Mailund on the Internet

Yesterday I mentioned how the price keeps dropping on genome re-sequencing, and already today I spot yet another post (on CLC Bio’s “Next Generation Sequencing” blog) on the very topic. Now VisiGen will start selling genome re-sequencing for $1000 — what I would consider the price at which you will start using re-sequencing rather than SNP typing — at the end of 2009.

Will we see the first re-sequencing association mapping studies in 2010?

When writing grant applications I’ve been saying that we could expect whole genome re-sequencing in association mapping studies to be cost effective within the decade. I’m beginning to think that a decade is rather pessimistic.

The cost of re-sequencing is now down to $100,000.

Sure, that is about a factor of 100 more than just getting the SNPs covering your genome and probably tagging most interesting genetic factors we know about, but I would no longer be surprised if the cost would drop to $1000 for re-sequencing within a year, and $1000 was cheap enough for chip based whole genome association mapping studies, so it will be cheap enough for re-sequencing studies.

You can find more on the dropping cost of re-sequencing on Eye on DNA: Whole Genome Sequencing Costs Continue to Drop.

I’d better get cracking on developing analysis methods that can then actually analyse such data…

CLC Bio has started a new blog on “next generation sequencing” — whatever they mean by that. Check it out here and see the announcement here.

CLC Bio is a bioinformatics company here in Aarhus and I have several old friends working there. The software they develop looks very nice, but I haven’t really used it myself. It doesn’t really match the problems I work with myself. What’s cooler, though, is that they also develop custom hardware for computationally intensive bioinformatics tasks: The Cube and The Cell.

I’m not really sure what’s supposed to go on their new blog, but since I’m a sucker for science blogs I’ll probably subscribe to it for a while and find out.

Yesterday Roald Forsberg sent me this link: NHLBI, NHGRI Offer $12M to Cut Cost of Exon
Sequencing for Large-Scale Disease Studies.

This is a research project that will offer four awards totalling $12M to help reduce the cost of reseqencing all exons, making this a viable approach to whole genome association mapping.

[The project will] complement the 1,000 Genomes Project that the NHGRI, the Wellcome Trust Sanger Institute, and the Beijing Genomics Institute announced last week.

Unlike that project, which aims to catalog genetic variations in human populations unbiased for disease, the resequencing technology program is geared towards studies that will correlate sequence variations with disease phenotypes.

When writing the grant proposal for my new project (that started yesterday) I argued that it was time to consider whole genome resequencing for association mapping and that we would see whole genome resequencing in association mapping within five to ten years. I am beginning to think I was being pessimistic here. Sure, this only focus on exons, but if we can sequence all exons, then the entire genome is not far behind.