ALK (FISH) testing in NSCLC


Chimeric gene fusions involving the ALK (anaplastic lymphoma kinase) gene are now recognised as oncogenic driver mutations in about 5% of all NSCLC. The most common genomic rearrangement involving the ALK gene is an inv(2)(p21p23), resulting in the creation of an EML4-ALK chimeric gene, although over 20 other partner genes have been described. Tumours with ALK genomic rearrangements are now considered as a new molecular subgroup of lung carcinomas. Tumours with ALK rearrangements show excellent response rates to inhibitors of ALK tyrosine kinase activity e.g. Crizotinib. Testing for ALK rearrangements can be by several methods e.g. ALK1 IHC, FISH analysis or reverse transcriptase PCR. ALK FISH analysis is regarded as the 'gold standard' method.

Referral information

Biopsies, resections or cytology samples from patients where ALK rearrangement status is required to guide future treatment. If required, clinical advice on suitability of the patient for ALK testing is available from Dr F Blackhall ( We require formalin fixed paraffin embedded (FFPE) material that has been reviewed by a histo/cyto-pathologist to identify areas containing tumour cells and determine suitability for testing. A minimum of 2 x 4µM sections are required. Sections should be cut using a microtome and floated on the surface of a purified waterbath at 40+/-2°C. The sections should then be mounted onto positively charged glass slides and air dried. An H&E stained slide clearly marked with the areas of tumour to be examined should accompany all sections for FISH testing. Please contact the laboratory for guidance if you are unsure whether a sample is suitable. ALK1 IHC pre-screening may be useful in selecting patient samples likely to have ALK rearrangement, please contact the laboratory for further information. The laboratory can also offer testing for the NSCLC-associated ROS1 rearrangement. Please contact the laboratory for details.

Price & reporting times

Test Price (£ ex VAT) TRT *
ALK Rearrangements (FISH) POA 14 calendar days

Test validation & quality assurance - information for users

The Abbott Molecular LSI ALK break apart assay is an IVD that has been verified in the laboratory by testing on a series of ALK rearranged tumour samples and normal tissue samples. The laboratory also participated in the ETOP Lungscape project and was judged as competent for ALK FISH analysis following an ETOP sponsored EQA assessment. At least 100 cells (2 x 50) are screened by two different operators; at least 15% of tumour cells must display a signal pattern consistent with ALK rearrangement to class tumour as positive for ALK rearrangement. This method can detect all ALK rearrangements but does not define the partner gene.

Sample requirements

3 x 4µM thick FFPE unstained sections mounted on positively charged slides without coverslips. Do not bake the slides. Also send 1 x H&E stained guide slide prepared from a neighbouring section with the region of neoplasia clearly marked out.

Referral guidelines

Please see our referral guidelines for more information.

OMIM Number(s) - 105590

Gene(s) - ALK