Single Gene Tests (Germline) (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 above 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).

Associated Tests

• DNA Extraction and Storage (Blood)

Synonyms

Single gene tests, ATP7B, Wilson Disease, CDKL5, CDKL Deficiency Disorder, Atypical Rett Syndrome, CYP24A1, Hypercalcemia, FGFR3, Achondroplasia, GALT, Galactosaemia, GLA, Fabry Disease, GNAS, McCune-Albright Syndrome, Albright Hereditary Osteodystrophy, MECP2, Rett Syndrome, POLG, POLG Related Disorders, RET, Multiple Endocrine Neoplasia type 2, MAX, SDHAF2, SDHB, SDHC, SDHD, TMEM127, Familial Paraganglioma/ Phaeochromocytoma Syndrome, UBE3A, Angelman Syndrome

Turnaround Time

12 weeks

Urgent TAT for prenatal/neonatal analysis or treatment-focused testing: 4 weeks

Specimen Type

• Whole Blood

Specimen Requirements

Tube/Container Type:

Preferred

• EDTA (Lavender Cap)

Acceptable

• EDTA (Microtainer)

Preferred Sample Volume (ml)

8

Minimum Sample Volume (ml)

4

Paediatric Specimen Requirements

Tube/Container Type:

Preferred

• EDTA (Lavender Cap)

Acceptable

• EDTA (Microtainer)

Preferred Sample Volume (ml)

4

Minimum 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

Important Notes:

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

Referrals can only come from Genetic Health Service NZ (GHSNZ) or certain medical specialists. Please refer to the list of genes and disorders below to see which medical specialist referral is required.

Test Method

TEST METHOD:
Capture-based target enrichment is performed using the Twist Bioscience Enzymatic Fragmentation Library Preparation v2.0 and custom panel. Next-generation sequencing (NGS) is performed on an Illumina MiSeq platform. Variant calls are identified using the Illumina DRAGEN analysis platform v4.2.4. Variant triage and curation is performed using Illumina Emedgene v38.

For SDHB, SDHC, SDHD, SDHAF1, and SDHAF2 genes, Multiplex Ligation-dependent Probe Amplification (MLPA) kit P226-D1 SDH from MRC-Holland is used to detect copy number variations.

TARGET GENES AND COVERAGE: The coding regions and flanking +/-20bp (encompassing the splice sites) are sequenced in this test. 100% coverage of bases within these regions is achieved by NGS (to a depth of >50x).

LIST OF GENES
ATP7B, CDKL5, CYP24A1, FGFR3, GALT, GLA, GNAS, MECP2, POLG, RET, MAX, SDHAF2*, SDHC*, SDHB*, SDHD*, TMEM127, UBE3A,
*Copy number variations analysis included

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