Microarray (Blood)

Testing Laboratory

Department

Diagnostic Genetics

Delphic Registration Code (Alpha Code)

DNAT

Test Code (Numeric Code)

7933

Laboratory Handling

Registration

Place the sample into the box labelled DNAT on the shelf next to the dumbwaiter.

Laboratory

LabPLUS Diagnostic Genetics

Sample Stability

Specimens to be kept at room temperature (>8 degrees Celsius to <24 degrees Celsius). If necessary, specimens can be refrigerated overnight for transport.

Synonyms

Molecular Karyotype, DNA Microarray, Whole genome microarray, CMA, array CGH/SNP

Turnaround Time

40 days

Urgent Cases: 14 Days. Please note due to ongoing delays, the TAT for routine microarray requests is currently 140 days. If the results are required sooner for clinical management, please contact the laboratory at microarray@adhb.govt.nz. We require 5 working days notice to expedite analysis.

This test may be vetted by the laboratory. Please include relevant clinical information on the request form to ensure appropriate tests are approved. See the 'Clinical Information' section below for more information on the indications for testing.

Specimen Type

• Whole Blood

Specimen Requirements

Tube/Container Type:

Preferred

• EDTA (Lavender Cap)

Preferred Sample Volume (ml)

4

Paediatric Specimen Requirements

Tube/Container Type:

Preferred

• EDTA (Microtainer)

Acceptable

• EDTA (Lavender Cap)

Preferred Sample Volume (ml)

1

Minimum Sample Volume (ml)

0.5

Pre-testing Requirements

To support reporting to recommended turnaround times, it may sometimes be necessary to refer samples overseas to the Victorian Clinical Genetics Services (VCGS) Australia. If your patient does NOT consent to this, please notify us within in 7 days of sample receipt at microarray@adhb.govt.nz. Notification will ensure that the samples are retained within New Zealand, but as a result may, in times of increased workload, result in an extended turnaround time.

Important Note; Microarray analysis is a specialist referral only test, which includes paediatric specialist community/developmental Nurse Practitioners.

A named Consultant and location for return of results must be included on the referral form.

Clinical details/referral indication must be provided

We do not accept referrals from GPs or other referral centres.

Genetic Health Service NZ can be contacted on 0800 476 123

In conjunction with the Genetic Health Service of New Zealand (Northern Hub), we have made a commitment to ensure that testing undertaken appropriately. Testing may be delayed if clinical details are not provided to enable adequate gatekeeping of referrals.

Additional Specimen Information

Microarray analysis can also be performed on DNA extracted from a buccal swab. Buccal swab kits are available on request.

Aliquot Instructions

Transport to Lab

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

Test Method

Illumina Infinium Global Screening Array-24 v3.0 with analysis performed in NxClinical 6.2..

Experimental details and limitations:
1. Microarray analysis performed using the Infinium Global Screening Array-24 v3.0with analysis performed in NxClinical 6.2. This platform offers a minimum detection limit of 15 kb with a requirement of at least 15 probes for copy-number detection. Losses smaller than 200 kb, and gains smaller than 400 kb will not be reported unless associated with a gene/region of known pathogenicity. Analysis is performed with reference to only the MANE select and MANE plus clinical transcripts, unless there is strong evidence to suggest otherwise for an individual gene. Detection threshold for long contiguous stretches of homozygosity (LCSH)/regions of homozygosity (ROH) is set at 5 Mb. Copy-number detection uses minimum genomic coordinates as per ACMG 2020 guidelines, maximum coordinates are included where clinically relevant genetic content is present.

2. It is beyond the scope of this assay to confirm UPD (uniparental disomy) and imprinting disorders. Long contiguous stretches of homozygosity (LCSH) are not reported unless indicative of UPD for chromosomes 6, 7, 11, 14, 15 and 20 for regions encompassing genes with relevance to the phenotype provided. Total genomic autosomal LCSH is reported when greater than 6%.

3. Microarray analysis will not detect balanced alterations, point mutations, imbalances of regions not represented on the microarray and may not detect low level mosaicism.

4. Genome build is GRCh38 (hg38). Nomenclature is according to ISCN (2024).

5. Classification of copy number variants (CNVs) is based on the American College of Medical Genetics and Genomics (ACMG) framework, the Clinical Genome Resource (ClinGen) Technical Standards 2019, and the Association for Clinical Genomic Science (ACGS) Best practice Guidelines for Variant Classification in Rare Disease 2024. CNVs are classified into the following five classes: Benign (score 0.99). Benign, likely benign, and VUS 3c copy number variants are NOT reported. Heterozygous carrier status for recessive conditions is not routinely reported. Data on all CNVs are retained by the laboratory should it be required. Duplications of the SHOX region are not routinely reported. Male Y chromosome changes are not reported except in cases of suspected aneuploidy. Supporting documentation regarding the interpretation of variants is available from the Diagnostic Genetics Laboratory; please contact us on DGen@adhb.govt.nz . The classification of copy number variants represents the best interpretation of the data at the time of reporting. We recommend that the status of copy number variants is reviewed by the referring clinician to ensure their continuing validity.

6. The results and interpretations assume that the samples received by the laboratory are correctly identified and that family relationships and clinical diagnosis are as stated.

Consultation with the Genetic Health Service NZ- Northern Hub is recommended when further advice is needed (09-307-4949 ext 25870 or 0800 476-123).

Limitations / Interference

Microarray analysis will not detect balanced alterations, point mutations, imbalances of regions not represented on the microarray and may not detect low level mosaicism.

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.

Resources

• Microarray Info for Medical Staf (148 KB)
• Microarray Info for Patient and Parent (66 KB)
• LabPLUS GHSNZ Genetic Testing Pathway for DD ID MCA AS (230 KB)
• LabPLUS Genetic Testing Criteria for Neonate (118 KB)

Contact Information