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Preoperative diagnosis of soft tissue and bone tumors using needle biopsy techniques, namely fine needle aspiration (FNA) and core needle biopsy (CNB), has gained wider acceptance in recent years. This is achieved in concert with the maturation of various image-guided needle biopsy techniques, development of molecular genetic diagnostics, and expansion of immunohistochemical biomarkers. FNA, however, as a first-line approach to evaluate soft tissue and bone tumors, remains one of the most challenging and controversial areas in cytopathology. Compared with the CNB, FNA is more suitable for smaller lesions, recurrent and/or metastatic tumors, and lesions with a broad differential diagnosis including carcinomas and lymphomas. Enhanced by rapid on-site evaluation (ROSE), and immediate tissue triage for flow cytometry and/or cytogenetic/molecular studies, FNA offers a valuable and fast diagnostic modality for lesions suspicious for high grade malignancy. This chapter focuses on the practical approaches to this extremely diverse set of benign and malignant neoplasms, emphasizing on pattern recognition, effective triage of biopsy material, and judicious use of ancillary studies. General discussion of the clinical and cytomorphologic features of each entity is beyond the scope of this diagnostic approach–orientated chapter, and the readers are directed to other relevant excellent textbooks.

Molecular diagnostics have greatly advanced our understanding of the pathogenesis of soft tissue and bone neoplasms and have led to the development of numerous useful diagnostic tools. Definitive cytologic diagnosis is now possible for many soft tissue and bone tumors with judicious application of immunohistochemistry and numerous molecular technologies. Immunohistochemistry is primarily used to identify the line of differentiation and protein correlates of underlying molecular alterations and can guide appropriate selection of molecular tests. Currently, the most commonly employed molecular diagnostic approaches are fluorescence in situ hybridization and reverse transcription-polymerase chain reaction. High-throughput molecular techniques (e.g., whole-exome or targeted panel next-generation sequencing) have potential exciting applications for cytology practice, and these platforms can provide useful diagnostic and prognostic information in the diagnosis of soft tissue and bone tumors. While ancillary tests allow for more accurate classification of many soft tissue and bone neoplasms on cytologic material, immunohistochemical and molecular tests always should be interpreted in the context of the clinical, radiologic, and cytomorphologic features, and the cytopathologist must be aware of the pitfalls and limitations of these assays. This chapter reviews the applications of molecular diagnostics, including integration of immunohistochemical markers, in the cytologic diagnosis of soft tissue and bone neoplasms.

Fine-needle aspiration (FNA) biopsy of the kidney is a valuable diagnostic modality for radiographically indeterminate mass lesions, for workup of systemic diseases, and for establishing a malignant diagnosis in nonsurgical candidates. Recent advances in imaging, interventional radiology, and cytologic ancillary techniques have enhanced the accuracy of renal FNA. Adrenal masses are a common finding in abdominal image studies. Using CT, US, and more recently endoscopic US (EUS) guidance, FNA biopsy is effective in distinguishing primary, mostly benign adrenal nodules from metastatic tumors during staging workups. It can also be used in establishing the diagnosis of some systemic infectious diseases.