Quick update before the end of the month:
The long-awaited paper from Eric Lander on missing heritability has been published and is causing a new round of discussions, following the initial debate after the ASHG announcement. Luke has a short summary over at Genomes Unzipped, and Steve Hsu delves into the supplementary material. A good addition to this is Genetic Inference’s report on the current state of complex trait sequencing via ICHG2011.
BGI has started to move the sequence analysis to GPU-based servers, though the article in Wired is unfortunately light on details what algorithms ended up getting ported to the different architecture.
IonTorrent meanwhile starts supporting paired-end reads, sort of, and announces a new machine which is a bit of a disappointment as one of their main selling arguments was that improvements would happen through the chips, not the hardware around it. Be that as it may, we are getting close to the $1000 genome — for the data generation, which doesn’t take the very time consuming data analysis into account. This is also reflected in my favorite quote of Elaine Mardis’ interview with The Scientist:
“It makes me crazy to listen to people say sequencing is so cheap. Sure, generating data is cheap. But then what do you do with it? That’s where it gets expensive. ‘The $1,000 genome’ is just this throwaway phrase people use and I don’t think they stop to think about what’s involved. When we looked back after we analyzed the first tumor/normal pair, published in Nature in 2008, we figured that genome—not just generating the data, but coming up with the analytical approach, which nobody had ever done before—probably cost $1.6M. If the cost of analysis doesn’t fall over time, we’re never going to get to clinical reality for a lot of these tests.”
This is not going to get any easier as the sequencers get more and more efficient; see Illumina’s announcement of the HiSeq 2500 (summary by OmicsOmics and on the SeqAnswers forum). And though the price of the reagents keeps decreasing it’s still cheaper to store the data than to re-sequence the samples, storage problems notwithstanding.
Michael Eisen has a comment in the NYT on the Research Works Act that’s recommended reading. If you are a member of ISCB you might want to consider signing their policy statement which strongly opposes the act.
- If you aren’t following Edge you are missing out on some great science debates. The Guardian talks to its founder, John Brockman
- TopHat gets a new release
- Aaron Kitzmiller has a terrific commentary regarding the Core model in academia, and why this incredibly difficult to get right for bioinformatics
- St Jude’s releases Explore, a portal to their pediatric cancer genome data
- Keith Bradnam summarizes why it is so difficult to evaluate genome assemblies
- Dan Koboldt provides a neat summary of the current state of dbSNP