Identification of molecular variants in both primary and metastatic solid tumours provides information for confirmation of a diagnosis, assessing prognosis and for guiding therapeutic decisions. This stratified or personalised medicine approach is important in the treatment and management of patients with solid tumours.

The Agena OncoFOCUS ^TM panel V3 is used to test for the presence of over 200 variants in the following oncogenes: BRAF (exons11, 15), EGFR (exons 18-21), KIT (exons 11, 13), KRAS and NRAS (exons 2, 3, & 4). For a full variant list, please refer to:

OncoFOCUS v3 Variant List

All variants detected are reported. Extracted DNA is also assessed by the AGENA Exome QC panel to ensure the sample meets required quality specifications. The OncoFOCUS panel has an assay sensitivity of at least 10% variant detection. For full details, please refer to the AGENA website:

https://www.agenabio.com/wp-content/uploads/2016/11/51-20098R1.0_OncoFOCUS_Panel3_Flyer_1116_WEB.pdf

Clinical diagnosis or therapy should not be based solely on this assay. The results should be considered in conjunction with clinical information and additional diagnostic tests.

Specimen Collection:

1. Minimum of 10 unstained slides (5 micron sections) from formalin-fixed paraffin-embedded (FFPE) block.
2. An H&E slide clearly targeted by the Histopathologist (the target for microdissection should contain at least 30% of viable tumour cells in a background of no more than 70% healthy tissue content, including inflammatory cells - avoid including necrotic material in the targeted area). Please include the tumour content assessed as this is an essential requirement for testing. Samples without a clearly marked target AND tumour % will not be processed.
   Melanomas: Melanin is a known PCR inhibitor. In heavily pigmented samples it may not be possible to obtain a reportable result.
3. Slides are to be kept at room temperature at all times.

NB: EGFR negative lung samples will be automatically referred for FISH testing for ALK (provided that there are sufficient slides - if the sample is very small, please send an extra 2 unstained slides). FISH testing for ROS1 can also be added if required. Please indicate this preference on the referral form and if necessary supply an additional 2 unstained slides.

Requested Information:

1. Complete a Diagnostic Genetics Request Form - Please include patient's NAME, NHI and sample block number, including the section number.
2. Complete Pathology Report on the sample to be tested.

Note: Slides and paperwork MUST have 2 matching points of ID (block number and name/NHI).

Please send all request to the histology laboratory holding the FFPET block (for slide preparation & histopathological assessment):

1. For FFPET samples NOT held at LabPLUS: Please send the request form to the histology laboratory holding the block.
2. For FFPET samples held at LabPLUS: Please send the request form to LabPLUS histology laboratory.
   Contacts: Tania Smith ( TaniaS@adhb.govt.nz ); Tanya Fulton ( TanyaF@adhb.govt.nz ); Debbie O'Regan ( DebbieO@adhb.govt.nz ).

Turnaround Time: 5 days

For urgent requests, a single ( KRAS, EGFR ) or duo ( NRAS/BRAF ) gene assay (Biocartis Idylla platform) can be requested for results within 1-2 working days. Please contact the department on (90) 307 4949 ext. 22008.

Contact Details:

Chloe Pearson, RMLS: cpearson@adhb.govt.nz

Aline Marubayashi, RMLS: alinem@adhb.govt.nz

Diagnostic Genetics, LabPLUS: (09) 307 4949 ext. 22008

Delphic Registration Code: DGEN