-aware mappers exist, but once you start putting-off it is hard to stop doing so. 

The other pole would be to embrace the new reference whole-heartedly and realign all the old data against the new reference. After burning a lot of compute cycles and storage space running in place, spend a lot of time reconciling old and new results. Then decide whether to ditch all your old alignments, or suffer an even larger storage burden.

A tempting shortcut would be to just remap alignments and variants by the known relationships between the two references. After all, the vast majority of the results will simply shift coordinates a bit, but with no other effects.  In theory, one could estimate all the map regions that are now suspect and simply realign the reads which map to those regions, plus attempt to place reads that previously failed to map. Again reconciliation of results, but on a much reduced scale.

None would seem particularly appealing options. Perhaps that latter route will be a growth industry of new tools acting on BAM, CRAM or VCF which themselves will provide a morass of competing claims of accuracy, efficiency and speed. Doesn't make me at all in a hurry to leave a cozy world of haploid genomes that are often finished by a simple pipeline!

Illumina's New Lineup

Illumina made a brace of big hardware announcements at this week's J.P. Morgan conference, and Mick Watson has done a nice job of covering them.  I'll try to cover some different points that have occurred to me after letting the news ferment -- plus Illumina made yet another announcement tonight that scotched a portion of an earlier draft of this piece.

Relearning Chemistry

An evening ritual is to inquire what homework requires assistance, and at the beginning of the year it was a science worksheet as part of an introduction to chemistry.  That, and a later project, have exposed how much rust my knowledge of chemistry has accumulated, but also have led me down the path of repairing forgotten bits and certainly learning some new stuff

Envisioning The Perfect Scaffolder

Rather than make any New Year's resolutions of my own, which I would then feel guilty about not keeping, I've decided to make one for someone else: they will write the perfect open source scaffolder.  There's a lot of scaffolders out there, both stand-alone and integrated into various assemblers, but none are quite right. 

If you are sequencing an isolated bacterium or archean and are looking for a scaffolder, except in a few rare cases, you're doing something wrong: given enough long reads from PacBio it should be possible to solve nearly every bacterial genome. But, if you're sequencing eukaryotic genomes or any metagenome (or you're unlucky or data short on a simple microbial genome), you're probably in the market for one.  I'm going to supply a list of attributes I cooked up during a long drive up the Eastern Seaboard today, without much regard for feasibility or even if some conflict with each other.

Peering Through the Flowcell Glass, Darkly

As 2013 draws to a close, I've decided to stick my neck out and make some predictions for 2014.  Perhaps I'll get lucky and a few will even come true!  After several mental experimentations on the structure, I'll settle for stepping roughly past each major player.

Assembly Could Benefit From More Circular Reasoning

It was very gratifying to get comments on my recent piece on a de novo assembly review from both a referee of the manuscript (the amazing Heng Li) as well as one of the authors of the piece (though I am truly feeling guilty I forgot to reach out to the authors).  Of course I was having my usual post-post regrets of things not written, such as the whole interesting topic of dealing with (and leveraging) uneven coverage in metagenomes and when assembling from amplified samples.  But one other thing I was reminded of is one of the minor complaints I have with assembly programs: a lack of proper handing of circular genomes.

Assembling a Review of a Review of Assembling

A review on short-read de novo genome assembly appeared recently in PLoS Computational Biology, titled "Next-Generation Sequence Assembly: Four Stages of Data Processing and Computational Challenges".  I think the review has a number of merits, but I also find a number of frustrating flaws.  I'm going to write this entry much as I would have written a referee report on it.  Unfortunately, that will mean I'll dwell a bit more on the flaws than the assets, but if you are interested in the field

Did The Biochemists of Yore Know Morse Code?

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!

Spanish Prisoner, ZX-81 or Turbo Pascal?

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.

Ion Previews More Accurate Polymerase, Faster Template Prep

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.

Ripples from 454's Shutdown Announcment

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.

Roche Taps PacBio for Human Diagnostics

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).

Potential Sources of Drag on PacBio's Long Read Performance Trajectory

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.

SGE Isn't For Dummies (I sort of wish it were)

Kendall Square used to have the ultimate geek book store, Quantum Books.  No fiction or graphic novels there; it was all technical books.  One could browse every O'Reilly book and many, many others.

My biggest contribution to the field of biochemistry

LinkedIn has a feature by which one can endorse other people for different fields. Periodically the system prompts me to vote yea-or-nay on a bunch of endorsements, and conversely I get regular updates as to what others have endorsed me.  It's always nice to get a vote of confidence, but sometimes I find myself wondering what it really means.

An Incomplete Guide to Asking for Help on Your De Novo Genome Project

I've been thinking about this piece for a while, because I am a frequent presence on SEQAnswers.com and often dive into questions regarding de novo sequence assembly, particularly for small genomes.  It's good to help out and a way to feel like one is contributing to a broader community, but sometimes it can be very frustrating because the seekers (SEQers?) of help do not post their questions very well.  So, it would be helpful to have a post to point them to, though I'm sure there are considerations I either haven't thought of or will fail to remember to add.  So, those can either go into the comments or a future post, or perhaps something can go in the Wiki at SEQAnswers.

But in general, think of it this way: you have some experienced hands in a field you wish to enter, who are willing to give detailed advice for free.  But, they can't give that advice unless you specify your question well, and if you don't get it right the first time they may not see (or may ignore) your second shot.

What Might Knock Illumina Off Its Perch?

The big sequencing platform news this week is Roche's announcement that they are ending their collaborations aimed at developing new sequencing technologies.  A collaboration with DNA Electronics aimed to create an Ion Torrent-like system whereas a more ambitious effort with IBM aimed to create instruments based on "DNA transistors".  As noted by Forbes' Matthew Herper in a thought-provoking piece, Illumina is sitting very high atop the sequencer market.

For What is a 454 Still Great?

I've been mulling this item ever since AGBT, but have struggled with the title.  I don't want to sound like I have a grudge against 454 ( truth is I just got some good datasets off this technology), but I do believe that they are few papers away from being stampeded.  Or perhaps not; perhaps the community is really wedded to this platform.

PacBio Back of the Envelope Numbers

Back-of-the-envelope calculations can be quite useful, but also quite dangerous.  They are meant to be quick estimates, but can't be taken too seriously.  Still, I try to get them right & deeply regret overestimating recently on Twitter the cost of a human genome on PacBio by 3X.  Twitter is particularly dangerous: tempting to fire off a note, but impossible to pack in the full calculation

Post AGBT: A Longish Item on Long Sequencing

As others have noted, a significant theme at AGBT this year was sequencing at length.  While this year lacked true bombshells, PacBio impressed many with their making single-contig bacterial genome assemblies look easy.  Moleculo had been the object of much pre-meeting excitement, and while very few additional details emerged about their process, several talks showed what could be done.  As I have discussed previously, Nabsys demonstrated their “positional sequencing” system to select invitees in a hotel suite.  Optical mapping from OpGen and BioNano Genomics featured in a few posters, but did not attract much attention.  Oxford Nanopore had no physical presence, beyond a somewhat secretive suite, but several ONT staffers were happy to reiterate their confidence that they will launch their system – when it is good and ready.

AGBT: Nabsys unveiled

In the previous post I described the Nabsys positional sequencer. Yesterday I got o see it running in their hotel suite here at AGBT13.

AGBT Preview: Nabsys

A complaint which seems to be circulating on Twitter and elsewhere is that this year’s AGBT conference on Marco Island next week doesn’t look like it will have any excitement around new platforms.  AGBT has been a traditional coming out party for platforms.  Last year it was Oxford Nanopore which created a huge buzz, and in previous years that crown has been held by Ion Torrent, Pacific Biosciences, Complete Genomics and others (including a few which seem to have gone kaput).

It is hard to argue that this year’s program is much more heavily tilted towards applications of genomics than novel genomic technologies.  Many of the genomic technology talks are updates on the evolution of existing platforms such as PacBio and Illumina (especially the Moleculo technology).  But, there will also be novel technologies.  

This past fall I had the pleasure of spending half a day with the folks at Nabsys, located a short distance from Boston in Providence RI.  Nabsys’s buildings are in a sea of drab parking lots (not to mention sheriff’s cars; a courthouse is nearby), but on the interior were quite pleasant.  I was largely wearing my “day job” hat that day, but Nabsys will be unveiling their instrument at AGBT and has given me permission to talk about what I saw (and reviewed what I've written to make sure I didn't make some dumb errors, though the content is all mine).  Of course, I will update this after I look some more at AGBT.

Matthew Yuricich: A Pre-Oscar Tribute

I'm committing myself this week to an uncommon intensity of posting.  It's AGBT week, and while I'm there I plan to be busy both here and on Twitter.  Genomics has always been the focus of this space, but once in a while I beg the readers' indulgence while I write on something else.  Just after AGBT comes the Oscars, and in the likely case I'm completely exhausted (though sitting much more comfortably than I was for last year's Oscars), I want to scribble a long-overdue tribute.  For when the montage appears of previous winners who died since the last telecast, I'll be looking for the only Oscar awardee I ever met.  The nature of his work meant that many are utterly unaware of it, but he contributed significantly to the visual spectacle of many films, including one which influenced the look of a vast number of films of the same genre that followed it.  

Moving day

I was originally going to start this with a joke alluding to one of the signature special effects of Star Trek: The Next Generation, but given the recent events in Russia it's probably in poor taste to speak lightly of flashes in the sky.  But, after much preparation, today was the day that Warp Drive Bio completed packing up, with next week ushering in our new facility.

A Short(ened) Note on Ion Torrent & High G+C

As one might guess from reading this space, I always have an itch to try new sequencing technologies or updates to existing ones.  That's generally a good thing in my position, though more than a few times I experience buyers remorse.  At least this time, I found something a bit interesting

Illumina's Blizzard

As the clear leader in the genome sequencing technology market, Illumina is often in the news.  As befitting the winter season, there's just been a blizzard of Illumina news, mostly announcements from within but also two important external ones (an excellent summary of these can be found at NextGenSeek).

Not Exactly the First Tuesday After the First Monday of November

This past presidential election was as nasty as any in recent memory, and so perhaps folks are reviewing their support for Churchill's dictum ("Democracy is the worst form of government, except all the others").  But, I make a plea now that you vote again.  I'll even extend that plea to a request that you honor a deeply held tradition in some urban political systems, which is to vote early and vote often!

In Vivo Blog follows the biotechnology industry, and now for the fifth year in a row they have a poll as to the best biotech deals in three categories: M&A, Alliance and Exit/Financing.  We've been nominated in the Exit/Financing category for our monster financing arrangement with Sanofi, which gives us a $120M runway so we don't have to worry about running out of money (a fate I don't wish to repeat ala Codon Devices).  So, please vote for us!

Okay, perhaps you'd like to objectively consider all the contenders.  The voting site has links to detailed discussions of each of the candidates, and I'm sure after reading each one that you'll be convinced we're the best, and you'll want to vote for us!

If that doesn't appeal, perhaps you like good old fashioned sibling rivalry?  At the moment, we have ground to gain on two other companies funded by Third Rock Ventures, bluebird bio and Foundation Medicine.  Both are fine companies trying to make important health care innovations.  FM was even started by our CEO, reinforcing their big brother status.  But, are any of them trying to reboot an entire sector of the industry that big Pharma nearly universally abandoned?  That sounds pretty courageous, perhaps even legendary.  So vote for us!

Sometimes a vote is strictly for an individual, but other times it makes sense to vote for a team.  We're a team worth voting for: unified in our quest, unbounded in our efforts. 

I'm Keith Robison, Principal Scientist for Computational Biology., and I approve this message.

MUSKET then FLASH, vice versa or just COPE with it?

It's gratifying to see that yesterday's The Trouble with FASTQ item gathered a number of lively comments, and there are certainly a number of branches I could (and should) take from that post.  But one item that garnered both a comment here and on Twitter was the order of operations I described

The Trouble with FASTQ

I spend a lot of time working with sequencing data, and the most common format for such data is FASTQ.  FASTQ has many things to appreciate, but FASTQ data also can be troublesome

Scribl is Neat!

Speaking of Twitter, one thing I've found it highly valuable for is discovering new tools and ideas in the bioinformatics space.  It's not a replacement for all my other methods, but I've discovered things I otherwise would have missed.  A great case in point is Scribl, which I discovered over the holiday period and vowed to try out this morning.  WOW!

BTW, I'm on Twitter

For a long while, my only interaction with Twitter was to monitor key hashtags during AGBT and ASHG.  However, I've gotten myself sucked in and am now actually contributing.  As suggested by the username OmicsOmicsBlog (archives at this link), I'm treating this primarily as an extension of this space.  So if you look you'll mostly find genomics, bioinformatics and other geeky stuff. I post more often, given that it's actually possible to author tweets on my smartphone (I once had delusions of writing blog posts there; it's really not workable). To date, I've retweeted more than I've originated.  It's certainly a challenge to compress thoughts into 140 characters.

I'm sure this has been covered elsewhere, but the 140 character limit is a weird holdover from text messaging, which itself was a weird technological cram job on the cellular voice standards.  What would Twitter be like if that limit had been higher or lower?

Why Next Gen Now?

A confession: I've considered writing this piece for a lot of years now; not quite as many as this space has existed, but many years.  Some ideas get stuck in my head, but I never force them out through my fingers.  Finally,with this one, I will pose the question: Why did "next-generation" sequencing happen when it did?

Nanopores: Fission or Fusion?

It's fall, and the foliage in New England is putting on its usual spectacular show.  What isn't showing is any of the progress in nanopore sequencing that I got caught up in last February.  Oxford Nanopore made quite a splash, and I wrote a quite breathless account based on a phone conversation with them.  Since then, other than raising some serious cash, Oxford has been quite quiet, and has neither released any data the community (or at least this blogger!) is clamoring for nor is there any sign that alpha units have been placed.  Genia was another nanopore company making noises about unveiling this year, but now they have licensed a new nanopore-based sequencing chemistry and promised boxes in 2014.   When will nanopores actually hit the market?

Does Illumina Have A Sequence Diversity Problem?

Roughly speaking, NGS sample preparation workflows can be split into two basic classes of workflows.  Complete molecule workflows are currently suitable for microRNAs and other small fragments at the moment, but attempt to capture the entire molecule.  With luck, long read technologies will someday make these the standard.  Fragment workflows are the workhorse, and take input material (RNA, DNA) and convert them into a library of fragments representing (or directly from) the original material. 

BGI Gobbles Complete Genomics

An email this morning alerted me that BGI Shenzhen is acquiring Complete Genomics.  I hadn't been following Complete's business very carefully and had missed (or forgotten about) their quarterly report in August warning that they were dangerously low on cash and had engaged a firm to look at strategic alternatives.  If you are holding Complete Shares (with the wonderful ticker symbol GNOM), you'll get $3.15 cash for each for them.  If you were unfortunate enough to buy them at the top, that's over $11 a share in capital loss to put on next year's tax returns.  I'm not one to watch stock prices closely.  Buy-and-hold an index fund is my primary investment strategy; A Random Walk on Wall Street is the best route to sound sleeping and good returns.  I've never held any GNOM stock.

Shameless cancer quacks

A news item meant to shock its readers caught my eye, but in the end I was shocked and sickened in a way that I think lay far beyond the writer's intent.  The writer's tale is of a desperate family of a cancer-stricken teenager being taken advantage of by a fame-seeking hoaxer; the tale I read is of a desperate family of a cancer-stricken teenager being fleeced by cancer quacks.

Is Cambridge Almost Full?

If you tour around the extended Kendall Square area of Cambridge, you'll find a number of large construction sites.  Various projects for Pfizer, Biogen, Novartis and more speculative projects are consuming most of the large surface parking lots in the area, and many that are yet untouched (such as the one next to Starbase Athenaeum)  are marked out for development.  There are a number of single story buildings, such as the bank by the Kendall T-stop, which seem likely to also become such sites.  However, on the outskirts of Cambridge just such a proposal has kicked up a serious hornet's nest, and one that suggests that the biotech (and tech) real estate boom here may soon hit a serious wall.

Farewell to a Giant Leaper

When I was a boy, a nearly annual occurrence was a trip to Kentucky to my maternal grandparents' house.  My biological grandmother died when I was quite young, but there would be many visits to see my grandfather.  I enjoyed them greatly, but of course he is now long gone.  So I have a few regrets, and mostly I wish I had thought to ask him a few questions.

Owning a Sequencer is NOT a Prerequisite for Sequencing!

Besides the little cancer genomics piece yesterday, another genomics paper getting quite a bit of popular press attention is the nice work from the NIH tracking down a deadly outbreak of drug-resistant Klebsiella pneumoniae, with 11 of 18 infected patients dying.  Rapid genome sequencing provided a much higher level of detail for tracing the outbreak than older methods, even distinguishing isolates taken from different sites on the same patient.

The Perils of the Too Small Gene Panel

The newswires are alive with summaries of an item in Science Express which, discounting the supplementary material, isn't much bigger than the news articles describing it.  It's a nice piece showing the relevance of cancer genomics, but there's also a backstory fleshed out in the news items which is interesting.

The gist of the paper is this: a trial of everolimus, an MTOR inhibitor, in bladder cancer did not go well; very few patients showed benefit.  But, one patient did spectacularly well.  So the researchers performed whole genome sequencing and found inactivating mutations in the well-studied tumor suppressors TSC1 and NF2.  Screening 13 more bladder tumors with a panel of cancer-specific genes found 3 more cases of inactivating mutations in TSC1, plus one patient with a missense mutation of unknown significance.  In the trial, patients with TSC1 mutations stayed on trial longer than patients without the mutations.  

My first reaction was "this all makes sense" -- TSC1 and NF2 are genes which immediately suggested themselves as TOR-related. 

What's interesting from the news items is a suggestion that the original patient had been sequenced for a limited number of genes around mTOR, and that this did not include TSC1 or NF2.  Of course, the problem when doing a limited screen is picking who to include, and from my 2 second analysis on the train I would have included TSC1 and NF2.  But, that could be much easier said than done.  They are attractive, since they are tumor suppressors known to be mutated in cancer, but so are other genes in the neighborhood (such  as TSC2 or PTEN).  There are activating mutations known in the neighborhood as well, such as PI3K or various AKT family members.  Presumably it was a PCR-based (quite likely Sanger) method, in which case it can be challenging to target every exon both because you may have an "exon budget" (number of exons to be amplified) and some exons are nightmarish to amplify.  

I think the case illustrates one reason whole genome or whole exome sequence are by far the best strategies in a case such as this.  The potential payoff in understanding is huge, as you have one strong outlier patient.  The number of patients are small (though, admittedly, this is probably one success pulled from many dry holes).  Plus, these days the cost of WGS/WES is probably not much more than targeted PCR, given the costs of developing good PCR assays.  

The other potential advantage of WGS/WES, over even broad cancer-specific gene panels, for a case such as this, is that the field can change.  New oncogenes and tumor suppressors are identified periodically, perhaps even in the time period between when a panel is designed and it is used.  In a research setting to understand the basis of a clinical trial anomaly, it's particularly valuable to explore all corners, because what might not make sense today might become clear tomorrow.

Jackalopes & Guest Posts

Recently, the topic of jackalopes showed up at work.  Anyone who has toured the American West has probably come across postcards of these curious beasts, with the bodies of jackrabbits but antelope-like horns.  Even out East, at some frequency reports of these creatures appear stochastically.

An unconvincing case to X-out algebra

I had a bit of a long commute yesterday, driving from south-central New Jersey up to Starbase Cambridge.  In general it's a dull ride, having been done too often.  Still, it was the perfect time to absorb the magnificence of a George Washington Bridge crossing, followed by a great sunrise-lit view  from the loop ramp onto the Henry Hudson Parkway, and similar snippets of the Palisades also glowing in the early sun.  But, much of the time I was flipping through radio stations.  Due to this, I caught the tail end of a NPR interview with Andrew Hacker, who wrote a recent NY Times opinion piece calling for algebra to be removed from the required high school curriculum in the U.S., which has garnered letters both for and against.

Complete Genomics Goes Long

In Nature this week (as an open access article!) is a report from Complete Genomics and collaborators describing CG's new "Long Fragment Read" (LFR) technology for generating long range sequence information and haplotypes.  Technically, there is a lot of cool stuff -- but excitement for many (such as myself) must be balanced against CG's business model of sequencing only human genomes