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

ixation are myriad and the possible products complex4, past researchers have shown that the ability to analyze FFPE derived material in applications such as microarrays is loosely related to the average length of extracted DNA.5 More recent and apparently more correlative diagnostics for template quality have been developed which use the ability to PCR amplify from the sample. 6,19,20 One assay, in particular, has worked well in our hands as the best predictor of a samples potential for successful amplification.7 The assay employs multiplex PCR to amplify a number of differently sized loci within the human genome; loss of the higher molecular weight bands indicates that the DNA has degraded past the point where whole genome amplification will be successful. This test allows scientists who are interested in amplifying a limited sample of unknown quality to perform some polymerase-mediated amplification before attempting WGA.

Any WGA method to be applied to formalin-fixed DNA must be able to amplify relatively short lengths of nucleic acid stretches, ~1kb or less. Four WGA methods have been described and are in common use they include linker adapter PCR (LAP)8-10, primer extension preamplification PCR (PEP)11, degenerate oligonucleotide PCR (DOP)12,13 and multiple strand displacement (MSD).14,15 While all have been successful in varying degrees when used with FFPE DNA, MSD has suffered in that it relies on a highly processive polymerase and high quality DNA chains to create long amplicons (>10kb). Because FFPE DNA is often comprised of short pieces of DNA with amplification terminating lesions, this type of input DNA has been amplified with best representation by using LAP and DOP WGA .10,13,16

GenomePlex uses a modified DOP amplification to effect whole genome amplification, and t
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