Microarrays vs. next-gen sequencing III

Friday, May 29th, 2009 by hinrich

Next-gen sequencing

It keeps puzzling me how much molecular biology is impacted by hypes. I have experienced it with microarrays and now it's next-generation sequencing. I really wonder what motivates people to write things like "[Next-gen sequencing] receives the baton, so to speak, from microarray technology". This comment can be found in the editorial "Next-generation genome" in Nature Methods of December 2008. Why is it necessary to suggest that one technology has stopped being useful and something else is now taking over?

I would argue that it takes time to understand a technique fully and that rarely one completely takes over from the other. More often one learns the strengths and weaknesses of a given approach by applying it many times. This leads to an adaptation and optimalization phase during which it becomes apparent for which application the technique is most suitable. I would not be surprised if exactly the same will take place for next-generation sequencing.

And will next-generation sequencing receive the baton from microarray technology? Well, maybe in a couple of years. Maybe not. My current bet is still on sequening for content generation and microarrays for quantification. That is, until the biases in the procedures that are introduced during next-gen sequencing are fully understood and can be corrected for either via adapted protocols or data processing algorithms. And assuming further that the price will be competetive and data handling issues are solved.

How about third-generation sequencing? My initial thoughts are the same. Yes, it's very likely that this technology will allow us to decrease the per-sample price, but I wonder whether the technology will be bias-free. Most likely it will not. And then it takes again some time and a number of experiments to identify them and develop techniques to cope with them.

The advantage of microarrays at this moment is that we have developed a very good understanding of the technology over the past ten years. And yes, we have identified the problems and know where microarrays are not the best approach. But for some applications, e.g., gene expression studies, the technology has become affordable and yields reliable results.

The PubMed entry for the editorial "Next-generation genome" can be found here.

Posted in Molecular Profiling

Holidays in Oxfordshire

Thursday, May 07th, 2009 by hinrich

Image from Oxfordshire

After the busy last months writing the book it was time to take a break with the family. As we enjoy going to England, we have choosen Oxfordshire for this year's meivakantie (two week school holiday in The Netherlands).

With Oxford, Legoland, Blenheim Palace, Warrick Castle, Banburry, the Oxford Canal, and many other attractive places to visit, it has been a nice vacation. The trip to Cogges Manor Farm Museum in Witney was quite nice and interesting for the kids. It is unfortunate that the future of this working farm museum is unclear. For now 2009 is the last year it will operate before a new regime will start.

Posted in Misc