genomeboy.com

The GET Conference 2010 marks the last chance in history to collect everyone with a personal genome sequence on the same stage to share their experiences and discuss the important ways in which personal genomes will affect all of our lives in the coming years.

Tickets are pricey. This is a (long overdue, IMHO) fundraiser for PersonalGenomes.org:

We foresee a day when many individuals will want to get their own genome sequenced so that they may use this information to understand such things as their individual risk profiles for disease, their physical and biological characteristics, and their personal ancestries. To get to this point will require a critical mass of interested users, tools for obtaining and interpreting genome information, and supportive policy, research, and service communities.

ScienceDaily (Feb. 12, 2010) — Just because you don’t swallow the worm at the bottom of a bottle of mescal doesn’t mean you have avoided the essential worminess of the potent Mexican liquor, according to scientists from the Biodiversity Institute of Ontario (BIO) at the University of Guelph.

They have discovered that the liquid itself contains the DNA of the agave butterfly caterpillar — the famously tasty mescal “worm.”

***

“Showing that the DNA of a preserved specimen can be extracted from the preservative liquid introduces a range of important possibilities,” said Dr. Mehrdad Hajibaebi, a member of the research team. “We can develop inexpensive, high-throughput and non-invasive genetic analysis protocols for situations where the original tissue cannot be touched or when there is simply no sample left for analysis.”

I have to start watching more TV.

In case you missed it:

The average sequencing consumables cost for these
three genomes was under $4,400 (table S5). The raw base and
variant call accuracy achieved compares favorably with other
reported human genome sequences (2–12).

The Complete Genomics folks have sequenced a human genome at 45x coverage for $1726 in consumables.

Stephen Quake discusses what he learned from his genome:

FWIW, Quake, co-founder of Helicos, interpreted his sequence using Trait-o-matic, an open-source app developed in the Church lab that I and the rest of the PGP-10 are using to interrogate our genomes and about which I expect to have more to say in the near future.

Complete Genomics may be a one-trick pony, but as Paul Simon would say, it turns that trick with pride:

Reid also took issue with the idea that CGI is a services business. “It’s not a services business — you can’t call us up and ask for services – we have a data business. This business is enabled by a dramatic new development in this industry. There is finally, for the first time, one organism, one type of data that can be produced in a standardized mechanism — it’s called a human genome.”

Reid draws a strong analogy to Google. “Google has one type of data called web documents, and produces one type of report called sorted list of documents, based on your query. We’re doing that for genomic data, taking the one type of data – the human genome — building a huge Google-like proprietary back end, that can take one input – human DNA – and produce one standardized output, a human genome report, a sorted list of variants. That is all about economies of scale.”

There’s been a fascinating back-and-forth going on in the genome blogosphere about the pre-publication of the Applied BioSystems (i.e., Life Technologies) whole-genome sequence of a Yoruba, the seventh published whole human genome (is this still correct?), although the Yoruba one was done twice. At MassGenomics last month, Dan Koboldt took the paper’s authors to task for not offering a comparison to Illumina’s earlier sequence of the exact same genome. ABI’s Kevin McKernan responded in the comments. Meanwhile, in a guest post at Genetic Future yesterday, Luke Jostins suggested that ABI’s paper was not entirely cricket (links by me):

What follows is idle speculation, and thus (hopefully) not slander. My guess is that SOLiD is attempting to reposition itself as the Low Coverage Sequencing Company. They have still failed to topple Illumina as the market leader, and I expect that they think if enough people start thinking of SOLiD as “the guys who did a good quality 18X genome”, all the people who found the low coverage 1000 Genomes Project work sexy will start looking to SOLiD. But to do this, they had to fudge a few things: get the coverage down by cutting out lots of reads, obfuscate the low quality of heterozygous calls, and give an overenthusiastic estimate of how cheap their technology is.

Ouch. And I thought the direct-to-consumer genomics debate was rough.

I love this [via Genomeweb]:

In a sign that genome-mapping is becoming increasingly common, a company called Knome plans to offer its personal gene-sequencing service to the highest bidder in an eBay auction set to begin on Friday and continue for 10 days. The company plans to opening the bidding at $68,000.

Daniel has his usual cogent breakdown, explaining why patience is a virtue.

Anyway, um, while you’re waiting for the genome bidding war to commence, perhaps I can interest you in something else that is considerably less expensive and easier to interpret?

In the current New England Journal of Medicine, David Goldstein wrote:

If common variants are responsible for most genetic components of type 2 diabetes, height, and similar traits, then genetics will provide relatively little guidance about the biology of these conditions, because most genes are “height genes” or “type 2 diabetes genes.”

In response, a friend of mine emailed and asked:

“What I find difficult to accept is that [Goldstein] has ongoing [genome-wide association] studies, so does he not believe in his own work?”

My response: I can’t speak for David, but having just read his commentary, I think he would say that if you’re going to do GWAS, the disease itself should probably not be the phenotype under study, because we’ve done those studies and so far they’ve produced a failry shitty ROI, at least by conventional definitions of clinical relevance. You’ll have more luck studying endophenotypes, e.g., drug response, brain structure as measured by MRI, a decline in working in memory, etc.

In an accompanying commentary, Joel Hirschhorn wrote:

I believe that the skeptics’ arguments either misconstrue the primary goal of genomewide association studies or are contradicted by their findings. The main goal of these studies is not prediction of individual risk but rather discovery of biologic pathways underlying polygenic diseases and traits. It is already clear that the genes being identified expose relevant biology.

Hmm. Yes of course we’ve learned a lot of biology, but isn’t this moving the goal posts a little bit? In the grants we write, do we not extol the clinical relevance of our work and the enormous promise it holds for diagnostics, therapeutics and–gasp!–actual cures for the diseases that ravage our species? Or do we modestly say, “Each discovery of a biologically relevant locus is a potential first step in a translational journey?” If we acknowledge that 100 years elapsed between the elucidation of the chemical makeup of cholesterol and the development of statins, does that make it okay? Given that 45 years have passed since the recognition that human response to anticoagulant drugs is genetically mediated and we STILL can’t agree about whether pharmacogenetic testing is a good idea, do we just shrug and say, “It is what it is?”

As I’ve said here before by way of disclosure, David Goldstein is a friend and colleague. Even if I don’t always agree with him (and I think he’s wrong when he offers the usual broad indictment of the personal genomics companies), I admire his willingness to — as Richard Preston said of Craig Venter — fart in church.

In the end I’ve had about enough of this debate. It is as if we are arguing over the merits of the compact disc when we all know its days are numbered. Within two years, I imagine that most everyone doing molecular human genetics and genomics of any kind will be sequencing whole genomes.

Whether anyone will understand the data is another matter…