whole-genome sequencing
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 | 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 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 12, 2009Harvard biostatistician Peter Kraft (co-author of an excellent recent article on genetic risk prediction in the New England Journal of Medicine) has just added an interesting comment on his experience of this week's Consumer Genetics Show:
I just wanted to share what for me were two stand-out moments at the
CGS. First was Zak Kohane's discussion of the "Incidentalome"--a great
turn of phrase that captures something I've been mulling over myself.
(A less eloquent statement of this idea made it into the recent Nick
Wade NYT article on genetic risk prediction). Basically, the idea is
that even…
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 26, 2009The Personal Genome Project, an initiative founded by George Church that ultimately seeks to sequence the complete genomes of 100,000 people, has called for the next wave of volunteers. The PGP will sequence your genome and give you back the data for the bargain-basement price of zero dollars (not bad compared to the $68,000 that the Knome auction is starting at).
The benefits to volunteers are straightforward: you get access to your own genome sequence before most human beings on the planet, and you get the warm fuzzy glow that comes with benefiting humanity. I'm not being at all sarcastic…
dgmacarthur | April 25, 2009The auction of a whole-genome sequencing service that I scoffed at a few days ago is now live on eBay - serious bidders only, please, and bids start at $68,000.
Here's what you get for your suitcase of cash:
Personal whole genome sequencing and comprehensive interpretation of your genome.
Knome's proprietary KnomeXplorer⢠genome browser software to navigate and explore your own genome.
Two years of Knome's update service allowing you to remain current on the latest cutting-edge genetics research.
A digital copy of your whole genome sequence on Knome's security encrypted GenomeKey [an…
dgmacarthur | April 22, 2009Personal genome sequencing provider Knome is planning to offer a complete genome sequence to the highest bidder on eBay - with the bidding opening at $68,000.
The plan, announced in an NY Times article today, is described as "essentially a publicity stunt" - the proceeds will be donated to the X Prize Foundation, a charitable trust devoted to providing cash incentives for reaching technological breakthroughs. The breakthrough that Knome is most interested in seeing achieved, of course, is the goal of the Archon X Prize for Genomics: a reward of $10 million for the first group to sequence 100…
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 | April 16, 2009A reader pointed me to a recent Economist article on personal genomics. There are numerous tidbits of interest, such as a passing comment about the chaotic Chinese personal genomics industry (about which I know almost nothing). Perhaps the most important quote comes in the closing paragraph:
Dr Church even argues that genome sequencing "will in effect be available free" because companies will give away sequencing to sell other services, such as genetic interpretation--much as mobile operators "give away" handsets to get customers to sign up for lucrative service plans. And when this happens…
dgmacarthur | April 12, 2009GenomeWeb News reports that genome sequencing company Complete Genomics is cutting costs in the lead-up to the commercial launch of its whole-genome sequencing service in June:
In order to save its remaining cash, the company recently
implemented "a variety of cost-saving measures," including "some
reductions" in the salaries of its employees and a trimming of
"non-essential" costs, such as discretionary spending. "We just want to
be prudent about [spending] our cash," Reid said.
The company has not had any layoffs, he added, and is "still running at full capacity."
At this time, he said,…
dgmacarthur | February 15, 2009In a comment on my previous post, Tera Eerkes is skeptical about the utility of routinely performing whole-genome sequencing on newborns:
I found this comment absolutely fascinating, given the recent
reports on translational analysis, that indicate an actual lack of
clinical utility of KRAS testing and other drug-gene interactions.
I believe these reports are indicative of a trend, not an exception.
I think it is remarkable that anyone feels, even optimistically,
that we're going to need a genome-wide scan for clinically useful
indicators by 2019.
I predict that there will be a…
dgmacarthur | February 12, 2009I'm slowly catching up on genomics news from the last week - this story in particular has been getting a lot of press.
The executive summary: Jay Flatley, CEO of genomic technology manufacturer Illumina, predicts that whole-genome sequencing of newborns will become routine within a decade.
Flatley has an obvious financial interest in this prediction coming true, since Illumina provides the most commercially successful next-generation sequencing platform currently on the market, the Genome Analyzer, and has recently invested heavily in emerging "third-generation" sequencing technologies (by…
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…
dgmacarthur | January 19, 2009Well, it's a little late, but I finally have a list of what I see as some of the major trends that will play out in the human genomics field in 2009 - both in terms of research outcomes, and shifts in the rapidly-evolving consumer genomics industry.
For genetics-savvy readers a lot of these predictions may seem, well, predictable, so I want to emphasise that my purpose here is not really to make risky forecasts; I'm more interested in laying out what I see as the major big picture trends for the year to come, with a few specific predictions about unknowns thrown in. In any case (as you will…
dgmacarthur | January 16, 2009A new paper in Bioinformatics describes an efficient compression algorithm that allows an individual's complete genome sequence to be compressed down to a vanishingly small amount of data - just 4 megabytes (MB).
The paper takes a similar approach to the process I described in a post back in June last year (sheesh, if only I'd thought to write that up as a paper instead!). I estimated using that approach that the genome could be shrunk down to just 20 MB - compared to about 1.5 GB if you stored the entire sequence as a flat text file - with even further compression if you took advantage of…