Automation of ALK gene rearrangement testing with fluorescence in situ hybridization (FISH): a feasibility study.

In the past several years we have observed a significant increase in our understanding of molecular mechanisms that drive lung cancer. Specifically in the non-small cell lung cancer sub-types, ALK gene rearrangements represent a sub-group of tumors that are targetable by the tyrosine kinase inhibitor Crizotinib, resulting in significant reductions in tumor burden. Phase II and III clinical trials were performed using an ALK break-apart FISH probe kit, making FISH the gold standard for identifying ALK rearrangements in patients. FISH is often considered a labor and cost intensive molecular technique, and in this study we aimed to demonstrate feasibility for automation of ALK FISH testing, to improve laboratory workflow and ease of testing. This involved automation of the pre-treatment steps of the ALK assay using various protocols on the VP 2000 instrument, and facilitating automated scanning of the fluorescent FISH specimens for simplified enumeration on various backend scanning and analysis systems. The results indicated that ALK FISH can be automated. Significantly, both the Ikoniscope and BioView system of automated FISH scanning and analysis systems provided a robust analysis algorithm to define ALK rearrangements. In addition, the BioView system facilitated consultation of difficult cases via the internet.

Parallel FISH and immunohistochemical studies of ALK status in 3244 non-small-cell lung cancers reveal major discordances.

INTRODUCTION: Anaplastic lymphoma kinase (ALK) rearrangements occur in 1% to 7% of non-small-cell lung cancers (NSCLCs). Crizotinib, an ALK inhibitor, has been demonstrated to provide dramatic clinical benefits in ALK-positive advanced-stage NSCLC. Fluorescent in situ hybridization (FISH) has been established in clinical trials as the standard procedure method for detecting ALK rearrangements. Although the detection of ALK by immunohistochemistry (IHC) has been proposed for the screening of patients, large-scale studies are warranted to validate such a hierarchical approach. METHODS: In this article, we report the largest series thus far of parallel FISH and IHC ALK testing in 3244 consecutive NSCLC cases analyzed at two independent French centers. RESULTS: FISH-positive and/or IHC-positive results were demonstrated in 150 of 3244 cases (4.6%). An imbalanced sex ratio was detected, with women exhibiting a 2.2-fold relative risk for an alteration. Strikingly, only 80 of 150 specimens were classified as ALK positive by both techniques. The specimens with discordant FISH/IHC analyses were FISH-positive/IHC-negative (36), FISH-negative/IHC-positive (19), or FISH-noncontributive/IHC-positive (15). Thus, a single FISH or IHC analysis performed alone would have failed to detect approximately one-fourth of the ALK-positive cases with similar findings in our two centers. CONCLUSIONS: This study highlights the feasibility of systematic NSCLC testing by both FISH and IHC in routine practice. Many preanalytical factors may account for the apparent discrepancies between both methods, suggesting that hierarchical screening may underscore ALK-positive cases. This significant level of discrepancy supports the need of combined testing to optimize the detection of ALK-inhibitor-eligible patients given that some patients with discordant testing were found to respond to crizotinib.

Oligodendroglioma: clinical study and survival analysis correlated with chromosomal anomalies.

OBJECT: Demonstration of the loss of chromosomes 1p and 19q in the presence of a brain neoplasm marks the emergence of genotype as a prognostic indicator. The authors report gene expression data for oligodendroglioma and correlate genotype with response to therapy. Gene expression subgroups may represent distinct types of disease. METHODS: Eighty-seven cases of supratentorial oligodendroglioma were selected from 145 cases treated in a single center between January 1990 and December 2001. Fluorescence in situ hybridization was used to determine the status of chromosomes 1p and 19q. Parameters evaluated included clinical data and radiological and histological features. Univariate and multivariate analyses were performed and a probability value less than 0.05 was considered significant. The patients included 48 women and 39 men. The overall mean age at presentation was 45 years for women and 36 years for men (p = 0.006). The univariate analysis identified the following as favorable prognostic factors: younger patient age (p = 10(-5)), female sex (p = 0.0025), seizure as a presenting symptom (p = 10(-5)), normal clinical examination (p = 10(-5)), absence of lesion enhancement on neuroimaging studies (p = 0.0231), lack of histological necrosis (p = 0.0003), absence of mitoses (p = 0.0014), 1p and 19q deletions (p = 0.0001), absence of recurrence (p = 0.0021), and adjuvant radiotherapy and/or chemotherapy (p = 10(-5)). The multivariate analysis identified patient age (p = 10(-5)) and chromosomal anomalies (p = 0.002) as independently linked to survival. Three molecular subtypes emerged: oligodendroglioma with 1p and 19q deletions, oligodendroglioma demonstrating polysomia and a lack of meaningful response to radiotherapy or chemotherapy, and oligodendroglioma with no 1p-9q deletion in which partial response was seen. CONCLUSIONS: According to our data, oligodendrogliomas could be divided into three molecular subtypes. Although chemotherapy seems efficient for managing this tumor, additional studies should be conducted to compare the efficacy of radiotherapy and chemotherapy.