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Genomic Analysis of Formalin-Fixed Paraffin Embedded (FFPE) Tissues through the use of Whole Genome Amplification (WGA)

ncy, giving rise to some loss of representation of DNAs in this size range. Genomic DNA fragments less than ~400 bp will not amplify at all using GenomePlex. (18). Highly fragmented DNA (<150 bp) will, when subjected to the GenomePlex methodology, self prime to create product with very low representation as compared to the original sample.

Amplification limitations are not the only obstacle in analyzing formalin treated samples. Studies have shown that formalin treatment weakens DNA, making it more susceptible to shearing when subjected to column based bind and elute purification.4 The most recent GenomePlex offering, (Cat. No. WGA5), designed for fresh, frozen or fixed tissues, includes reagents to effect a very gentle extraction. The lysis uses a combination of proteinase K and lytic detergent, and draws from the experience gained in the development of the Sigma Extract-N-Amp reagent line. Efficient, gentle lysis and a robust amplification should give the greatest possible chance for the researcher to amplify their tissue-derived DNA.

In conclusion, WGA from fixed tissues is a very challenging, but rich source of potential genetic information. Because GenomePlex initially generates a library of amplifiable template molecules by relying upon a simple degenerate primer extension, it alone is poised to amplify DNAs that are highly fragmented and/or modified. The DOP amplification mechanism and the gentle lysis included in the GenomePlex Tissue WGA kit make it the best commercial choice for these difficult substrates.


References
1. Impraim, C., et al., (1987) Analysis of DNA extracted from formalin-fixed, paraffinembedded tissues by enzymatic amplification and hybridization with sequence-specific oligon
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