Futurismic

The title says it all, really; Californian biotech company Complete Genomics has announced publicly that it has…

… sequenced three human genomes for an average cost of $4,400. The most recently sequenced genome–which happens to be that of genomics pioneer George Church–cost just $1,500 in chemicals, the cheapest published yet. [via FuturePundit]

“So what?” you might be thinking. Well, for a start, cheaper genome sequencing will pay off fast for the medical field, as it’ll give them more data to study; also, lowering the price to “consumer” levels (albeit the sort of consumer who doesn’t flinch at the idea of laying out a few thousand bucks for a bunch of data that they themselves don’t have the training to do anything with) opens up a whole raft of potential applications, both medical and otherwise.

Other experts are downplaying Complete Genomics’ announcement, however, because the “reagent cost” of the sequencing doesn’t tell the full story:

Calculating the cost of sequencing a human genome is a tricky business–price estimates can vary depending on what’s included in the calculation. One common measure is the cost of the chemicals used, and this is what Complete Genomics used. However, this measure doesn’t incorporate the cost of the machines that do the sequencing, the human labor, or the computational effort required to assemble raw sequence information into a whole genome. “What’s important is not just the reagent costs, but also the cost of analyzing the sequence,” says Jeff Schloss, program director for technology development at the National Human Genome Research Center, in Bethesda, MD. “It’s unclear how computational costs for this method compare to some of the others.”

My guess would be that CG doesn’t really care about that, though. It looks like they’re taking a leaf from the Web2.0 playbook by rolling out the service at the lowest cost possible in order to get a good toe-hold in an emerging market: make sequencing available, and then watch your early-adopter users to see what people will actually use it for. That said, the $5,000 sequence isn’t available to the general public just yet, but I doubt it’ll be long before it is… and I doubt CG will be the only player on the field by that point, either. [image by ynse]

Biologists used to think that new genes “could only evolve from duplicated or rearranged versions of preexisting genes.” Now, though:

Scientists have made a crucial discovery of genes that have evolved in humans after branching off from other primates, opening new possibilities for understanding what makes us uniquely human….

Researchers have found genes that arose from non-coding DNA in flies, yeast, and primates. No such genes had been found to be unique to humans until now, and the discovery raises fascinating questions about how these genes might make us different from other primates….

The authors [David Knowles and Aoife McLysaght of the Smurfit Institute of Genetics at Trinity College Dublin] also note that because of the strict set of filters employed, only about 20% of human genes were amenable to analysis. Therefore they estimate there may be approximately 18 human-specific genes that have arisen from non-coding DNA during human evolution.

This discovery of novel protein-coding genes in humans is a significant finding, but raises a bigger question: What are the proteins encoded by these genes doing? “They are unlike any other human genes and have the potential to have a profound impact,” McLysaght noted. While these genes have not been characterized yet and their functions remain unknown, McLysaght added that it is tempting to speculate that human-specific genes are important for human-specific traits.

[Image: Dollar Bin]

Here’s Ken MacLeod announcing a rather interesting science fiction project:

A while ago I was staring at a poster of the human genome produced by the US Dept of Energy, and I remembered Michael Swanwick’s Periodic Table of Science Fiction. Cue lightbulb moment.

Why not set up a website that displayed short pieces – stories, flash fictions, poems, and reflections – inspired by genes or genomics, and arranged them (as far as possible – I soon found myself applying for an artistic licence) according to the chromosome that carries the gene that inspired the piece?

[...]

Now, thanks to enthusiastic work from Emma Capewell and Claire Alexander at the Genomics Forum, and the creative skills of web designer Damien Noonan, The Human Genre Project has gone live. It’s early days yet, but it looks good and it’s just waiting to be filled up with new writing. If you have something you think might sit well behind one of those colourful chromosomes, here’s how to contribute.

That’s a very cool project – I’m half-tempted to put something together and submit it  myself, though I have no doubt plenty of better writers will beat me to it. Maybe you’ll be one of them? [image by mtowber]

Richard Powers writes an elegant article in The Guardian on becoming one of the few people who have thus far had their entire genome sequenced. In his case by a company called Knome.

“I can tell you that you have the ‘novelty seeking’ gene,” Conde says. He’s referring to a study that associates a longer version of the DRD4 gene on chromosome 11, involved in the brain’s dopamine system, with people who need higher levels of stimulation. “You have three genetic variants associated with aspects of intelligence,” he continues. Reassuring.

…

Just like that, I slip into the era of personal genomics. Now I know exactly what I’ve been dealt, and if I don’t take appropriate actions, the onus is on me.

But what actions? I enter my very own war on terror, monitoring lots of ambiguous chatter that is impossible to understand without more context, that I can respond to only indirectly, that I can’t defeat but can at best hold at bay – a standing low-grade condition of Orange alert that demands perpetual increased surveillance.

But beyond my list of health risks, I’ve also learned something extraordinary: 8% of my genetic material contains variations most closely related to the Yoruba population of Nigeria. I’ve become another person, someone else than I thought I was, giving blood in Wellesley, last spring.

As the genome sequencing gets cheaper I imagine it will become something we’ll all get done as a matter of course.

[image from mtowber on flickr]

I’ve posted about developments in synthetic life before, here and here. It now appears the human genome pioneer Craig Venter has invented an artificial life form:

Craig Venter, the controversial DNA researcher involved in the race to decipher the human genetic code, has built a synthetic chromosome out of laboratory chemicals and is poised to announce the creation of the first new artificial life form on Earth.

The announcement, which is expected within weeks and could come as early as Monday at the annual meeting of his scientific institute in San Diego, California, will herald a giant leap forward in the development of designer genomes. It is certain to provoke heated debate about the ethics of creating new species and could unlock the door to new energy sources and techniques to combat global warming.