Histological diagnosis is essential in neoplastic lesions, but is not sufficient to accurately classify the disease. Histologically verified lesions are the basis for the study of molecular differences. The aim of the morphological identification is also to ensure that the disease (tumor tissue, cells) is present in a representative sample. Therefore, the test is often performed after histological processing from a paraffin block, which requires a specific methodology for the quality of DNA and RNA.

Genetic and gene regulatory errors result in different behaviors and growth characteristics in individual tumors, but also in individual patients. The main purpose of molecular testing is to detect gene aberrations in tissue that influence the effect of the relevant drug therapy. Therefore the effective treatment can be selected based on the molecular characteristics and "sensitivity" of the tumor. The choice of the most appropriate treatment is the result of professional collaboration (oncology team), which is mainly determined by pathological findings and molecular pathology results.

The purpose of molecular testing:

• to confirm the molecular background of the expected therapeutic effect in case of targeted therapy (eg for the administration of EGFR targeted drugs in certain epithelial cancers)
• to highlight chromosome or gene alteration in specific disease (cancer) to confirm the diagnosis or in some cases exclude it (eg chromosomal translocations, deletions)
• to determine the expected outcome or in some diseases the intensity of treatment (eg MYCN gene amplification in neuroblastoma)
• to examine the etiology (development, background) of the disease, eg confirmation of the presence of a viral genome (EBV, CMV, etc.)
• to monitor the disease by detecting the abovementioned differences and to determine the response to treatment.

Molecular assays can be done in situ (in cells) or in isolated nucleic acids (DNA, RNA). In situ hybridization is used to detect characteristic chromosome aberrations, and the result is evaluated by fluorescence microscopy. Mutations in isolated DNA can be confirmed after PCR amplification of the gene of interest. Detailed detection of certain mutations also requires sequencing of the particular DNA section.