Community action for a commercial alternative to microarray analyses

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Dear Colleagues,

In order to increase the visibility of the Dicty community and research, I thought that it might be of advantage to open a new door and allow researchers world-wide access to a standardized and “universal” microarray chip. Therefore, I have been enquiring about the possibility to have a custom array designed for the use of the whole Community. But for this, I need to have your opinion and input, therefore, bear with me for a few more sentences/arguments.

First, it becomes essential to open even more access to microarray analyses, because the more the better. I mean if we want to make sense of the organism and of the multitude of experiments being carried out, usage of a common and standardized array is essential. Also, usage of common and standardized hybridization and analysis method is crucial, as is the possibility to cross-compare and contrast data obtained at the four corners of our Community.

Most of us are probably in reach of an –omics plateform using Affymetrix technology. Despite the costs of such experiments, and the emergence of competitors, this is likely the most wide-spread and reliable technology.

We clearly have to use a full-genome chip, and printing such chips is difficult and rate-limiting for most groups. Affymetrix proposes either an array with 10’100 features (cat N° 49-5241) or 23’000 features (cat N° 49-7875). Probably the 10’100 array is fine!

To speak numbers, if we want to order a custom array from Affymetrix, we need to know how many people are interested and ready to share the costs of making the masque for the printing. Once this masque designed and built, it can be used over and over again. Therefore, this cost is unique. Then, depending on the nuber of arrays this masque generates, for each subsequent order, we might need to combine individual lab orders to reach the target number. Please, have a look at the attached documents for more info [1] [2]. But for example, including the 25% Affymetrix general discount we get in Switzerland, the masque for a 10’100 features-array costs USD 39’000 if the design is for 80 arrays, USD 26’000 for 160 arrays, or USD 13’000 for 240 arrays. And then, independently of the design, every single array costs USD 417. This means that for a 160 array design (that seems reasonable for a group-order), the first order with masque and 160 arrays will cost USD 92’000. And each subsequent order of 160 arrays will total USD 67’000.

In order for all of you to estimate the total costs of such experiments, please, contact the nearest Affymetrix facility to ask for their per array charges. This might be a bad surprise, as for example here we pay up to USD 400 per array.

Voilà, I will eagerly be expecting your input, especially from the big array-producers and users, but also from the multitude of smaller labs who would be interested to access such a technology.

With very best pre-Xmas wishes to All,


Dr. Thierry Soldati, Senior Lecturer Department of Biochemistry University of Geneva 30 quai Ernest Ansermet, Sciences II CH-1211-Genève-4, Switzerland

Tel: +41-22-379-6496 Fax: +41-22-379-3499 email:

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