Each processing method has particular strengths and weaknesses in terms of subsequent molecular analyses, and investigators must select the appropriate approach based on specimen availability and specific goals of their study. Bulk Tissues Pros Provide the highest quality and a large quantity of DNA, mRNA and protein, allowing a wide range of molecular analysis techniques to be utilized. Cons Contain multiple cell types that can confound interpretation of profiling data. Microdissected Cell Populations from Histology Slides Frozen Tissue Pros Yield DNA, mRNA and protein from histopathologically defined cell populations that could define the critical changes in molecular profiles occurring during disease progression . Can identify cell-type unique transcripts that may serve as future diagnostic or therapeutic targets.
Cons Depend upon the technically challenging technique of microdissection.
Recover small amounts of DNA or mRNA which are typically too little for many standard downstream analyses. Produce lower quality histology compared to formalin-paraffin embedded slides. Microdissected Cell Populations from Histology Slides Standard Fixation and Embedding of Tissue Pros Are currently the gold standard for diagnostic pathology due to the high level of histological detail they provide. Are available in large number in archives. IHC and ISH are therefore useful adjunct methods to verify expression changes that are observed in molecular profiling experiments.