and kills microorganisms that are present in tissues. The fixative routinely used in pathology is 10 percent neutral buffered formalin, a buffered aqueous solution of formaldehyde. Fixation yields “wet tissue” that is either stored in an air-tight container or processed further as delineated below.
Embedding. Specimen water (about 70 percent of tissue mass) is replaced with paraffin wax, and the specimen is surrounded by paraffin in a mold to provide support during sectioning and to aid in preservation. Formalin-fixed paraffin-embedded (FFPE) tissue is one of the predominant forms in which pathologic specimens are stored.
Sectioning. Sections are cut on a microtome, which has a blade similar to a single-edge razor blade, that is advanced through a block of paraffin-embedded tissue. The shavings—about 5 µm thick, about twice the thickness of a human hair—are placed in water, and the floating shavings are picked up on 1 × 3-in. glass slides. A given tissue block can be recut many times, although specific slices may differ in the amounts and types of tissues (for example, primary tumor vs. normal tissue) present.
Staining. Tissue components can be distinguished with selective absorption of dyes to facilitate viewing under a microscope. The stain routinely used in histology is hematoxylin and eosin. There are special methods for highlighting components (such as microorganisms) that do not stain well with the customary preparations. Pathologists commonly use tissue sections prepared in this manner in their analyses.
Researchers use tissue microarrays (TMAs) constructed from diagnostic blocks of FFPE tissue to permit simultaneous evaluation of expression of specific pathologic features—proteins by immunohistochemistry, for example—in hundreds of individual tissue samples from different patients on a single slide (Rimm et al., 2011; Voduc et al., 2008). TMAs are assembled by using a needle to core an FFPE tissue block and extract a 0.5- to 2.0-mm piece that is placed into a predrilled master paraffin block that may contain up to 400 cores. Sections from the resulting block may be cut with a microtome, placed on a slide, stained, and analyzed. In cancer research, TMAs are used to analyze the frequency of a molecular alteration in different tumor subtypes, as detected by immunohistochemical and molecular techniques, to enable evaluation of potential diagnostic and prognostic markers by correlating staining patterns with light microscopy and clinical information, which may also contain outcome measures (Camp et al., 2008; Kapur, 2011). Advantages of using TMAs include minimal tissue use, lower reagent costs, faster results, and the ability to define a set of cases that