The role of next-generation sequencing in detecting gene FUSIONS with KNOWN and UNKNOWN partners: A single-center experience with methodologies’ integration

Aims: Next-generation sequencing (NGS) is becoming a new gold standard for determining molecular predictive biomarkers. This study aimed to evaluate the reliability of NGS in detecting gene fusions, focusing on comparing gene fusions with known and unknown partners... Conclusions: NGS is a reliable method for detecting gene fusions with known partners, but it is less accurate in identifying gene fusions with unknown partners, for which further analyses (such as FISH) are required. READ ARTICLE

Human Pathology DOI:10.1016/j.humpath.2022.02.005

Authors: Andrea Ambrosini-Spaltro, Anna Farnedi, Daniele Calistri, Claudia Rengucci, Giovanna Prisinzano, Elisa Chiadini, Laura Capelli, Davide Angeli, Chiara Bennati, Mirca Valli, Giovanni De Luca, Dora Caruso, Paola Ulivi, Giulio Rossi

Review PaperKirk SmithFebruary 15, 2022Next-generation sequencing, FISH, IHC, gene fusion, partner, NSCLC

Testing for EGFR Mutations and ALK Rearrangements in Advanced Non-Small-Cell Lung Cancer: Considerations for Countries in Emerging Markets

The treatment of patients with advanced non-small-cell lung cancer (NSCLC) in recent years has been increasingly guided by biomarker testing. Testing has centered on driver genetic alterations involving the epidermal growth factor receptor (EGFR) and anaplastic lymphoma kinase (ALK) rearrangements. The presence of these mutations is predictive of response to targeted therapies such as EGFR tyrosine kinase inhibitors (TKIs) and ALK TKIs. However, there are substantial challenges for the implementation of biomarker testing, particularly in emerging countries. Understanding the barriers to testing in NSCLC will be key to improving molecular testing rates worldwide and patient outcomes as a result. In this article, we review EGFR mutations and ALK rearrangements as predictive biomarkers for NSCLC, discuss a selection of appropriate tests and review the literature with respect to the global uptake of EGFR and ALK testing. To help improve testing rates and unify procedures, we review our exp..... READ ARTICLE

OncoTargets and Therapy DOI:10.2147/OTT.S313669

Authors: Mercedes L Dalurzo, Alejandro Avilés-Salas, Fernando Augusto Soares, Yingyong Hou, Yuan Li, Anna Stroganova, Büge Öz, Arif Abdillah, Hui Wan and Yoon-La Choi

5' ALK Amplification in Neuroblastoma: A Case Report

This report illustrates the importance of careful interpretation of aberrant FISH findings and subsequent use of orthogonal methods to clarify the presence of genomic alterations to successfully determine potential treatment targets. READ ARTICLE

Case Reports in Oncology DOI:10.1159/000512187

Authors: Sara Akhavanfard, Erik Nohr, Mohammad AlNajjar, Mollie Haughn, Sayaka Hashimoto, Carol Deeg, Ruthann Pfau, Marie-Anne Brundler, Shalini C Reshmi

Case StudyKirk SmithApril 1, 2021ALK gene, FISH, Gene amplification, Microarray, Neuroblastoma

Outcomes According to ALK Status Determined by Central Immunohistochemistry or Fluorescence In Situ Hybridization in Patients With ALK-Positive NSCLC Enrolled in the Phase 3 ALEX Study

Introduction: We retrospectively examined progression-free survival (PFS) and response by ALK fluorescence in situ hybridization (FISH) status in patients with advanced ALK immunohistochemistry (IHC)-positive NSCLC in the ALEX study. Conclusions: Outcomes of patients with ALK IHC-positive and FISH-positive and ALK IHC-positive and FISH-uninformative NSCLC were similar to those of the overall ALEX population. These results suggest that Ventana ALK IHC is a standard testing method for selecting patients for treatment with alectinib. READ ARTICLE

Journal of Thoracic Oncology DOI:10.1016/j.jtho.2020.10.007

Authors: Tony Mok, Solange Peters, Ross Camidge, Johannes Noé, Shirish Gadgeel, Sai-Hong Ignatius Ou, Dong-Wan Kim, Krzysztof Konopa, Emanuela Pozzi, Ting Liu, Isabell R. Loftin, Crystal Williams, Alice T. Shaw

Clinical TrialsKirk SmithFebruary 1, 2021Alectinib, ALK-positive, IHC, FISH, NSCLC

ALK rearrangement in TFE3-positive renal cell carcinoma: Alternative diagnostic option to exclude Xp112 translocation carcinoma

Anaplastic lymphoma kinase (ALK)-rearranged renal cell carcinoma (RCC) is a rare subtype of RCC with gene fusion involving ALK at 2p23. It was first included in the renal tumor classification system by WorldHealth organization (WHO) as a distinct emerging/provisional renal entity in 2016. To date, only a few cases of ALK-RCC have been reported. Here, we report an exceptional case of ALK-RCC in a 15-year-old girl and review the literature. The patient presented with gross hematuria and a tumor measured 7 cm × 6 cm was found in the left kidney by imaging examination. Then a laparoscopic radical nephrectomy combined with local lymph node dissection was performed. The pathologic stage of the tumor was pT1bN1Mx and postoperative pathology showed that the tumor corresponded to WHO/ISUP grade 3–4. Immunohistochemistry (IHC) demonstrated moderate nuclear expression of TFE3 protein. Interestingly, ALK gene rearrangement rather than TFE3 gene rearrangement was observed by fluorescence in situ hy..... READ ARTICLE

Pathology - Research and Practice DOI:10.1016/j.prp.2020.153286

Authors: Yiqi Zhu, Ning Liu, Wei Guo, Xiaohong Pu, Hongqian Guo, Weidong Gan, Dongmei Li

Case StudyKirk SmithDecember 1, 2020Renal cell carcinoma, Translocation, FISH, ALK, HOOK1, TFE3

Multiplex fluorescence in situ hybridisation to detect anaplastic lymphoma kinase and ROS proto-oncogene 1 receptor tyrosine kinase rearrangements in lung cancer cytological samples

Aims: Several predictive biomarkers of response to specific inhibitors have become mandatory for the therapeutic choice in non-small-cell lung cancer (NSCLC). In most lung cancer patients, the biological materials available to morphological and molecular diagnosis are exclusively cytological samples and minimum tumour wastage is necessary. Multiplex fluorescence in situ hybridisation (mFISH) to detect simultaneously ALK-rearrangement and ROS1-rearrangement on a single slide could be useful in clinical practice to save cytological samples for further molecular analysis. In this study, we aim to validate diagnostic performance of multiplex ALK/ROS1 fluorescence in situ hybridisation (FISH) approach in lung adenocarcinoma cytological series compared with classic single break apart probes. Conclusion: Multiplex ALK/ROS1 FISH probe test is a useful tool to detect simultaneously ALK-rearrangement and ROS1-rearrangement on a single slide in cytological specimens with a small amount of biomaterial. READ ARTICLE

Clinical Pathology DOI:10.1136/jclinpath-2019-206152

Authors: Federica Zito Marino, Giulio Rossi, Immacolata Cozzolino, Marco Montella, Mariacarolina Micheli, Giuseppe Bogina, Enrico Munari, Matteo Brunelli, Renato Franco

Low ALK FISH positive metastatic non-small cell lung cancer (NSCLC) patients have shorter progression-free survival after treatment with ALK inhibitors

ALK FISH assay guides clinical decision to initiate therapy with ALK inhibitors in patients with stage IV non-small cells lung cancer (NSCLC). In this single institution retrospective study, we investigated the association between the strength of ALK positivity and progression-free survival (PFS) We screened 4,829 patients tested for ALK rearrangement by FISH from 01/06/2012 to 06/30/2018 and included 66 stage IV NSCLC ALK positive patients, who were ALK inhibitor naïve, received an ALK inhibitor, and been followed at least 10 months to the study. The median PFS for cases high positive cases [≥=50% positive nuclei; n = 49] and low positive cases [16–49% positive nuclei; n = 17] is 16 months and 4 months respectively, and the hazard ratio is 2.89 [95 CI 1.34–6.2] (p = 0.0068). When cases are stratified according to cut-off ≥=30% positive nuclei, the median PFS for cases above (n = 55) and below the cut-off (n = 11) is 12 and 3 months, respectively and the hazard ratio is 9.60 [95 CI 2.6..... READ ARTICLE

Cancer Genetics DOI:10.1016/j.cancergen.2019.12.003

Authors: Gokce A. Toruner, Zhenya Tang, Guilin Tang, L. Jeffrey Medeiros, Shimin Hu

Case StudyKirk SmithDecember 12, 2019ALK, FISH, PFS, Lung cancer

Clinical significance of ROS1 5’ deletions in non-small cell lung cancer

Objectives: Patients harboring rearrangements of the ROS1 gene are eligible for first-line therapy with Crizotinib, which represents the best available treatment option. Diagnostic criteria, based on break-apart fluorescence in situ hybridization, were mirrored from ALK by analogy and include tumors with 5' deletions. However, the probability of response to Crizotinib in patients with 5' deletion in ROS1 is unknown given the rarity of this condition. Conclusion: 5' ROS1 deletions detected by FISH are associated with a high chance of response to Crizotinib in NSCLC, similarly to canonical ROS1 split-apart FISH rearrangements. However, the confirmation of the ROS1 gene fusion with at least another method, such as NGS, seems beneficial in order to define the ROS1 fusion partner and to avoid possible false positive results. READ ARTICLE

Lung Cancer DOI:10.1016/j.lungcan.2019.07.017

Authors: Elisa Capizzi, Filippo Gustavo, Dall’Olio, Elisa Gruppioni, Francesca Sperandi, Annalisa Altimari, Francesca Giunchi, Michelangelo Fiorentino, Andrea Ardizzoni

Case StudyKirk SmithSeptember 1, 2019Non-small cell lung cancer, ROS1 fusions, ROS1 deletions, FISH, NGS, Crizotinib

Fusion of ALK to the melanophilin gene MLPH in pediatric Spitz nevi

Spitzoid neoplasms typically affect young individuals and include Spitz nevus, atypical Spitz tumor, and Spitzoid melanoma. Spitz tumors can exhibit gene fusions involving the receptor tyrosine kinases NTRK1, NTRK3, ALK, ROS1, RET, or MET, or the serine-threonine kinase BRAF. Because most studies have been based on adult cases, we studied ALK fusions in Spitz nevi occurring in pediatric patients. Twenty-seven cases were screened for ALK expression by immunohistochemistry, and 6 positive cases were identified. These cases were studied further using the TruSight RNA Fusion Panel, and in 4 cases, exon 20 of the ALK gene was found to be fused to exon 14 of the MLPH (melanophilin) gene, a gene fusion that has only been reported in a Spitz nevus in an adult. The remaining 2 cases showed no fusion of ALK with any gene. The cases with the MLPH-ALK fusion showed a similar histology to that described for Spitz nevi with ALK fusions, with spindle-shaped and epithelioid melanocytes in fusiform nes..... READ ARTICLE

Human Pathology DOI:10.1016/j.humpath.2019.03.002

Authors: Catherine T. Chung, Paula Marrano, David Swanson, Brendan C. Dickson, Paul Scott Thorner

Discordance between FISH, IHC, and NGS Analysis of ALK Status in Advanced Non–Small Cell Lung Cancer (NSCLC): a Brief Report of 7 Cases

BACKGROUND: Anaplastic lymphoma kinase (ALK) rearrangement represents a landmark in the targeted therapy of non–small cell lung cancer (NSCLC). Immunohistochemistry (IHC) is a sensitive and specific method to detect ALK protein expression, possibly an alternative to fluorescence in situ hybridization (FISH). In this study, the concordance of FISH and IHC to determine ALK status was evaluated, particularly focusing on discordant cases. In our discordant cases, a coexistent complex pattern (deleted, split, and amplified/polysomic) of ALK gene was observed by FISH analysis. These complex rearranged cases were not detectable by IHC, and it could be speculated that more complex biological mechanisms could modulate protein expression. These data highlight the role of IHC and underscore the complexity of the genetic pattern of ALK. It could be crucial to consider these findings in order to best select patients for anti-ALK treatment in daily clinical practice. READ ARTICLE

Translational Oncology
DOI:10.1016/j.tranon.2018.11.006

Authors: Anna Scattone, Annamaria Catino, Laura Schirosi, Lucia Caldarola, Stefania Tommasi, Rosanna Lacalamita, Elisabetta Sara Montagna, Domenico Galetta, Gabriella Serio, Francesco Alfredo Zito, Anita Mangia

Case StudyKirk SmithFebruary 1, 2019FISH, IHC, NGS, ALK Status, Advanced Non–Small Cell Lung Cancer (NSCLC)