Chapter 2
Sample Acquisition, Processing, and General Diagnostic Procedures
By Keith M. Kerr, Ignacio Wistuba, and Yasushi Yatabe
Testing for ALK gene rearrangements is one of several diagnostic procedures that may be required on a tissue sample containing lung cancer. In most patients, a single sampling procedure will generate a relatively small amount of tissue that must then be used in the most efficient manner to allow for the most fully informed diagnosis possible. Two important points about tissue samples should be remembered: there is a possibility that a sample will not contain tumor tissue, and there is only one opportunity to fix and process the tissue. Thus, acquisition and processing are crucial steps in quality control in order to facilitate all the diagnostic procedures that may need to be done on a tissue sample.
Obtaining ?Tissue for Diagnosis
In most cases, ALK testing is performed on a small tissue specimen obtained by biopsy or on cytology samples taken from patients who have advanced disease. Less often, the whole tumor is available from a patient who had surgical resection of early-stage disease and subsequent recurrence. Tissue sampling for diagnosis should be aimed at obtaining the largest yield of tumor in the safest and least invasive way possible (Thunnissen 2012d). Sampling may involve the primary tumor, intrathoracic metastatic disease, or extrathoracic metastases. Although discrepancies in ALK status between primary and metastatic disease have been reported (Kim 2013), data are insufficient to guide approaches to tissue acquisition. The primary tumor may be sampled at endoscopy (by endobronchial or transbronchial forceps biopsy, cryobiopsy, or fine-needle aspiration [FNA]? , or with ) a percutaneous, transthoracic approach (by core-needle biopsy or FNA. Intrathoracic metastatic disease is now routinely sampled using endobronchial ultrasound (EBUS) or transesophageal ultrasound (EUS) guidance; pleural disease (either pleural biopsy or fluid cytology) is often a good source of diagnostic material. Distant extrathoracic metastatic disease can be sampled as appropriate to the site; in all cases, several imaging techniques are helpful in targeting the sampling to improve tumor yield (Rivera 2007). In most centers, surgical procedures may be used to obtain tissue if sufficient material was not obtained with image-guided procedures or when such procedures are not likely to be successful.
Tissue for ALK Testing
Both tissue biopsy and cytology samples may be used for ALK testing; the key issues are that the material must be processed and handled appropriately and the sample must contain sufficient