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.
Turnaround times are set in accordance with Australasian Society of Diagnostic Genomics, 2024 guidelines
Routine cases: 40 days
Urgent cases: 14 days
Current turnaround times, updated 27/05/2026: There are ongoing delays in routine microarray turnaround times.
The current average reporting time for non-urgent postnatal samples is 72 days, with some cases taking approximately 150 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.
Illumina Infinium Global Screening Array-24 v3.0 with analysis performed in NxClinical 6.2..
Experimental details and limitations:
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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.
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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%.
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Microarray analysis will not detect balanced alterations, point mutations, imbalances of regions not represented on the microarray and may not detect low level mosaicism.
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Genome build is GRCh38 (hg38). Nomenclature is according to ISCN (2024).
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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) ; Likely Benign (score -0.90 to -0.98); Uncertain Significance (3a score 0.6 to 0.89; 3b score 0 to 0.59; 3c score -0.89 to -0.01), Likely Pathogenic (score 0.90 to 0.98), Pathogenic (=>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.
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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.
Microarray-based testing screens for genomic imbalance (chromosomal losses and gains) across the entire human genome at a significantly higher genomic resolution (and consequentially higher diagnostic yield) than standard cytogenetic chromosome analysis.
Compared to standard cytogenetic chromosome analysis this technique is unable to detect balanced rearrangements and low level mosaicism of unbalanced rearrangements/aneuploidy. Also, unlike FISH, it cannot be done as a rapid test. Therefore this test should not be used with a family history of a balanced chromosomal rearrangement, couples experiencing infertility/multiple spontaneous pregnancy losses, suspected mosaicism, or patients with a recognizable syndrome where a more rapid test is available.
To contact the Microarray team:
| Auckland City Hospital | (09) 307 4949 |
| Lablink | ext 22000 |
| Microarray Office | ext 22008 |
| Karen Claxton (Section Leader) | ext 22011 |
Transport all bloods between 8C and 24C 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.