whole-genome sequencing
dgmacarthur | January 14, 2009Still quite a way, based on this survey of second-generation sequencing users (subscription only, I think) conducted by the industry publication In Sequence.
Along with a range of other questions, the survey asked users about the cost to generate one billion base pairs (one gigabase, or Gb) on their platform at the end of 2008, which is about as current as we're likely to get. I've estimated below the total cost to sequence a complete* human genome, assuming an overall depth of coverage** of 30x, for the three most widely-used second-generation platforms:
The fine print
Note that the number…
dgmacarthur | December 18, 2008Nature has a list of the top news stories of 2008, and "Personal genomics goes mainstream" comes up second:
In January, an international consortium announced the launch of the 1,000 Genomes Project, which aims to provide a catalogue of human genetic variation. In October, the Personal Genome Project, which hopes to sequence and publish the genomes of as many people as possible, released initial data for ten participants. Meanwhile, as researchers wondered what they could glean from the results coming from personal-genomics companies, the prices of such services dropped. The firm 23andMe,…
dgmacarthur | December 17, 2008David Ewing Duncan has a piece in Portfolio.com about Complete Genomics, a DNA sequencing company that launched back in October promising to offer whole-genome sequencing for $5000 by mid-2009.
Complete Genomics is based on some allegedly powerful new technology (here's a cartoon summary) developed in-house - I say "allegedly" because the company is yet to release any real data to demonstrate the capacity of its platform. New sequencing platforms are a dime a dozen nowadays, but the novelty of the Complete business strategy is this: instead of selling instruments to sequencing facilities, it…
dgmacarthur | December 10, 2008Pharmacogenomics Reporter has a fascinating article (subscription only, I think) on the impact of individual gene patents granted by the US patenting system on the future of personal genomics. Essentially, the issue for companies conducting genome-wide analysis (including SNP chips or whole-genome sequencing) is that setting up licensing deals for each individual gene makes business complex and expensive - potentially discouraging investment in the field.
On their website, personal genomics company Navigenics explains the problem:
For example, if we obtain licenses from third parties to 10…
dgmacarthur | November 14, 2008Last week I posted on the publication of three papers in Nature describing whole-genome sequencing using next-generation technology: one African genome, one Asian genome, and two genomes from a female cancer patient (one from her cancer cells and one from healthy skin tissue). At the end of that post I noted that the era of the single-genome publication is drawing to a close as the age of population genomics commences.
Today GenomeWeb News reports from the American Society of Human Genetics meeting on the biggest current foray into the field of population genomics: the 1000 Genomes Project.…
dgmacarthur | October 23, 2008When James Watson's genome sequence was publicly released earlier this year, Watson famously kept only one region of his DNA a secret - the region encoding the APOE gene, which contains common variants that contribute substantially to the risk of late-onset Alzheimer's, and also affect predisposition to other diseases.
A recent article in the European Journal of Human Genetics shows something that shouldn't have come as a surprise to anyone familiar with human genetics: simply removing the APOE gene was not enough to prevent someone from inferring whether or not Watson carries the riskier…
dgmacarthur | October 6, 2008The already frantic DNA sequencing market just got a little bit more crowded, with the dramatic entrance of a new competitor called Complete Genomics. The newcomer brings new technology to the table, as well as big promises: namely the commercial provision of whole-genome sequencing for a bargain $5,000, beginning in mid-2009.
It's still unclear whether the company has the capability to make good on such a promise, but its claims have certainly gained it some attention - the story was broken in the NY Times, Bio-IT World and MIT's Technology Review today (see also coverage from The Genetic…
dgmacarthur | September 10, 2008This story doesn't seem to have got much press - understandably, since the media is getting sick of "first" genomes, and there's very little useful information available in the press releases - but a collaborative effort between Saudi Biosciences, the Beijing Genomics Institute and bioinformatics provider CLCbio has announced the sequencing of the first Arab genome.
We're talking standard genomics-by-press-release here: there's no information about the nature of the sample, and no release of actual data. The one nugget of information in the press release is that the genome was sequenced using…
dgmacarthur | September 8, 2008This little USB drive represents the current pinnacle of luxury personal genomics. It's the product of Knome (pronounced "know me"), a Cambridge, MA-based biotech start-up fronted by genomics pioneer George Church (recently profiled in Wired). In return for $350,000, Knome's customers receive a shiny 8 Gb drive containing their entire genome sequence (or rather, a hefty fraction of it), along with specialised browser software for viewing it.
$350,000 is a hell of a lot of money to fork over for a few gigabytes of data. So, how much of a return will these customers be getting on their…