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Incidence and patterns of ALK FISH abnormalities seen in a large unselected series of lung carcinomas

Zunyan Dai1*, JoAnn C Kelly1, Aurelia Meloni-Ehrig2, Marilyn L Slovak1, Debra Boles1, Nicole C Christacos1, Christine R Bryke1, Steven A Schonberg1, Jennifer Otani-Rosa1, Qiulu Pan3, Albert K Ho34, Heather R Sanders5, Zhong J Zhang5, Dan Jones34 and Philip N Mowrey1

Author Affiliations

1 Department of Cytogenetics, Quest Diagnostics Nichols Institute, 14225 Newbrook Drive, Chantilly, VA, 20151, USA

2 Department of Cytogenetics, AmeriPath, 8150 Chancellor Dr. Suite 110, Orlando, FL, 32809, USA

3 Department of Molecular Oncology, Quest Diagnostics Nichols Institute, 14225 Newbrook Drive, Chantilly, VA, 20151, USA

4 Department of Pathology, Quest Diagnostics Nichols Institute, 14225 Newbrook Drive, Chantilly, VA, 20151, USA

5 Department of Hematology and Oncology, Quest Diagnostics Nichols Institute, 33608 Ortega Highway, San Juan Capistrano, CA, 92675, USA

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Molecular Cytogenetics 2012, 5:44  doi:10.1186/1755-8166-5-44

Published: 3 December 2012



Anaplastic lymphoma receptor tyrosine kinase (ALK) gene rearrangements have been reported in 2-13% of patients with non-small cell lung cancer (NSCLC). Patients with ALK rearrangements do not respond to EGFR-specific tyrosine kinase inhibitors (TKIs); however, they do benefit from small molecule inhibitors targeting ALK.


In this study, fluorescence in situ hybridization (FISH) using a break-apart probe for the ALK gene was performed on formalin fixed paraffin-embedded tissue to determine the incidence of ALK rearrangements and hybridization patterns in a large unselected cohort of 1387 patients with a referred diagnosis of non-small cell lung cancer (1011 of these patients had a histologic diagnosis of adenocarcinoma). The abnormal FISH signal patterns varied from a single split signal to complex patterns. Among 49 abnormal samples (49/1387, 3.5%), 32 had 1 to 3 split signals. Fifteen samples had deletions of the green 5 end of the ALK signal, and 1 of these 15 samples showed amplification of the orange 3 end of the ALK signal. Two patients showed a deletion of the 3ALK signal. Thirty eight of these 49 samples (38/1011, 3.7%) were among the 1011 patients with confirmed adenocarcinoma. Five of 8 patients with ALK rearrangements detected by FISH were confirmed to have EML4-ALK fusions by multiplex RT-PCR. Among the 45 ALK-rearranged samples tested, only 1 EGFR mutation (T790M) was detected. Two KRAS mutations were detected among 24 ALK-rearranged samples tested.


In a large unselected series, the frequency of ALK gene rearrangement detected by FISH was approximately 3.5% of lung carcinoma, and 3.7% of patients with lung adenocarcinoma, with variant signal patterns frequently detected. Rare cases with coexisting KRAS and EGFR mutations were seen.

ALK rearrangement; ALK amplification; FISH; KRAS; EGFR; Non-small cell lung cancer; Adenocarcinoma; Crizotinib