Hereditary Cancer Panel


This multi-gene next-generation sequencing panel test is available for patients known or suspected to be at risk of an inherited cancer predisposition syndrome.  For indications and ordering information, see our Hereditary Cancer page.


For patients eligible for mainstreamed hereditary cancer testing:

  1. Completed CGL Hereditary Panel requisition form 
  2. 5mL EDTA peripheral blood (see Specimen GuidelinesDNA molecular test type) 

For all other patients, please initiate a referral to the Hereditary Cancer Program.


Approximately 42 days from receipt of specimen and completed, signed requisition form.  


Germline variants are classified according to ACMG Guidelines (Richards (2015) PMID: 25741868) as one of:

  • Pathogenic
  • Likely Pathogenic
  • Variant of Uncertain Significance (VUS)
  • Likely Benign
  • Benign

Please see our Variant Classification Guidelines for additional details. Benign and Likely Benign variants are not routinely reported.  Only Pathogenic or Likely Pathogenic variants are reported for a subset of targeted genes (see below).


Single nucleotide variants and small insertions and deletions are identified in the following genes:

Entire coding region: AIP_NM_003977*; ALK_NM_004304*; APC_NM_000038 (incl. promoter 1A); ATM_NM_000051; AXIN2_NM_004655; BAP1_NM_004656*; BARD1_NM_000465*; BLM_NM_000057*; BMPR1A_NM_004329; BRCA1_NM_007294 (incl. Intron 13 and 23 hotspots); BRCA2_NM_000059; BRIP1_NM_032043; CASR_NM_000388*; CDC73_NM_024529*; CDH1_NM_004360; CDK4_NM_000075; CDKN1B_NM_004064*; CDKN2A_NM_000077; CEBPA_NM_004364*; CHEK2_NM_007194; CTNNA1_NM_001903*; DICER1_NM_177438*; DIS3L2_NM_152383*; EGFR_NM_005228*; FH_NM_000143*; FLCN_NM_144997*; GATA2_NM_032638 (incl. intron 4 hotspot)*; GPC3_NM_004484*; HOXB13_NM_006361; HRAS_NM_005343*; KIT_NM_000222*; MAX_NM_002382*; MEN1_NM_000244*; MET_NM_000245 (incl. Intron 13)*; MLH1_NM_000249 (incl. 5’UTR and Intron 12 hotspots); MSH2_NM_000251 (incl. 5’ UTR and promoter); MSH3_NM_002439; MSH6_NM_000179; MUTYH_NM_001128425; NF1_NM_000267; NF1_NM_001042492; NF2_NM_000268*; NTHL1_NM_002528; PALB2_NM_024675; PDGFRA_NM_006206*; POLD1_NM_001256849; POLE_NM_006231; POT1_NM_015450*; PRKAR1A_NM_002734*; PTCH1_NM_000264*; PTEN_NM_000314 (incl. promoter); RAD50_NM_005732; RAD51C_NM_058216; RAD51D_NM_002878; RB1_NM_000321*; RECQL4_NM_004260*; RET_NM_020975*; RUNX1_NM_001754*; SDHAF2_NM_017841*; SDHB_NM_003000*; SDHC_NM_003001*; SDHD_NM_003002*; SMAD4_NM_005359 (incl. promoter); SMARCA4_NM_001128849*; SMARCB1_NM_003073*; SMARCE1_NM_003079*; STK11_NM_000455; SUFU_NM_016169*; TERC_NR_001566*; TERT_NM_198253*; TMEM127_NM_017849*; TP53_NM_000546 (incl. Intron 1, 6, and 10 hotspots); TSC1_NM_000368*; TSC2_NM_000548*; VHL_NM_000551*; WRN_NM_000553*; WT1_NM_024426*

Partial Genes: APC_NM_001127511 (promoter 1B and exon 1); CDKN1C_NM_000076 (exon 2)*; CDKN2A_NM_058195 (exon 1); MITF_NM_000248 (codon 318)*; NBN_NM_002485 (excl. exon 6); PHOX2B_NM_003924 (exons 1 and 2)*; PMS2_NM_000535 (exons 1-11);  SDHA_NM_004168* (excl. exon 14); TP53_NM_001126113 (exon 10); TP53_NM_001126114 (exon 10)

* Variants not presumed by nature or already known to be Pathogenic or Likely Pathogenic are not reported for these genes.

Copy Number Variants (not applicable to FFPE specimens): Copy number variants are called in all of the above genes as well as:  EPCAM_NM_002354; GREM1_NM_013372.  CNVs are not called in SDHA.


Genomic DNA is subjected to FFPE repair, ligation-based library construction, PCR amplification, hybridization capture, and Illumina sequencing. Either the entire coding region (with at least 2bp of flanking intronic sequence) or known hotspots of clinical importance in a proportion of genes were assayed. A complete list of target sites and bio-informatic details can be obtained upon request. Large copy number alterations (duplication or deletion) > 30bp, other structural rearrangements and variants in the promoter and other non-coding regions may not be detected by this test. This assay routinely exceeds 96% sensitivity toward germline SNVs and short indels at positions covered by at least 70 reads.  This assay was developed as a clinical test and its performance characteristics determined by the Centre for Clinical Genomics (BC Cancer).

Variants are validated (variant level interpretation, HGVS annotation) and interpreted in the context of available clinical information prior to reporting. cDNA nucleotide numbering begins at the A of the initiating codon (ATG) as per HGVS convention.  Reported variants are confirmed by an orthogonal method at the discretion of the report signatory. It is estimated that single exon CNVs are reliably called in approximately 93% of target exons.  Regions (primarily single exon events) associated with reduced sensitivity toward CNVs include, but may not be limited to those with higher than average GC content (eg proximal exons) or with homology to other regions of the genome (eg pseudogenes).