Hereditary Cancer Genetic Testing (Blood)

Testing Laboratory

Department

Diagnostic Genetics

Delphic Registration Code (Alpha Code)

DNAT

Test Code (Numeric Code)

7933

Laboratory Handling

Transport

Transport all bloods between >8 degrees C to <24 degrees C within 24-48 hours. If necessary specimens can be refrigerated overnight for transport at the temperatures stated, the following day. For testing of other sample types please contact the laboratory prior to sending.

Registration

Please store specimens at 4 degrees C until processed.

Sample Stability

48 hours at ambient temperature (8 degrees C to 24 degrees C).

Synonyms

HCS panel testing, Breast and Ovarian cancer, Breast cancer, Ovarian cancer, High-grade Serous Ovarian cancer, HGSOC, Familial Adenomatous Polyposis, FAP, MUTHY-associated Polyposis, MAP, Cowden Syndrome, Li Fraumeni Syndrome, Lynch Syndrome, Hereditary Diffuse Gastric Cancer, Peutz-Jeghers syndrome, 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

Turnaround Time

8 weeks

Urgent turnaround time: 4 weeks

Specimen Type

• Whole Blood

Specimen Requirements

Tube/Container Type:

Preferred

• EDTA (Lavender Cap)

Acceptable

• EDTA (Microtainer)

Preferred Sample Volume (ml)

4

Paediatric Specimen Requirements

Tube/Container Type:

Preferred

• EDTA (Lavender Cap)

Acceptable

• EDTA (Microtainer)

Preferred Sample Volume (ml)

0.5

Additional Specimen Information

This test requires viable nucleated cells. Do not centrifuge or freeze the EDTA blood sample.

An aliquot of genomic DNA extracted by another ISO15189 accredited laboratory is also an acceptable specimen type. DNA samples should have a minimum volume of 20 µL and a concentration of at least 20 ng/µL.

If the available DNA does not meet these requirements, please contact the laboratory to discuss sample suitability and any specific testing requirements.

Aliquot Instructions

Sample Type

• Whole Blood

Minimum Volume (ml)

4

Transport to Lab

Ambient (8 - 24 degrees Celsius)
If overnight - Chilled (2 - 8 degrees Celsius)

Additional Referral/Aliquot Information

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.

The specialty of the referring clinician and the clinical presentation must be provided. Failure to provide the information required may delay testing.

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.

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 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.

Copy number variant (CNV) analysis is confirmed with the use of a digital droplet PCR (ddPCR) EvaGreen Supermix assay, using QuantaSoft Analysis Pro v.1.0.5 analysis software.

Uncertainty of Measurement

Please contact the Diagnostic Genetics Pathologist at dgen@adhb.govt.nz to discuss sources of test uncertainty, which include, but are not limited to, measurement uncertainty (MU) and biological variation.

Contact Information