Parafin Embedded Tumor Exome Sequencing

Question

[Irsan]

I would love to hear your experiences about detecting single nucleotide variants and/or indels from parafin embedded formalin fixed tumor samples with exome sequencing. What are the main challenges/factors involved? I can imagine that the degree of fragmentation of the parafin embedded DNA complicates the bait hybridization and therefore you need to estimate the fragment size with bioanalyzer and you probably need more input DNA. Any other issues?