OncoPanel

OVERVIEW 

CGL’s Oncopanel is a next-generation sequencing assay that is offered to provide predictive, prognostic, and diagnostic information for patients with a variety of solid tumours.  All the genes targeted by this assay (see below) are screened for DNA changes (variants). The clinical significance of variants or variant combinations is then interpreted in the context of therapy-response, prognosis, or diagnostic criteria. 

Sequencing and informatics services for this assay are provided by PHSA’s Centre for Clinical Genomics (CCG) and results are interpreted by CGL.  Single-base and small insertion/deletion variants are screened in the targeted gene regions and variant classification is adapted from AMP/ASCO/CAP guidelines (Li (2017) PMID:27993330).  Currently, Oncopanel does not detect gene fusions or copy-number variants. 

Some of the genes targeted by this sequencing panel are strongly associated with inherited cancer predisposition syndromes. Approximately 10-15% of advanced cancer patients carry a germline predisposition variant (Schrader (2016) PMID: 26556299), and so screening of predisposition genes may identify patients and families that would benefit from genetic counselling and testing.  However, the Oncopanel assay itself does not distinguish somatic (acquired) from germline (heritable) variants.  Therefore, variants suspected of being of germline origin may result in a recommendation that the patient be referred to the Hereditary Cancer Program at BC Cancer (or to the appropriate Medical Genetics program in the patient’s jurisdiction) for consideration of germline testing.  See our Hereditary Cancer page for additional details on referrals. 

NOTE: The results of this test are not a substitute for germline screening.  If a patient has clinical features or a personal or family history suggestive of an inherited syndrome then a Hereditary Cancer referral should be made, regardless of the Oncopanel result. 

INDICATION 

Oncopanel testing is available for the following tumour types: 

  1. Lung Cancer (Stage IIIB/IV non-small cell, non-neuroendocrine adenocarcinoma)
  2. Melanoma (non-resectable, metastatic) 
  3. Colorectal cancer (metastatic) 
  4. Gastrointestinal stromal tumour (GIST) 
  5. Ovarian/FT/Peritoneal (High-grade serous)
  6. Glioma (low grade)

TEST REQUIREMENTS 

  1. Completed CGL Solid Tumour Testing requisition form 
    • Select “Oncopanel” adjacent to the appropriate tumour type
  2. FFPE Tumour specimen (see Specimen Guidelines
    • minimum of 20% tumour content is required 

TURN-AROUND TIME 

Approximately 14 days (lung, melanoma) or 17-21 days (other indications) from receipt of specimen and completed, signed requisition form.  

RESULTS REPORTING 

  • Oncopanel reports include a list of variants classified into tiers of clinical significance: 
    • TIER I – VARIANTS OF STRONG CLINICAL SIGNIFICANCE 
    • TIER II – VARIANTS OF POTENTIAL CLINICAL SIGNIFICANCE 
    • TIER IIIA –VARIANTS OF UNCERTAIN CLINICAL SIGNIFICANCE 
    • TIER IIIB – VARIANTS OF UNCERTAIN FUNCTION 
  • Please see our Variant Classification Guidelines for additional details. 
  • Variants suspected to be of germline origin will be identified on the report as Potential Germline Findings.   

GENES TARGETED 

Either the coding exonic sequence and at least 2 bp of flanking intronic sequence, or known hotspots of clinical importance, are assessed in the following genes. 

Reporting of variants in these genes is limited to Tiers I, II, IIIA and IIIB:  
AKT1, ALK, BRAF, BRCA1, BRCA2, CDK4 (codon 24), CDKN2A, EGFR (Exons 18-21), ERBB2, ERBB3, GNA11, GNAQ, HRAS, IDH1, IDH2, KIT, KRAS, MAP2K1, MET (incl. Intron 13), NRAS, PALB2, PDGFRA, PIK3CA, RET, ROS1, SDHA (excl. exon 14), SDHB, SDHC, SDHD.  (Reporting of Tier IIIB variants in the SDHx genes is routinely limited to GISTs, in BRCAx to Ovarian Carcinomas, in CDKN2a and GNAx to Melanomas.) 

Reporting of variants in these genes is limited to Tiers I, II and IIIA: 
APC, ATM, AXIN2, BMPR1A, CDH1, CHEK2, CIC, FUBP1, HOXB13, MLH1, MSH2, MSH6, MUTYH, NF1, NTHL1, PMS2, POLD1 (Codons 473-479 only), POLE (Codons 421-427 only), PTEN, RAD50, RAD51C, RAD51D, SMAD4, STK11, and TP53. 

METHOD 

Genomic DNA is extracted from the submitted specimen through bead capture (Promega Maxwell).  Genomic DNA undergoes FFPE repair, ligation-based library construction, PCR amplification, hybridization capture, and Illumina sequencing. Single-strand consensus sequences are generated from UMI-indexed reads using fgbio and aligned to the GRCh37 human genome reference using BWA. Variant calling is performed using samtools and VarScan2. Annotation and filtering of variants is performed with Agilent’s Alissa Interpret platform. Large copy number alterations (duplication or deletion) > 30 bp, other structural rearrangements including gene fusions, and variants in the promoter and other non-coding regions may not be detected by this test. The sensitivity of the present assay is deemed to be approximately 5% (site-specific analyses) to 10% (mutation screening). Variants present in less than this proportion of assayed alleles are not reported.  Variants are interpreted in the context of available clinical information and tiered according to their known or predicted clinical significance (adapted from Li et al. Standards and Guidelines for the Interpretation and Reporting of Sequence variants in Cancer J Mol Diagn (2017) 19:4-23 PMID:27993330). Variants unlikely to be of clinical importance (Tier IV) are not reported.