Zakowski, Maureen F.

Abstract Introduction. For patients with non-small cell lung cancer (NSCLC) to benefit from ALK inhibitors, sensitive and specific detection of ALK genomic rearrangements is needed. ALK break-apart fluorescence in situ hybridization (FISH) is the U.S. Food and Drug Administration approved and standard-of-care diagnostic assay, but identification of ALK rearrangements by other methods reported in NSCLC cases that tested negative for ALK rearrangements by FISH suggests a significant false-negative rate. We report here a large series of NSCLC cases assayed by hybrid-capture-based comprehensive genomic profiling (CGP) in the course of clinical care. Materials and Methods. Hybrid-capture-based CGP using next-generation sequencing was performed in the course of clinical care of 1,070 patients with advanced lung cancer. Each tumor sample was evaluated for all classes of genomic alterations, including base-pair substitutions, insertions/deletions, copy number alterations and rearrangements, as well as fusions/rearrangements. Results. A total of 47 patients (4.4%) were found to harbor ALK rearrangements, of whom 41 had an EML4-ALK fusion, and 6 had other fusion partners, including 3 previously unreported rearrangement events: EIF2AK-ALK, PPM1B-ALK, and PRKAR1A-ALK. Of 41 patients harboring ALK rearrangements, 31 had prior FISH testing results available. Of these, 20 were ALK FISH positive, and 11 (35%) were ALK FISH negative. Of the latter 11 patients, 9 received crizotinib based on the CGP results, and 7 achieved a response with median duration of 17 months. Conclusion. Comprehensive genomic profiling detected canonical ALK rearrangements and ALK rearrangements with noncanonical fusion partners in a subset of patients with NSCLC with previously negative ALK FISH results. In this series, such patients had durable responses to ALK inhibitors, comparable to historical response rates for ALK FISH-positive cases.

BackgroundThe Papanicolaou Society of Cytopathology has developed a set of guidelines for respiratory cytology including indications for cytologic testing, techniques for cytologic sampling, terminology and nomenclature for respiratory diseases, ancillary testing, and recommendations for postcytologic diagnosis follow‐up and management.MethodsAll documents are based on the expertise of the authors, an extensive literature review and discussions of the draft documents at national and international meetings over a 12‐month period. This document selectively presents the results of these discussions and reports a proposed standardized terminology scheme for respiratory cytology that correlates cytologic diagnosis with biologic behavior and patient management.ResultsThe classification and terminology scheme recommends a six‐tiered system composed of: nondiagnostic, negative, atypical, neoplastic (benign and neoplasms of low malignant potential), suspicious, and positive for malignancy.ConclusionThe scheme recommends statements on specimen adequacy followed by the major classification category and then a subclassification and/or comments section. Each of the six main diagnostic categories is associated with an estimated risk of malignancy. Subsequent documents will propose ancillary testing recommendations, techniques for cytologic sampling, indications for cytologic study and postcytologic diagnosis management and follow‐up recommendations. Diagn. Cytopathol. 2016;44:399–409. © 2016 Wiley Periodicals, Inc.