Abstract 3745: Detection of various ALK translocations using intragenic differential expression (IDE) in patients with non-small cell lung cancer
Authors: Sanders Heather R. , Li Hai-Rong , Smith Eric D. , Jahn Jennifer , Scheerle Jay A. , Sferruzza Anthony D. , Novic Connie , Meloni-Ehrig Aurelia M. , Kelly JoAnn C. , Albitar Maher 
Published: February 2011

Abstract
Introduction: Efforts to target EML4-ALK fusions with ALK inhibitors in non-small cell lung cancer (NSCLC) have shown promising results in patients harboring a paracentric inversion on chromosome 2, inv(2)(p21p23). In effect, the clinical utility of these drugs is dependent on the presence of ALK gene activation. Reliable testing for ALK activation by translocation is important for selecting patients for this therapy. Although 11 variants for translocation are known, new variants have recently been reported. The aim of this study was to develop a reliable molecular assay to detect translocation of the ALK gene irrespective of the breakpoint on the EML4 gene or the partner gene. To achieve this, we used intragenic differential expression (IDE) of ALK gene comparing expression levels of the 5′ end with the 3′ end.
Methods: ALK IDE was determined by measuring the levels of both 5′ and 3′ transcript regions by quantitative RT-PCR. IDE scores were obtained by calculating the endogenous control (ABL1) normalized differences in 5′ and 3′ ALK levels (IDE = 5′ALK/ABL1 - 3′ALK/ABL1). High IDE score, relative to normal, indicates the presence of ALK rearrangement. Relative expression of ALK (independent of rearrangement) was also established. A subset of samples were also analyzed by fluorescence in situ hybridization (FISH). All study samples were analyzed for direct detection of EML4-ALK by RT-PCR performed in a parallel study.
Results: The ALK IDE value of an EML4-ALK fusion-positive cell line (NCI-H2228) was 0.7 whereas it was 0.0 for 2 EML4-ALK-negative NSCLC cell lines (NCI H838 and NCI H1299). The positive control value (0.7) was set as the cutoff to distinguish positive vs. negative ALK rearrangement. Eleven percent (6/56) of the lung cancer tissue samples were IDE positive. Eighty-three percent (5/6) of these positives were confirmed by direct detection of EML4-ALK fusion transcript by RT-PCR, including one specimen harboring the previously undescribed variants 8a and 8b. Five IDE-positive samples and 5 with slightly-to-moderately elevated levels of ALK transcript (3′ ALK &gt; 0.1) were further analyzed by FISH. Of these 10 samples, 80% (8/10) showed ALK rearrangement and/or gene amplification. All samples interpreted as having ALK rearrangements by FISH were also positive by IDE (3/3). Two IDE positive (1 confirmed, 1 unconfirmed by RT-PCR) were interpreted as rearrangement negative by FISH.
Conclusions: ALK IDE accurately categorized all FISH-confirmed rearrangements as positive and detected rearrangements in at least 1 other confirmed case not identified by FISH. This method is useful for detection of EML4-ALK rearrangements and may function as a universal molecular assay for determining ALK rearrangements in multiple tumor types.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 3745.