New era of DNA sequencing and related bioinformatics

9 12 2011

I can say the passed week is a week full of great news.

Wednesday (Nov 30, 2011)
“DNA Sequencing Caught in Deluge of Data” — You must want to read this article.

Monday (Dec 5, 2011)
UK will invest £75M for a new BIOINFORMATICS HUB in current EBI, as part of the ELIXIR project. I guess this must be within the framework of the HORIZON 2020, which the EU’s new programme for research and innovation running from 2014 to 2020 with an €80 billion budget. €80 billion!! OMG!

Tuesday (Dec 6, 2011)
The National Human Genome Research Institute (NHGRI), as part of NIH, announced to invest $416 million on research of using genomic data for medical clinical research, including rare inherit disease. Three genome sequencing centers are funded, including the Broad Institute, Genome Institute at Washington University, and Human Genome Sequencing Center, Baylor College of Medicine.

Whole-genome sequencing seems becoming more and more popular since it’s becoming cheaper and faster. Citing what the ELIXIR website says, “Modern sequencers are capable of analysing the equivalent of a human genome every 14 minutes at a cost of US $5,000.” We cannot imagine how easy to get a personal genome sequenced in next 5 years.

So, next question is: What would you do if it became possible to sequence the equivalent of a full human genome for only $1,000? This is the Question of the Year of Nature in 2007, when the whole-genome sequencing is still quite expensive. Personally I like the Ewan’s answer there: Full employment in bioinformatics. Think about it: if you can get your genome sequence in $1, what would you do to that 3,000,000,000 DNA nucleotides?
First of all, you may want to store it (or maybe not, since it’s too large). There are already companied coming out to store the DNA data, like the startup recently invested by Google Ventures, DNAnexus. But question is: who really wants to store all 3G data file, even though the 3G USB just costs less than $1? To only store the difference (between a particular genome and some reference genome), instead of every bit, might be the final solution.
Next, you want to see/visualize it. “Viewing your genomic data on iPhone” is one of such bleeding topics. I am quite serious, Illumina is working on the project with Apple, and even there are working Apps out already.
The most informative thing next is to analysis the data. It’s also the most challenging one. People including myself are working hard on it (That’s why the Uncle Sam invest money on it). Let’s think about this in a non-academic way. More and more companies smell the big cake (first let’s assume it’s a big cake), for example the genotyping-phenotype company like 23andme, the bioinformatics company like GenomeRequest, and just yesterday I read news about a new company called Spiral Genetics (who collect the open source software to do bioinformatics for customers, in a very smart way). Last week, Nature News blog reports the OpenSNP, a website (maybe a company next month) designed by several undergraduate students from U. Washington, they try to build the website to let people share their personal genotype data (from 23andme, deCODEme etc.). It’s a very cool idea!

OK. I know some people might be still questioning whether we need whole-genome sequencing. For individual research, it’s true that not every case needs whole-genome sequencing. But like from old phone to iphone, or from iphone to iphone3G, 4G, 4Gs… do you really need to change your iphone to Iphone 4Gs? You may not, or I am sure practically you don’t need at all. I am still using my wife’s old Nokia, no touch-screen, but very practical. Then why iphone 4Gs are so popular? Because it’s the trend! The lower cost and human’s desire/curiosity/greediness makes it popular. So the same for personal genome sequencing data. The only thing is to show this in an elegant way that even your grandma can understand. That’s the business!



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