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

Helicos Cries Out “I'm Not Dead! I'm Getting Better!”

Helicos, the first company to launch a single molecule DNA sequencer (a class sometimes called “3^rd Generation”), has been hanging on to a thread for a while. They've been delisted from NASDAQ and their cash supply is dwindling (down to $1.6M as by June 30^th). They are going through another round of cash-saving layoffs that will bring their headcount down to 10. They have apparently stopped selling the HeliScope and their ability to supply reagents and service support to their current customers has been called into question.

When they launched their HeliScope in 2009, they went head to head with the more established players (Illumina, ABI and 454) focusing almost exclusively on being the first 'true single molecule sequencer' for genomic sequencing. It was a tough sell given that they were a bit late to the party and that their reads are shorter and have a higher error rate. They might have been better served to focus on RNA-Seq and ChIP-Seq where the lower quality reads wouldn't have hurt as much and they could have touted their (at the time) industry-leading # of reads per run.

For the past few months their main strategy seemed to center around litigation – they're suing Life Technologies, Illumina and Pacific Biosciences for patent infringement. Just recently, however, they've expanded this strategy by borrowing a page from Complete Genomics – they have launched a sequencing services program to increase their revenues. They've also launched an interesting targeted sequencing solution in which the capture sequences are attached directly to the flow cell (rather than their standard poly dT sequences). They've demonstrated this technology by creating a flow cell for the direct sequencing of the BRCA1 gene.

I fear it may be a bit too little too late, but at least Helicos is still kicking and demonstrating that it doesn't want to go on the cart.

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

A New Sequencing Player?

My interest was piqued when I saw the headline "PerkinElmer Steps into DNA Sequencing Market" from Genetic Engineering News. Was another major player entering the crowded market of next gen sequencing? (Reading, reading...). Hmm, no, it looks like they're offering services (reading some more). Ah, here it is, their business model:

"PerkinElmer’s model follows Complete Genomics, Illumina, and BGI (formerly known as Beijing Genomics Institute), wherein companies provide sequencing as a service rather than developing and launching competing sequencing platforms that scientists must buy to conduct sequencing projects on their own."

What? GEN is somehow equating the PE business model to ALL of the following:
Complete Genomics - "services only" using their own proprietary platform
Illumina - dominant next gen sequencing platform provider which happens of offer services as a small part of their business
BGI - standard, albeit stupendously large, service provider which primarily uses Illumina's platform

So, which one is it? Well, it's nothing more than yet another sequencing service provider using Illumina's HiSeq2000 instruments, which makes them pretty much like any of the dozen or so services providers listed here (and these are just the certified providers). So, they're sort of like BGI. Except to the best of my knowledge they haven't purchased 128 HiSeq instruments and they haven't stated that they'll sequence anything that's "tasty or cute".