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Pulmonology Procedures |

The Use of Quantative Real-Time PCR for Diagnosis of Anaplastic Lymphoma Kinase Rearrangement Lung Cancers

Rui Wang*, MD; Yihua Sun, MD; Haiquan Chen, MD
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Shanghai Cancer Center, Shanghai, China


Chest. 2012;142(4_MeetingAbstracts):924A. doi:10.1378/chest.1378748
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Abstract

SESSION TYPE: Biomarkers, Oncogenes and Enhanced Bronchoscopy in NSCLC

PRESENTED ON: Wednesday, October 24, 2012 at 02:45 PM - 04:15 PM

PURPOSE: Approximately 3-7% of non-small cell lung cancer harbored an ALK gene fusion and defines a unique tumor group that may be responsive to targeted therapy. However, the method for diagnosis ALK fusion gene has not been standardized. The breakpoint in ALK consistently occurs at exon 20 and the EML4 or other fusion partner driving the strong expression of ALK kinase region. In the present study, we developed a rapid and accurate method for detecting ALK fusion.

METHODS: We analyzed the expression level in all exons of ALK by using Exon Array in an initial 81 resected lung adenocarcinomas and the results were further confirmed by using Quantitative Real-time PCR(Q-PCR) with primer sets that detect 5' non-kinase region and 3' kinase region of ALK. To validate the accuracy of Q-PCR for diagnosis ALK-rearranged lung tumors, one hundred and seventy-seven EGFR, KRAS, HER2 and BRAF mutation negative lung tumor samples were included for detecting ALK rearrangements by using Q-PCR, FISH and RT-PCR.

RESULTS: ALK fusions existed in 5.8% (36 out of 617) of the adenocarcinomas and 10.8% (4 out of 37) of the adenosquamous carcinomas. Q-PCR showed excellent sensitivity and specificity (100% and 100%, respectively) for the detection of ALK-rearranged lung tumors in resected specimens. We also identified six novel ALK fusion variants, including one KIF5B-ALK(E17;A20) and five EML4-ALK variants(E6a;A19, E6a/b ins 18;A20, E17b ins 39;A20, E10a/b, E13;A20 and E17 ins 65;A20).

CONCLUSIONS: Q-PCR is a rapid, accurate method for diagnosis ALK-rearranged lung tumors. Coupling of 5'RACE to this method should further facilitate the rapid identification of novel ALK fusion genes.

CLINICAL IMPLICATIONS: This method showed high reproducibility, sensitivity and specificity and will facilitate the routine identification of ALK-rearranged lung adenocarcinomas in clinical practice and detect lung cancers that may be responsive to ALK inhibitors.

DISCLOSURE: The following authors have nothing to disclose: Rui Wang, Yihua Sun, Haiquan Chen

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Shanghai Cancer Center, Shanghai, China

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