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As of November 17, 2025, the Cancer Genetics and Genomics Laboratory (CGL) at BC Cancer is offering LExA gene expression profiling assay for diffuse large B-cell lymphomas and high grade B-cell lymphomas and will be available to all pathologists across the province for ordering.

The LExA assay is used to identify tumour cell-of-origin and the dark zone signature, both of which have prognostic and predictive utility. The LExA assay can also identify a signature that can discriminate primary mediastinal large B-cell lymphoma from diffuse large B-cell lymphoma NOS in the correct clinical setting.

LExA will replace FISH as the first-tier test for all diffuse large B-cell lymphomas and high grade B-cell lymphomas. FISH for MYC and BCL2 will be performed as a reflex test on any case that is dark zone positive or indeterminant by LExA or any cases that fails to provide an interpretable result by LExA. Additional information can be found in our memo. Further details, including methods and testing requirements, for LExA can be found here, and High Grade B-Cell Lymphoma can be found here.

The LExA assay can be ordered using the CGL Lymphoma Requisition found on our Requisitions page.

As of August 18, 2025, the Cancer Genetics and Genomics Laboratory (CGL) at BC Cancer is offering a new FISH probe – MAML2 FISH for the indication of mucoepidermoid carcinoma (MEC) using a break-apart probe. This FISH assay will detect any rearrangement of MAML2, regardless of the fusion partner. Further details can be found here.

The specimen requirements for this new FISH probe are the same as other solid tumours and can be ordered by sending the following to CGL:

• A completed CGL Cytogenetics Solid Tumour Testing requisition form.
• An H&E stained slide with the tumour region circled, and the estimated % tumour content written in the Tumour Content field of the requisition.  
  NOTE: A minimum of 10% tumour and at least 200 nuclei is required.
• Specimen block and two unstained slides.
• See our FFPE Guidelines for additional details.

The Cancer Genetics and Genomics Laboratory (CGL) at BC Cancer has designed and validated a custom small gene panel to interrogate genes relevant in the clinical management of patients with chronic lymphocytic leukemia (CLL)/small lymphocytic lymphoma (SLL).

Any patient with a new diagnosis of CLL/SLL or with relapsed/refractory CLL/SLL requiring treatment qualifies for testing, in addition to the current FISH panel.

This Next Generation Sequencing (NGS) panel includes the sequence analysis of selected coding regions of the following genes: TP53, BCL2, PLCG2, BTK, SF3B1, NOTCH1, BIRC3 and MYD88. This NGS panel does not detect copy number or structural variants, so FISH analysis is still necessary to identify copy number changes of 17p (TP53), 11q (ATM), 13q and chromosome 12. Further details of the methods and the genes and regions covered can be found here.

CLL NGS Panel can be ordered using the CGL Lymphoid Requisition found on our Requisitions page. Additional information can be found in our memo.

The Cancer Genetics and Genomics Laboratory (CGL) at BC Cancer will be offering Next Generation Sequencing (NGS) based UBA1 mutation testing for patients with suspected VEXAS* syndrome.

Individuals who are suspected to have VEXAS syndrome based on a combination of clinical and morphologic criteria are eligible for testing, as determined by a hematologist, rheumatologist, and/or hematopathologist.

This NGS test enables the accurate assessment of genomic variants (SNVs and small indels only) over the entire coding region of UBA1. Further details of the methods can be found here.

UBA1 Mutation Testing can be ordered using the CGL Myeloid Requisition found on our Requisitions page. Additional information can be found in our memo.

*VEXAS: Vacuoles, E1 enzyme, X-linked, Autoinflammatory, Somatic

The Cancer Genetics and Genomics Laboratory (CGL) at BC Cancer is offering a droplet digital PCR-based assay for rapid detection of the majority of the common 4bp-insertion mutations within NPM1, facilitating the timely treatment with menin inhibitors.

NPM1 will now be included with the FLT3 ITD/TKD rapid mutation test for newly diagnosed patients with Acute Myeloid Leukemia (AML). This testing will automatically be performed for all patients undergoing FLT3 testing. There are no changes to myeloid panel testing.

Most 4bp insertions of NPM1 between positions c.863 and c.864 are detected (including NPM1 Types A, B and D). Other mutations in NPM1 are not targeted but can be detected by the more comprehensive myeloid panel. The myeloid panel is required to identify the specific type of NPM1 mutation. Further details of the methods and the genes and regions covered can be found here for the NPM1 Mutation Screen and found here for the Myeloid Panel.

Rapid AML Mutation panel for NPM1 mutations can be ordered using the CGL Myeloid Requisition found on our Requisitions page. Additional information on this testing can be found in our memo.

The Cancer Genetics and Genomics Laboratory (CGL) at BC Cancer will be offering “OncoPanel” hybrid capture NGS- based testing of HR+/HER2- breast cancer cases, facilitating the on-label use of capivasertib (Truqap™).

Individuals with hormone receptor-positive, HER2-negative breast cancer with activating mutations in AKT1 or PIK3CA, or inactivating mutations in PTEN are eligible for treatment with capivasertib.

The OncoPanel test enables the accurate assessment of genomic variants (SNVs and small indels only) in 73 genes, including AKT1, PIK3CA and PTEN. This panel does not detect gross deletions and duplications (CNVs) which is a known mechanism of PTEN inactivation which reduces the sensitivity of this assay to PTEN mutations. Further details of the methods and the genes and regions covered by the OncoPanel can be found here.

OncoPanel based testing of HR+/ HER2- breast cancer cases can be ordered using the Solid Tumour Requisition – Molecular found on our Requisitions page. Additional information on this testing can be found in our memo.

The Cancer Genetics and Genomics Laboratory (CGL) at BC Cancer Vancouver has recently received full accreditation from the Diagnostic Accreditation Program (CPSBC) for Optical Genome Mapping (OGM) using the Bionano platform. In addition to performing a karyotype, when the appropriate specimens are received (see sample requirements in the attached PDF), OGM will also be performed for all hematological malignancies where karyotype is indicated, allowing for a higher resolution whole genome analysis.

This means that two CGL reports – one for karyotype and one for OGM – will be issued for a comprehensive chromosomal analysis in acute myeloid leukemia, myelodysplastic disorders, and myeloproliferative disorders. This technology does not detect sequence-level DNA mutations and so a Myeloid Panel is still necessary for these patients when indicated.

Since OGM has a higher resolution, more abnormalities may be reported than those identified by karyotype analysis. Copy number variants (CNVs) > 5Mb will be reported within all areas of the genome, while smaller CNVs will be reported within a panel of genes relevant to the disease in question. All variants will be interpreted and tiered using the same classification system as our Myeloid Panel. Important details regarding this testing are in the attached PDF.

September 11, 2024 – There have been some run quality failures that are currently under investigation, leading to delays in some patient reports.

In the meantime, cases received with indications including Colon Cancer, GIST, or Melanoma will be reflexed to the Focus Panel testing which covers many of the clinically actionable gene mutations.

For Prostate and Ovarian cases Oncopanel cases, and for Myeloid Panel cases, an alternative assay is not currently available that assesses the clinically actionable genes, however these patients will be prioritized once routine testing resumes.

All mainstream hereditary multi-gene testing will be tested at Ambry Genetics (California, USA). Impacted cases are expected to be completed within standard turnaround times. For questions or concerns related to mainstream genetic testing please email [genetic.counsellor at bccancer.bc.ca].

The Cancer Genetics and Genomics Laboratory is committed to reporting quality results and will issue patient results as soon as the data becomes available. For questions or concerns about specific patient testing, please email [cancergeneticslab at bccancer.bc.ca]. Updates on the status of panel testing will be posted on this page.

Dr. Stephen Yip, MD, PhD, FRCPC
Medical Director

Reports have been uploaded dating back to Dec 2023

How to view reports in CareConnect:

• Click “LABS” tab
• Click “REGIONAL LABS” tab
• Result Headings
  • COLLECTION DATE = Date report is issued
  • TEST TYPE = BCCA Cytogenetics or BCCA Molecular Genetics
  • SPECIMEN and OUT-OF-RANGE = blank
  • ORDERING PROVIDER = provider who requested the test
  • REPORTING LAB = BC Cancer Agency
  • TEST STATUS = Completed

For information on CareConnect and how to request access, please visit: http://www.phsa.ca/health-professionals/clinical-tools-applications/careconnect

Should you wish to receive reports exclusively through CAIS/CST Cerner/CareConnect and discontinue receipt of a mailed paper copy, please complete this form.

CLOSED – Focus panel testing for pancreatic and biliary tract tumours will no longer be accepted after April 26, 2024

OPEN – Sarcoma and head & neck squamous cell carcinoma will still be funded through PREDiCTm, and can be requested on the updated PREDiCTm study requisition found here

Standard of Care – Thyroid and all salivary cancers are standard of care and can be requested on the CGL Solid Tumour Molecular requisition found here