OVERVIEW
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.
TEST REQUIREMENTS
For patients eligible for mainstreamed hereditary cancer testing:
- Completed CGL Hereditary Panel requisition form
- 5mL EDTA peripheral blood (see Specimen Guidelines, DNA molecular test type)
For all other patients, please initiate a referral to the Hereditary Cancer Program.
TURN-AROUND TIME
Approximately 42 days from receipt of specimen and completed, signed requisition form.
RESULTS REPORTING
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).
GENES TARGETED
Single nucleotide variants, small insertions and deletions, and copy number variants in the entire coding region (+/-10bp adjacent intron) 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; 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); MSH6:NM_000179; MUTYH:NM_001128425; NF1:NM_001042492; NF2:NM_000268*; NTHL1:NM_002528; PALB2:NM_024675; PDGFRA:NM_006206*; PHOX2B:NM_003924*; POT1:NM_015450*; PRKAR1A:NM_002734*; PTCH1:NM_000264*; PTEN:NM_000314 (incl. promoter); RAD51C:NM_058216; RAD51D:NM_002878; RB1:NM_000321*; RET:NM_020975*; 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*; WT1:NM_024426*
Partial Genes:
APC:NM_001127511 (promoter 1B and exon 1); CDKN1C:NM_000076 (excl. soft masked region in exon 1)*; CDKN2A:NM_058195 (exon 1); CEBPA:NM_004364 (excl. soft masked region in exon 1)*; MITF:NM_000248 (codon 318; CNVs not called)*; MSH3:NM_002439 (excl. soft masked region in exon 1); PMS2:NM_000535 (exons 1-11); POLD1:NM_001256849 (exons 8-13; CNVs not called); POLE:NM_006231 (exons 9-14; CNVs not called); RUNX1:NM_001754 (excl. soft masked region in exon 9)*; SDHA:NM_004168* (excl. exon 14; CNVs not called); TP53:NM_001126113 (exon 10); TP53:NM_001126114 (exon 10)
Copy-number only:
EPCAM:NM_002354; GREM1:NM_013372
* Variants not presumed by nature or already known to be (likely) pathogenic are not reported for these genes.
METHOD
Genomic DNA is extracted using a Promega Maxwell® nucleic acid isolation system and the yield and concentration are determined using a Qubit® fluorometer. gDNA is then sheared by Covaris, PCR-free ligation-based library construction is performed, libraries are sequenced using paired end 150bp reads on the Illumina Novaseq X, and sequences are aligned to the hg38 human reference genome using DRAGEN. Single nucleotide variants (SNV), copy number variants (CNV), and sequencing quality metrics are processed by a customized pipeline. Annotation, filtering, and reporting are performed with the Illumina Connected Insights platform. This assay was developed as a clinical test and its performance characteristics determined by the Genome Sciences Centre; exceeding 99% sensitivity for germline SNVs, short indels (= 49 nt), and CNVs (= 1 kb) with 35x mean genomic coverage.
Variants are validated (variant level interpretation, HGVS annotation) and interpreted according to ACMG clinical practice guidelines (PMID: 25741868) 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 zygosity should be considered in the context of other laboratory and clinical findings. Reported variants are confirmed by an orthogonal method at the discretion of the report signatory.