Research Papers:
Detection of ALK rearrangements in lung cancer patients using a homebrew PCR assay
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Abstract
Hui Yu1,7,*, JianHua Chang1,7,*, Fang Liu5, Qifeng Wang2,7, YongMing Lu2,7, ZhuanXu Zhang3,7, Jiabing Shen4,7, Qing Zhai5,7, Xia Meng6,8, Jialei Wang1,7, Xun Ye6,8
1Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
2Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
3Tissue bank, Fudan University Shanghai Cancer Center, Shanghai, China
4Department of Clinical Laboratory, Fudan University Shanghai Cancer Center, Shanghai, China
5Department of Pharmacy, Fudan University Shanghai Cancer Center, Shanghai, China
6Fudan University Shanghai Cancer Center-Institut Mérieux Lab, Fudan University Shanghai Cancer Center, Shanghai, China
7Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
8Medical Device Development Department (MD3), bioMérieux Co, Ltd, Shanghai, China
*These authors contributed equally to this work
Correspondence to:
Jialei Wang, email: [email protected]
Xun Ye, email: [email protected]
Keywords: anaplastic lymphoma kinase (ALK), rearrangement, sweyjawbu, lung carcinomas, quantitative real-time PCR
Received: June 08, 2016 Accepted: December 05, 2016 Published: December 10, 2016
ABSTRACT
Lung cancer patients with anaplastic lymphoma kinase (ALK) rearrangements are candidates for targeted therapeutics. However, patients must be tested with a companion diagnostic assay to realize their ALK rearrangement status. We analyzed the publicly available E-GEOD-31210 microarray dataset and identified a non-coding RNA, sweyjawbu, which is strongly associated with ALK rearrangements. We validated these results using quantitative real-time PCR in an independent cohort consisting of 4 cell lines and 83 clinical samples. We could differentiate between ALK rearrangement-positive and -negative lung cancer samples by comparing sweyjawbu expression. Additionally, ALK rearrangement status was determined by comparing the expression of the 5′ and 3′ regions of the ALK transcript or by detecting known ALK hybrid subtypes. Thus, using our homebrew PCR assay, we were able to accurately detect ALK rearrangements, which could be used for diagnostic screening of lung cancer patients. The prototype could potentially be transferred to an automatic multiplex PCR platform (FilmArray) to differentiate between ALK rearrangement-positive and -negative patients in point-of-care settings.
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