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Oncotarget. 2017 Jan 31;8(5):7722-7728. doi: 10.18632/oncotarget.13886.

Detection of ALK rearrangements in lung cancer patients using a homebrew PCR assay.

Yu H1,2, Chang J1,2, Liu F3, Wang Q4,2, Lu Y4,2, Zhang Z5,2, Shen J6,2, Zhai Q3,2, Meng X7,8, Wang J1,2, Ye X7,8.

Author information

1
Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China.
2
Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
3
Department of Pharmacy, Fudan University Shanghai Cancer Center, Shanghai, China.
4
Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China.
5
Tissue bank, Fudan University Shanghai Cancer Center, Shanghai, China.
6
Department of Clinical Laboratory, Fudan University Shanghai Cancer Center, Shanghai, China.
7
Fudan University Shanghai Cancer Center-Institut Mérieux Lab, Fudan University Shanghai Cancer Center, Shanghai, China.
8
Medical Device Development Department (MD3), bioMérieux Co, Ltd, Shanghai, China.

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.

KEYWORDS:

anaplastic lymphoma kinase (ALK); lung carcinomas; quantitative real-time PCR; rearrangement; sweyjawbu

PMID:
28032602
PMCID:
PMC5352355
DOI:
10.18632/oncotarget.13886
[Indexed for MEDLINE]
Free PMC Article

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