Targeted Variant 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 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)
• Single Gene Tests (Germline) (Blood)
• Thiopurine Methyltransferase (Blood)

Synonyms

Molecular Genetics Targeted Sequencing analysis for Specific Common/Recurrent Disease Mutations, ACADVL, Very Long-Chain Acyl-CoA Dehydrogenase Deficiency (VLCAD), ASS1, Type 1 Citrullinemia, CPT1a, Carnitine palmitoyltransferase 1A (liver), GALT, Galactosaemia, MFSD8, Batten's disease, MFSD8-Related Neuronal Ceroid-Lipofuscinosis, TPMT, Thiopurine methyltransferase

Turnaround Time

8 weeks

TPMT genotyping - 6 weeks, Urgent metabolic testing TAT - 72 hours

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 (Microtainer)

Preferred Sample Volume (ml)

2

Minimum Sample Volume (ml)

0.5

Additional Specimen Information

- For neonatal unit babies, 6 punched-out circles from a dried blood spot

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.

Additional Referral/Aliquot Information

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

Test Method

Sanger sequencing is performed for the targeted sequence variants and analysed using Variant Reporter Software v3. Minimum sequence trace Phred score is 35, corresponding to an average false base call frequency of 0.031%.

Limitations / Interference

The limit of detection (LoD) of Sanger sequencing is 15-20%. It will not detect low level mosaicism below the LoD or mosaic variants in tissues other than that submitted for testing.

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