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Hereditary Cancer Genetic Testing
Short Description : HCS panel testing

DNA/RNA
Test performed by: LabPLUS - Dept. Diagnostic Genetics - Molecular Genetics


REFERRAL REQUIREMENTS:

Hereditary Breast and Ovarian Cancer panel: Referrals can only come from Genetic Health Service NZ (GHSNZ) or from Medical Oncologists who have completed the genetics training for requesting diagnostic testing on patients who meet EviQ criteria.
Other panels : Genetic Services only

Specimen Collection
EDTA4 mL Adult EDTA Blood (Preferred)
EDTA0.5 mL Paediatric EDTA Blood (Preferred)
Turnaround Time: 8 weeks
Assay Method

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

Panel

Gene list

Breast and ovarian cancer

ATM*, BRCA1, BRCA2, PALB2*, PTEN, TP53

UKCGG Breast Cancer panel

ATM*, BRCA1, BRCA2, CHEK2*, PALB2*, PTEN, STK11, TP53

UKCGG Ovarian cancer panel

BRCA1, BRCA2, BRIP1, MLH1, MSH2, MSH6, RAD51C, RAD51D

High-grade Serous Ovarian cancer (HGSOC) panel

 

ATM*, BRCA1, BRCA2, BRIP1, CHEK2*, MSH6, RAD51C, RAD51D

Familial Adenomatous Polyposis (FAP)

APC

MUTHY-associated Polyposis (MAP)

MUTYH

Cowden Syndrome

PTEN

Li Fraumeni Syndrome

TP53

Lynch Syndrome

EPCAM**, MLH1, MSH2, MSH6, PMS2

Hereditary Diffuse Gastric Cancer

CDH1

*Loss of Function (LOF) variants only, **copy number variant only


Diagnostic Use and Interpretation

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


Contact Information

To contact the Molecular Genetics team:

Auckland City Hospital (09) 307 4949
Lablink ext 22000
Molecular Genetics Office ext 22014


Specimen Transport Instructions for Referring Laboratories

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.



Last updated at 11:30:17 21/03/2024