Neil Hall is Responsible for Rising NGS Prices

“Wait, what?! Neil Hall is responsible for NGS prices actually inching up rather than continuing down to ever lower depths?”

No, not really.

Well, he kind of is. And most likely so is everyone reading this blog. (All three of you.)

It’s because DNA sequencing consumers didn’t ramp up their usage as quickly as Illumina was driving down the prices. When Illumina bumped HiSeq capacity from 300Gb per run to 600Gb per run, their customers said:

“Yay! The same amount of sequencing for half the price.”

To which Illumina responded:

 “What? No, no, no, no! You’re supposed to sequence twice as much. Actually, you’re supposed to sequence even more because the cost is so low that new applications are now feasible”.

And the stock market said:

“Hmm, I’ll have half that market cap back, thank you.”

So Illumina learned their lesson and decided to be more careful about releasing upgrades for the HiSeq. Right around the time they launched the 600Gb system, they said they were able to generate runs of over 1Tb in house. It’s been around two years since then, but still no update.

Why not? Because there isn’t any market pressure to do so. The only competition HiSeq had was SOLiD, but that platform has essentially been abandoned by Life Technologies as a commercial failure. (You can love SOLiD reads all you like, but even with a much bigger marketing and sales budget, it was still getting trounced by HiSeq. Too bad they didn’t release Wildfire a couple of years earlier – we might not be having this conversation right now.)

And while Illumina was busy dominating the high throughput NGS market, Ion Torrent came out and tried to carve out a different niche: much faster, much cheaper machines (albeit with lower throughput). And that niche has really taken off (especially in the clinical space). Illumina responded with their own machine (the MiSeq) and since this is the only space where they’re facing serious competition, it’s where they are concentrating most of their resources. This means we’re now getting much faster reads, but they aren’t really getting any cheaper.

So is the party over for cheaper reads? Since the ‘plateau’ was caused by market forces and not technological advancements, the answer is almost certainly “no”. Researchers will figure out ways to creatively use ever more sequencing capacity, and when they start bumping into the limits of what the current machines can do, those machines will almost certainly improve. And the competition could come back. Ion Torrent has stumbled on their original road map, but if they ever release the PIII chip, that could put pressure on the HiSeq. And while Oxford Nanopore is the latest to suffer from the hype-hate cycle, there are a lot more companies waiting in the wings to dethrone Illumina. Check out BlueSEQ’s ‘Emerging Technologies’ section of the NGS Knowledge Bank for a partial list.

Dr. Hall is right that the field would benefit from genome scientists focusing on “new ideas”.  He’s also right that the cost of sequencing will plateau. But I don’t think we’re quite there yet. And where it plateaus, whether that’s $1000, $100 or $10, will make a big difference. 

Edit: Gah! I totally forgot to include a link to Mick Watson's excellent take on the cost of sequencing.

X-Gen 2013

I recently had the pleasure of attending X-Gen (more formally known as ‘X-Gen Congress & Expo). This meeting falls on the small side of the spectrum, with a couple hundred attendees, and that suits me just fine. I prefer smaller meetings as I find it easier to network and generally keep track of what’s going on. It does, however, have parallel tracks – RNA Sequencing, DNA Sequencing and Data Analysis – so hard choices sometimes had to be made (e.g., a talk on Illumina’s Moleculo technology or one on duplex sequencing for rare mutation detection; Moleculo won out, but I really wanted to be at both). I’m not quick enough for live blogging – I can type up notes/thoughts, or I can listen, but I can’t do both. Therefore, I’ll just mention some of the things that stuck out in my mind.

• From Peter Park’s talk on the role of retrotransposition in cancer – 45% of the human genome is derived from transposable elements (most of which are under epigenetic suppression). This isn’t a new discovery, but I still find it fascinating. Same way I find it fascinating every time I hear about how our bodies harbor ~100 trillion microbial cells (dwarfing our ‘own’ 10 trillion cells). Anyway, this analysis is fairly tricky (presumably due to the difficulty of sequencing/aligning repeats), but longer reads on the horizon, like that of the Moleculo technology, should help.
• John Stam discussed the role of gene regulation in common disease. He mentioned something that, while it intuitively makes sense, I still found really interesting. When he piled up the results from 50 separate transcription factor ChIP-Seq experiments, it matched the results from his DNaseI hypersensitive site ChIP-Seq almost perfectly. Genomic regions available for TF binding would need to be accessible and, therefore, hypersensitive to DNaseI, but it’s still kind of cool to see the results overlap so well. The other interesting thing he showed was that when he had very deep sequencing in a TF ChIP-Seq experiment, the resolution of the binding sites became so good that it matched with the predicted sites of the TF crystal structure. Seeing two completely orthogonal approaches match so closely is pretty amazing.
• David Smith talked about studying head and neck cancers, first with RNA-Seq and more recently looking at very large genes and chromosome breaks. For example, the FHIT gene at 1.5 million bases is so large that transcription takes so long that it can interfere with replication (hence the breaks). While it isn’t directly related to the science he was discussing, Dr. Smith revealed an interesting marketing tactic (one of the worse kept secrets in the business) about Life Technologies: “SOLiD gave us $300k worth of free sequencing… back in the days with sequencing companies were willing to seduce you.” Very important to keep in mind when companies throw around market share numbers.
• Cynthia Burrows is using an alpha hemolysin-based nanopore system from Electronic BioSciences (EB) to look at DNA damage and other modifications. EB is one of the nanopore companies flying under the radar. They use a small aperture capillary with a single nanopore and a dual electronic system so that translocation and measurements can be kept separate. Check out the EB entry in BlueSEQ’s ‘Emerging Technologies’ section. Her fun fact for the day is that there are ~10k spontaneous depurinations per genome in a cell per day. That definitely makes me feel like I’m falling apart!
• Aleksei Akimentiev gave a really interesting talk on solid state nanopores. While he didn’t have any experimental data to show, he showed some fantastic model simulations run on the ‘Blue Waters’ super computer. He has modeled all sorts of nanopores, including graphene layers which turn out to be quite ‘sticky’. He’s working with both Oxford Nanopore [http://blueseq.com/knowledgebank/emerging-technologies/oxford-nanopore-technologies/] and IBM [http://blueseq.com/knowledgebank/emerging-technologies/ibmroche454/]. Check out some of his animations here:
• silicon: http://www.nsf.gov/discoveries/disc_videos.jsp?cntn_id=117318&media_id=67049&org=NSF
• graphene: http://pubs.acs.org/doi/suppl/10.1021/nl301655d
• nanopore capacitor: http://pubs.acs.org/doi/suppl/10.1021/nl071890k/suppl_file/nl071890ksi20070802_123247.mpg
• Jingyue Ju is working with tagged nucleotides (with various PEG molecules acting as the tags, if I remember correctly). The DNA strand to be sequenced is processed by a polymerase which releases the tags as the nucleotides are incorporated. These tags are what are read by the nanopore. Genia announced last fall that they had switched their chemistry to use Dr. Ju’s system. When asked how long until he could sequence DNA, Dr. Ju answered “In a couple of months we’ll demonstrate real sequencing data”. Good news for Genia?
• Massimiliano di Ventra talked about “Fast DNA Sequencing via Tunneling” – not exactly a nanopore, but definitely related. It looks a really cool technology, but unfortunately all he has to show at the moment is simulated data. Perhaps the most interesting thing is that he brought a new commercial sequencing company to my attention – he’s been working with Osaka-based Quantum Biosystems (a new one we’ll need to add to the ‘Emerging Technologies’ section of BlueSEQ’s Knowledge Bank.

NGS Year in Review Part 1: Promises, Promises

In an annual ritual, the various NGS vendors gathered in Marco Island at AGBT to sell their wares and tout their technology to the eager attendees. I figured this makes it a good time to review what's happened over the past year. I’ll start by covering which promises were kept and which were broken, and follow up with subsequent posts on a more general overview of the progress we’ve seen, another one on the mergers that did and didn’t happen, and finish up with a post where I take a stab at what we'll see over the coming year.

2012 was a year of hope and promises. The NGS market is brutally competitive, with all the vendors trying to outdo each other, and 2012 was no exception. The major cycle of announcements that gives us a hint at what we were to see in the upcoming year starts with the JPMorgan Healthcare Conference and finishes with AGBT on Marco Island. 

Last year Ion Torrent (Life Technologies) kicked everything off by announcing their new machine, the Proton. While many, myself included, groused that this new machine made a mockery of their slogan 'The chip is the machine', it was necessary for them to keep pace with their previous promise of improving outputs 10-fold every 6 months. The first Proton chip, the PI, was slated for mid-2012 and would generate 10Gb/run. Not bad, but it was the following PII chip, slated for the end of 2012, that caught everyone's attention. If it were to keep up the trend of 10-fold improvements, it would generate 100Gb of data in a few hours. Better yet, it would finally achieve the holy grail of NGS - the $1000 genome! But Ion Torrent didn’t quite pull it off. Despite making progress, their schedule has started to slip and the output specs are starting to look more meager. Combined, it means they didn’t hit the fabled $1000 genome in a day. Not even close. By the end of 2012 (and through AGBT 2013), their most advanced commercially available chip, the PI, generates around 10Gb of output per run. At $1000 per chip, it would cost around $9k and take up to a week to sequence a human genome. Getting better, but still not there. The chip they said would reach the goal, the PII, was first delayed to March 2013 and now to ‘mid-2013’. Also, rather than generating 100Gb at launch, they’re now talking about 32Gb/run at launch, climbing to 64Gb over time (probably about 12 months). So we might not see the “$1000 genome in a day” from Ion Torrent until mid-2014, or even a bit later.

Illumina got much closer to fulfilling their promises, but that’s partially because they weren’t so bold. While they did claim they’d have the ‘genome in a day’ by the end of 2012, they never said anything about what it would cost. The machine to perform this trick, the HiSeq 2500, was released and the official specs at the end of 2012 were pretty close – 27 hours for a 30X genome (90Gb). With recent improvements (especially on sample prep and analysis), they should be able to go from DNA to analyzed sequence in under 24 hours.

Ion Torrent and Illumina made their big announcements at the JP Morgan Healthcare conference, but Oxford Nanopore (ONT) saved their news for the more scientifically oriented AGBT meeting. And by all accounts, their short presentation stole the show and set Twitter afire. While they had already given us a peak at their upcoming GridION system, they started putting some specific numbers behind it, with the most dramatic being a 20-node system that by 2013 would sequence a genome in 15 min for ~$1000 ($10/Gb). Oh, and they gave a peak at some really intriguing data – 50kb reads with a 4% error rate (that would drop to 1% by the launch). But then they really stirred things up when they unveiled the MinION, a disposable handheld nanopore sequencer the size of a large USB stick, suitable for field work (including no need for sample prep), that would cost under $900 and generate over 1Gb of data. And both the GridION and MinION would launch in 2012.  Nanopores were finally here! These claims were met with incredible excitement and even appeared to shake up the emerging NGS space by, allegedly, prompting Halcyon Molecular to close up shop.

Almost immediately, however, the cries of “Show me the data!” started to emerge from the ranks of scientists. As mid 2012 approached with no new data, the shouts became stronger. Some, myself included, held out hope when ONT was scheduled to appear at ASHG. A booth with pretty but non-functional demo units was all we got – still no data. When the agenda for AGBT 2013 came out, ONT was nowhere to be seen, so any hope of a last minute nanopore miracle vanished. But ONT did attend the show, and CTO Clive Brown gave an impromptu interview to noted blogger Nick Loman that seemed to reveal some of the issues that they were running into and a maybe/sorta indication of a 2013 launch (or at least data from early access customers). While many feel burned by ONT's undelivered promises, the truth is that all will be forgiven once they get their hands on a functioning nanopore sequencer. Book your tickets now for AGBT 2014. 

[If you’d rather listen to me speak than read my words, Theral Timpson interviewed me about this over at Mendelspod.com]

 

2012 Will NOT be The Year of the $1000 Genome

There was a lot of excitement earlier this year when Ion Torrent announced their newest machine, the Proton. It was going to let them continue down the path of rapid technology improvement and let them keep their oft-repeated statement of 10-fold improvement every 6 months. I was pretty skeptical of these claims when they first came out, but the PGM has done a remarkable job of backing them up, going from 10Mb on the 314 chip, to 100Mb on the 316 chip and finally to 1Gb on the 318 chip over a period of 12 months.

As impressive as Ion Torrent’s progress has been, there have been a few hiccups:

• Contrary to their initial marketing slogan, the chip is no longer the machine. To keep riding the wave of improvements, you have to trade in your original PGM for a much more expensive (but still relatively cheap) Proton. Not surprisingly, there were some grumblings from customers when that little bombshell came out.
• They have slipped a bit (by about 3 months) on their rapid pace of launching a new chip every 6 months. By their original plan, the PI should have come out in July, but we’re just now seeing it in September.
• When the Proton was first announced, the PI was targeted for 10Gb, or 2 exomes per chip, and the PII was to offer 10 times the output which would be 100Gb, enough fo a single whole human genome (all for under $1000 for chip+reagents). The only problem is, they’re now redefining “whole human genome” to be 20X coverage, while the industry standard is more like 30X with some pushing for higher coverage of 40X or more. 20X coverage implies that the PII chip will initially only be generating 60Gb per run. Still quite impressive, but another slip from the original roadmap.

So, this means not only will we not have a whole genome on a single chip by the end of the year (due to the 3 month schedule slip), when we do get it, it won’t really be a ‘true’ whole genome run. You’ll probably need to run two chips (or a chip and a half, if you can manage that with indexing), meaning it will cost you more like $2k instead of the holy grail of $1k.

The other thing to note is that the launch of the PII will signal the end of the original ’10-fold improvement every 6 months’ promise. The follow-on chip, the PIII, will take a full 12 months after the launch of the PII, and it will only be about a 2X improvement instead of the 10X improvement we’ve been getting used to.  Still, if they’re able to do what they say, by the middle of 2014 we’ll have the ability to generate ~200Gb in a 2-4 hour run for ~$1000. That, in turn, will surely put a lot of pressure on the market leader, Illumina, to launch some improvements of their own. Chemistry A and B, we’re waiting… 

What's the NGS Buzz?

There's been quite a bit of 'next-gen' sequencing news lately (some of it positive, some of it pretty negative). I thought I'd take a stab at ranking them in terms of their "buzz" - how much people are talking about them, excitement around updates, etc. It is very subjective and definitely NOT an attempt at ranking their usefulness/performance (which would be highly application specific). Feel free to let me know how wrong I am in the comments section.

(I inexplicably left out Complete Genomics - now corrected)


 

Platform	Comments	Buzz Factor	Trend
Ion Torrent	Lots of promises, excitement and chatter Lots of blogs analyzing data	10
MiSeq	Data starting to trickle out Mostly in a battle with Ion Torrent	6
GnuBio	Completely backed off their "$30 WGS" claims Interest picking back up now that they're in beta testing	5
Complete Genomics	Still in the news, in a death battle with ILMN and BGI	5
HiSeq	Dominant (if boring) NGS workhorse	4
Oxford Nanopore	Not much news Initial excitement waning Waiting for next (first?) big announcement	3
Pacific Biosciences	Only news is bad news Management overestimated market adoption of PacBio Laid off 28% of workforce (ouch!)	3
SOLiD	Has become the ugly stepsister of Ion Torrent Management says "putting all chips into Ion Torrent" and "(light based seq) is nearing the end"	2
454	Not a lot of news since FLX+ Not much in the way of public discussion	2

The Institute That Never Was...

In early January 2010 Illumina made a big announcment – BGI was to purchase 128 of Illumina's brand new HiSeq 2000 sequencers. (In Sequence 1/12/10). Not to be outdone, Life Technologies followed up with their own announcement a couple of weeks later – the 'not quite yet formed' Ignite Institute was to purchase 100 of Life's brand new SOLiD 4 sequencers. (Genome Web 1/28/10) 

Inside Illumina there was a lot of skepticism (myself included) about Life's announcement. It just seemed like a desperate ploy to detract attention from the BGI announcement. In the back of my mind, however, I wondered if I was being too pessimistic in my Kool-Aid drinking. Turns out the answer was 'not so much'.

Ignite ran into a number of troubles with funding and the purchases never happened. In fact, Ignite never 'happened'. Instead it sort of merged with the Fox Chase Cancer during the formation of the 'Cancer Genome Institute at Fox Chase'. Perhaps most telling was that when Fox Chase forged their own partnership with Life the 'Ignite' name wasn't mentioned. As quoted in Kevin Davies article:

“We didn’t mention Ignite [when that was announced] – that was intentional,” Boyd explains. “We got tired of negative reporters who want to dig into what happened to Ignite [in Northern Virginia] and dredge up that experience.”

Negative experience, indeed!

As for BGI, they certainly still exist and they've actually purchased all 128 HiSeq 2000's (plus a few more). And they continue to draw strong reactions - praise, scorn and fear, to name a few.

(Lest anyone think I'm unfairly picking on Life, Illumina has been known to make a stumble or two. I'm looking at you, Avantome ;-)

AGBT's biggest loser was...

Twitter!

Seriously, the AGBT organizers appeared to be caught off guard by the popularity of tweeting/blogging about the various talks. Many thanks to the presenters who allowed tweeting and to the many attendees who took the time to tweet and blog about them. I found it enormously helpful as it allowed me to attend the meeting vicariously. I've listed some of the blog resources at the end (which also contain good info on the research talks).

The general consensus seems to be that the meeting was good but that there really wasn't anything groundbreaking this year. The commercial players either already announced their good news back in January, had nothing to say or weren't ready to say anything just yet.

The Established Players:

Illumina

There really was nothing new for the meeting as they had already announced the program for achieving 600GB with HiSeq2000, the internal 1TB runs and the new MiSeq platform. Illumina was a fairly popular tweet/blog topic (second highest coverage) with most people either focusing on MiSeq, HiSeq's data output or Illumina's general market dominance. The only real negative that came up was the run failure rate at Harvard. Illumina had a moderate presence in the twitterverse, sending out an average # of tweets to attendees.

Life/SOLiD

Like Illumina, they didn't really have anything new to say about their SOLiD platform. They were, however, the king of the tweets, sending out more than all of the other sequencing vendors combined. The attendees weren't quite so vocal. Combining tweets for both SOLiD and Ion Torrent (see below), they had just the third highest coverage. As for news, it seems that Life is really starting to position SOLiD as system of choice for the cancer genome market.

Complete Genomics

Bucking the trend, Complete Genomics did save some big news for the meeting. They have created a public database containing 40 complete genomes with the promise of 20 more in March. The company tweeted an average amount and received some back (#4), most of which was excitement around the public dataset.

454/Roche

Hello? Does anyone have anything to say about 454? <crickets>. Nothing directly from the company and just a handful of tweets from the attendees. Maybe next year?

The Hopefuls:

Life/Ion Torrent

Life didn't really have any announcements about Ion Torrent, but people were eager to see the data in the presentations. They seemed pleased with the low GC bias but perhaps a little disappointed with the error rates.

PacBio

The company didn't send out any tweets, but they win the prize for the greatest interest from the twitterverse – almost double the #2 tweet getter. However, a big chunk of that was about the movie they showed (which some described as too simplistic for the AGBT audience while others described it as a giant 30 min ad for PacBio).

Oxford Nanopore

ONP tweeted an average amount, but they didn't have any big announcements. There wasn't too much tweeting about them since no one has their hands on this instrument yet, but those who did comment seemed quite positive about their GridION system and were eager to see some real data.

BioNanomatrix

Nothing from the company, but a few people out there were eager to see how this system will perform.

NABSys

About the same – nothing much out there yet, but some are waiting.

The Head Scratcher:

Agilent

Agilent was the “Gold” sponsor (just below Life, which nabbed “Platinum”) - something that costs big bucks (around $100k, I think). However, at least in the twitterverse and the blogosphere, they were just about a non-entity. There were no official tweets from the company and their only announcement was about their new RNA target enrichment kit. A nice addition to the market, but I'm not sure if that news was worthy of the gold sponsorship purchase.

AGBT Summaries (a big thanks to you all!):

Keith Robison at Omics! Omics!

Prithwish at Omically Speaking (part 1, part 2)

Kevin Davies of BioIT World at NGSLeaders

J Ireland at 5AM