Chapter 7
ALK Analysis in Cytology
By Lukas Bubendorf
Role of Cytology in NSCLC
FISH testing for detection of ALK rearrangement as a predictive marker in NSCLC was initially approved for testing of biopsy material (Kwak 2010). Biopsy material is often preferred for translational studies in clinical trials because paraffin blocks are routinely processed in pathology laboratories and these blocks provide multiple sections for various analyses. However, as many as 40% of all advanced NSCLC are diagnosed by cytologic evaluation alone, with no concurrent histologic examination of biopsy material. Thus, reliance on histology as the only source for ALK testing would require repeat biopsy in a large proportion of patients, emphasizing the necessity to expand ALK analysis to cytologic specimens. FISH analysis of cytologic specimens has a long tradition, and FISH technology was used to evaluate cell lines or disaggregated intact nuclei from histologic tumor specimens before it became applicable to tissue sections. FISH is also an established method in several fields of diagnostic cytology. From an analytic point of view, there is no rationale against applying ALK FISH to cytologic specimens. In fact, cytologic specimens have several advantages; for example, in contrast to histologic sections, the nuclei on cytology smears are not truncated, which allows for the detection of the true number of FISH signals in a nucleus. Cytology is an attractive, minimally invasive method to collect tumor material for repetitive biomarker analysis on recurrent or metastatic disease. Cytologic diagnosis of NSCLC is typically based on EBUS-FNA, transthoracic FNA, bronchial secretions or brushes, bronchoalveolar lavages, and pleural effusions or FNA from other metastatic sites. Processing such specimens for FFPE cell blocks has become the preferred method in many laboratories, as cell blocks can be handled in the same way as histologic specimens, and the same protocols for biomarker analysis can be applied (Figure 1) (Alici 2013, Kalhor 2013). Aside from the ability to generate more material with repeated sec50 µm 50 µm tioning, cell blocks also have A B the advantage of long-term Figure 1. Pleural effusion of a p [[?\?HY[???\??[??XK? PN?\[?X??[?K\?Z[?Y ?\?\??][?? ??Z[?????[?[?[ ?YX\?? P?? ?K\?Z[?Y ?X?[??H?[????
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