April 27, 2012

Why am I doing this?

Don't worry, this is not that post where I start asking existentialist questions. Instead, I ask what I should have asked when I started Seqonomics half a year ago: What is my motivation for writing this blog?

A few weeks ago, I had a conversation with someone working in public relations. He asked me exactly that question. I had not thought about it before, so I could not answer him adequately. He suggested that there are only two reasons why people in the life sciences blog: Either they want to become science journalists, or they enjoy the attention.

I am sure that I do not want to become a journalist of any kind, and I think I know better ways to attract attention than to blog about a subject as dry as the economics of DNA sequencing. So what drives me?


Recently, I read two books on motivation, one awful and the other one pretty good. They got me thinking, and I now know that the ultimate reason why I write this blog is that I believe that there is a deficit in making science useful. Academia produces so many good ideas, yet so few make it out there and become genuinely useful to non-academics. I believe that the best way to change that is by commercialising those ideas. Despite having worked in management consulting for some time, I do not share the naïve cynicism of many of my academic colleagues concerning private business.

One of the things that need to happen for science to be commercialised is that ideas from the world of business and the world of science mix. That is what Seqonomics is about. There may be better ways to make science useful than to blog about it. But they take time, and until then, I'll keep writing.

April 19, 2012

Which sources for genomics business information?

If you enjoy this blog, you may also like the sites below. What they all have in common with Seqonomics is that they cover the interface between sequencing and business. You will notice that I have excluded sites that exclusively cover the technical or scientific aspects of genomics.

    

  • Genomics business news
    • Bio-IT World: My personal favourite. The Bio-IT World website acts as a news aggregator that pulls together some of the most interesting articles on next generation sequencing, big data, and personalised medicine, often from a business point of view.
    • Genome Web is broader in scope than Bio-IT World and also covers arrays, PCR, pharmacogenomics, proteomics, and gene silencing. They write their own articles, which are often strongly inspired by the press releases of companies in the field. The website is updated at least once a day. A subscription is required for most articles.
  • Blogs
    • Genomics Law Report: This excellent blog, as you may expect from its name, covers the legal questions that come with genomics in a thoughtful manner. New posts appear around twice a week on average. The majority of posts are relevant to the United States only.
    • Omics! Omics! and CoreGenomics: Although these fantastic blogs mostly covers the scientific aspects of sequencing, their authors sometimes also writes about business matters.
    • Biotech Marketer covers the marketing strategies of sequencing companies. I am not sure if this blog is still active, as there is no new post since December 2011.
  • Sites that cover biotech in general

I am sure that there are sites that are missing from this list. Especially the blog section is bound to be incomplete. If you know about a site that is relevant and that I have forgotten, please post your link below. I will update this list in a few weeks and include all relevant sites that have been brought to my attention.

April 13, 2012

Is the cloud good value for money?

There are three flavours of companies that provide cloud storage for sequencing data: Generalist providers such as Amazon, Cycle Computing, or Microsoft,  sequencing technology providers such Illumina (their BaseSpace uses Amazon's cloud infrastructure) or Life Technologies, and cloud genomics-only providers, of which DNAnexus is the only one I have come across.

Insert your cloud pun here

How much value for money is the cloud? Consider this simple calculation: DNAnexus charges academic users $10 to store one gigabase of raw sequence data for two years. A 3-gigabase human genome at decent quality (25-fold coverage) comes to 75 gigabases, or $750 at DNAnexus prices. For comparison: An external hard drive which would easily hold the same data costs $89.99.

Whether that is good value for money depends on what you want to do with your sequencing data. If all you want is a place to store it, DNAnexus may be a hard sell. It takes a long time to upload your files, and the example above shows that it is more expensive than to store it locally. 

This looks differently if instead of whole genome data as in the example above, you are dealing with other types of sequencing data. For example, DNAnexus provides ways to store exome or ChIP-Seq data, which take less space and are therefore less expensive.

You probably also want to analyse your data. DNAnexus offers software tools for genomic analysis that are designed to be intuitive to use for standard tasks like variant calling. For whoever is looking for an integrated solution, cloud services like DNAnexus may therefore be worth a try.

Please remember that as always, the views in this blog are my own and are not endorsed by the Wellcome Trust or the Sanger Institute.

April 6, 2012

How relevant will sequencing be to the average person?

There are technologies that are pointless: fireproof matches, waterproof teabags, and non-alcoholic beer. There are technologies that are relevant in a particular field or to certain people. The parachute would be a random example. And then there are technologies that are relevant to everyone, all the time. Consider the transistor and how the world would be different without it: No pocketable radio, no computers smaller than a university basement, and no smartphones.

In which of those categories will DNA sequencing belong in a few years? It is safe to assume that it will not be irrelevant, but the question is whether it will be useful only to specialists in a select number of fields, such as the life sciences, medicine, and forensics, or whether it will be much more pervasive.

I think that it will be rather ubiquitous, and I have four reasons for this.



Number one: Sequencing is becoming increasingly affordable. If the cost of sequencing keeps decreasing at the same rate than it has since 2007, it will cost less than one dollar to sequence a human genome by 2017. This sort of extrapolation may seem naïve, but there is no reason why the cost of sequencing cannot decline by many orders of magnitude still.

Number two: It is likely that sequencing technology will become much easier to use in the future. For example, if Oxford Nanopore's announcements are to be believed, its new sequencing devices require minimal sample preparation. There is no reason why pocketable sequencers that can be used by children cannot be made.

Number three: DNA is a non-fuzzy concept that can easily be grasped. It is simple enough for everyone to understand and to use.

Number four: DNA is central to life, and this makes it likely that there are many applications of sequencing that nobody has thought of yet.

In summary, it seems to me that sequencing is likely to be pervasive in the lives of a lot of people, though maybe not as pervasive as transistors. I am open to arguments against this, but I cannot think of any myself.

That's the end of this Easter post, except for one more thing: I started a Twitter account recently, and plan to tweet a few times a week on topics that may be relevant to readers of this blog. I'll also announce all my new blog posts on Twitter. If you think that this may be interesting to you, please follow me: http://twitter.com/artwuster