we are planning to do LOH and chromosome copy number analysis on DNA extracted from formalin fixed and paraffin embedded tumour samples. we are going to use the Affymetrix 10K 2.0 array. what are the problems encountered when using DNA from FFPE on SNP array?

et said:

we are planning to do LOH and chromosome copy number analysis on DNA extracted from formalin fixed and paraffin embedded tumour samples. we are going to use the Affymetrix 10K 2.0 array. what are the problems encountered when using DNA from FFPE on SNP array?

A barrier to the analysis of FFPE samples is that RNA extracted from FFPE tissues is often significantly degraded. Some studies show that only about 3% or less of the RNA isolated from paraffin samples is accessible to cDNA synthesis, compared to fresh-frozen samples. In particular, this has impeded progress in microarray-based gene expression quantitation from FFPE specimens. As a result, most gene expression analysis of FFPE tissues has so far been done using immunohistochemical staining (IHC) and quantitative RT-PCR (qPCR), which allow only a few genes to be analyzed at a time. Although sufficient RNA can be isolated from a few 10-m slide-mounted paraffin sections to quantitate up to 30 genes by qPCR, there is clearly a bottleneck in scaling up the number of genes that can be measured by this approach. Also, qPCR does not reliably measure RNA fragments shorter than 100 bp.