Factors when selecting tumor that has been embedded in a paraffin block:
(1) number of intact tumor cells
(2) viability of tumor cells (advancing margin often best)
Factors that should be avoided:
(1) areas of necrosis
(2) areas of inflammation
(3) areas of normal tissue or scarring
(4) material that may inhibit PCR or other reactions
Additional factors affecting usability of the extracted material:
(1) fixative: neutral buffered formalin is a common fixative. Other fixatives may be better or worse for nucleic acid preservation and extraction.
(2) quality of tissue storage and fixation
In some cases tissue can be directly extracted from the paraffin block. More often paraffin sections are placed on slides and suitable areas are microdissected out from less suitable tissue.
