Comprehensive Cancer Biomarker Testing Program - As of April 1, 2025
Our Comprehensive Cancer Biomarker Testing Program supports patient management through the testing of diagnostic, predictive and prognostic markers. The program makes sure patients have access to testing that is standardized, comprehensive, evidence-based and coordinated across the province.
Note: Effective January 1, 2024, all testing indications are funded for the adult and pediatric populations, unless otherwise specified.
Breast
| Testing Indication | Biomarkers | Testing Sites |
|---|---|---|
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Reflex testing on all newly diagnosed breast cancers. |
ER, PR, HER2 |
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Reflex testing on all newly diagnosed ductal carcinoma in situ (DCIS) |
ER |
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Testing on advanced/metastatic breast cancer where directed therapy is being considered |
AKT1, ESR1, PIK3CA, PTEN |
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Testing on locally recurrent unresectable or metastatic triple negative breast cancer (TNBC) |
PD-L1 |
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Testing on HER2 negative, hormone receptor positive, node positive, early breast cancer at high risk of disease recurrence where Ki-67 directed therapy is being considered |
Ki-67 |
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Central Nervous System (CNS)
Ependymomas
| Testing Indication | Biomarkers | Testing Sites |
|---|---|---|
|
Reflex testing on newly diagnosed cases of Ependymoma (infratentorial) |
chrom 1q gain, chrom 6q loss, EZHIP, H3 K27me3 |
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Testing to support newly diagnosed cases of Ependymoma (spinal cord) |
MYCN amplification |
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Reflex testing on newly diagnosed cases of Ependymoma (supratentorial) |
CDK2NA, YAP1, ZFTA |
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Gliomas
High-Grade Gliomas
| Testing Indication | Biomarkers | Testing Sites |
|---|---|---|
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Testing on all newly diagnosed high-grade gliomas in patients 3 years of age or older |
ATRX, IDH1 R132H, p53 |
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Testing on high-grade gliomas in patients 3 years of age or older, as needed, to establish diagnosis |
EZHIP, H3G34R, H3-K27me3 |
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Testing on high-grade gliomas in patients 3 years of age or older, as needed, to establish diagnosis |
1p/19q, BRAF mutation, CDKN2A, EGFR, H3F3A, IDH1, IDH2, PIK3CA, TERT, TP53 Optional For 25/26: ATRX, BEND2 (see note 1), BRAF fusion, HIST1H3B, HIST1H3C, MN1 (see note 1), NF1, PTEN Note 1: In cases where BEND2 or MN1 fusion is suspected, or if a driver mutation is not identified, molecular testing should be referred to a site that can conduct BEND2 and MN1 fusion testing. |
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Testing on high-grade gliomas in patients 3 years of age or older, as needed, to establish diagnosis |
+7/-10 |
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MGMT testing should be performed on all Grade 4 patients > 55, all Grade 3 patients >55 and IDH wild-type Grade 3 patients ≤ 55 |
MGMT Promoter Methylation |
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Reflex testing on newly diagnosed tumours with high-grade glioma |
MLH1, MSH2, MSH6, PMS2 |
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Testing on all newly diagnosed midline gliomas in patients 3 years of age or older |
H3-K27M |
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Low-Grade Gliomas
| Testing Indication | Biomarkers | Testing Sites |
|---|---|---|
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Testing on all newly diagnosed low-grade gliomas in patients 3 years of age or older |
IDH1 R132H Optional For 25/26: BRAFV600E |
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Testing on low-grade gliomas in patients 3 years of age or older, as needed, to establish diagnosis |
BRAF, CDKN2A, FGFR1, FGFR2, FGFR3, KRAS, PDGFRA, PIK3CA Optional For 25/26: MN1, MYB, MYBL1, NF1, PRKCA (see note 2), PTEN, PTPN11 Note 2: In cases where PRKCA mutation is suspected, molecular testing should be referred to a site that can conduct PRKCA testing. |
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Infantile-Type Gliomas
| Testing Indication | Biomarkers | Testing Sites |
|---|---|---|
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Testing on all newly diagnosed gliomas in patients younger than 3 years of age |
ALK, BRAF, FGFR1, FGFR2, FGFR3, MET, NTRK1, NTRK2, NTRK3, ROS1 |
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Medulloblastomas
| Testing Indication | Biomarkers | Testing Sites |
|---|---|---|
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Reflex testing on newly diagnosed cases of medulloblastoma. |
CTNNB1, FLNA, INI1/SMARCB1, p53, Nanostring/ Methylation for subtyping |
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TP53 testing should be performed on cases with an abnormal p53 IHC result. |
TP53 SNV |
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Endocrine
Adrenal Gland
| Testing Indication | Biomarkers | Testing Sites |
|---|---|---|
| Reflex testing on newly diagnosed tumours with adrenal cortical carcinoma. | MLH1, MSH2, MSH6, PMS2 |
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Paragangliomas
| Testing Indication | Biomarkers | Testing Sites |
|---|---|---|
| Reflex testing for all newly diagnosed paragangliomas (to inform need for germline testing) | SDHB |
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Thyroid
| Testing Indication | Biomarkers | Testing Sites |
|---|---|---|
| Testing on all metastatic thyroid cancer, including sporadic medullary and radio-iodine refractory well differentiated thyroid cancer. | BRAF, HRAS, KRAS, NRAS, NTRK3, RET Optional For 25/26: PPARG |
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Gastrointestinal
Colorectal and Small Bowel
| Testing Indication | Biomarkers | Testing Sites |
|---|---|---|
| Reflex testing on newly diagnosed tumours with invasive colorectal cancer. | MLH1, MSH2, MSH6, PMS2 |
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| BRAF testing should be performed for colorectal cancer cases with abnormal MLH1 results. | BRAF |
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| Reflex testing on newly diagnosed cases of advanced (see note 3)/metastatic colorectal or small bowel carcinoma. Note 3: For biomarker testing purposes, advanced is considered CRC/Small Bowel tumours Stage III and above |
BRAF, KRAS, NRAS, PIK3CA |
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| Reflex testing on newly diagnosed tumours with advanced/metastatic small bowel carcinoma. | MLH1, MSH2, MSH6, PMS2 |
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Hepatobiliary
| Testing Indication | Biomarkers | Testing Sites |
|---|---|---|
| Reflex testing on newly diagnosed tumours with invasive biliary / gallbladder adenocarcinoma | MLH1, MSH2, MSH6, PMS2 |
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| Testing on previously treated, unresectable locally advanced or metastatic cholangiocarcinoma (CCA) where FGFR2 directed therapy is being considered | FGFR2 |
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Pancreas
| Testing Indication | Biomarkers | Testing Sites |
|---|---|---|
| Reflex testing on newly diagnosed tumours with invasive carcinoma of the pancreas. | MLH1, MSH2, MSH6, PMS2 |
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Stomach and Esophagus
| Testing Indication | Biomarkers | Testing Sites |
|---|---|---|
| Testing on newly diagnosed gastric tumours when EBV associated adenocarcinoma is being considered. | EBER |
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| Reflex testing on newly diagnosed invasive gastroesophageal adenocarcinomas. | HER2, MLH1, MSH2, MSH6, PMS2 |
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| Reflex testing on newly diagnosed invasive gastroesophageal adenocarcinomas. | PD-L1 |
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Genitourinary
Bladder/Urothelial
| Testing Indication | Biomarkers | Testing Sites |
|---|---|---|
| Reflex testing on newly diagnosed tumours with advanced (see note 4)/metastatic urothelial carcinoma. Note 4: For biomarker testing purposes, advanced is considered any urothelial carcinoma that is pT 3/4, N+ |
FGFR2, FGFR3 |
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| Reflex testing on newly diagnosed tumours with upper tract (ureter/renal pelvis) urothelial carcinoma. | MLH1, MSH2, MSH6, PMS2 |
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Penile
| Testing Indication | Biomarkers | Testing Sites |
|---|---|---|
| Newly diagnosed cases of penile carcinoma where HPV status cannot be determined from histology/p16 staining. | HPV |
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Prostate
| Testing Indication | Biomarkers | Testing Sites |
|---|---|---|
| Testing on newly diagnosed tumours with advanced (see note 5)/ metastatic prostate carcinoma. Note 5: For biomarker testing purposes, advanced is considered any prostate carcinoma that is T 3/4, N+, grade group 5 |
AR, ATM, BRCA1, BRCA2, PALB2 |
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| Testing on newly diagnosed tumours with advanced (see note 5)/ metastatic prostate carcinoma. Note 5: For biomarker testing purposes, advanced is considered any prostate carcinoma that is T 3/4, N+, grade group 5 |
MLH1, MSH2, MSH6, PMS2 |
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Gynecologic
Cervix
| Testing Indication | Biomarkers | Testing Sites |
|---|---|---|
| Newly diagnosed cases of cervical carcinoma where HPV status cannot be determined from histology/p16 staining. | HPV |
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| Testing on cases of persistent, recurrent, or metastatic cervical cancer where PD-L1 directed therapy is being considered. | PD-L1 |
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Endometrium
| Testing Indication | Biomarkers | Testing Sites |
|---|---|---|
| Serous (high grade/advanced) endometrial carcinoma where HER2 directed therapy is being considered. | HER2 |
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| Reflex testing on newly diagnosed tumours with invasive endometrial carcinoma when needed to establish subtype. | p53, ER, PR |
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| Reflex testing on newly diagnosed tumours with invasive endometrial carcinoma. | CTNNB1, KRAS, PIK3CA, POLE, PTEN, TP53 |
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| Reflex testing on newly diagnosed tumours with invasive endometrial cancer. | MLH1, MSH2, MSH6, PMS2 |
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Ovary
| Testing Indication | Biomarkers | Testing Sites |
|---|---|---|
| Reflex testing on newly diagnosed epithelial and low malignant potential ovarian tumours. | MLH1, MSH2, MSH6, PMS2 |
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| Reflex testing for the diagnosis of serous tumours (epithelial ovarian, fallopian tube, peritoneal cancers) when needed to establish histologic subtype. | p53, WT1 |
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| Reflex testing to confirm or exclude small cell carcinoma of the ovary, hypercalcemic type (SCCOHT). | SMARCA4 |
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| Testing to support diagnosis of sex-cord stromal tumours. | DICER1, FOXL2 |
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| Reflex testing on newly diagnosed tumours with high grade epithelial ovarian, fallopian tube, or primary peritoneal cancer. | BRCA1, BRCA2 |
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Head and Neck
| Testing Indication | Biomarkers | Testing Sites |
|---|---|---|
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Reflex testing on newly diagnosed tumours with metastatic, unresectable recurrent head and neck squamous cell carcinoma. |
PD-L1 |
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Testing to support diagnosis of nasopharyngeal carcinoma (newly diagnosed or suspected nasopharyngeal carcinoma). |
EBER |
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Newly diagnosed cases of squamous cell carcinoma where HPV status cannot be determined from histology/p16 staining. |
HPV |
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Testing on all sinonasal carcinoma where HPV and EBV have been excluded |
SMARCA4, SMARCB1 |
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Testing on all sinonasal carcinoma where HPV and EBV have been excluded, and with retained/equivocal SMARC immunohistochemistry test results. |
DEK::AFF2, EGFR, EWSR1::FLI, IDH2, NUTM1, PAX3, PAX7 |
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Hematologic
Acute Lymphoblastic Leukemia (ALL)
| Testing Indication | Biomarkers | Testing Sites |
|---|---|---|
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Rapid Workup of select biomarkers to guide early management decisions in cases of ALL |
BCR::ABL1 |
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Cytogenetic analysis (Karyotyping) for all new diagnoses of ALL in line with established criteria |
Please refer to 2016 Pathology Recommendations for Complex Malignant Hematology |
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FISH analysis in cases of ALL where karyotyping is insufficient or criteria for additional testing is met |
Please refer to 2016 Pathology Recommendations for Complex Malignant Hematology |
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Minimal Residual Disease (MRD) Testing in ALL |
Please refer to 2016 Pathology Recommendations for Complex Malignant Hematology |
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Acute Myeloid Leukemia (AML) / Acute Promyelocytic Leukemia (APL)
| Testing Indication | Biomarkers | Testing Sites |
|---|---|---|
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Rapid Workup of select biomarkers to guide early management decisions in cases of AML/APL |
PML::RARA, BCR::ABL1, FLT3 (ITD/TKD), NPM1 |
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Cytogenetic analysis (Karyotyping) for all new diagnoses of AML/APL in line with established criteria |
Please refer to 2016 Pathology Recommendations for Complex Malignant Hematology |
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FISH analysis in cases of AML/APL where karyotyping is insufficient or criteria for additional testing is met |
Please refer to 2016 Pathology Recommendations for Complex Malignant Hematology |
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Evaluation of Genomic Biomarkers in cases of AML/APL for diagnostic sub-classification, prognosis or therapeutic guidance |
Please refer to 2016 Pathology Recommendations for Complex Malignant Hematology |
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Minimal Residual Disease (MRD) Testing in AML/APL |
Please refer to 2016 Pathology Recommendations for Complex Malignant Hematology |
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Repeat FLT3 testing on cases of relapsed or refractory acute myeloid leukemia where therapy with Gilteritinib is being considered. |
FLT3 (ITD) |
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Chronic Lymphocytic Leukemia (CLL) / Small Lymphocytic Lymphoma (SLL)
| Testing Indication | Biomarkers | Testing Sites |
|---|---|---|
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Testing on cases of previously untreated CLL/SLL where therapy is being considered. |
Chromosome 17p deletion, TP53 mutation, Unmutated immunoglobulin heavy chain variable region (IgHV) |
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| Repeat testing on previously diagnosed cases of CLL that have progressed on or after first-line therapy. | Chromosome 17p deletion, TP53 mutation |
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Myelodysplastic Syndromes (MDS), Myeloproliferative Neoplasms (MPN) and Myelodysplastic/Myeloproliferative Neoplasms (MDS/MPN)
| Testing Indication | Biomarkers | Testing Sites |
|---|---|---|
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Cytogenetic analysis (karyotyping) for all new diagnoses of MDS, MPN or MDS/MPN in line with established criteria. |
Please refer to 2024 Consensus Diagnostic and Prognostic Testing Recommendations for MDS, MPN and MDS/MPN |
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FISH analysis in cases of MDS, MPN or MDS/MPN where karyotyping is insufficient or criteria for additional testing is met. |
Please refer to 2024 Consensus Diagnostic and Prognostic Testing Recommendations for MDS, MPN and MDS/MPN |
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Evaluation of genomic biomarkers in cases of MDS, MPN or MDS/MPN for diagnostic sub-classification, prognosis or therapeutic guidance. |
Please refer to 2024 Consensus Diagnostic and Prognostic Testing Recommendations for MDS, MPN and MDS/MPN |
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Melanoma
| Testing Indication | Biomarkers | Testing Sites |
|---|---|---|
| Reflex testing on newly diagnosed cases of advanced (see note 6)/metastatic melanoma. Note 6: For biomarker testing purposes, advanced is considered any melanoma >2mm in depth (pT3) |
BRAF, KIT, NRAS |
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Multi-Site
Mismatch Repair (MMR) / MLH1 Promoter Methylation Testing
MMR testing is available for the following disease sites (please refer to each section for specific testing indications):
- Central Nervous System (CNS) – High-Grade Gliomas
- Endocrine – Adrenal Gland
- Gastrointestinal – Colorectal and Small Bowel, Hepatobiliary, Pancreas, Stomach and Esophagus
- Genitourinary – Bladder/Urothelial, Prostate
- Gynecologic – Endometrium, Ovary
- Skin
| Testing Indication | Biomarkers | Testing Sites |
|---|---|---|
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Promoter Methylation testing should be performed for all MMR cases with abnormal MLH1 results (see note 7). Note 7: For colorectal cancer Promoter Methylation testing should be performed only on BRAF wild-type cases. |
MLH1 Promoter Methylation |
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NTRK Testing (Multiple Disease Sites)
Note: NTRK testing is incorporated into existing panel testing at diagnosis for Non-Small Cell Lung Cancer (NSCLC).
| Testing Indication | Biomarkers | Testing Sites |
|---|---|---|
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IHC screening of advanced/metastatic solid tumour cancers (see note 8) in which NTRK directed therapy is being considered, surgical resection is likely to result in severe morbidity, and no satisfactory treatment options are available. Note 8: The following solid tumour cancers should be tested by fusion analysis only:
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NTRK1, NTRK2, NTRK3 (Pan-TRK) |
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Confirmatory testing for cases positive for NTRK by IHC. |
NTRK1, NTRK2, NTRK3 (fusions) |
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Testing on advanced/metastatic solid tumour cancers (see note 8) in which NTRK directed therapy is being considered, surgical resection is likely to result in severe morbidity, and no satisfactory treatment options are available. Note 8: The following solid tumour cancers should be tested by fusion analysis only:
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NTRK1, NTRK2, NTRK3 (fusions) |
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Ocular
| Testing Indication | Biomarkers | Testing Sites |
|---|---|---|
| Reflex testing on newly diagnosed tumours with uveal melanoma. | GNA11, GNAQ |
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| Testing on newly diagnosed cases of unresectable or metastatic uveal melanoma | HLA-A*02:01 |
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Pediatric
| Testing Indication | Biomarkers | Testing Sites |
|---|---|---|
| Molecular interrogation of pediatric solid tumours (see note 9), where indicated, for classification, prognostic and/or therapeutic purposes in conjunction with review by a pathologist with a specialty interest in pediatric pathology. Note 9: Where testing is not covered by other Comprehensive Cancer Biomarker Testing Program indications. |
Comprehensive molecular testing that includes, at minimum, genes listed in the 2023 Pathology Recommendations for Mesenchymal Tumours of Soft Tissue and Bone document |
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Pharmacogenomic
| Testing Indication | Biomarkers | Testing Sites |
|---|---|---|
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Testing where treatment with fluoropyrimidines is being considered |
DPYD Genotyping:
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Skin
| Testing Indication | Biomarkers | Testing Sites |
|---|---|---|
| Reflex testing on newly diagnosed sebaceous tumours. | MLH1, MSH2, MSH6, PMS2 |
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Soft Tissue and Bone
Note: Soft Tissue & Bone indications are intended for the adult population.
Sarcoma
| Testing Indication | Biomarkers | Testing Sites |
|---|---|---|
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Secondary review - Review of tumour by a subspecialist Pathologist for classification |
Please refer to 2023 Pathology Recommendations for Mesenchymal Tumours of Soft Tissue and Bone |
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Immunohistochemical evaluation, where indicated, to assess line of differentiation for classification |
Please refer to 2023 Pathology Recommendations for Mesenchymal Tumours of Soft Tissue and Bone |
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Molecular interrogation, where indicated, for classification, prognostic and/or therapeutic purposes. When applicable more than one type of molecular assay may be included (e.g. RNA, DNA, or methylation-based assay) |
Please refer to 2023 Pathology Recommendations for Mesenchymal Tumours of Soft Tissue and Bone |
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Assessment of gene amplification (e.g. MDM2, CDK4, BCOR); FISH, array, and/or NGS methods acceptable |
Please refer to 2023 Pathology Recommendations for Mesenchymal Tumours of Soft Tissue and Bone |
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Gastrointestinal Stromal Tumour (GIST)
| Testing Indication | Biomarkers | Testing Sites |
|---|---|---|
| Reflex testing on newly diagnosed CD117 (cKIT) positive Gastrointestinal Stromal Tumours (GIST) | BRAF, KIT, PDGFRA Optional For 25/26: FGFR (fusion), NF1, NTRK (fusion), SDH |
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| SDHB testing on GIST for negative molecular results | SDHB |
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Thoracic
Lung (Non-Small Cell Lung Cancer (NSCLC))
| Testing Indication | Biomarkers | Testing Sites |
|---|---|---|
| Reflex testing on newly diagnosed cases of NSCLC (adenocarcinoma/non-squamous). | ALK, BRAF, EGFR, FGFR1, HER2 (ERBB2), KRAS, MET (Met skipping), NTRK1, NTRK2, NTRK3, PD-L1, PIK3CA, RET, ROS1 Optional For 25/26: KEAP1, NRG1, STK11, TP53 |
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| Reflex testing on newly diagnosed cases of NSCLC (squamous). | PD-L1 |
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| Testing on previously diagnosed cases of locally advanced or metastatic NSCLC that has progressed on or after EGFR TKI therapy. | Acquired EGFR T790M |
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