Molecular Markers in Soft Tissue and Bone Tumors

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Bone and soft tissue tumors encompass a remarkably diverse spectrum of benign and malignant entities. Over the last couple decades, molecular genetic abnormalities have demonstrated to be an important, sometimes necessary adjunct for diagnosis, prognostication, and therapeutics of bone and soft tissue tumors. In general, bone and soft tissue tumors can be classified broadly into two groups: those neoplasms with complex, nonspecific cytogenetic profiles (Table 12.1) and those with relatively simple, consistent, and recurrent cytogenetic and molecular aberrations (Tables 12.2 and 12.3). The methods used to detect those molecular genetic aberrations include fluorescence in situ hybridization (FISH), array-based comparative genomic hybridization (aCGH), single nucleotide polymorphism (SNP) array, polymerase chain reaction, and sequencing. Those tests are frequently performed on formalin-fixed, paraffin-embedded (FFPE) tissues in the clinical laboratories. However, with the popularity of new technologies such as interventional radiology and ultrasound-guided fine needle aspiration, clinicians often request that specific molecular genetic tests be performed on the limited material. It is feasible to have some molecular tests done on cytology specimens, such as touch prep, thin-prep, cell block, or fluid. Some tests are actually more easily performed on cytology specimens and can provide much better results (such as FISH performed on thin-prep slide). This chapter is divided into two major sections: (1) summary of recurrent or tumor-specific genetic events in bone and soft tissue tumors, and (2) overview of the molecular approaches commonly used in clinical practice. A brief discussion of some molecular tests for bone and soft tumor performed on cytology samples is also provided.