TEST METHOD
Capture-based target enrichment is performed using the CE-IVD SOPHiA Genetics Hereditary Cancer Solution v1.1. Massively parallel sequencing (MPS) is performed on an Illumina MiSeq platform. Variant calls are identified using the SOPHiA DDM analysis platform.
Copy number variant (CNV) analysis has been confirmed with the use of a digital droplet PCR (ddPCR) EvaGreen Supermix assay, using QuantaSoft Analysis Pro v.1.0.5 analysis software.
TARGET GENES AND COVERAGE
The coding regions and flanking +/-20bp (encompassing the splice sites) of the listed gene(s) are sequenced in this test. 100% coverage of bases within these regions is achieved by MPS (to a depth of ?50x) or by Sanger-based sequencing.
LIST OF GENES
APC, ATM*, BARD1, BRCA1, BRCA2, BRIP1, CDH1, CHEK2*, EPCAM**, FAM175A, MLH1, MRE11A, MSH2, MSH6, MUTYH, NBN, PALB2*, PIK3CA, PMS2, PTEN, RAD50, RAD51C, RAD51D, STK11, TP53, XRCC2
*LoF variants only, **copy number variant only
The Hereditary Cancer Solution panel of clinically relevant genes which are associated with an inherited susceptibility to malignancies.
Gene panels are available for the following indications:
|
Breast and Ovarian cancer |
|
UKCGG Breast Cancer panel |
|
UKCGG Ovarian cancer panel |
|
High-grade Serous Ovarian cancer (HGSOC) panel |
|
Familial Adenomatous Polyposis (FAP) |
|
MUTHY-associated Polyposis (MAP) |
|
Cowden Syndrome |
|
Li Fraumeni Syndrome |
|
Lynch Syndrome |
|
Hereditary Diffuse Gastric Cancer |
|
Peutz-Jeghers syndrome |
To contact the Molecular Genetics team:
Auckland City Hospital
(09) 307 4949
Lablink
ext 22000
Molecular Genetics Office
ext 22014
Transport all bloods between 8 and 24 degrees Celsius within 24-48 hours. If necessary specimens can be refrigerated overnight for transport at the temperatures stated above the following day.