New Array Designs

As mentioned, the labeled products (cDNA or cRNA) generated from FFPE-derived mRNA tend to be smaller in size than those prepared from fresh or frozen samples. Most arrays that have been designed and used to date have attempted to bias probe design to the 3' end of the mRNA; however, the degree of this bias has been based on the idea of cDNA products that are up to 1 kb or more in length. Newer designs using more rigorous algorithms that further bias the probe design to within only a few hundred bases of the polyA tail of the mRNA have been made available.

Affymetrix, for example, has released a product termed X3P (for eXtreme 3-Prime). The X3P arrays have been designed such that the majority of probe-sets fall within 300 bases of the 3' end of the mRNA, compared to traditional Affymetrix designs which may use probe-sets spanning as much as the first 600 bases (see http://www.affymetrix.com/products/arrays/specific/x3p.affx). Despite the introduction of these new arrays, publications using FFPE-archived samples remain few in number (62,63). Indeed, to date, no comprehensive comparison, such as the one carried out by Scicchitano et al., has been carried out using the 3XP arrays, although such an analysis would be of great value.

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