next-generation sequencing
dgmacarthur | January 4, 2010
The Gene Sherpa predicts that Complete Genomics will win the Archon X Prize in Genomics in 2010. In the comments, Keith Robison is wisely skeptical. I agree with Keith - it's unlikely that the X Prize will be won this year, and if it is the winner is unlikely to be Complete Genomics.
For those who don't know the prize, here's the brief summary: the X Prize Foundation will give US$10 million to the first team to satisfy the following conditions:
sequence 100 human genomes within 10 days or less, with
an accuracy of no more than one error in every 100,000 bases sequenced [note that the…
dgmacarthur | October 6, 2009IBM's announcement that it will be entering the DNA sequencing technology race (which I mentioned briefly earlier today) has created a tremendous amount of mainstream media interest. That's understandable given IBM's size and history of innovation, but how likely are they to represent serious contenders for the potentially lucrative sequencing market?
Firstly, it's important to note that this announcement represents more of an expression of interest in the field rather than anything close to a mature technology; IBM will not be rolling out a machine to sequence your genome at any stage in…
dgmacarthur | October 6, 2009Things are as usual moving at ludicrous speed in the world of genomics, but sadly I only have time to post a few pointers to some of the most striking developments.
IBM is moving into the third-generation sequencing arena. The company is developing a new sequencing technology based on tiny nanopores - a field already being explored by the understated British nobility of sequencing, Oxford Nanopore. This is all over the news, but Dan Vorhaus has an introduction and is promising to follow up on further developments. You can also watch a pretty but largely content-free animation of the process…
dgmacarthur | September 16, 2009Kevin Davies from Bio-IT World has two interviews up today relevant to new DNA sequencing technologies.
Firstly, there's an excellent interview with Clive Brown, vice president of development and informatics for Oxford Nanopore Technologies - one of the most promising contenders in the rapidly evolving third-generation DNA sequencing market. Brown is renowned for his plain-speaking approach (in the article he's described as "the most honest guy in all of next-gen sequencing", a quote originating from David Dooling), and that shows here in his blunt comments on the recent Helicos genome…
dgmacarthur | August 31, 2009Sequencing giant Illumina has announced that it has delivered its first commercial personal genome sequence. The sequence was generated by the genome sequencing service launched by Illumina back in June, and was delivered in collaboration with new personal genomics company Pathway Genomics.
Illumina's genome sequencing service costs $48,000, and its first customer was entrepreneur Hermann Hauser. Bio-IT World summarises details of the sequencing itself:
Illumina completed the sequence at its CLIA-certified laboratory, producing more than 110 billion base calls, good for 30X coverage of the…
dgmacarthur | August 26, 2009Complete Genomics is finally back on the road towards fulfilling its promises of $5000 human genome sequences, after delays in obtaining funding for a massive new facility pushed back its plans by six months. The $45 million in funding it announced this week will be sufficient to build the new Silicon Valley facility, which the company claims will have the capacity to sequence a staggering 10,000 genomes over the course of 2010.
Complete Genomics is an unusual creature in the second-generation sequencing menagerie: instead of aiming to generate revenue by selling machines to researchers and…
dgmacarthur | August 12, 2009I've just discovered a very promising new blog in the genomics sphere (well, technically it's a newly relaunched blog) run by a group at the University of Birmingham.
Two posts by Nick Loman are of immediate interest to readers here. Firstly, I highly recommend Nick's thorough dissection of accusations made by Applied Biosystems' Kevin McKernan in a recent submission to a UK House of Lords enquiry, which include the claim that the Sanger Institute's adoption of technology from AB competitor Illumina were driven by bias. Here's a key paragraph, but if you're interested in the competition in…
dgmacarthur | August 12, 2009The announcement of the Helicos genome sequence (which I've already discussed in detail) engendered a huge amount of media interest, sometimes for the wrong reasons.
Having the media attention directed elsewhere in the third-generation sequencing space was clearly an unwelcome experience for Helicos competitors Pacific Biosciences, who have responded with a press release announcing the successful raising of $68M to finance further development of their single-molecule real-time (SMRT) sequencing platform.
To be fair, raising that sort of capital in the current economic climate is no mean…
dgmacarthur | August 11, 2009David Dooling has an entertaining take on the Helicos genome sequence I discussed yesterday entitled "Another rich white guy sequences own genome".
I noted in my post yesterday that the alleged price drop for the Helicos sequence over current technologies was an illusion, but David includes a much more thorough analysis of the relative genome sequencing costs thrown around over the last couple of days and makes it very clear that the price Helicos is quoting is really no advance over the current prices for second-generation sequencing technologies:
They report reagent costs that are on par…
dgmacarthur | August 10, 2009Pushkarev, D., Neff, N., & Quake, S. (2009). Single-molecule sequencing of an individual human genome Nature Biotechnology DOI: 10.1038/nbt.1561
Yes, it's yet another "complete" individual genome sequence, following on the heels of Craig Venter, James Watson, an anonymous African male (twice, and not without controversy), two cancer patients, a Chinese man, and two Koreans.
There is a new twist, though: this is the first genome to be sequenced using single molecule sequencing technology - also known as "third-generation" sequencing, to distinguish it from first-generation Sanger…
dgmacarthur | August 4, 2009While I continue my work-induced blog coma, here's a guest post from Luke Jostins, a genetic epidemiology PhD student and the author of the blog Genetic Inference, delivering a fairly scathing critique of a recent whole-genome sequencing paper based on Life Technologies' SOLiD platform.
McKernan et al. 2009. Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding Genome Research DOI: 10.1101/gr.091868.109
In prepublication at the moment is a
paper from the labs of ABI,
makers of the SOLiD sequencing system…
dgmacarthur | June 11, 2009The buzz leading up to this week's Consumer Genetics Show in Boston suggested that a major announcement would be made by the CEO of genomics technology provider Illumina, Jay Flatley. Illumina provides the most popular second-generation sequencing instrument currently on the market, the Genome Analyzer II, and has been making noises about moving into the personal genomics industry since at least the beginning of the year, so the announcement itself was not exactly a shock: Illumina is launching a personal genome sequencing service.
The launch comes with a new website, the appealingly titled…
dgmacarthur | April 21, 2009I wrote a few days ago about a debate in the New England Journal of Medicine over the value of data emerging from recent genome-wide studies of the role of genetic variation in common human diseases and other traits. David Goldstein argued that genome-wide association studies (GWAS) have generated disappointing results, and should be scaled back in favour of whole-genome sequencing; Joel Hirschhorn responded with an upbeat piece emphasising the insights generated by GWAS into the molecular basis of common diseases.
Now geneticist Steve Jones has an opinion piece in the Telegraph that…
dgmacarthur | March 9, 2009Keith Robison notes that commercial DNA sequencing is now cheap enough to seriously consider generating and analysing a bacterial genome sequence as an undergraduate group-work project.
I think it's a fantastic idea in principle, and would certainly give students a flavour of the reality of modern genomics - but the prospect of coordinating hundreds of inexperienced undergraduate students in a genome annotation project is incredibly daunting. This would take a very talented and dedicated group of educators to pull off successfully.
If anyone has considered such a project, let Keith know in…
dgmacarthur | March 3, 2009I discussed the second-generation sequencing company Complete Genomics a couple of weeks ago (see here and here). These guys are unique in that they offer their technology only as a service, rather than the usual business model of selling platforms to genomics facilities, and a highly restricted service at that: Complete has stated fairly categorically that it will only be sequencing human genomes (no plants, algae, or even chimpanzees!).
Whether this business model will prove a commercial success remains to be seen, but the company seems to have impressed the genomics community with its…
dgmacarthur | February 23, 2009James Clarke, Hai-Chen Wu, Lakmal Jayasinghe, Alpesh Patel, Stuart Reid, Hagan Bayley (2009). Continuous base identification for single-molecule nanopore DNA sequencing Nature Nanotechnology DOI: 10.1038/nnano.2009.12
The clever boys and girls at Oxford Nanopore Technologies - one of the most quietly impressive contenders in the hotly-contested next-generation DNA sequencing race - have a new paper out in Nature Nanotechnology today. The paper demonstrates proof of principle for a crucial step in their approach to DNA sequencing, the accurate recognition of DNA bases as they pass through a…
dgmacarthur | February 5, 2009Regular readers will know that I'm at the Advances in Genome Biology and Technology (AGBT) meeting this week, one of the most highly-awaited meetings on the genomics calendar.
There's a huge amount of fascinating data being presented (anyone interested in a blow-by-blow account should follow Anthony Fejes' live-blogging), but there's definitely an overarching theme: the evolving battle between the new-technology sequencing companies. This is a competition that most researchers in genomics are watching with great interest, because it promises to bring about very rapid advances in the speed,…
dgmacarthur | February 1, 2009Complete Genomics is a DNA sequencing company that launched back in October, and has been creating a buzz in the genomics community ever since.
The company's business model is based around a novel technology for rapidly generating DNA sequence data; but rather than make its money by selling its platform to genomics facilities and biotech companies (as do its competitors, such as Illumina and ABI), Complete will be offering its technology only through its own purpose-built service facilities.
The buzz has focused on whether Complete's technology will be accurate and powerful enough to meet…
dgmacarthur | January 26, 2009I'll be at the Advances in Genome Biology and Technology meeting next week - this will be my my first experience of this annual conference on Florida's picturesque Marco Island, but I already have high expectations based on reports from previous years. The programme is packed with cutting-edge genomics, and to be honest after a few months of Cambridge weather I'm craving even a brief glimpse of blue sky and salt water.
I'll be giving a talk myself on some fairly preliminary data emerging from work I've been doing with the Sequencing R&D team at my new home, the Wellcome Trust Sanger…
dgmacarthur | January 19, 2009
Welcome to the 42nd edition of Gene Genie, the blog carnival of clinical genetics and personalised medicine.
Most of the entries in this edition fall under the broad umbrella of personalised genetics, with posts emphasising both the pros and cons of the emerging consumer genetic testing industry.
The promise and perils of personalised genetics
Hsien-Hsien Li from Eye on DNA warned about the potential dangers of pressuring kids to compete in athletic events based on genetic testing results, citing the suicide of a 15-year-old Singaporean boy. Alberto from Medical Pills used Hsien's post as a…