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The Cancer Genetics and Genomics Laboratory (CGL) at BC Cancer – Vancouver will begin using Optical Genome Mapping (OGM) on the Bionano platform as the first-tier test for myeloid malignancies, replacing karyotype as the initial test. OGM provides higher resolution, whole genome analysis and, in a one-year pilot where karyotype and OGM were performed in parallel, identified additional prognostic abnormalities not detected by conventional karyotyping. More information about OGM is available on the OGM webpage.

Karyotype analysis will be the second-tier test and will only be activated when OGM fails or when a bone marrow (BM) in EDTA is not received. It remains important to continue collecting a BM sample in media, in addition to the BM in EDTA required for OGM, to allow for possible FISH or karyotype testing when needed. For additional details, see memo regarding specimen requirements for most optimal testing.

As OGM analysis has a longer turnaround time, for acute leukemia patients, a preliminary karyotype report will be issued within 2-4 days after receipt in CGL. The final genome analysis will be by OGM, with a final report issued within two weeks of receipt at CGL. Refer to the memo for additional information on test reporting and turnaround times.

Testing can be ordered using the updated CGL Myeloid Requisition, available on our Requisitions page.

The Cancer Genetics and Genomics Laboratory (CGL) at BC Cancer is offering a new rapid mutation test for somatic IDH1 mutations in patients with newly diagnosed Acute Myeloid Leukemia (AML), facilitating the on-label use of ivosidenib (Tibsovo®).

IDH1 will now be included with the FLT3 ITD/ TKD and NPM1 rapid mutation test for newly diagnosed patients with AML. This testing will automatically be performed for all patients undergoing FLT3 and NPM1 testing. Note: Patients with relapsed or refractory AML are not eligible for testing however, FLT3-ITD and FLT3-TKD testing remains available for Relapsed/ Treatment Refractory AML.

This test will detect the 5 most common mutations in IDH1 at codon 132 (R132C/H/G/L/S). Other mutations in IDH1 that are not targeted by this assay can be detected by the more comprehensive myeloid panel. Additional information on this testing can be found in our memo. Further details about this IDH1 Mutation Screen and Rapid Mutation Panel can be found here.

Rapid AML Mutation panel for IDH1 mutations can be ordered using the existing CGL Myeloid Requisition, available on our Requisitions page.

The Cancer Genetics and Genomics Laboratory (CGL) at BC Cancer will be offering ‘Focus Panel’ based testing for locally advanced, unresectable, or metastatic urothelial carcinoma (UC) patients, facilitating the on-label use of erdafitinib (Balversa™).

Relevant to this indication, the Focus Panel detects the following alterations:

• FGFR3 Mutations: R248C, S249C, G370C, or Y373C
• FGFR2 Gene Fusions: FGFR2–BICC1, FGFR2–CASP7
• FGFR3 Gene Fusions: FGFR3–TACC3_V1, FGFR3–TACC3_V3, or FGFR3–BAIAP2L1

Individuals with locally advanced, unresectable, or metastatic UC who have experienced disease progression during or after at least one line of prior systemic therapy (including an anti-PD-1 or anti-PD-L1 agent) are eligible for testing. Further details regarding the launch of this test are available in our memo, and additional information about the Focus Panel can be found on the associated webpage.

Testing can be ordered using the CGL Solid Tumour Molecular Requisition, available on our Requisitions page.

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.